diff --git a/data/schiPomb_972H/schiPomb-mitotRNAs.fa b/data/schiPomb_972H/schiPomb-mitotRNAs.fa
new file mode 100644
index 0000000..36cb8b6
--- /dev/null
+++ b/data/schiPomb_972H/schiPomb-mitotRNAs.fa
@@ -0,0 +1,75 @@
+>URS000040774E_4896|Schizosaccharomyces_pombe|9606|Trp|TCA
+AAGAGTATAGTTTAATTGGTAAAACTTCTGATTCCAAATTAGACATTGTTCGTTCAAGTC
+GGACTGCTCTTG
+>URS000052E18F_4896|Schizosaccharomyces_pombe|9606|Cys|GCA
+GATAATGTTCAGTGGTCTGAAATTGAATTTGCAAAATTTGATATATGAGTTCAATTCTCA
+TCATTATCT
+>URS00002C4932_4896|Schizosaccharomyces_pombe|9606|Val|TAC
+AGGAGAATAGCTTAATTGGTAGAGCACTTACCTTACAAGTAAGATTATAAGGGTTCAAAT
+CCCTTTTCTCCTA
+>URS00003B0065_4896|Schizosaccharomyces_pombe|9606|Leu|TAG
+GCAGATGTGATGAAATTGGTAAACATGTTTACCTTAGGAGTAAAATCTTGAAGGTTCGAA
+TCCTTCCATCTGTA
+>URS00001AD663_4896|Schizosaccharomyces_pombe|9606|Leu|TAA
+GCCTAAATGCTGGAATTTGGTAGACAGAACAAACTTAAGATTTGTCGCTTTCGAGCGTGT
+TGGTTCGAGTCCAACTTTAGGTA
+>URS00001DDDAC_4896|Schizosaccharomyces_pombe|9606|Ile|GAT
+AGTTCTTTAACTTAAAAGGTCAGAGTGCAGACTTGATAAGTCTGTGGTATTGGTTCGATT
+CCAATAAGAACTA
+>URS00000E510A_4896|Schizosaccharomyces_pombe|9606|Ser|TGA
+GGAAGGGTGTCCGAGTGGTTTAAGGAGCGATATTTGAGCTATTGTGATTTATTCATCGCA
+GGTTCGAATCCTGCCCCTTTCG
+>URS00000B84DA_4896|Schizosaccharomyces_pombe|9606|Arg|TCG
+GCACTTTTAGCTTAATTGGTTAGAGTAACAATCTTCGAAATTGTTAGTATAGGTTCAAAT
+CCTATAAAGTGTT
+>URS00005E6A72_4896|Schizosaccharomyces_pombe|9606|Gly|TCC
+GCAGATATAAGTCAATTGGCAGACCTTCTGATTTCCACTTAGATTATGTTCGTTCGAATC
+GGACTATCTGCA
+>URS00000E1077_4896|Schizosaccharomyces_pombe|9606|Asn|GTT
+GTTGTTGTAGCTCAATGGTAGAGCAAGTCACTGTTAATGACCTGATAGTGGTTCGATTCC
+ACTCAATAACG
+>URS00000A90BD_4896|Schizosaccharomyces_pombe|9606|Lys|TTT
+GGGGATGTAGCTCAATGGTTAGAGCTTTCGCCTTTTAAGCGATAGGATAAGGGTTCAAAT
+CCCTTCAGACCCA
+>URS0000226DF4_4896|Schizosaccharomyces_pombe|9606|Glu|TTC
+GGCTCTATTGTCTAATGGTTAAGACCTTACATCTTCATTGTAAATATCTTGGTTCGATTC
+CAAGTAGGGCTA
+>URS000027C703_4896|Schizosaccharomyces_pombe|9606|Ser|GCT
+GGAAAAATAGTTCTAATTGGTAAGAAGGATACTTGCTACGTATCTGGTGAATAACCTTGT
+GAGTTCGAGTCTCACTTTTTCCG
+>URS000012A615_4896|Schizosaccharomyces_pombe|9606|Thr|TGT
+GCTAATTTAACTCAATTGGTAGAGTGCGTACCTTGTAAGTACGAAGTTAGAGGTTCAATT
+CCTCTAATTAGCA
+>URS0000519C3F_4896|Schizosaccharomyces_pombe|9606|Glu|TTC
+TGGGTTGTTGACTAATAGGTAAGTCCCTGAAATTTGACTTCAGTCTATGTAAGTTCGAAT
+CTTACCATCCCAT
+>URS0000101C2D_4896|Schizosaccharomyces_pombe|9606|Met|CAT
+TGCGATTTAATGTAATTGGTTAACATCTCTGACTCATGATCAGTGTATTAAGGTTCAAGT
+CCTTAGGTCGCAC
+>URS00003C6042_4896|Schizosaccharomyces_pombe|9606|Ile|GAT
+AGGATTATAGCTTAACGGTTAAAGCAGAGAGCTCATAACTCTTGTATATTGGTTCGATTC
+CAGTTTGTCCTA
+>URS0000409C5E_4896|Schizosaccharomyces_pombe|9606|Phe|GAA
+GCTCTGATAACTTAACGGTTAAAGTGCAGTATTGAAGCTGCTGAGATATTGGTTCGATTC
+CATTTCAGAGCA
+>URS00001B646E_4896|Schizosaccharomyces_pombe|9606|Met|CAT
+GTTGGTATAGTTTAATTGGTTAAAATAATCTCCTCATGTGAGATTGATCTATAGGTTCGA
+GCCCTTTTACCAACT
+>URS00000FEDF7_4896|Schizosaccharomyces_pombe|9606|Ala|TGC
+GGGGATTTAATTTAATTGGTTAGAATATTGTGTTTGCACCACAAAAATCTGGTTTCGAGT
+ACCAGAATCTCCA
+>URS000045D66C_4896|Schizosaccharomyces_pombe|9606|His|GTG
+GGTGATTGTAATTCAATGGTAGAATGCTTATTTGTGGCATAAGAAGTTCTTGGTTCGATT
+CCAAGTAATCACC
+>URS000023E104_4896|Schizosaccharomyces_pombe|9606|Asp|GTC
+GAATCTGTAGCTTAAAGTAAAGTATCGCCTTGTCACGGTGATGGATGCCCACTCGTACTG
+GGTCAGATTCG
+>URS000025B7E6_4896|Schizosaccharomyces_pombe|9606|Pro|TGG
+CGGATAGAAACATGTATTGGTTCATGTACTTGCTTTGGGTGTGAGAATTTGTTAGTTCGA
+ATCTAACCTATCCGA
+>URS00004A6ED0_4896|Schizosaccharomyces_pombe|9606|Tyr|GTA
+GGGGAGAATTCTTATGTTGGTTTTAAGAGGTGAGTTGTAGCCTCATTAGGTCAATCCTAT
+CGCAGGTTCGATTCCTGCTCTCCTCA
+>URS00003FFD19_4896|Schizosaccharomyces_pombe|9606|Arg|TCG
+GTCTGTATAGCTCAATGGTAGAGCATCTCACTTCTAATGAGTCGATCTAAGTTCGATTCT
+TAGTACAGATTCCACAC
diff --git a/data/schiPomb_972H/schiPomb_972H-tRNAs.fa b/data/schiPomb_972H/schiPomb_972H-tRNAs.fa
index 63537b2..73ab98b 100644
--- a/data/schiPomb_972H/schiPomb_972H-tRNAs.fa
+++ b/data/schiPomb_972H/schiPomb_972H-tRNAs.fa
@@ -1,504 +1,504 @@
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-TGG-1-1 (chrI.trna1-ProTGG) chrI:365155-365226 (+) Pro (TGG) 72 bp Sc: 65.3
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-TGG-1-1 (chrI.trna1-ProTGG) chrI:365155-365226 (+) Pro (TGG) 72 bp Sc: 65.3
 GGCTTCGTGGTGTAGTGGTAGCATACTTCGTTTGGGTCGAAGTGGtCAGGGGTTCGATCC
 CCCTCGAAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-2 (chrI.trna10-ThrAGT) chrI:2433048-2433119 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-2 (chrI.trna10-ThrAGT) chrI:2433048-2433119 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-2-2 (chrI.trna11-LysTTT) chrI:2441963-2442037 (+) Lys (TTT) 75 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-2-2 (chrI.trna11-LysTTT) chrI:2441963-2442037 (+) Lys (TTT) 75 bp Sc: 69.6
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 GTCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-2-1 (chrI.trna12-CysGCA) chrI:2510538-2510610 (+) Cys (GCA) 73 bp Sc: 63.7
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-2-1 (chrI.trna12-CysGCA) chrI:2510538-2510610 (+) Cys (GCA) 73 bp Sc: 63.7
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCACTGGTTCAAAT
 CCGGTTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-TAT-1-1 (chrI.trna13-IleTAT) chrI:2578426-2578524 (+) Ile (TAT) 99 bp Sc: 64.5
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-TAT-1-1 (chrI.trna13-IleTAT) chrI:2578426-2578524 (+) Ile (TAT) 99 bp Sc: 64.5
 GCTCCCGTGGCCAAGCTGGTtAAGGCCTCATGCTTATAtgatactccccttaggaggtgt
 gttACGTGGAAAtCGCGAGTTCGATCCTCGCCGGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-3 (chrI.trna14-LysCTT) chrI:3086310-3086392 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-3 (chrI.trna14-LysCTT) chrI:3086310-3086392 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-TGC-1-2 (chrI.trna15-AlaTGC) chrI:3157430-3157501 (+) Ala (TGC) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-TGC-1-2 (chrI.trna15-AlaTGC) chrI:3157430-3157501 (+) Ala (TGC) 72 bp Sc: 67.9
 GGGCATGTGATGCAGTGGTAGCATGCTCGCTTTGCATGCGAGTCGtCCTGGGTTCAATCC
 CCAGCGTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-CGT-1-1 (chrI.trna16-ThrCGT) chrI:3164749-3164820 (+) Thr (CGT) 72 bp Sc: 72.5
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-CGT-1-1 (chrI.trna16-ThrCGT) chrI:3164749-3164820 (+) Thr (CGT) 72 bp Sc: 72.5
 GCTCTTGTAGCTCAGTGGTAGAGCGCCTGTCTCGTAAACAGGAGGtCCAGTGTTCGAGTC
 ACTGCCGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-CCG-1-1 (chrI.trna17-ArgCCG) chrI:3443055-3443144 (+) Arg (CCG) 90 bp Sc: 30.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-CCG-1-1 (chrI.trna17-ArgCCG) chrI:3443055-3443144 (+) Arg (CCG) 90 bp Sc: 30.8
 GGCCTCGTGGCCTAGAAGTAAGGCGTTGGTTTCCGGtggaggagactccaggttCGCCAA
 AGAtCGCGAGTGCAAATCTCGCCGTGGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAG-1-1 (chrI.trna18-LeuTAG) chrI:3591948-3592044 (+) Leu (TAG) 97 bp Sc: 54.3
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAG-1-1 (chrI.trna18-LeuTAG) chrI:3591948-3592044 (+) Leu (TAG) 97 bp Sc: 54.3
 GGATGGGTGTCCGAGTGGTtATGGAGCTGGCTTTAGGtgcgttcaacgcattgcaCGCCA
 GTGCGAAAGCTCGCGGGTTCGAGTCCCGTCCCATTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-1-2 (chrI.trna19-CysGCA) chrI:3700665-3700737 (+) Cys (GCA) 73 bp Sc: 65.6
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-1-2 (chrI.trna19-CysGCA) chrI:3700665-3700737 (+) Cys (GCA) 73 bp Sc: 65.6
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCGCTGGTTCAAAT
 CCGGCTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Val-CAC-1-1 (chrI.trna2-ValCAC) chrI:446000-446071 (+) Val (CAC) 72 bp Sc: 64.7
+>Schizosaccharomyces_pombe_972h_tRNA-Val-CAC-1-1 (chrI.trna2-ValCAC) chrI:446000-446071 (+) Val (CAC) 72 bp Sc: 64.7
 AGTCCCGTGTTCTAGTGGTATGATTTCTCCTTCACACGGAGAAGGtCCCGGGTTCGATCC
 CCGGCGGGACTA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-1 (chrI.trna20-PheGAA) chrI:3701556-3701628 (+) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-1 (chrI.trna20-PheGAA) chrI:3701556-3701628 (+) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-1 (chrI.trna21-ArgACG) chrI:3736520-3736592 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-1 (chrI.trna21-ArgACG) chrI:3736520-3736592 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-1 (chrI.trna22-IleAAT) chrI:3768290-3768363 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-1 (chrI.trna22-IleAAT) chrI:3768290-3768363 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-2 (chrI.trna23-GluCTC) chrI:3776768-3776839 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-2 (chrI.trna23-GluCTC) chrI:3776768-3776839 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-2 (chrI.trna24-AlaAGC) chrI:3777192-3777265 (+) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-2 (chrI.trna24-AlaAGC) chrI:3777192-3777265 (+) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-TGA-1-1 (chrI.trna25-SerTGA) chrI:4265149-4265245 (+) Ser (TGA) 97 bp Sc: 84.7
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-TGA-1-1 (chrI.trna25-SerTGA) chrI:4265149-4265245 (+) Ser (TGA) 97 bp Sc: 84.7
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTTGAAtcctgtattctagtcATCTAATG
 GGCTTTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-2 (chrI.trna26-MetCAT) chrI:4265253-4265324 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-2 (chrI.trna26-MetCAT) chrI:4265253-4265324 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-1 (chrI.trna27-AspGTC) chrI:4532857-4532927 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-1 (chrI.trna27-AspGTC) chrI:4532857-4532927 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-3 (chrI.trna28-ThrAGT) chrI:4715431-4715502 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-3 (chrI.trna28-ThrAGT) chrI:4715431-4715502 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-CGC-1-1 (chrI.trna29-AlaCGC) chrI:4796977-4797059 (+) Ala (CGC) 83 bp Sc: 66.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-CGC-1-1 (chrI.trna29-AlaCGC) chrI:4796977-4797059 (+) Ala (CGC) 83 bp Sc: 66.3
 GGGGATGTAGTTTAGGGGTATAACGTTTCATTCGCAtagttcgcaccTTGAAAAGGtCCC
 GGGTTCGATTCCCGGCATCTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-2 (chrI.trna3-GluTTC) chrI:957183-957254 (+) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-2 (chrI.trna3-GluTTC) chrI:957183-957254 (+) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-2 (chrI.trna30-SerAGA) chrI:5437747-5437828 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-2 (chrI.trna30-SerAGA) chrI:5437747-5437828 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-2 (chrI.trna31-AspGTC) chrI:5232917-5232987 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-2 (chrI.trna31-AspGTC) chrI:5232917-5232987 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-2 (chrI.trna32-ArgACG) chrI:5045132-5045204 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-2 (chrI.trna32-ArgACG) chrI:5045132-5045204 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-2-1 (chrI.trna33-LeuAAG) chrI:4059028-4059106 (-) Leu (AAG) 79 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-2-1 (chrI.trna33-LeuAAG) chrI:4059028-4059106 (-) Leu (AAG) 79 bp Sc: 58.4
 GGAAGGTTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACACCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-2 (chrI.trna34-IleAAT) chrI:3773910-3773983 (-) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-2 (chrI.trna34-IleAAT) chrI:3773910-3773983 (-) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-1 (chrI.trna35-GluCTC) chrI:3765434-3765505 (-) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-1 (chrI.trna35-GluCTC) chrI:3765434-3765505 (-) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-1 (chrI.trna36-AlaAGC) chrI:3765008-3765081 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-1 (chrI.trna36-AlaAGC) chrI:3765008-3765081 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-2 (chrI.trna37-PheGAA) chrI:3752334-3752406 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-2 (chrI.trna37-PheGAA) chrI:3752334-3752406 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-2 (chrI.trna38-ValAAC) chrI:3710739-3710821 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-2 (chrI.trna38-ValAAC) chrI:3710739-3710821 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-1 (chrI.trna39-TrpCCA) chrI:3559754-3559826 (-) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-1 (chrI.trna39-TrpCCA) chrI:3559754-3559826 (-) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-CGA-1-1 (chrI.trna4-SerCGA) chrI:1096369-1096466 (+) Ser (CGA) 98 bp Sc: 83.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-CGA-1-1 (chrI.trna4-SerCGA) chrI:1096369-1096466 (+) Ser (CGA) 98 bp Sc: 83.9
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTCGAAttcctacattcgtggcATCTAAT
 GGGCTCTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-1 (chrI.trna40-SerAGA) chrI:3047677-3047758 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-1 (chrI.trna40-SerAGA) chrI:3047677-3047758 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-1-1 (chrI.trna41-ThrAGT) chrI:2844674-2844745 (-) Thr (AGT) 72 bp Sc: 81.0
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-1-1 (chrI.trna41-ThrAGT) chrI:2844674-2844745 (-) Thr (AGT) 72 bp Sc: 81.0
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCGAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAA-1-1 (chrI.trna42-LeuTAA) chrI:2802761-2802858 (-) Leu (TAA) 98 bp Sc: 57.0
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAA-1-1 (chrI.trna42-LeuTAA) chrI:2802761-2802858 (-) Leu (TAA) 98 bp Sc: 57.0
 GCGGCTATGCCCGAGTGGTctAAGGGGGCAGATTTAAGaggcttctgccttgatcccTGC
 TGTTGTAAAACGCGAGAGTTCGAACCTCTCTGGCCGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-2 (chrI.trna43-LysCTT) chrI:2684683-2684765 (-) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-2 (chrI.trna43-LysCTT) chrI:2684683-2684765 (-) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-2 (chrI.trna44-GlyGCC) chrI:2249180-2249250 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-2 (chrI.trna44-GlyGCC) chrI:2249180-2249250 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-1 (chrI.trna45-ValAAC) chrI:2214733-2214814 (-) Val (AAC) 82 bp Sc: 58.9
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-1 (chrI.trna45-ValAAC) chrI:2214733-2214814 (-) Val (AAC) 82 bp Sc: 58.9
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtgctagttCGCAGACGGtCCCA
 AGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-2-1 (chrI.trna46-LysTTT) chrI:1733764-1733838 (-) Lys (TTT) 75 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-2-1 (chrI.trna46-LysTTT) chrI:1733764-1733838 (-) Lys (TTT) 75 bp Sc: 69.6
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 GTCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-1 (chrI.trna47-GlyGCC) chrI:1646292-1646362 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-1 (chrI.trna47-GlyGCC) chrI:1646292-1646362 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-1 (chrI.trna48-ThrAGT) chrI:1603305-1603376 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-1 (chrI.trna48-ThrAGT) chrI:1603305-1603376 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAG-1-1 (chrI.trna49-LeuCAG) chrI:1527088-1527181 (-) Leu (CAG) 94 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAG-1-1 (chrI.trna49-LeuCAG) chrI:1527088-1527181 (-) Leu (CAG) 94 bp Sc: 67.2
 GGCGAAGTGGCCGAGTGGTctATGGCGCTAGCTTCAGGtgaaagcaatTGCTAGTCTACG
 TATGTGGGCGTGGGTTCGAACCCCACCTTCGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-1 (chrI.trna5-MetCAT) chrI:1096474-1096545 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-1 (chrI.trna5-MetCAT) chrI:1096474-1096545 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-1 (chrI.trna50-MetCAT) chrI:1484979-1485061 (-) Met (CAT) 83 bp Sc: 54.7
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-1 (chrI.trna50-MetCAT) chrI:1484979-1485061 (-) Met (CAT) 83 bp Sc: 54.7
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAttatgacacAGGGGAAGGtCGT
 GAGTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-1 (chrI.trna51-ProAGG) chrI:1449398-1449469 (-) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-1 (chrI.trna51-ProAGG) chrI:1449398-1449469 (-) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-CGG-1-1 (chrI.trna52-ProCGG) chrI:1314924-1315020 (-) Pro (CGG) 97 bp Sc: 49.9
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-CGG-1-1 (chrI.trna52-ProCGG) chrI:1314924-1315020 (-) Pro (CGG) 97 bp Sc: 49.9
 GGCCTAATAGTGTAGTGGTtAACATACCTCTTTCGGGtaatccccacttgtatgctgagt
 tTAGAGGTGAtCCCTGGTTCGAATCCTGGTTAGGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-TGC-1-1 (chrI.trna53-AlaTGC) chrI:1195592-1195663 (-) Ala (TGC) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-TGC-1-1 (chrI.trna53-AlaTGC) chrI:1195592-1195663 (-) Ala (TGC) 72 bp Sc: 67.9
 GGGCATGTGATGCAGTGGTAGCATGCTCGCTTTGCATGCGAGTCGtCCTGGGTTCAATCC
 CCAGCGTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-1 (chrI.trna54-GluTTC) chrI:718119-718190 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-1 (chrI.trna54-GluTTC) chrI:718119-718190 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-TAC-1-1 (chrI.trna55-ValTAC) chrI:703075-703147 (-) Val (TAC) 73 bp Sc: 70.5
+>Schizosaccharomyces_pombe_972h_tRNA-Val-TAC-1-1 (chrI.trna55-ValTAC) chrI:703075-703147 (-) Val (TAC) 73 bp Sc: 70.5
 GCATCTGTAGTCTAGTGGTtATGATTTCTGCTTTACACGCAGACGGtCCCAGGTTCGATC
 CCTGGTAGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-1-1 (chrI.trna6-CysGCA) chrI:1421149-1421221 (+) Cys (GCA) 73 bp Sc: 65.6
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-1-1 (chrI.trna6-CysGCA) chrI:1421149-1421221 (+) Cys (GCA) 73 bp Sc: 65.6
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCGCTGGTTCAAAT
 CCGGCTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-1 (chrI.trna7-LysCTT) chrI:1704582-1704664 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-1 (chrI.trna7-LysCTT) chrI:1704582-1704664 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtaATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-1 (chrI.trna8-TyrGTA) chrI:1746464-1746547 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-1 (chrI.trna8-TyrGTA) chrI:1746464-1746547 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAtttcgatgatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-2-1 (chrI.trna9-IleAAT) chrI:1772296-1772369 (+) Ile (AAT) 74 bp Sc: 59.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-2-1 (chrI.trna9-IleAAT) chrI:1772296-1772369 (+) Ile (AAT) 74 bp Sc: 59.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCAGTTCGAA
 CCTGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-CTG-1-1 (chrII.trna1-GlnCTG) chrII:257454-257525 (+) Gln (CTG) 72 bp Sc: 67.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-CTG-1-1 (chrII.trna1-GlnCTG) chrII:257454-257525 (+) Gln (CTG) 72 bp Sc: 67.8
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTCTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-TGT-2-1 (chrII.trna10-ThrTGT) chrII:1503953-1504024 (+) Thr (TGT) 72 bp Sc: 75.3
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-TGT-2-1 (chrII.trna10-ThrTGT) chrII:1503953-1504024 (+) Thr (TGT) 72 bp Sc: 75.3
 GCCTCTATGGCTTAGTGGTACAGCATCGCACTTGTAATGCGAAGAtCCTTGGTTCGATTC
 CGAGTGGAGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-2 (chrII.trna11-TyrGTA) chrII:1598511-1598594 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-2 (chrII.trna11-TyrGTA) chrII:1598511-1598594 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAttataaagatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-4 (chrII.trna12-LysCTT) chrII:1599706-1599788 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-4 (chrII.trna12-LysCTT) chrII:1599706-1599788 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAcgaatggtATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-3 (chrII.trna13-IleAAT) chrII:1600086-1600159 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-3 (chrII.trna13-IleAAT) chrII:1600086-1600159 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-3 (chrII.trna14-ArgACG) chrII:1602188-1602260 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-3 (chrII.trna14-ArgACG) chrII:1602188-1602260 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-4 (chrII.trna15-IleAAT) chrII:1618293-1618366 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-4 (chrII.trna15-IleAAT) chrII:1618293-1618366 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-5 (chrII.trna16-ValAAC) chrII:1629159-1629241 (+) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-5 (chrII.trna16-ValAAC) chrII:1629159-1629241 (+) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-5 (chrII.trna17-AlaAGC) chrII:1629902-1629975 (+) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-5 (chrII.trna17-AlaAGC) chrII:1629902-1629975 (+) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-3 (chrII.trna18-TyrGTA) chrII:1643849-1643932 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-3 (chrII.trna18-TyrGTA) chrII:1643849-1643932 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAttataaagatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-5 (chrII.trna19-LysCTT) chrII:1645044-1645126 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-5 (chrII.trna19-LysCTT) chrII:1645044-1645126 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAcgaatggtATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-3-1 (chrII.trna2-GlyTCC) chrII:326235-326305 (+) Gly (TCC) 71 bp Sc: 58.7
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-3-1 (chrII.trna2-GlyTCC) chrII:326235-326305 (+) Gly (TCC) 71 bp Sc: 58.7
 GCATCAGTGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGTTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-6 (chrII.trna20-IleAAT) chrII:1645424-1645497 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-6 (chrII.trna20-IleAAT) chrII:1645424-1645497 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-3 (chrII.trna21-TrpCCA) chrII:1774860-1774932 (+) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-3 (chrII.trna21-TrpCCA) chrII:1774860-1774932 (+) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-3 (chrII.trna22-ProAGG) chrII:1877221-1877292 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-3 (chrII.trna22-ProAGG) chrII:1877221-1877292 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-2 (chrII.trna23-AsnGTT) chrII:2032160-2032233 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-2 (chrII.trna23-AsnGTT) chrII:2032160-2032233 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-CCC-1-1 (chrII.trna24-GlyCCC) chrII:2069487-2069557 (+) Gly (CCC) 71 bp Sc: 59.7
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-CCC-1-1 (chrII.trna24-GlyCCC) chrII:2069487-2069557 (+) Gly (CCC) 71 bp Sc: 59.7
 GCATTAGTGGTGTAGCGGTAACATTGGAGCTTCCCATGCTCTAGcTCCGGGTTCGACTCC
 CGGCTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-4 (chrII.trna25-ProAGG) chrII:2319292-2319363 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-4 (chrII.trna25-ProAGG) chrII:2319292-2319363 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-5 (chrII.trna26-ProAGG) chrII:2939715-2939786 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-5 (chrII.trna26-ProAGG) chrII:2939715-2939786 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-1 (chrII.trna27-SerGCT) chrII:3350594-3350688 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-1 (chrII.trna27-SerGCT) chrII:3350594-3350688 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-6 (chrII.trna28-LysCTT) chrII:3814134-3814216 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-6 (chrII.trna28-LysCTT) chrII:3814134-3814216 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-1-1 (chrII.trna29-TyrGTA) chrII:3814558-3814641 (+) Tyr (GTA) 84 bp Sc: 62.6
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-1-1 (chrII.trna29-TyrGTA) chrII:3814558-3814641 (+) Tyr (GTA) 84 bp Sc: 62.6
 CTCCTGATGGTGTAGTTGGTtATCACATCCGGCTGTAAttaaaacgatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-1-2 (chrII.trna3-GlnTTG) chrII:355920-355991 (+) Gln (TTG) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-1-2 (chrII.trna3-GlnTTG) chrII:355920-355991 (+) Gln (TTG) 72 bp Sc: 67.9
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTTTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-2 (chrII.trna30-LeuAAG) chrII:3914043-3914121 (+) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-2 (chrII.trna30-LeuAAG) chrII:3914043-3914121 (+) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-4 (chrII.trna31-AspGTC) chrII:3939227-3939297 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-4 (chrII.trna31-AspGTC) chrII:3939227-3939297 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-3 (chrII.trna32-AsnGTT) chrII:4031743-4031816 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-3 (chrII.trna32-AsnGTT) chrII:4031743-4031816 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-4 (chrII.trna33-GluCTC) chrII:4107639-4107710 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-4 (chrII.trna33-GluCTC) chrII:4107639-4107710 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-2-1 (chrII.trna34-AsnGTT) chrII:4210053-4210126 (-) Asn (GTT) 74 bp Sc: 75.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-2-1 (chrII.trna34-AsnGTT) chrII:4210053-4210126 (-) Asn (GTT) 74 bp Sc: 75.5
 GGTCGGGTAGCGTAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-TGG-2-1 (chrII.trna35-ProTGG) chrII:3360519-3360590 (-) Pro (TGG) 72 bp Sc: 65.1
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-TGG-2-1 (chrII.trna35-ProTGG) chrII:3360519-3360590 (-) Pro (TGG) 72 bp Sc: 65.1
 GGTTTCGTGGTGTAGTGGTAGCATACTTCGTTTGGGTCGAAGTGGtCACGGGTTCAATCC
 CCGTCGAAACCC
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-2-2 (chrII.trna36-LeuAAG) chrII:3209139-3209217 (-) Leu (AAG) 79 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-2-2 (chrII.trna36-LeuAAG) chrII:3209139-3209217 (-) Leu (AAG) 79 bp Sc: 58.4
 GGAAGGTTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACACCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-4 (chrII.trna37-ThrAGT) chrII:2790375-2790446 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-4 (chrII.trna37-ThrAGT) chrII:2790375-2790446 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-1 (chrII.trna38-LeuAAG) chrII:2768257-2768335 (-) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-1 (chrII.trna38-LeuAAG) chrII:2768257-2768335 (-) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-1-1 (chrII.trna39-PheGAA) chrII:2576376-2576448 (-) Phe (GAA) 73 bp Sc: 68.2
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-1-1 (chrII.trna39-PheGAA) chrII:2576376-2576448 (-) Phe (GAA) 73 bp Sc: 68.2
 GTCGCGATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTCGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-1 (chrII.trna4-HisGTG) chrII:464238-464309 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-1 (chrII.trna4-HisGTG) chrII:464238-464309 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-3 (chrII.trna40-MetCAT) chrII:2434303-2434374 (-) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-3 (chrII.trna40-MetCAT) chrII:2434303-2434374 (-) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-2 (chrII.trna41-ProAGG) chrII:1825787-1825858 (-) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-2 (chrII.trna41-ProAGG) chrII:1825787-1825858 (-) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-4 (chrII.trna42-ArgACG) chrII:1647283-1647355 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-4 (chrII.trna42-ArgACG) chrII:1647283-1647355 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-4 (chrII.trna43-GluTTC) chrII:1646829-1646900 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-4 (chrII.trna43-GluTTC) chrII:1646829-1646900 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-6 (chrII.trna44-ValAAC) chrII:1646305-1646387 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-6 (chrII.trna44-ValAAC) chrII:1646305-1646387 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-6 (chrII.trna45-AlaAGC) chrII:1645571-1645644 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-6 (chrII.trna45-AlaAGC) chrII:1645571-1645644 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-6 (chrII.trna46-GlyGCC) chrII:1644675-1644745 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-6 (chrII.trna46-GlyGCC) chrII:1644675-1644745 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-2 (chrII.trna47-LeuCAA) chrII:1644080-1644183 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-2 (chrII.trna47-LeuCAA) chrII:1644080-1644183 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-5 (chrII.trna48-IleAAT) chrII:1630049-1630122 (-) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-5 (chrII.trna48-IleAAT) chrII:1630049-1630122 (-) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-4 (chrII.trna49-ValAAC) chrII:1619174-1619256 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-4 (chrII.trna49-ValAAC) chrII:1619174-1619256 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-4 (chrII.trna5-GlyGCC) chrII:570156-570226 (+) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-4 (chrII.trna5-GlyGCC) chrII:570156-570226 (+) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-4 (chrII.trna50-AlaAGC) chrII:1618440-1618513 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-4 (chrII.trna50-AlaAGC) chrII:1618440-1618513 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-3 (chrII.trna51-AspGTC) chrII:1602347-1602417 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-3 (chrII.trna51-AspGTC) chrII:1602347-1602417 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-3 (chrII.trna52-GluTTC) chrII:1601491-1601562 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-3 (chrII.trna52-GluTTC) chrII:1601491-1601562 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-3 (chrII.trna53-ValAAC) chrII:1600967-1601049 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-3 (chrII.trna53-ValAAC) chrII:1600967-1601049 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-3 (chrII.trna54-AlaAGC) chrII:1600233-1600306 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-3 (chrII.trna54-AlaAGC) chrII:1600233-1600306 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-5 (chrII.trna55-GlyGCC) chrII:1599337-1599407 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-5 (chrII.trna55-GlyGCC) chrII:1599337-1599407 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-1 (chrII.trna56-LeuCAA) chrII:1598742-1598845 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-1 (chrII.trna56-LeuCAA) chrII:1598742-1598845 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-3 (chrII.trna57-MetCAT) chrII:1598075-1598155 (-) Met (CAT) 81 bp Sc: 54.8
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-3 (chrII.trna57-MetCAT) chrII:1598075-1598155 (-) Met (CAT) 81 bp Sc: 54.8
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAtgatgatAGGGGAAGGtCGTGA
 GTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-1 (chrII.trna58-AsnGTT) chrII:1597996-1598069 (-) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-1 (chrII.trna58-AsnGTT) chrII:1597996-1598069 (-) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAA-1-2 (chrII.trna59-LeuTAA) chrII:1402444-1402541 (-) Leu (TAA) 98 bp Sc: 57.0
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAA-1-2 (chrII.trna59-LeuTAA) chrII:1402444-1402541 (-) Leu (TAA) 98 bp Sc: 57.0
 GCGGCTATGCCCGAGTGGTctAAGGGGGCAGATTTAAGaggcctcggccttgatcccTGC
 TGTTGTAAAACGCGAGAGTTCGAACCTCTCTGGCCGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-2 (chrII.trna6-MetCAT) chrII:658451-658531 (+) Met (CAT) 81 bp Sc: 54.8
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-2 (chrII.trna6-MetCAT) chrII:658451-658531 (+) Met (CAT) 81 bp Sc: 54.8
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAtaatgacAGGGGAAGGtCGTGA
 GTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-CCT-1-1 (chrII.trna60-ArgCCT) chrII:1160893-1160994 (-) Arg (CCT) 102 bp Sc: 53.0
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-CCT-1-1 (chrII.trna60-ArgCCT) chrII:1160893-1160994 (-) Arg (CCT) 102 bp Sc: 53.0
 TTACGCGTGGCGCAATGGTAGCGCATCTCATTCCTAtacgacctgatcgttgttggggag
 tgaattACGAGAAGGtTGCGGGTTCGAGTCCCGTCGTGTAAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-3 (chrII.trna61-SerAGA) chrII:744754-744835 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-3 (chrII.trna61-SerAGA) chrII:744754-744835 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-1-1 (chrII.trna62-LysTTT) chrII:602625-602699 (-) Lys (TTT) 75 bp Sc: 72.0
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-1-1 (chrII.trna62-LysTTT) chrII:602625-602699 (-) Lys (TTT) 75 bp Sc: 72.0
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 ATCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCT-2-1 (chrII.trna63-ArgTCT) chrII:326652-326724 (-) Arg (TCT) 73 bp Sc: 63.5
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCT-2-1 (chrII.trna63-ArgTCT) chrII:326652-326724 (-) Arg (TCT) 73 bp Sc: 63.5
 GCTCCCGTGGCCTAATGGCtAGGGCATTTGACTTCTAATCAAGGGAtTGTGGGTTCGAGT
 CCCGCCGGGAGCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-1-1 (chrII.trna64-GlyTCC) chrII:285389-285459 (-) Gly (TCC) 71 bp Sc: 63.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-1-1 (chrII.trna64-GlyTCC) chrII:285389-285459 (-) Gly (TCC) 71 bp Sc: 63.8
 GCATCGATGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGTCGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-CTG-1-2 (chrII.trna65-GlnCTG) chrII:258848-258919 (-) Gln (CTG) 72 bp Sc: 67.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-CTG-1-2 (chrII.trna65-GlnCTG) chrII:258848-258919 (-) Gln (CTG) 72 bp Sc: 67.8
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTCTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-1-1 (chrII.trna66-GlnTTG) chrII:257908-257979 (-) Gln (TTG) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-1-1 (chrII.trna66-GlnTTG) chrII:257908-257979 (-) Gln (TTG) 72 bp Sc: 67.9
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTTTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-3 (chrII.trna67-GlyGCC) chrII:180994-181064 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-3 (chrII.trna67-GlyGCC) chrII:180994-181064 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-2 (chrII.trna7-TrpCCA) chrII:717076-717148 (+) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-2 (chrII.trna7-TrpCCA) chrII:717076-717148 (+) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-3 (chrII.trna8-GluCTC) chrII:820491-820562 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-3 (chrII.trna8-GluCTC) chrII:820491-820562 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-2 (chrII.trna9-HisGTG) chrII:960729-960800 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-2 (chrII.trna9-HisGTG) chrII:960729-960800 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-3 (chrIII.trna1-HisGTG) chrIII:71400-71471 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-3 (chrIII.trna1-HisGTG) chrIII:71400-71471 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-3 (chrIII.trna10-LeuAAG) chrIII:1069166-1069244 (+) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-3 (chrIII.trna10-LeuAAG) chrIII:1069166-1069244 (+) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-7 (chrIII.trna11-LysCTT) chrIII:1071093-1071175 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-7 (chrIII.trna11-LysCTT) chrIII:1071093-1071175 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-6 (chrIII.trna12-AspGTC) chrIII:1092437-1092507 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-6 (chrIII.trna12-AspGTC) chrIII:1092437-1092507 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-8 (chrIII.trna13-ValAAC) chrIII:1092934-1093016 (+) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-8 (chrIII.trna13-ValAAC) chrIII:1092934-1093016 (+) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-4 (chrIII.trna14-LeuCAA) chrIII:1102809-1102912 (+) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-4 (chrIII.trna14-LeuCAA) chrIII:1102809-1102912 (+) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-6 (chrIII.trna15-ThrAGT) chrIII:1105840-1105911 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-6 (chrIII.trna15-ThrAGT) chrIII:1105840-1105911 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-8 (chrIII.trna16-ArgACG) chrIII:1106327-1106399 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-8 (chrIII.trna16-ArgACG) chrIII:1106327-1106399 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-2 (chrIII.trna17-SerGCT) chrIII:1253193-1253287 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-2 (chrIII.trna17-SerGCT) chrIII:1253193-1253287 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-9 (chrIII.trna18-LysCTT) chrIII:1475034-1475116 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-9 (chrIII.trna18-LysCTT) chrIII:1475034-1475116 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-TGA-2-1 (chrIII.trna19-SerTGA) chrIII:1689713-1689809 (+) Ser (TGA) 97 bp Sc: 84.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-TGA-2-1 (chrIII.trna19-SerTGA) chrIII:1689713-1689809 (+) Ser (TGA) 97 bp Sc: 84.0
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTTGAAtcctgtattctagtcATCTAATG
 GGCTCTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-5 (chrIII.trna2-GluCTC) chrIII:140967-141038 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-5 (chrIII.trna2-GluCTC) chrIII:140967-141038 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-4 (chrIII.trna20-MetCAT) chrIII:1689817-1689888 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-4 (chrIII.trna20-MetCAT) chrIII:1689817-1689888 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-5 (chrIII.trna21-AsnGTT) chrIII:1701899-1701972 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-5 (chrIII.trna21-AsnGTT) chrIII:1701899-1701972 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-6 (chrIII.trna22-ProAGG) chrIII:1788949-1789020 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-6 (chrIII.trna22-ProAGG) chrIII:1788949-1789020 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-4 (chrIII.trna23-HisGTG) chrIII:1844639-1844710 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-4 (chrIII.trna23-HisGTG) chrIII:1844639-1844710 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-2-1 (chrIII.trna24-GlnTTG) chrIII:1863131-1863202 (+) Gln (TTG) 72 bp Sc: 65.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-2-1 (chrIII.trna24-GlnTTG) chrIII:1863131-1863202 (+) Gln (TTG) 72 bp Sc: 65.2
 GGTTGTATGGTGTAGCGGTtAGCACGCGAGATTTTGATTCTCGAGaTCTGGGTTCGACTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-2-1 (chrIII.trna25-GlyTCC) chrIII:2037352-2037422 (+) Gly (TCC) 71 bp Sc: 63.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-2-1 (chrIII.trna25-GlyTCC) chrIII:2037352-2037422 (+) Gly (TCC) 71 bp Sc: 63.2
 GCATCAGTGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGCTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-3 (chrIII.trna26-SerGCT) chrIII:2072080-2072174 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-3 (chrIII.trna26-SerGCT) chrIII:2072080-2072174 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-8 (chrIII.trna27-AspGTC) chrIII:2139408-2139478 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-8 (chrIII.trna27-AspGTC) chrIII:2139408-2139478 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-2-2 (chrIII.trna28-GlnTTG) chrIII:2074991-2075062 (-) Gln (TTG) 72 bp Sc: 65.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-2-2 (chrIII.trna28-GlnTTG) chrIII:2074991-2075062 (-) Gln (TTG) 72 bp Sc: 65.2
 GGTTGTATGGTGTAGCGGTtAGCACGCGAGATTTTGATTCTCGAGaTCTGGGTTCGACTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-7 (chrIII.trna29-SerAGA) chrIII:1775992-1776073 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-7 (chrIII.trna29-SerAGA) chrIII:1775992-1776073 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCT-1-1 (chrIII.trna3-ArgTCT) chrIII:578847-578919 (+) Arg (TCT) 73 bp Sc: 68.4
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCT-1-1 (chrIII.trna3-ArgTCT) chrIII:578847-578919 (+) Arg (TCT) 73 bp Sc: 68.4
 GCTCCCGTGGCCTAATGGCtAGGGCATTTGACTTCTAATCAAGGGAtTGCGGGTTCGAGT
 CCCGCCGGGAGCT
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-TGT-1-1 (chrIII.trna30-ThrTGT) chrIII:1361090-1361161 (-) Thr (TGT) 72 bp Sc: 76.0
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-TGT-1-1 (chrIII.trna30-ThrTGT) chrIII:1361090-1361161 (-) Thr (TGT) 72 bp Sc: 76.0
 GCCCCTATGGCTTAGTGGTACAGCATCGCACTTGTAATGCGAAGAtCCTTGGTTCGATTC
 CGAGTGGGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-TAC-1-2 (chrIII.trna31-ValTAC) chrIII:1206747-1206819 (-) Val (TAC) 73 bp Sc: 70.5
+>Schizosaccharomyces_pombe_972h_tRNA-Val-TAC-1-2 (chrIII.trna31-ValTAC) chrIII:1206747-1206819 (-) Val (TAC) 73 bp Sc: 70.5
 GCATCTGTAGTCTAGTGGTtATGATTTCTGCTTTACACGCAGACGGtCCCAGGTTCGATC
 CCTGGTAGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-4 (chrIII.trna32-PheGAA) chrIII:1142192-1142264 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-4 (chrIII.trna32-PheGAA) chrIII:1142192-1142264 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-8 (chrIII.trna33-LysCTT) chrIII:1139536-1139618 (-) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-8 (chrIII.trna33-LysCTT) chrIII:1139536-1139618 (-) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-7 (chrIII.trna34-AspGTC) chrIII:1106487-1106557 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-7 (chrIII.trna34-AspGTC) chrIII:1106487-1106557 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-9 (chrIII.trna35-ValAAC) chrIII:1105978-1106060 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-9 (chrIII.trna35-ValAAC) chrIII:1105978-1106060 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-6 (chrIII.trna36-GluCTC) chrIII:1097499-1097570 (-) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-6 (chrIII.trna36-GluCTC) chrIII:1097499-1097570 (-) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-3 (chrIII.trna37-LeuCAA) chrIII:1096082-1096185 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-3 (chrIII.trna37-LeuCAA) chrIII:1096082-1096185 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-5 (chrIII.trna38-ThrAGT) chrIII:1093083-1093154 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-5 (chrIII.trna38-ThrAGT) chrIII:1093083-1093154 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-7 (chrIII.trna39-ArgACG) chrIII:1092595-1092667 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-7 (chrIII.trna39-ArgACG) chrIII:1092595-1092667 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-2-2 (chrIII.trna4-IleAAT) chrIII:817425-817498 (+) Ile (AAT) 74 bp Sc: 59.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-2-2 (chrIII.trna4-IleAAT) chrIII:817425-817498 (+) Ile (AAT) 74 bp Sc: 59.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCAGTTCGAA
 CCTGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-6 (chrIII.trna40-ArgACG) chrIII:1068182-1068254 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-6 (chrIII.trna40-ArgACG) chrIII:1068182-1068254 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCG-1-1 (chrIII.trna41-ArgTCG) chrIII:1067092-1067164 (-) Arg (TCG) 73 bp Sc: 62.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCG-1-1 (chrIII.trna41-ArgTCG) chrIII:1067092-1067164 (-) Arg (TCG) 73 bp Sc: 62.8
 GGGTGTGTAGCCTAATGGTtAAGGCGTTGGTTTTCGGCACCAAAGAcTGCAGGTTCGAGT
 CCTGTCACACTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-7 (chrIII.trna42-ValAAC) chrIII:1065778-1065860 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-7 (chrIII.trna42-ValAAC) chrIII:1065778-1065860 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-8 (chrIII.trna43-GlyGCC) chrIII:820567-820637 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-8 (chrIII.trna43-GlyGCC) chrIII:820567-820637 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-4 (chrIII.trna44-SerAGA) chrIII:473199-473280 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-4 (chrIII.trna44-SerAGA) chrIII:473199-473280 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-3 (chrIII.trna45-PheGAA) chrIII:331228-331300 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-3 (chrIII.trna45-PheGAA) chrIII:331228-331300 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-7 (chrIII.trna46-GlyGCC) chrIII:113716-113786 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-7 (chrIII.trna46-GlyGCC) chrIII:113716-113786 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-5 (chrIII.trna5-SerAGA) chrIII:847701-847782 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-5 (chrIII.trna5-SerAGA) chrIII:847701-847782 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-5 (chrIII.trna6-ArgACG) chrIII:925852-925924 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-5 (chrIII.trna6-ArgACG) chrIII:925852-925924 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-4 (chrIII.trna7-AsnGTT) chrIII:947262-947335 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-4 (chrIII.trna7-AsnGTT) chrIII:947262-947335 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-6 (chrIII.trna8-SerAGA) chrIII:1066628-1066709 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-6 (chrIII.trna8-SerAGA) chrIII:1066628-1066709 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-5 (chrIII.trna9-AspGTC) chrIII:1068029-1068099 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-5 (chrIII.trna9-AspGTC) chrIII:1068029-1068099 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
diff --git a/data/schiPomb_eColitK/schiPomb-mitotRNAs.fa b/data/schiPomb_eColitK/schiPomb-mitotRNAs.fa
new file mode 100644
index 0000000..36cb8b6
--- /dev/null
+++ b/data/schiPomb_eColitK/schiPomb-mitotRNAs.fa
@@ -0,0 +1,75 @@
+>URS000040774E_4896|Schizosaccharomyces_pombe|9606|Trp|TCA
+AAGAGTATAGTTTAATTGGTAAAACTTCTGATTCCAAATTAGACATTGTTCGTTCAAGTC
+GGACTGCTCTTG
+>URS000052E18F_4896|Schizosaccharomyces_pombe|9606|Cys|GCA
+GATAATGTTCAGTGGTCTGAAATTGAATTTGCAAAATTTGATATATGAGTTCAATTCTCA
+TCATTATCT
+>URS00002C4932_4896|Schizosaccharomyces_pombe|9606|Val|TAC
+AGGAGAATAGCTTAATTGGTAGAGCACTTACCTTACAAGTAAGATTATAAGGGTTCAAAT
+CCCTTTTCTCCTA
+>URS00003B0065_4896|Schizosaccharomyces_pombe|9606|Leu|TAG
+GCAGATGTGATGAAATTGGTAAACATGTTTACCTTAGGAGTAAAATCTTGAAGGTTCGAA
+TCCTTCCATCTGTA
+>URS00001AD663_4896|Schizosaccharomyces_pombe|9606|Leu|TAA
+GCCTAAATGCTGGAATTTGGTAGACAGAACAAACTTAAGATTTGTCGCTTTCGAGCGTGT
+TGGTTCGAGTCCAACTTTAGGTA
+>URS00001DDDAC_4896|Schizosaccharomyces_pombe|9606|Ile|GAT
+AGTTCTTTAACTTAAAAGGTCAGAGTGCAGACTTGATAAGTCTGTGGTATTGGTTCGATT
+CCAATAAGAACTA
+>URS00000E510A_4896|Schizosaccharomyces_pombe|9606|Ser|TGA
+GGAAGGGTGTCCGAGTGGTTTAAGGAGCGATATTTGAGCTATTGTGATTTATTCATCGCA
+GGTTCGAATCCTGCCCCTTTCG
+>URS00000B84DA_4896|Schizosaccharomyces_pombe|9606|Arg|TCG
+GCACTTTTAGCTTAATTGGTTAGAGTAACAATCTTCGAAATTGTTAGTATAGGTTCAAAT
+CCTATAAAGTGTT
+>URS00005E6A72_4896|Schizosaccharomyces_pombe|9606|Gly|TCC
+GCAGATATAAGTCAATTGGCAGACCTTCTGATTTCCACTTAGATTATGTTCGTTCGAATC
+GGACTATCTGCA
+>URS00000E1077_4896|Schizosaccharomyces_pombe|9606|Asn|GTT
+GTTGTTGTAGCTCAATGGTAGAGCAAGTCACTGTTAATGACCTGATAGTGGTTCGATTCC
+ACTCAATAACG
+>URS00000A90BD_4896|Schizosaccharomyces_pombe|9606|Lys|TTT
+GGGGATGTAGCTCAATGGTTAGAGCTTTCGCCTTTTAAGCGATAGGATAAGGGTTCAAAT
+CCCTTCAGACCCA
+>URS0000226DF4_4896|Schizosaccharomyces_pombe|9606|Glu|TTC
+GGCTCTATTGTCTAATGGTTAAGACCTTACATCTTCATTGTAAATATCTTGGTTCGATTC
+CAAGTAGGGCTA
+>URS000027C703_4896|Schizosaccharomyces_pombe|9606|Ser|GCT
+GGAAAAATAGTTCTAATTGGTAAGAAGGATACTTGCTACGTATCTGGTGAATAACCTTGT
+GAGTTCGAGTCTCACTTTTTCCG
+>URS000012A615_4896|Schizosaccharomyces_pombe|9606|Thr|TGT
+GCTAATTTAACTCAATTGGTAGAGTGCGTACCTTGTAAGTACGAAGTTAGAGGTTCAATT
+CCTCTAATTAGCA
+>URS0000519C3F_4896|Schizosaccharomyces_pombe|9606|Glu|TTC
+TGGGTTGTTGACTAATAGGTAAGTCCCTGAAATTTGACTTCAGTCTATGTAAGTTCGAAT
+CTTACCATCCCAT
+>URS0000101C2D_4896|Schizosaccharomyces_pombe|9606|Met|CAT
+TGCGATTTAATGTAATTGGTTAACATCTCTGACTCATGATCAGTGTATTAAGGTTCAAGT
+CCTTAGGTCGCAC
+>URS00003C6042_4896|Schizosaccharomyces_pombe|9606|Ile|GAT
+AGGATTATAGCTTAACGGTTAAAGCAGAGAGCTCATAACTCTTGTATATTGGTTCGATTC
+CAGTTTGTCCTA
+>URS0000409C5E_4896|Schizosaccharomyces_pombe|9606|Phe|GAA
+GCTCTGATAACTTAACGGTTAAAGTGCAGTATTGAAGCTGCTGAGATATTGGTTCGATTC
+CATTTCAGAGCA
+>URS00001B646E_4896|Schizosaccharomyces_pombe|9606|Met|CAT
+GTTGGTATAGTTTAATTGGTTAAAATAATCTCCTCATGTGAGATTGATCTATAGGTTCGA
+GCCCTTTTACCAACT
+>URS00000FEDF7_4896|Schizosaccharomyces_pombe|9606|Ala|TGC
+GGGGATTTAATTTAATTGGTTAGAATATTGTGTTTGCACCACAAAAATCTGGTTTCGAGT
+ACCAGAATCTCCA
+>URS000045D66C_4896|Schizosaccharomyces_pombe|9606|His|GTG
+GGTGATTGTAATTCAATGGTAGAATGCTTATTTGTGGCATAAGAAGTTCTTGGTTCGATT
+CCAAGTAATCACC
+>URS000023E104_4896|Schizosaccharomyces_pombe|9606|Asp|GTC
+GAATCTGTAGCTTAAAGTAAAGTATCGCCTTGTCACGGTGATGGATGCCCACTCGTACTG
+GGTCAGATTCG
+>URS000025B7E6_4896|Schizosaccharomyces_pombe|9606|Pro|TGG
+CGGATAGAAACATGTATTGGTTCATGTACTTGCTTTGGGTGTGAGAATTTGTTAGTTCGA
+ATCTAACCTATCCGA
+>URS00004A6ED0_4896|Schizosaccharomyces_pombe|9606|Tyr|GTA
+GGGGAGAATTCTTATGTTGGTTTTAAGAGGTGAGTTGTAGCCTCATTAGGTCAATCCTAT
+CGCAGGTTCGATTCCTGCTCTCCTCA
+>URS00003FFD19_4896|Schizosaccharomyces_pombe|9606|Arg|TCG
+GTCTGTATAGCTCAATGGTAGAGCATCTCACTTCTAATGAGTCGATCTAAGTTCGATTCT
+TAGTACAGATTCCACAC
diff --git a/data/schiPomb_eColitK/schiPomb_972H-tRNAs.fa b/data/schiPomb_eColitK/schiPomb_972H-tRNAs.fa
index 24d8b73..38b6fb7 100644
--- a/data/schiPomb_eColitK/schiPomb_972H-tRNAs.fa
+++ b/data/schiPomb_eColitK/schiPomb_972H-tRNAs.fa
@@ -1,507 +1,507 @@
 >Escherichia_coli_str_K_12_substr_MG1655_tRNA-eColiLys-TTT-1-1 (tRNAscan-SE ID: chr.trna9) chr:780554-780629 (+) Lys (TTT) 76 bp Sc: 94.9
 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGtCGCAGGTTCGAAT
 CCTGCACGACCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-TGG-1-1 (chrI.trna1-ProTGG) chrI:365155-365226 (+) Pro (TGG) 72 bp Sc: 65.3
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-TGG-1-1 (chrI.trna1-ProTGG) chrI:365155-365226 (+) Pro (TGG) 72 bp Sc: 65.3
 GGCTTCGTGGTGTAGTGGTAGCATACTTCGTTTGGGTCGAAGTGGtCAGGGGTTCGATCC
 CCCTCGAAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-2 (chrI.trna10-ThrAGT) chrI:2433048-2433119 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-2 (chrI.trna10-ThrAGT) chrI:2433048-2433119 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-2-2 (chrI.trna11-LysTTT) chrI:2441963-2442037 (+) Lys (TTT) 75 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-2-2 (chrI.trna11-LysTTT) chrI:2441963-2442037 (+) Lys (TTT) 75 bp Sc: 69.6
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 GTCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-2-1 (chrI.trna12-CysGCA) chrI:2510538-2510610 (+) Cys (GCA) 73 bp Sc: 63.7
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-2-1 (chrI.trna12-CysGCA) chrI:2510538-2510610 (+) Cys (GCA) 73 bp Sc: 63.7
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCACTGGTTCAAAT
 CCGGTTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-TAT-1-1 (chrI.trna13-IleTAT) chrI:2578426-2578524 (+) Ile (TAT) 99 bp Sc: 64.5
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-TAT-1-1 (chrI.trna13-IleTAT) chrI:2578426-2578524 (+) Ile (TAT) 99 bp Sc: 64.5
 GCTCCCGTGGCCAAGCTGGTtAAGGCCTCATGCTTATAtgatactccccttaggaggtgt
 gttACGTGGAAAtCGCGAGTTCGATCCTCGCCGGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-3 (chrI.trna14-LysCTT) chrI:3086310-3086392 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-3 (chrI.trna14-LysCTT) chrI:3086310-3086392 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-TGC-1-2 (chrI.trna15-AlaTGC) chrI:3157430-3157501 (+) Ala (TGC) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-TGC-1-2 (chrI.trna15-AlaTGC) chrI:3157430-3157501 (+) Ala (TGC) 72 bp Sc: 67.9
 GGGCATGTGATGCAGTGGTAGCATGCTCGCTTTGCATGCGAGTCGtCCTGGGTTCAATCC
 CCAGCGTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-CGT-1-1 (chrI.trna16-ThrCGT) chrI:3164749-3164820 (+) Thr (CGT) 72 bp Sc: 72.5
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-CGT-1-1 (chrI.trna16-ThrCGT) chrI:3164749-3164820 (+) Thr (CGT) 72 bp Sc: 72.5
 GCTCTTGTAGCTCAGTGGTAGAGCGCCTGTCTCGTAAACAGGAGGtCCAGTGTTCGAGTC
 ACTGCCGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-CCG-1-1 (chrI.trna17-ArgCCG) chrI:3443055-3443144 (+) Arg (CCG) 90 bp Sc: 30.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-CCG-1-1 (chrI.trna17-ArgCCG) chrI:3443055-3443144 (+) Arg (CCG) 90 bp Sc: 30.8
 GGCCTCGTGGCCTAGAAGTAAGGCGTTGGTTTCCGGtggaggagactccaggttCGCCAA
 AGAtCGCGAGTGCAAATCTCGCCGTGGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAG-1-1 (chrI.trna18-LeuTAG) chrI:3591948-3592044 (+) Leu (TAG) 97 bp Sc: 54.3
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAG-1-1 (chrI.trna18-LeuTAG) chrI:3591948-3592044 (+) Leu (TAG) 97 bp Sc: 54.3
 GGATGGGTGTCCGAGTGGTtATGGAGCTGGCTTTAGGtgcgttcaacgcattgcaCGCCA
 GTGCGAAAGCTCGCGGGTTCGAGTCCCGTCCCATTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-1-2 (chrI.trna19-CysGCA) chrI:3700665-3700737 (+) Cys (GCA) 73 bp Sc: 65.6
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-1-2 (chrI.trna19-CysGCA) chrI:3700665-3700737 (+) Cys (GCA) 73 bp Sc: 65.6
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCGCTGGTTCAAAT
 CCGGCTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Val-CAC-1-1 (chrI.trna2-ValCAC) chrI:446000-446071 (+) Val (CAC) 72 bp Sc: 64.7
+>Schizosaccharomyces_pombe_972h_tRNA-Val-CAC-1-1 (chrI.trna2-ValCAC) chrI:446000-446071 (+) Val (CAC) 72 bp Sc: 64.7
 AGTCCCGTGTTCTAGTGGTATGATTTCTCCTTCACACGGAGAAGGtCCCGGGTTCGATCC
 CCGGCGGGACTA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-1 (chrI.trna20-PheGAA) chrI:3701556-3701628 (+) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-1 (chrI.trna20-PheGAA) chrI:3701556-3701628 (+) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-1 (chrI.trna21-ArgACG) chrI:3736520-3736592 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-1 (chrI.trna21-ArgACG) chrI:3736520-3736592 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-1 (chrI.trna22-IleAAT) chrI:3768290-3768363 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-1 (chrI.trna22-IleAAT) chrI:3768290-3768363 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-2 (chrI.trna23-GluCTC) chrI:3776768-3776839 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-2 (chrI.trna23-GluCTC) chrI:3776768-3776839 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-2 (chrI.trna24-AlaAGC) chrI:3777192-3777265 (+) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-2 (chrI.trna24-AlaAGC) chrI:3777192-3777265 (+) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-TGA-1-1 (chrI.trna25-SerTGA) chrI:4265149-4265245 (+) Ser (TGA) 97 bp Sc: 84.7
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-TGA-1-1 (chrI.trna25-SerTGA) chrI:4265149-4265245 (+) Ser (TGA) 97 bp Sc: 84.7
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTTGAAtcctgtattctagtcATCTAATG
 GGCTTTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-2 (chrI.trna26-MetCAT) chrI:4265253-4265324 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-2 (chrI.trna26-MetCAT) chrI:4265253-4265324 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-1 (chrI.trna27-AspGTC) chrI:4532857-4532927 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-1 (chrI.trna27-AspGTC) chrI:4532857-4532927 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-3 (chrI.trna28-ThrAGT) chrI:4715431-4715502 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-3 (chrI.trna28-ThrAGT) chrI:4715431-4715502 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-CGC-1-1 (chrI.trna29-AlaCGC) chrI:4796977-4797059 (+) Ala (CGC) 83 bp Sc: 66.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-CGC-1-1 (chrI.trna29-AlaCGC) chrI:4796977-4797059 (+) Ala (CGC) 83 bp Sc: 66.3
 GGGGATGTAGTTTAGGGGTATAACGTTTCATTCGCAtagttcgcaccTTGAAAAGGtCCC
 GGGTTCGATTCCCGGCATCTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-2 (chrI.trna3-GluTTC) chrI:957183-957254 (+) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-2 (chrI.trna3-GluTTC) chrI:957183-957254 (+) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-2 (chrI.trna30-SerAGA) chrI:5437747-5437828 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-2 (chrI.trna30-SerAGA) chrI:5437747-5437828 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-2 (chrI.trna31-AspGTC) chrI:5232917-5232987 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-2 (chrI.trna31-AspGTC) chrI:5232917-5232987 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-2 (chrI.trna32-ArgACG) chrI:5045132-5045204 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-2 (chrI.trna32-ArgACG) chrI:5045132-5045204 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-2-1 (chrI.trna33-LeuAAG) chrI:4059028-4059106 (-) Leu (AAG) 79 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-2-1 (chrI.trna33-LeuAAG) chrI:4059028-4059106 (-) Leu (AAG) 79 bp Sc: 58.4
 GGAAGGTTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACACCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-2 (chrI.trna34-IleAAT) chrI:3773910-3773983 (-) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-2 (chrI.trna34-IleAAT) chrI:3773910-3773983 (-) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-1 (chrI.trna35-GluCTC) chrI:3765434-3765505 (-) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-1 (chrI.trna35-GluCTC) chrI:3765434-3765505 (-) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-1 (chrI.trna36-AlaAGC) chrI:3765008-3765081 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-1 (chrI.trna36-AlaAGC) chrI:3765008-3765081 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-2 (chrI.trna37-PheGAA) chrI:3752334-3752406 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-2 (chrI.trna37-PheGAA) chrI:3752334-3752406 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-2 (chrI.trna38-ValAAC) chrI:3710739-3710821 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-2 (chrI.trna38-ValAAC) chrI:3710739-3710821 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-1 (chrI.trna39-TrpCCA) chrI:3559754-3559826 (-) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-1 (chrI.trna39-TrpCCA) chrI:3559754-3559826 (-) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-CGA-1-1 (chrI.trna4-SerCGA) chrI:1096369-1096466 (+) Ser (CGA) 98 bp Sc: 83.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-CGA-1-1 (chrI.trna4-SerCGA) chrI:1096369-1096466 (+) Ser (CGA) 98 bp Sc: 83.9
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTCGAAttcctacattcgtggcATCTAAT
 GGGCTCTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-1 (chrI.trna40-SerAGA) chrI:3047677-3047758 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-1 (chrI.trna40-SerAGA) chrI:3047677-3047758 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-1-1 (chrI.trna41-ThrAGT) chrI:2844674-2844745 (-) Thr (AGT) 72 bp Sc: 81.0
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-1-1 (chrI.trna41-ThrAGT) chrI:2844674-2844745 (-) Thr (AGT) 72 bp Sc: 81.0
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCGAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAA-1-1 (chrI.trna42-LeuTAA) chrI:2802761-2802858 (-) Leu (TAA) 98 bp Sc: 57.0
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAA-1-1 (chrI.trna42-LeuTAA) chrI:2802761-2802858 (-) Leu (TAA) 98 bp Sc: 57.0
 GCGGCTATGCCCGAGTGGTctAAGGGGGCAGATTTAAGaggcttctgccttgatcccTGC
 TGTTGTAAAACGCGAGAGTTCGAACCTCTCTGGCCGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-2 (chrI.trna43-LysCTT) chrI:2684683-2684765 (-) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-2 (chrI.trna43-LysCTT) chrI:2684683-2684765 (-) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-2 (chrI.trna44-GlyGCC) chrI:2249180-2249250 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-2 (chrI.trna44-GlyGCC) chrI:2249180-2249250 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-1 (chrI.trna45-ValAAC) chrI:2214733-2214814 (-) Val (AAC) 82 bp Sc: 58.9
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-1 (chrI.trna45-ValAAC) chrI:2214733-2214814 (-) Val (AAC) 82 bp Sc: 58.9
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtgctagttCGCAGACGGtCCCA
 AGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-2-1 (chrI.trna46-LysTTT) chrI:1733764-1733838 (-) Lys (TTT) 75 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-2-1 (chrI.trna46-LysTTT) chrI:1733764-1733838 (-) Lys (TTT) 75 bp Sc: 69.6
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 GTCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-1 (chrI.trna47-GlyGCC) chrI:1646292-1646362 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-1 (chrI.trna47-GlyGCC) chrI:1646292-1646362 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-1 (chrI.trna48-ThrAGT) chrI:1603305-1603376 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-1 (chrI.trna48-ThrAGT) chrI:1603305-1603376 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAG-1-1 (chrI.trna49-LeuCAG) chrI:1527088-1527181 (-) Leu (CAG) 94 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAG-1-1 (chrI.trna49-LeuCAG) chrI:1527088-1527181 (-) Leu (CAG) 94 bp Sc: 67.2
 GGCGAAGTGGCCGAGTGGTctATGGCGCTAGCTTCAGGtgaaagcaatTGCTAGTCTACG
 TATGTGGGCGTGGGTTCGAACCCCACCTTCGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-1 (chrI.trna5-MetCAT) chrI:1096474-1096545 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-1 (chrI.trna5-MetCAT) chrI:1096474-1096545 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-1 (chrI.trna50-MetCAT) chrI:1484979-1485061 (-) Met (CAT) 83 bp Sc: 54.7
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-1 (chrI.trna50-MetCAT) chrI:1484979-1485061 (-) Met (CAT) 83 bp Sc: 54.7
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAttatgacacAGGGGAAGGtCGT
 GAGTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-1 (chrI.trna51-ProAGG) chrI:1449398-1449469 (-) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-1 (chrI.trna51-ProAGG) chrI:1449398-1449469 (-) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-CGG-1-1 (chrI.trna52-ProCGG) chrI:1314924-1315020 (-) Pro (CGG) 97 bp Sc: 49.9
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-CGG-1-1 (chrI.trna52-ProCGG) chrI:1314924-1315020 (-) Pro (CGG) 97 bp Sc: 49.9
 GGCCTAATAGTGTAGTGGTtAACATACCTCTTTCGGGtaatccccacttgtatgctgagt
 tTAGAGGTGAtCCCTGGTTCGAATCCTGGTTAGGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-TGC-1-1 (chrI.trna53-AlaTGC) chrI:1195592-1195663 (-) Ala (TGC) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-TGC-1-1 (chrI.trna53-AlaTGC) chrI:1195592-1195663 (-) Ala (TGC) 72 bp Sc: 67.9
 GGGCATGTGATGCAGTGGTAGCATGCTCGCTTTGCATGCGAGTCGtCCTGGGTTCAATCC
 CCAGCGTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-1 (chrI.trna54-GluTTC) chrI:718119-718190 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-1 (chrI.trna54-GluTTC) chrI:718119-718190 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-TAC-1-1 (chrI.trna55-ValTAC) chrI:703075-703147 (-) Val (TAC) 73 bp Sc: 70.5
+>Schizosaccharomyces_pombe_972h_tRNA-Val-TAC-1-1 (chrI.trna55-ValTAC) chrI:703075-703147 (-) Val (TAC) 73 bp Sc: 70.5
 GCATCTGTAGTCTAGTGGTtATGATTTCTGCTTTACACGCAGACGGtCCCAGGTTCGATC
 CCTGGTAGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Cys-GCA-1-1 (chrI.trna6-CysGCA) chrI:1421149-1421221 (+) Cys (GCA) 73 bp Sc: 65.6
+>Schizosaccharomyces_pombe_972h_tRNA-Cys-GCA-1-1 (chrI.trna6-CysGCA) chrI:1421149-1421221 (+) Cys (GCA) 73 bp Sc: 65.6
 GGGGTCATAGCTCAGTGGTtAGAGTGAGGGATTGCAGATCCCCAGGtCGCTGGTTCAAAT
 CCGGCTGGTCCCT
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-1 (chrI.trna7-LysCTT) chrI:1704582-1704664 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-1 (chrI.trna7-LysCTT) chrI:1704582-1704664 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtaATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-1 (chrI.trna8-TyrGTA) chrI:1746464-1746547 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-1 (chrI.trna8-TyrGTA) chrI:1746464-1746547 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAtttcgatgatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-2-1 (chrI.trna9-IleAAT) chrI:1772296-1772369 (+) Ile (AAT) 74 bp Sc: 59.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-2-1 (chrI.trna9-IleAAT) chrI:1772296-1772369 (+) Ile (AAT) 74 bp Sc: 59.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCAGTTCGAA
 CCTGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-CTG-1-1 (chrII.trna1-GlnCTG) chrII:257454-257525 (+) Gln (CTG) 72 bp Sc: 67.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-CTG-1-1 (chrII.trna1-GlnCTG) chrII:257454-257525 (+) Gln (CTG) 72 bp Sc: 67.8
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTCTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-TGT-2-1 (chrII.trna10-ThrTGT) chrII:1503953-1504024 (+) Thr (TGT) 72 bp Sc: 75.3
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-TGT-2-1 (chrII.trna10-ThrTGT) chrII:1503953-1504024 (+) Thr (TGT) 72 bp Sc: 75.3
 GCCTCTATGGCTTAGTGGTACAGCATCGCACTTGTAATGCGAAGAtCCTTGGTTCGATTC
 CGAGTGGAGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-2 (chrII.trna11-TyrGTA) chrII:1598511-1598594 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-2 (chrII.trna11-TyrGTA) chrII:1598511-1598594 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAttataaagatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-4 (chrII.trna12-LysCTT) chrII:1599706-1599788 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-4 (chrII.trna12-LysCTT) chrII:1599706-1599788 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAcgaatggtATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-3 (chrII.trna13-IleAAT) chrII:1600086-1600159 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-3 (chrII.trna13-IleAAT) chrII:1600086-1600159 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-3 (chrII.trna14-ArgACG) chrII:1602188-1602260 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-3 (chrII.trna14-ArgACG) chrII:1602188-1602260 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-4 (chrII.trna15-IleAAT) chrII:1618293-1618366 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-4 (chrII.trna15-IleAAT) chrII:1618293-1618366 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-5 (chrII.trna16-ValAAC) chrII:1629159-1629241 (+) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-5 (chrII.trna16-ValAAC) chrII:1629159-1629241 (+) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-5 (chrII.trna17-AlaAGC) chrII:1629902-1629975 (+) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-5 (chrII.trna17-AlaAGC) chrII:1629902-1629975 (+) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-2-3 (chrII.trna18-TyrGTA) chrII:1643849-1643932 (+) Tyr (GTA) 84 bp Sc: 61.7
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-2-3 (chrII.trna18-TyrGTA) chrII:1643849-1643932 (+) Tyr (GTA) 84 bp Sc: 61.7
 CTCCTGATGGTGTAGTTGGTtATCACACCCGGCTGTAAttataaagatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-5 (chrII.trna19-LysCTT) chrII:1645044-1645126 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-5 (chrII.trna19-LysCTT) chrII:1645044-1645126 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAcgaatggtATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-3-1 (chrII.trna2-GlyTCC) chrII:326235-326305 (+) Gly (TCC) 71 bp Sc: 58.7
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-3-1 (chrII.trna2-GlyTCC) chrII:326235-326305 (+) Gly (TCC) 71 bp Sc: 58.7
 GCATCAGTGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGTTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-6 (chrII.trna20-IleAAT) chrII:1645424-1645497 (+) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-6 (chrII.trna20-IleAAT) chrII:1645424-1645497 (+) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-3 (chrII.trna21-TrpCCA) chrII:1774860-1774932 (+) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-3 (chrII.trna21-TrpCCA) chrII:1774860-1774932 (+) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-3 (chrII.trna22-ProAGG) chrII:1877221-1877292 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-3 (chrII.trna22-ProAGG) chrII:1877221-1877292 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-2 (chrII.trna23-AsnGTT) chrII:2032160-2032233 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-2 (chrII.trna23-AsnGTT) chrII:2032160-2032233 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-CCC-1-1 (chrII.trna24-GlyCCC) chrII:2069487-2069557 (+) Gly (CCC) 71 bp Sc: 59.7
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-CCC-1-1 (chrII.trna24-GlyCCC) chrII:2069487-2069557 (+) Gly (CCC) 71 bp Sc: 59.7
 GCATTAGTGGTGTAGCGGTAACATTGGAGCTTCCCATGCTCTAGcTCCGGGTTCGACTCC
 CGGCTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-4 (chrII.trna25-ProAGG) chrII:2319292-2319363 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-4 (chrII.trna25-ProAGG) chrII:2319292-2319363 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-5 (chrII.trna26-ProAGG) chrII:2939715-2939786 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-5 (chrII.trna26-ProAGG) chrII:2939715-2939786 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-1 (chrII.trna27-SerGCT) chrII:3350594-3350688 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-1 (chrII.trna27-SerGCT) chrII:3350594-3350688 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-6 (chrII.trna28-LysCTT) chrII:3814134-3814216 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-6 (chrII.trna28-LysCTT) chrII:3814134-3814216 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Tyr-GTA-1-1 (chrII.trna29-TyrGTA) chrII:3814558-3814641 (+) Tyr (GTA) 84 bp Sc: 62.6
+>Schizosaccharomyces_pombe_972h_tRNA-Tyr-GTA-1-1 (chrII.trna29-TyrGTA) chrII:3814558-3814641 (+) Tyr (GTA) 84 bp Sc: 62.6
 CTCCTGATGGTGTAGTTGGTtATCACATCCGGCTGTAAttaaaacgatACCGGTTGGtCG
 CTAGTTCGATTCTGGCTCAGGAGA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-1-2 (chrII.trna3-GlnTTG) chrII:355920-355991 (+) Gln (TTG) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-1-2 (chrII.trna3-GlnTTG) chrII:355920-355991 (+) Gln (TTG) 72 bp Sc: 67.9
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTTTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-2 (chrII.trna30-LeuAAG) chrII:3914043-3914121 (+) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-2 (chrII.trna30-LeuAAG) chrII:3914043-3914121 (+) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-4 (chrII.trna31-AspGTC) chrII:3939227-3939297 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-4 (chrII.trna31-AspGTC) chrII:3939227-3939297 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-3 (chrII.trna32-AsnGTT) chrII:4031743-4031816 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-3 (chrII.trna32-AsnGTT) chrII:4031743-4031816 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-4 (chrII.trna33-GluCTC) chrII:4107639-4107710 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-4 (chrII.trna33-GluCTC) chrII:4107639-4107710 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-2-1 (chrII.trna34-AsnGTT) chrII:4210053-4210126 (-) Asn (GTT) 74 bp Sc: 75.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-2-1 (chrII.trna34-AsnGTT) chrII:4210053-4210126 (-) Asn (GTT) 74 bp Sc: 75.5
 GGTCGGGTAGCGTAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-TGG-2-1 (chrII.trna35-ProTGG) chrII:3360519-3360590 (-) Pro (TGG) 72 bp Sc: 65.1
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-TGG-2-1 (chrII.trna35-ProTGG) chrII:3360519-3360590 (-) Pro (TGG) 72 bp Sc: 65.1
 GGTTTCGTGGTGTAGTGGTAGCATACTTCGTTTGGGTCGAAGTGGtCACGGGTTCAATCC
 CCGTCGAAACCC
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-2-2 (chrII.trna36-LeuAAG) chrII:3209139-3209217 (-) Leu (AAG) 79 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-2-2 (chrII.trna36-LeuAAG) chrII:3209139-3209217 (-) Leu (AAG) 79 bp Sc: 58.4
 GGAAGGTTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACACCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-4 (chrII.trna37-ThrAGT) chrII:2790375-2790446 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-4 (chrII.trna37-ThrAGT) chrII:2790375-2790446 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-1 (chrII.trna38-LeuAAG) chrII:2768257-2768335 (-) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-1 (chrII.trna38-LeuAAG) chrII:2768257-2768335 (-) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-1-1 (chrII.trna39-PheGAA) chrII:2576376-2576448 (-) Phe (GAA) 73 bp Sc: 68.2
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-1-1 (chrII.trna39-PheGAA) chrII:2576376-2576448 (-) Phe (GAA) 73 bp Sc: 68.2
 GTCGCGATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTCGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-1 (chrII.trna4-HisGTG) chrII:464238-464309 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-1 (chrII.trna4-HisGTG) chrII:464238-464309 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-3 (chrII.trna40-MetCAT) chrII:2434303-2434374 (-) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-3 (chrII.trna40-MetCAT) chrII:2434303-2434374 (-) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-2 (chrII.trna41-ProAGG) chrII:1825787-1825858 (-) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-2 (chrII.trna41-ProAGG) chrII:1825787-1825858 (-) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-4 (chrII.trna42-ArgACG) chrII:1647283-1647355 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-4 (chrII.trna42-ArgACG) chrII:1647283-1647355 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-4 (chrII.trna43-GluTTC) chrII:1646829-1646900 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-4 (chrII.trna43-GluTTC) chrII:1646829-1646900 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-6 (chrII.trna44-ValAAC) chrII:1646305-1646387 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-6 (chrII.trna44-ValAAC) chrII:1646305-1646387 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-6 (chrII.trna45-AlaAGC) chrII:1645571-1645644 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-6 (chrII.trna45-AlaAGC) chrII:1645571-1645644 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-6 (chrII.trna46-GlyGCC) chrII:1644675-1644745 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-6 (chrII.trna46-GlyGCC) chrII:1644675-1644745 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-2 (chrII.trna47-LeuCAA) chrII:1644080-1644183 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-2 (chrII.trna47-LeuCAA) chrII:1644080-1644183 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-1-5 (chrII.trna48-IleAAT) chrII:1630049-1630122 (-) Ile (AAT) 74 bp Sc: 62.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-1-5 (chrII.trna48-IleAAT) chrII:1630049-1630122 (-) Ile (AAT) 74 bp Sc: 62.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCGGTTCGAA
 CCCGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-4 (chrII.trna49-ValAAC) chrII:1619174-1619256 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-4 (chrII.trna49-ValAAC) chrII:1619174-1619256 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-4 (chrII.trna5-GlyGCC) chrII:570156-570226 (+) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-4 (chrII.trna5-GlyGCC) chrII:570156-570226 (+) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-4 (chrII.trna50-AlaAGC) chrII:1618440-1618513 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-4 (chrII.trna50-AlaAGC) chrII:1618440-1618513 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-3 (chrII.trna51-AspGTC) chrII:1602347-1602417 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-3 (chrII.trna51-AspGTC) chrII:1602347-1602417 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-TTC-1-3 (chrII.trna52-GluTTC) chrII:1601491-1601562 (-) Glu (TTC) 72 bp Sc: 55.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-TTC-1-3 (chrII.trna52-GluTTC) chrII:1601491-1601562 (-) Glu (TTC) 72 bp Sc: 55.8
 TCCGTTGTGGTCCAACGGCtAGGATTCGTCGCTTTCACCGACGCGGTCGGGGTTCGACTC
 CCCGCAACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-3 (chrII.trna53-ValAAC) chrII:1600967-1601049 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-3 (chrII.trna53-ValAAC) chrII:1600967-1601049 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ala-AGC-1-3 (chrII.trna54-AlaAGC) chrII:1600233-1600306 (-) Ala (AGC) 74 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Ala-AGC-1-3 (chrII.trna54-AlaAGC) chrII:1600233-1600306 (-) Ala (AGC) 74 bp Sc: 59.9
 GGGCATGTGGTGTAGATGGTtATCACGCTTCCTTAGCATGGAAGAGGtCCCAGATTCGAG
 TTCTGGCTTGTCCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-5 (chrII.trna55-GlyGCC) chrII:1599337-1599407 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-5 (chrII.trna55-GlyGCC) chrII:1599337-1599407 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-1 (chrII.trna56-LeuCAA) chrII:1598742-1598845 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-1 (chrII.trna56-LeuCAA) chrII:1598742-1598845 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-3 (chrII.trna57-MetCAT) chrII:1598075-1598155 (-) Met (CAT) 81 bp Sc: 54.8
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-3 (chrII.trna57-MetCAT) chrII:1598075-1598155 (-) Met (CAT) 81 bp Sc: 54.8
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAtgatgatAGGGGAAGGtCGTGA
 GTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-1 (chrII.trna58-AsnGTT) chrII:1597996-1598069 (-) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-1 (chrII.trna58-AsnGTT) chrII:1597996-1598069 (-) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-TAA-1-2 (chrII.trna59-LeuTAA) chrII:1402444-1402541 (-) Leu (TAA) 98 bp Sc: 57.0
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-TAA-1-2 (chrII.trna59-LeuTAA) chrII:1402444-1402541 (-) Leu (TAA) 98 bp Sc: 57.0
 GCGGCTATGCCCGAGTGGTctAAGGGGGCAGATTTAAGaggcctcggccttgatcccTGC
 TGTTGTAAAACGCGAGAGTTCGAACCTCTCTGGCCGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-2-2 (chrII.trna6-MetCAT) chrII:658451-658531 (+) Met (CAT) 81 bp Sc: 54.8
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-2-2 (chrII.trna6-MetCAT) chrII:658451-658531 (+) Met (CAT) 81 bp Sc: 54.8
 GCTTCTGTAGCTCAGTCGGTgGTAGCATCCCTCTCATAtaatgacAGGGGAAGGtCGTGA
 GTTCGAGCCTCACCAGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-CCT-1-1 (chrII.trna60-ArgCCT) chrII:1160893-1160994 (-) Arg (CCT) 102 bp Sc: 53.0
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-CCT-1-1 (chrII.trna60-ArgCCT) chrII:1160893-1160994 (-) Arg (CCT) 102 bp Sc: 53.0
 TTACGCGTGGCGCAATGGTAGCGCATCTCATTCCTAtacgacctgatcgttgttggggag
 tgaattACGAGAAGGtTGCGGGTTCGAGTCCCGTCGTGTAAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-3 (chrII.trna61-SerAGA) chrII:744754-744835 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-3 (chrII.trna61-SerAGA) chrII:744754-744835 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-TTT-1-1 (chrII.trna62-LysTTT) chrII:602625-602699 (-) Lys (TTT) 75 bp Sc: 72.0
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-TTT-1-1 (chrII.trna62-LysTTT) chrII:602625-602699 (-) Lys (TTT) 75 bp Sc: 72.0
 TCCCGTTTAGCTCAATCGGCttAGAGCGTCCGGCTTTTAACCGGAAGGtTGCGAGTTCGA
 ATCTCGCAGTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCT-2-1 (chrII.trna63-ArgTCT) chrII:326652-326724 (-) Arg (TCT) 73 bp Sc: 63.5
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCT-2-1 (chrII.trna63-ArgTCT) chrII:326652-326724 (-) Arg (TCT) 73 bp Sc: 63.5
 GCTCCCGTGGCCTAATGGCtAGGGCATTTGACTTCTAATCAAGGGAtTGTGGGTTCGAGT
 CCCGCCGGGAGCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-1-1 (chrII.trna64-GlyTCC) chrII:285389-285459 (-) Gly (TCC) 71 bp Sc: 63.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-1-1 (chrII.trna64-GlyTCC) chrII:285389-285459 (-) Gly (TCC) 71 bp Sc: 63.8
 GCATCGATGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGTCGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-CTG-1-2 (chrII.trna65-GlnCTG) chrII:258848-258919 (-) Gln (CTG) 72 bp Sc: 67.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-CTG-1-2 (chrII.trna65-GlnCTG) chrII:258848-258919 (-) Gln (CTG) 72 bp Sc: 67.8
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTCTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-1-1 (chrII.trna66-GlnTTG) chrII:257908-257979 (-) Gln (TTG) 72 bp Sc: 67.9
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-1-1 (chrII.trna66-GlnTTG) chrII:257908-257979 (-) Gln (TTG) 72 bp Sc: 67.9
 GGTTGTATGGTGTAATGGTtAGCACGTGAGATTTTGATTCTCGAGaCCTGGGTTCGATTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-3 (chrII.trna67-GlyGCC) chrII:180994-181064 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-3 (chrII.trna67-GlyGCC) chrII:180994-181064 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Trp-CCA-1-2 (chrII.trna7-TrpCCA) chrII:717076-717148 (+) Trp (CCA) 73 bp Sc: 69.6
+>Schizosaccharomyces_pombe_972h_tRNA-Trp-CCA-1-2 (chrII.trna7-TrpCCA) chrII:717076-717148 (+) Trp (CCA) 73 bp Sc: 69.6
 GGCCCCTTAACTCAGTTGGTAGAGTGTGAGATTCCAAATCTCAAAGtCAAGTGTTCAAGT
 CACTTAGGGGTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-3 (chrII.trna8-GluCTC) chrII:820491-820562 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-3 (chrII.trna8-GluCTC) chrII:820491-820562 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-2 (chrII.trna9-HisGTG) chrII:960729-960800 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-2 (chrII.trna9-HisGTG) chrII:960729-960800 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-3 (chrIII.trna1-HisGTG) chrIII:71400-71471 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-3 (chrIII.trna1-HisGTG) chrIII:71400-71471 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-AAG-1-3 (chrIII.trna10-LeuAAG) chrIII:1069166-1069244 (+) Leu (AAG) 79 bp Sc: 59.9
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-AAG-1-3 (chrIII.trna10-LeuAAG) chrIII:1069166-1069244 (+) Leu (AAG) 79 bp Sc: 59.9
 GGAAGGGTGTCCGAGTGGTtATGGAGCTAGTTTAAGGCACTAGTGCGAAAGCTCGTGGGT
 TCGAGTCCCACCCCTTTCA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-7 (chrIII.trna11-LysCTT) chrIII:1071093-1071175 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-7 (chrIII.trna11-LysCTT) chrIII:1071093-1071175 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-6 (chrIII.trna12-AspGTC) chrIII:1092437-1092507 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-6 (chrIII.trna12-AspGTC) chrIII:1092437-1092507 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-8 (chrIII.trna13-ValAAC) chrIII:1092934-1093016 (+) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-8 (chrIII.trna13-ValAAC) chrIII:1092934-1093016 (+) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-4 (chrIII.trna14-LeuCAA) chrIII:1102809-1102912 (+) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-4 (chrIII.trna14-LeuCAA) chrIII:1102809-1102912 (+) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-6 (chrIII.trna15-ThrAGT) chrIII:1105840-1105911 (+) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-6 (chrIII.trna15-ThrAGT) chrIII:1105840-1105911 (+) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-8 (chrIII.trna16-ArgACG) chrIII:1106327-1106399 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-8 (chrIII.trna16-ArgACG) chrIII:1106327-1106399 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-2 (chrIII.trna17-SerGCT) chrIII:1253193-1253287 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-2 (chrIII.trna17-SerGCT) chrIII:1253193-1253287 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-9 (chrIII.trna18-LysCTT) chrIII:1475034-1475116 (+) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-9 (chrIII.trna18-LysCTT) chrIII:1475034-1475116 (+) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-TGA-2-1 (chrIII.trna19-SerTGA) chrIII:1689713-1689809 (+) Ser (TGA) 97 bp Sc: 84.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-TGA-2-1 (chrIII.trna19-SerTGA) chrIII:1689713-1689809 (+) Ser (TGA) 97 bp Sc: 84.0
 GTCACTATGTCCGAGTGGTtAAGGAGTTAGACTTGAAtcctgtattctagtcATCTAATG
 GGCTCTGCCCGCGCAGGTTCAAATCCTGCTGGTGACG
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-5 (chrIII.trna2-GluCTC) chrIII:140967-141038 (+) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-5 (chrIII.trna2-GluCTC) chrIII:140967-141038 (+) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Met-CAT-1-4 (chrIII.trna20-MetCAT) chrIII:1689817-1689888 (+) Met (CAT) 72 bp Sc: 67.2
+>Schizosaccharomyces_pombe_972h_tRNA-Met-CAT-1-4 (chrIII.trna20-MetCAT) chrIII:1689817-1689888 (+) Met (CAT) 72 bp Sc: 67.2
 TGCGCGGTAGGAGAGTGGAACTCCGACGGGCTCATAACCCGTAGGtCCCAGGATCGAAAC
 CTGGCCGCGCAA
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-5 (chrIII.trna21-AsnGTT) chrIII:1701899-1701972 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-5 (chrIII.trna21-AsnGTT) chrIII:1701899-1701972 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Pro-AGG-1-6 (chrIII.trna22-ProAGG) chrIII:1788949-1789020 (+) Pro (AGG) 72 bp Sc: 58.4
+>Schizosaccharomyces_pombe_972h_tRNA-Pro-AGG-1-6 (chrIII.trna22-ProAGG) chrIII:1788949-1789020 (+) Pro (AGG) 72 bp Sc: 58.4
 GGCCGTTTGGTCTAGTGGTATGATACCATCTTAGGGTGATGGTGGtCGTGGGTTCGATTC
 CCACAACAGCCC
->Schizosaccharomyces_pombe_972h-_tRNA-His-GTG-1-4 (chrIII.trna23-HisGTG) chrIII:1844639-1844710 (+) His (GTG) 72 bp Sc: 65.4
+>Schizosaccharomyces_pombe_972h_tRNA-His-GTG-1-4 (chrIII.trna23-HisGTG) chrIII:1844639-1844710 (+) His (GTG) 72 bp Sc: 65.4
 GCTCACATGGTCCAGTGGTtAAGACTCATCGTTGTGGCCGATGCGaCCCAGGTTCGATTC
 CTGGTGTGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-2-1 (chrIII.trna24-GlnTTG) chrIII:1863131-1863202 (+) Gln (TTG) 72 bp Sc: 65.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-2-1 (chrIII.trna24-GlnTTG) chrIII:1863131-1863202 (+) Gln (TTG) 72 bp Sc: 65.2
 GGTTGTATGGTGTAGCGGTtAGCACGCGAGATTTTGATTCTCGAGaTCTGGGTTCGACTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-TCC-2-1 (chrIII.trna25-GlyTCC) chrIII:2037352-2037422 (+) Gly (TCC) 71 bp Sc: 63.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-TCC-2-1 (chrIII.trna25-GlyTCC) chrIII:2037352-2037422 (+) Gly (TCC) 71 bp Sc: 63.2
 GCATCAGTGGTGTAGCGGTAACATCAATGCCTTCCAAGCATTAGcTCCGGGTTCGACTCC
 CGGCTGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-GCT-1-3 (chrIII.trna26-SerGCT) chrIII:2072080-2072174 (+) Ser (GCT) 95 bp Sc: 75.2
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-GCT-1-3 (chrIII.trna26-SerGCT) chrIII:2072080-2072174 (+) Ser (GCT) 95 bp Sc: 75.2
 GACAACGTGGCCGAGTGGTtttAAGGCGTTCGCCTGCTAttctgtagcccAGCGGATTCC
 CTTTGGGAGCGCAGGTTCGAATCCTGCCGTTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-8 (chrIII.trna27-AspGTC) chrIII:2139408-2139478 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-8 (chrIII.trna27-AspGTC) chrIII:2139408-2139478 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Gln-TTG-2-2 (chrIII.trna28-GlnTTG) chrIII:2074991-2075062 (-) Gln (TTG) 72 bp Sc: 65.2
+>Schizosaccharomyces_pombe_972h_tRNA-Gln-TTG-2-2 (chrIII.trna28-GlnTTG) chrIII:2074991-2075062 (-) Gln (TTG) 72 bp Sc: 65.2
 GGTTGTATGGTGTAGCGGTtAGCACGCGAGATTTTGATTCTCGAGaTCTGGGTTCGACTC
 CCAGTACGACCT
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-7 (chrIII.trna29-SerAGA) chrIII:1775992-1776073 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-7 (chrIII.trna29-SerAGA) chrIII:1775992-1776073 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCT-1-1 (chrIII.trna3-ArgTCT) chrIII:578847-578919 (+) Arg (TCT) 73 bp Sc: 68.4
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCT-1-1 (chrIII.trna3-ArgTCT) chrIII:578847-578919 (+) Arg (TCT) 73 bp Sc: 68.4
 GCTCCCGTGGCCTAATGGCtAGGGCATTTGACTTCTAATCAAGGGAtTGCGGGTTCGAGT
 CCCGCCGGGAGCT
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-TGT-1-1 (chrIII.trna30-ThrTGT) chrIII:1361090-1361161 (-) Thr (TGT) 72 bp Sc: 76.0
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-TGT-1-1 (chrIII.trna30-ThrTGT) chrIII:1361090-1361161 (-) Thr (TGT) 72 bp Sc: 76.0
 GCCCCTATGGCTTAGTGGTACAGCATCGCACTTGTAATGCGAAGAtCCTTGGTTCGATTC
 CGAGTGGGGGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Val-TAC-1-2 (chrIII.trna31-ValTAC) chrIII:1206747-1206819 (-) Val (TAC) 73 bp Sc: 70.5
+>Schizosaccharomyces_pombe_972h_tRNA-Val-TAC-1-2 (chrIII.trna31-ValTAC) chrIII:1206747-1206819 (-) Val (TAC) 73 bp Sc: 70.5
 GCATCTGTAGTCTAGTGGTtATGATTTCTGCTTTACACGCAGACGGtCCCAGGTTCGATC
 CCTGGTAGATGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-4 (chrIII.trna32-PheGAA) chrIII:1142192-1142264 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-4 (chrIII.trna32-PheGAA) chrIII:1142192-1142264 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Lys-CTT-1-8 (chrIII.trna33-LysCTT) chrIII:1139536-1139618 (-) Lys (CTT) 83 bp Sc: 70.2
+>Schizosaccharomyces_pombe_972h_tRNA-Lys-CTT-1-8 (chrIII.trna33-LysCTT) chrIII:1139536-1139618 (-) Lys (CTT) 83 bp Sc: 70.2
 TCCCGAGTGGCTCAATCGGTttAGAGCGTCTGACTCTTAtgatggtcATCAGAAGGtTGC
 GAGTTCGAGTCTCGCCTTGGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-7 (chrIII.trna34-AspGTC) chrIII:1106487-1106557 (-) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-7 (chrIII.trna34-AspGTC) chrIII:1106487-1106557 (-) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-9 (chrIII.trna35-ValAAC) chrIII:1105978-1106060 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-9 (chrIII.trna35-ValAAC) chrIII:1105978-1106060 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Glu-CTC-1-6 (chrIII.trna36-GluCTC) chrIII:1097499-1097570 (-) Glu (CTC) 72 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Glu-CTC-1-6 (chrIII.trna36-GluCTC) chrIII:1097499-1097570 (-) Glu (CTC) 72 bp Sc: 68.8
 TCCGTCATGGTCCAGTGGCtAGGATTCATCGCTCTCACCGATGCGGCGGGGGTTCGATTC
 CCCCTGACGGAG
->Schizosaccharomyces_pombe_972h-_tRNA-Leu-CAA-1-3 (chrIII.trna37-LeuCAA) chrIII:1096082-1096185 (-) Leu (CAA) 104 bp Sc: 62.5
+>Schizosaccharomyces_pombe_972h_tRNA-Leu-CAA-1-3 (chrIII.trna37-LeuCAA) chrIII:1096082-1096185 (-) Leu (CAA) 104 bp Sc: 62.5
 GGCCAGTTGGCCGAGCGGTctATGGCGCAGCACTCAAGtaatacttggacgatagtcTTG
 CTGTATCGAAAGATGCGAGGGTTCGAATCCCTCACTGGTCACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Thr-AGT-2-5 (chrIII.trna38-ThrAGT) chrIII:1093083-1093154 (-) Thr (AGT) 72 bp Sc: 79.8
+>Schizosaccharomyces_pombe_972h_tRNA-Thr-AGT-2-5 (chrIII.trna38-ThrAGT) chrIII:1093083-1093154 (-) Thr (AGT) 72 bp Sc: 79.8
 GCTCTTGTAGCTCAGTGGTAGAGCGCTTGCCTAGTAAGCAAGAGGcCCAGTGTTCAAGTC
 ACTGCTGGAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-7 (chrIII.trna39-ArgACG) chrIII:1092595-1092667 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-7 (chrIII.trna39-ArgACG) chrIII:1092595-1092667 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ile-AAT-2-2 (chrIII.trna4-IleAAT) chrIII:817425-817498 (+) Ile (AAT) 74 bp Sc: 59.0
+>Schizosaccharomyces_pombe_972h_tRNA-Ile-AAT-2-2 (chrIII.trna4-IleAAT) chrIII:817425-817498 (+) Ile (AAT) 74 bp Sc: 59.0
 GGTCGCATGATGTAGTCGGTtATCATGTCGATCTAATAAGTCGAATGtCGCCAGTTCGAA
 CCTGGCTGTGACCA
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-6 (chrIII.trna40-ArgACG) chrIII:1068182-1068254 (-) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-6 (chrIII.trna40-ArgACG) chrIII:1068182-1068254 (-) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-TCG-1-1 (chrIII.trna41-ArgTCG) chrIII:1067092-1067164 (-) Arg (TCG) 73 bp Sc: 62.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-TCG-1-1 (chrIII.trna41-ArgTCG) chrIII:1067092-1067164 (-) Arg (TCG) 73 bp Sc: 62.8
 GGGTGTGTAGCCTAATGGTtAAGGCGTTGGTTTTCGGCACCAAAGAcTGCAGGTTCGAGT
 CCTGTCACACTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Val-AAC-1-7 (chrIII.trna42-ValAAC) chrIII:1065778-1065860 (-) Val (AAC) 83 bp Sc: 58.8
+>Schizosaccharomyces_pombe_972h_tRNA-Val-AAC-1-7 (chrIII.trna42-ValAAC) chrIII:1065778-1065860 (-) Val (AAC) 83 bp Sc: 58.8
 GGTCGTGTGGTTTAGATGGTtATAATTTCTGCTTAACAtttacagttCGCAGACGGtCCC
 AAGTTCGAGTCTTGGCACGATCA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-8 (chrIII.trna43-GlyGCC) chrIII:820567-820637 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-8 (chrIII.trna43-GlyGCC) chrIII:820567-820637 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-4 (chrIII.trna44-SerAGA) chrIII:473199-473280 (-) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-4 (chrIII.trna44-SerAGA) chrIII:473199-473280 (-) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Phe-GAA-2-3 (chrIII.trna45-PheGAA) chrIII:331228-331300 (-) Phe (GAA) 73 bp Sc: 67.1
+>Schizosaccharomyces_pombe_972h_tRNA-Phe-GAA-2-3 (chrIII.trna45-PheGAA) chrIII:331228-331300 (-) Phe (GAA) 73 bp Sc: 67.1
 GTCGCAATGGTGTAGTTGGGAGCATGACAGACTGAAGATCTGTTGGtCATCGGTTCGATC
 CCGGTTTGTGACA
->Schizosaccharomyces_pombe_972h-_tRNA-Gly-GCC-1-7 (chrIII.trna46-GlyGCC) chrIII:113716-113786 (-) Gly (GCC) 71 bp Sc: 70.8
+>Schizosaccharomyces_pombe_972h_tRNA-Gly-GCC-1-7 (chrIII.trna46-GlyGCC) chrIII:113716-113786 (-) Gly (GCC) 71 bp Sc: 70.8
 GCTTTGGTGGTTTAGTGGTATAATGAATCGTTGCCATCGATTCGaCCCGGGTTCGATTCC
 CGGCCAAAGCA
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-5 (chrIII.trna5-SerAGA) chrIII:847701-847782 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-5 (chrIII.trna5-SerAGA) chrIII:847701-847782 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Arg-ACG-1-5 (chrIII.trna6-ArgACG) chrIII:925852-925924 (+) Arg (ACG) 73 bp Sc: 68.8
+>Schizosaccharomyces_pombe_972h_tRNA-Arg-ACG-1-5 (chrIII.trna6-ArgACG) chrIII:925852-925924 (+) Arg (ACG) 73 bp Sc: 68.8
 GGTCTCGTGGCCCAATGGTtAAGGCGCTTGACTACGGATCAAGAGAtTCCAGGTTCGACT
 CCTGGCGGGATCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asn-GTT-1-4 (chrIII.trna7-AsnGTT) chrIII:947262-947335 (+) Asn (GTT) 74 bp Sc: 81.5
+>Schizosaccharomyces_pombe_972h_tRNA-Asn-GTT-1-4 (chrIII.trna7-AsnGTT) chrIII:947262-947335 (+) Asn (GTT) 74 bp Sc: 81.5
 GGTCGGGTAGCATAGTTGGTtATTGCGCACGACTGTTAATCGTGAGGtCGAGGGTTCGAG
 TCCCTCCCTGACCG
->Schizosaccharomyces_pombe_972h-_tRNA-Ser-AGA-1-6 (chrIII.trna8-SerAGA) chrIII:1066628-1066709 (+) Ser (AGA) 82 bp Sc: 86.3
+>Schizosaccharomyces_pombe_972h_tRNA-Ser-AGA-1-6 (chrIII.trna8-SerAGA) chrIII:1066628-1066709 (+) Ser (AGA) 82 bp Sc: 86.3
 GACACTATGCCTGAGTGGTtAAAGGGACAGACTAGAAATCTGTTGCGGTCTCCGCGCGCA
 GGTTCAAATCCTGCTGGTGTCG
->Schizosaccharomyces_pombe_972h-_tRNA-Asp-GTC-1-5 (chrIII.trna9-AspGTC) chrIII:1068029-1068099 (+) Asp (GTC) 71 bp Sc: 66.2
+>Schizosaccharomyces_pombe_972h_tRNA-Asp-GTC-1-5 (chrIII.trna9-AspGTC) chrIII:1068029-1068099 (+) Asp (GTC) 71 bp Sc: 66.2
 TCTCCTTTAGTATAGGGGTAGTACACAAGCCTGTCACGCTTGCAGCCCGGGTTCGAATCC
 CGGAGGGAGAG
diff --git a/dependencyList.txt b/dependencyList.txt
index 692d785..7db3fe2 100644
--- a/dependencyList.txt
+++ b/dependencyList.txt
@@ -3,13 +3,11 @@ Python packages:
 	- pandas 0.22.0
 	- numpy 1.14.0 
 	- pyfiglet 0.7.5
-	- pybedtools 0.7.10
 	- pysam 0.14.1
 	- seaborn 0.8.1
 	- matplotlib 2.1.2
 INFERNAL 1.1.2 (July 2016) 
 blast 2.7.1
-Subread package (for featureCounts) v1.6.2
 GMAP-GSNAP version 2019-02-26
 samtools version 1.6
 usearch v10.0.240
diff --git a/docs/source/start.rst b/docs/source/start.rst
index 746887c..e8edbd3 100644
--- a/docs/source/start.rst
+++ b/docs/source/start.rst
@@ -25,8 +25,6 @@ Please install all dependencies below before running mim-tRNAseq. In most cases,
 +-----------------+-------------------+-----------+
 |Tool             | Version >=        | Link      |
 +=================+===================+===========+
-| Subread package | 1.6.2             | subread_  |
-+-----------------+-------------------+-----------+
 | GMAP-GSNAP      | 2019-02-26        | GSNAP_    |
 +-----------------+-------------------+-----------+
 | samtools        | 1.7               | samtools_ |
@@ -42,7 +40,6 @@ Please install all dependencies below before running mim-tRNAseq. In most cases,
 | BLAST           | 2.7.1             | BLAST_    |
 +-----------------+-------------------+-----------+
 
-.. _subread: http://subread.sourceforge.net/
 .. _GSNAP: http://research-pub.gene.com/gmap/
 .. _samtools: http://www.htslib.org/
 .. _usearch: https://www.drive5.com/usearch/
@@ -116,8 +113,6 @@ Please install all dependencies below before running mim-tRNAseq. In most cases,
 +------------+------------+-------------+
 | pyfiglet   | 0.7.5      | pyfiglet_   |
 +------------+------------+-------------+
-| pybedtools | 0.7.10     | pybedtools_ |
-+------------+------------+-------------+
 | pysam      | 0.14.1     | pysam_      |
 +------------+------------+-------------+
 | pandas     | 0.22.0     | pandas_     |
@@ -127,7 +122,6 @@ Please install all dependencies below before running mim-tRNAseq. In most cases,
 
 .. _Biopython: https://biopython.org/
 .. _pyfiglet: https://pypi.org/project/pyfiglet/0.7/
-.. _pybedtools: https://daler.github.io/pybedtools/
 .. _pysam: https://pysam.readthedocs.io/en/latest/api.html
 .. _pandas: https://pandas.pydata.org/
 .. _NumPy: https://numpy.org/
diff --git a/scripts/__pycache__/getCoverage.cpython-36.pyc b/scripts/__pycache__/getCoverage.cpython-36.pyc
index 13c6f1b..34d9a71 100644
Binary files a/scripts/__pycache__/getCoverage.cpython-36.pyc and b/scripts/__pycache__/getCoverage.cpython-36.pyc differ
diff --git a/scripts/__pycache__/mmQuant.cpython-36.pyc b/scripts/__pycache__/mmQuant.cpython-36.pyc
index 25f6417..0258216 100644
Binary files a/scripts/__pycache__/mmQuant.cpython-36.pyc and b/scripts/__pycache__/mmQuant.cpython-36.pyc differ
diff --git a/scripts/__pycache__/splitReads.cpython-36.pyc b/scripts/__pycache__/splitReads.cpython-36.pyc
index 95ab971..117df57 100644
Binary files a/scripts/__pycache__/splitReads.cpython-36.pyc and b/scripts/__pycache__/splitReads.cpython-36.pyc differ
diff --git a/scripts/__pycache__/ssAlign.cpython-36.pyc b/scripts/__pycache__/ssAlign.cpython-36.pyc
index a5dcba2..ee0d547 100644
Binary files a/scripts/__pycache__/ssAlign.cpython-36.pyc and b/scripts/__pycache__/ssAlign.cpython-36.pyc differ
diff --git a/scripts/__pycache__/tRNAmap.cpython-36.pyc b/scripts/__pycache__/tRNAmap.cpython-36.pyc
index bac4226..18cfd93 100644
Binary files a/scripts/__pycache__/tRNAmap.cpython-36.pyc and b/scripts/__pycache__/tRNAmap.cpython-36.pyc differ
diff --git a/scripts/__pycache__/tRNAtools.cpython-36.pyc b/scripts/__pycache__/tRNAtools.cpython-36.pyc
index 281c3a0..5e073ee 100644
Binary files a/scripts/__pycache__/tRNAtools.cpython-36.pyc and b/scripts/__pycache__/tRNAtools.cpython-36.pyc differ
diff --git a/scripts/coveragePlot.R b/scripts/coveragePlot.R
index f0cddd6..43c308d 100644
--- a/scripts/coveragePlot.R
+++ b/scripts/coveragePlot.R
@@ -56,6 +56,7 @@ if (length(args)==0) {
 				facet_wrap(~bam, ncol = 4) + 
 				xlab("Gene (%)") + ylab("Normalised coverage (coverage/uniquely mapped reads)") + 
 				labs(fill = "Isotype") + 
+				guides(fill=guide_legend(ncol=2)) +
 				scale_fill_manual(values = getPalette(mit_colourCount)) + 
 				theme_bw()
 			ggsave(paste(out_dir, "mitocoverage_byaa_norm.pdf", sep = ''), mitocov_byaa_norm, height = ceiling(facetCount/4) * 4, width = 14)	
@@ -101,7 +102,8 @@ if (length(args)==0) {
 				geom_bar(stat = "identity", alpha = 0.8) + facet_wrap(~bam, ncol = 4) + 
 				xlab("Gene (%)") + 
 				ylab("Scaled normalised coverage") + 
-				labs(fill = "Isotype") + 
+				labs(fill = "Isotype") +
+				guides(fill=guide_legend(ncol=2)) + 
 				scale_y_continuous(breaks = seq(0,1,0.25)) + 
 				scale_fill_manual(values = getPalette(mit_colourCount)) + 
 				theme_bw()
diff --git a/scripts/deseq.R b/scripts/deseq.R
index 11d1659..1d39590 100644
--- a/scripts/deseq.R
+++ b/scripts/deseq.R
@@ -59,13 +59,9 @@ setwd(file.path(outdir))
 # Filter out mito counts
 anticodon_countdata = read.table("Anticodon_counts.txt", header=TRUE, row.names=1, check.names = FALSE)
 anticodon_countdata = anticodon_countdata[!grepl("mito", rownames(anticodon_countdata)),]
-if (cluster_id == 1) {
-  isodecoder_countdata = read.table("counts.txt", header=TRUE, row.names=1, check.names = FALSE)
-  isodecoder_countdata = isodecoder_countdata[, -c(1,2,3,4,5), drop = FALSE]
-} else {
-  isodecoder_countdata = read.table("Isodecoder_counts.txt", header=TRUE, row.names=1, check.names = FALSE)
-  isodecoder_countdata$Single_isodecoder = NULL
-}
+isodecoder_countdata = read.table("Isodecoder_counts.txt", header=TRUE, row.names=1, check.names = FALSE)
+isodecoder_countdata = isodecoder_countdata[grepl("True", isodecoder_countdata$Single_isodecoder),]
+isodecoder_countdata$Single_isodecoder = NULL
 isodecoder_countdata = isodecoder_countdata[!grepl("mito", rownames(isodecoder_countdata)),]
 coldata = read.table(paste(sampleData, sep=""), header=FALSE, sep = "\t", row.names=1)
 
diff --git a/scripts/getCoverage.py b/scripts/getCoverage.py
index 97a983f..2fdaae8 100755
--- a/scripts/getCoverage.py
+++ b/scripts/getCoverage.py
@@ -10,37 +10,18 @@
 import os, logging
 from functools import partial
 from collections import defaultdict
-from pybedtools import BedTool
 from multiprocessing import Pool
 
 log = logging.getLogger(__name__)
 
-def filterCoverage (bedtool_cov, min_cov):
-# returns BedTool features with less than min_cov reads as list
+def filterCoverage (cov_table, min_cov):
+# returns isodecoders as list from counts table with less than min_cov reads (excluding mito clusters)
 	
-	filtered_list = list()
-	for i in bedtool_cov:
-		if (int(i[6]) < min_cov) and not ("mito" in i[0]):
-			filtered_list.append(i[0])
-
-	return(filtered_list)
+	filtered_list = list(cov_table[(cov_table.values < min_cov).any(1) & (~cov_table.index.str.contains('mito'))].index)
 
+	log.info("{} clusters filtered out according to minimum coverage threshold: {}".format(len(filtered_list), min_cov))
 
-def bedtools_mp (tRNAbed, out_dir, min_cov, inputs):
-# runs pybedtools coverage for input data
-# multiprocessing of coverage tasks
-	
-	a = BedTool(tRNAbed)
-	b = BedTool(inputs)
-	log.info("Running bedtools coverage on {}...".format(inputs))
-	cov = a.coverage(b, s = True, counts = True)
-	filtered = filterCoverage(cov, min_cov)
-	cov_filtered = cov.filter(lambda x: (int(x[6]) >= min_cov) or ("mito" in x[0]))
-	a_filtered = a.intersect(cov_filtered)
-	cov_pernucl_filtered = a_filtered.coverage(b, d = True, s = True).saveas(out_dir + inputs.split("/")[-1] + "_coverage.txt")
-	log.info("Coverage calculation complete for {}".format(inputs))	
-
-	return(filtered)
+	return(filtered_list)
 
 def getBamList (sampleGroups):
 # reads sampleGroups file and creates dictionary of bam and groups
@@ -60,7 +41,7 @@ def getBamList (sampleGroups):
 	return(baminfo, bamlist)
 	sampleGroups.close()
 
-def getCoverage(tRNAbed, sampleGroups, out_dir, max_multi, min_cov, control_cond):
+def getCoverage(sampleGroups, out_dir, min_cov, control_cond, filtered_cov):
 # Uses bedtools coverage and pandas generate coverage in 5% intervals per gene and isoacceptor for plotting
 
 	log.info("\n+-----------------------------------+\
@@ -70,44 +51,27 @@ def getCoverage(tRNAbed, sampleGroups, out_dir, max_multi, min_cov, control_cond
 	baminfo, bamlist = getBamList(sampleGroups)
 	cov_mean = list()
 
-	# multiprocessing of bedtools coverage
-
-	if max_multi > len(bamlist):
-		max_multi = len(bamlist)
-
-	# create process pool, make partial function of bedtools_mp (above) with some inputs, 
-	# map partial function with bam inputs to pool of prcoesses for multithreaded coverage calculation
-	pool = Pool(max_multi)
-	func = partial(bedtools_mp, tRNAbed, out_dir, min_cov)
-	filtered = pool.map(func, bamlist)
-	filtered = list(set([item for sublist in filtered for item in sublist]))
-	pool.close()
-	pool.join()
-
-	log.info("{} clusters filtered out according to minimum coverage threshold: {}".format(len(filtered), min_cov))
-
 	for bam, info in baminfo.items():
 
-		coverage = pd.read_csv(out_dir + bam.split("/")[-1] + "_coverage.txt", header = None, index_col = 0, sep = "\t")[[6,7]] 
+		coverage = pd.read_csv(out_dir + bam.split("/")[-1] + "_coverage.txt", index_col = 0, sep = "\t") 
 		coverage['aa'] = coverage.index.format()
 		coverage.loc[coverage.aa.str.contains('mito'), 'aa'] = "mito" + coverage[coverage.aa.str.contains('mito')].aa.str.split("-").str[-4]
 		coverage.loc[coverage.aa.str.contains('nmt'), 'aa'] = "nmt" + coverage[coverage.aa.str.contains('nmt')].aa.str.split("-").str[-4]
 		coverage.loc[~coverage.aa.str.contains('mito') & ~coverage.aa.str.contains('nmt'), 'aa'] = coverage[~coverage.aa.str.contains('mito') & ~coverage.aa.str.contains('nmt')].aa.str.split("-").str[-4]
-		coverage.columns = ['pos','cov','aa']
+		coverage = coverage[['pos','cov','aa','bam']]
 		coverage['condition'] = info[0]
+		coverage['cov'] = coverage['cov'].astype(float)
 		coverage['cov_norm'] = coverage['cov'] / info[1]
 
 		# bin by grouping by each gene and cutting into 20 - i.e. 5% bins by gene length (pos)
 		coverage['bin'] = coverage.groupby([coverage.index])['pos'].transform(lambda x: pd.qcut(x, 25, labels=range(4,104,4)))
-		# add bam name to distinguish samples with same condition - NB for mmQuant mismatch counting and normalisation to coverage
-		coverage['bam'] = bam
 		# append big coverage table and remove original coverage output
 		cov_mean.append(coverage)
-		os.remove(out_dir + bam.split("/")[-1] + "_coverage.txt")	 
+		#os.remove(out_dir + bam.split("/")[-1] + "_coverage.txt")	 
 
 	# concatenate all tables together, groupby + mean
 	cov_mean = pd.concat(cov_mean, axis = 0)
-	cov_mean = cov_mean[~cov_mean.index.isin(filtered)]
+	cov_mean = cov_mean[~cov_mean.index.isin(filtered_cov)]
 	cov_mean_gene = cov_mean.copy()
 	cov_mean_gene['Cluster'] = cov_mean_gene.index.format()
 	cov_mean_gene.loc[cov_mean_gene.Cluster.str.contains("mito"), "Cluster"] = "mito" + cov_mean_gene[cov_mean_gene.Cluster.str.contains("mito")].Cluster.str.split("-").str[1:].str.join('-')
@@ -146,7 +110,7 @@ def getCoverage(tRNAbed, sampleGroups, out_dir, max_multi, min_cov, control_cond
 	sorted_aa = sorted(cov_ratios, key = cov_ratios.get)
 	sorted_aa = "_".join(str(e) for e in sorted_aa)
 
-	return(cov_mean, filtered, sorted_aa)
+	return(sorted_aa)
 
 def plotCoverage(out_dir, mito_trnas, sorted_aa):
 	
@@ -158,4 +122,3 @@ def plotCoverage(out_dir, mito_trnas, sorted_aa):
 	except Exception as e:
 		logging.error("Error in {}".format(command), exc_info=e)
 		raise
-
diff --git a/scripts/mim-seq.py b/scripts/mim-seq.py
index 345deff..e7fc5b1 100755
--- a/scripts/mim-seq.py
+++ b/scripts/mim-seq.py
@@ -13,9 +13,10 @@
 # github: https://github.com/drewjbeh/mim-tRNAseq
 
 import tRNAtools, tRNAmap, getCoverage, mmQuant, CCAanalysis, ssAlign, splitReads
-import sys, os, subprocess, logging, datetime
+import sys, os, subprocess, logging, datetime, copy
 import argparse
 from pyfiglet import figlet_format
+from collections import defaultdict
 
 def restrictedFloat(x):
 ## Method for restricting cluster_id argument to float between 0 and 1
@@ -28,7 +29,7 @@ def restrictedFloat(x):
 		raise argparse.ArgumentTypeError('{} not a real number'.format(x))
 
 def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_cond, threads, max_multi, snp_tolerance, \
-	keep_temp, mode, cca, min_cov, mismatches, remap, remap_mismatches, misinc_thresh, mito_trnas, sample_data):
+	keep_temp, cca, min_cov, mismatches, remap, remap_mismatches, misinc_thresh, mito_trnas, sample_data):
 	
 # Main wrapper
 
@@ -57,7 +58,6 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 	log.info("mim-tRNAseq run with command:")
 	log.info(" ".join(sys.argv))
 
-
 	########
 	# main #
 	########
@@ -77,30 +77,30 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 	bams_list, coverageData = tRNAmap.mainAlign(sample_data, name, genome_index_path, genome_index_name, \
 		snp_index_path, snp_index_name, out, threads, snp_tolerance, keep_temp, mismatches, map_round)
 
-	# Coverage and plots
-	cov_table, filtered_list, sorted_aa = getCoverage.getCoverage(coverage_bed, coverageData, out, max_multi, min_cov, control_cond)
-	getCoverage.plotCoverage(out, mito_trnas, sorted_aa)
+	# define unique mismatches/insertions to assign reads to unique tRNA sequences
+	if cluster and not cluster_id == 1:
+		cluster_dict2 = copy.deepcopy(cluster_dict) # copy so splitReadsIsodecoder does not edit main cluster_dict
+		unique_isodecoderMMs, splitBool, isodecoder_sizes = splitReads.splitReadsIsodecoder(isodecoder_count, tRNA_dict, cluster_dict2, mismatch_dict, insert_dict, cluster_perPos_mismatchMembers, out, name)
+	else:
+		unique_isodecoderMMs = defaultdict(dict)
+		splitBool = list()
+		isodecoder_sizes = defaultdict(int)
 
 	# if remap and snp_tolerance are enabled, skip further analyses, find new mods, and redo alignment and coverage
 	if remap and (snp_tolerance or not mismatches == 0.0):
-		new_mods, new_Inosines, clusterMMTable = mmQuant.generateModsTable(coverageData, out, threads, cov_table, min_cov, mismatch_dict, filtered_list, cca, remap, misinc_thresh, mod_lists, tRNA_dict, Inosine_clusters)
+		new_mods, new_Inosines, filtered_cov = mmQuant.generateModsTable(coverageData, out, threads, min_cov, mismatch_dict, cluster_dict, cca, remap, misinc_thresh, mod_lists, tRNA_dict, Inosine_clusters, unique_isodecoderMMs, splitBool, isodecoder_sizes)
 		Inosine_clusters = tRNAtools.newModsParser(out, name, new_mods, new_Inosines, mod_lists, Inosine_lists, tRNA_dict, cluster)
 		map_round = 2
 		genome_index_path, genome_index_name, snp_index_path, snp_index_name = tRNAtools.generateGSNAPIndices(name, out, map_round, snp_tolerance, cluster)
 		bams_list, coverageData = tRNAmap.mainAlign(sample_data, name, genome_index_path, genome_index_name, \
 			snp_index_path, snp_index_name, out, threads, snp_tolerance, keep_temp, remap_mismatches, map_round)
-		cov_table, filtered_list, sorted_aa = getCoverage.getCoverage(coverage_bed, coverageData, out, max_multi, min_cov, control_cond)
-		getCoverage.plotCoverage(out, mito_trnas, sorted_aa)
 		remap = False
 	else:
 		log.info("\n*** New modifications not discovered as remap is not enabled ***\n")
 
-	# featureCounts
-	tRNAmap.countReads(bams_list, mode, threads, out)
-
 	# Misincorporation analysis
 	if snp_tolerance or not mismatches == 0.0:
-		new_mods, new_Inosines, clusterMMTable = mmQuant.generateModsTable(coverageData, out, threads, cov_table, min_cov, mismatch_dict, filtered_list, cca, remap, misinc_thresh, mod_lists, tRNA_dict, Inosine_clusters)
+		new_mods, new_Inosines, filtered_cov = mmQuant.generateModsTable(coverageData, out, threads, min_cov, mismatch_dict, cluster_dict, cca, remap, misinc_thresh, mod_lists, tRNA_dict, Inosine_clusters, unique_isodecoderMMs, splitBool, isodecoder_sizes)
 	else:
 		log.info("*** Misincorporation analysis not possible; either --snp-tolerance must be enabled, or --max-mismatches must not be 0! ***\n")
 
@@ -118,9 +118,9 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 		if cca:
 			CCAanalysis.plotDinuc(out)
 
-	# split read counts by isodecoder
-	if cluster and not cluster_id == 1:
-		splitReads.splitReadsIsodecoder(isodecoder_count, clusterMMTable, tRNA_dict, cluster_dict, mismatch_dict, insert_dict, cluster_perPos_mismatchMembers, out, name)
+	# Coverage and plots
+	sorted_aa = getCoverage.getCoverage(coverageData, out, min_cov, control_cond, filtered_cov)
+	getCoverage.plotCoverage(out, mito_trnas, sorted_aa)
 
 	# DESeq2
 	sample_data = os.path.abspath(coverageData)
@@ -192,13 +192,6 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 	outputs.add_argument('--keep-temp', required = False, dest='keep_temp', action = 'store_true', help = \
 		'Keeps multi-mapping and unmapped bam files from GSNAP alignments. Default is false.')
 
-	featurecounts = parser.add_argument_group("featureCounts options")
-	featurecounts.add_argument('--count-mode', metavar = 'featureCounts mode', required = False, dest = 'mode', help = \
-		"featureCounts mode to handle reads overlapping more than one feature. Choose from 'none' (multi-overlapping reads are not counted)\
-		,'all' (reads are assigned and counted for all overlapping features), or 'fraction' (each overlapping feature receives a fractional count\
-		of 1/y, where y is the number of features overlapping with the read). Default is 'none'",\
-	 	choices = ['none','all','fraction'])
-
 	bedtools = parser.add_argument_group("Bedtools coverage options")
 	bedtools.add_argument('--min-cov', metavar = 'Minimum coverage per cluster', required = False, dest = 'min_cov', type = int, \
 		help = "Minimum coverage per cluster to include this cluster in coverage plots, modification analysis, and 3'-CCA analysis. Clusters with \
@@ -219,7 +212,7 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 
 	parser.add_argument('sampledata', help = 'Sample data sheet in text format, tab-separated. Column 1: full path to fastq (or fastq.gz). Column 2: condition/group.')
 
-	parser.set_defaults(threads=1, out="./", mode = 'none', max_multi = 3, min_cov = 0, mito = '')
+	parser.set_defaults(threads=1, out="./", max_multi = 3, min_cov = 0, mito = '')
 
 
 	#############################
@@ -252,5 +245,5 @@ def mimseq(trnas, trnaout, name, out, cluster, cluster_id, posttrans, control_co
 		else:
 			mimseq(args.trnas, args.trnaout, args.name, args.out, args.cluster, args.cluster_id, \
 				args.posttrans, args.control_cond, args.threads, args.max_multi, args.snp_tolerance, \
-				args.keep_temp, args.mode, args.cca, args.min_cov, args.mismatches, args.remap, args.remap_mismatches, \
+				args.keep_temp, args.cca, args.min_cov, args.mismatches, args.remap, args.remap_mismatches, \
 				args.misinc_thresh, args.mito, args.sampledata)
diff --git a/scripts/mmQuant.py b/scripts/mmQuant.py
index 3dabb14..49918d1 100755
--- a/scripts/mmQuant.py
+++ b/scripts/mmQuant.py
@@ -8,7 +8,8 @@
 import os, logging
 import re
 import pysam
-from getCoverage import getBamList
+import tRNAtools
+from getCoverage import *
 from multiprocessing import Pool
 from functools import partial
 import pandas as pd
@@ -18,42 +19,57 @@
 
 log = logging.getLogger(__name__)
 
-def unknownMods(inputs, out_dir, knownTable, modTable, misinc_thresh, cov_table, min_cov, tRNA_dict, cons_pos_dict):
+def unknownMods(inputs, out_dir, knownTable, cluster_dict, modTable, misinc_thresh, cov_table, min_cov, tRNA_dict, remap):
 # find unknown modifications with a total misincorporation threshold >= misinc_thresh
 
 	log.info('Finding potential unannotated mods for {}'.format(inputs))
-	new_mods =  defaultdict(list)
-	new_Inosines = defaultdict(list)
+	new_mods_cluster =  defaultdict(list)
+	new_inosines_cluster = defaultdict(list)
+	new_mods_isodecoder = defaultdict(list)
+	new_inosines_isodecoder = defaultdict(list)
 	cons_anticodon = ssAlign.getAnticodon()
 	
-	for cluster, data in modTable.items():
+	for isodecoder, data in modTable.items():
+		cluster = [parent for parent, child in cluster_dict.items() if isodecoder in child][0]
 		anticodon = ssAlign.clusterAnticodon(cons_anticodon, cluster)
 		for pos, type in data.items():
-			cov = cov_table[(cov_table.pos == pos) & (cov_table.bam == inputs)].loc[cluster]['cov']
-			if (sum(modTable[cluster][pos].values()) >= misinc_thresh and cov >= min_cov and pos-1 not in knownTable[cluster]): # misinc above threshold, cov above threshold and not previously known
+			cov = cov_table[isodecoder][pos]
+			if (sum(modTable[isodecoder][pos].values()) >= misinc_thresh and cov >= min_cov and pos-1 not in knownTable[cluster]): # misinc above threshold, cov above threshold and not previously known
 				# if one nucleotide dominates misinc. pattern (i.e. >= 0.9 of all misinc, likely a true SNP or misalignment)
-				if (max(modTable[cluster][pos].values()) / sum(modTable[cluster][pos].values()) >= 0.90):
+				if (max(modTable[isodecoder][pos].values()) / sum(modTable[isodecoder][pos].values()) >= 0.90):
 					# if mod seems to be an inosine (i.e. A with G misinc at 34) add to list and modification SNPs file (see tRNAtools.ModsParser())
-					if (tRNA_dict[cluster]['sequence'][pos-1] == 'A' and list(modTable[cluster][pos].keys())[list(modTable[cluster][pos].values()).index(max(modTable[cluster][pos].values()))] == 'G' and pos-1 == min(anticodon)):
-						new_Inosines[cluster].append(pos-1)
+					if (tRNA_dict[isodecoder]['sequence'][pos-1] == 'A' and list(modTable[isodecoder][pos].keys())[list(modTable[isodecoder][pos].values()).index(max(modTable[isodecoder][pos].values()))] == 'G' and pos-1 == min(anticodon)):
+						new_inosines_cluster[cluster].append(pos-1)
+						new_inosines_isodecoder[isodecoder].append(pos-1)
 				else:
-					new_mods[cluster].append(pos-1) #modTable had 1 based values - convert back to 0 based for snp index
+					new_mods_cluster[cluster].append(pos-1) #modTable had 1 based values - convert back to 0 based for snp index
+					new_mods_isodecoder[isodecoder].append(pos-1)
 
-	with open(out_dir + "mods/predictedModstemp.csv", "w") as predMods:
-		for cluster, data in new_mods.items():
+	with open(inputs + "_predictedModstemp.csv", "a") as predMods:
+		#predMods.write("isodecoder\tpos\tidentity\tbam\n")
+		for isodecoder, data in new_mods_isodecoder.items():
 			for pos in data:
-				predMods.write(cluster + "\t" + \
+				predMods.write(isodecoder + "\t" + \
 					str(pos) + "\t" + \
-					str(sum(modTable[cluster][pos+1].values())) + "\n")
-
-	return(new_mods, new_Inosines)
-
-def countMods_mp(out_dir, cov_table, min_cov, info, mismatch_dict, cca, filtered_list, tRNA_struct, remap, misinc_thresh, knownTable, tRNA_dict, cons_pos_dict, inputs):
+					str(tRNA_dict[isodecoder]['sequence'][int(pos)]) + "\t" + \
+					inputs.split("/")[-1] + "\n")
+		if not remap: # only write inosines on second round (or if remap is disabled) to prevent writing entries twice
+			for isodecoder, data in new_inosines_isodecoder.items():
+				for pos in data:
+					predMods.write(isodecoder + "\t" + \
+						str(pos) + "\t" + \
+						"I" + "\t" + \
+						inputs.split("/")[-1] + "\n")
+
+	return(new_mods_cluster, new_inosines_cluster)
+
+def bamMods_mp(out_dir, min_cov, info, mismatch_dict, cluster_dict, cca, tRNA_struct, remap, misinc_thresh, knownTable, tRNA_dict, unique_isodecoderMMs, splitBool, isodecoder_sizes, inputs):
 # modification counting and table generation, and CCA analysis
 	
 	modTable = defaultdict(lambda: defaultdict(lambda: defaultdict(int)))
-	clusterMMTable = defaultdict(lambda: defaultdict(lambda: defaultdict(int)))
 	stopTable = defaultdict(lambda: defaultdict(int))
+	counts = defaultdict(lambda: defaultdict(int))
+	cov = defaultdict(lambda: defaultdict(int))
 	geneCov = defaultdict(int)
 	condition = info[inputs][0]
 
@@ -71,9 +87,6 @@ def countMods_mp(out_dir, cov_table, min_cov, info, mismatch_dict, cca, filtered
 	for read in bam_file.fetch(until_eof=True):
 		query = read.query_name
 		reference = read.reference_name
-		if reference in filtered_list:
-			continue
-		geneCov[reference] += 1
 
 		#########################
 		# Modification analysis #
@@ -100,64 +113,27 @@ def countMods_mp(out_dir, cov_table, min_cov, info, mismatch_dict, cca, filtered
 			soft_clip = int(cigar_list[-2])
 			read_seq = read_seq[:-soft_clip]
 
-		# get offset of read mapping position to reference start in order to adjust mismatch position 
+		# get offset of read mapping position to reference start in order to adjust mismatch position, and end of alignment for coverage calculation
 		# (offset is simply start position of read alignment realtive to reference)
 		offset = read.reference_start
+		aln_end = read.reference_end
 		
-		# offset + 1 (0 to 1 based) is start of alignment - i.e. any start > 1 indicates a stop to RT at this position
-		stopTable[reference][offset+1] += 1
-		
-		# build mismatch dictionary ignoring inserts in reference ('^') due to alignment algorithm and adding offset only to first interval of MD tag
-		# build clusterMMTable to count reads with known mismatches between cluster members to later split reads by isodecoders
+		# map mismatches to reference and count mods
 		ref_pos = 0
 		read_pos = 0
-		for index, interval in enumerate(md_list):
-			if index == 0 and not interval.startswith('^'):
-				if interval.isdigit(): # stretch of matches
-					read_pos += int(interval)
-					interval = int(interval) + offset
-					ref_pos += interval
-				elif interval.isalpha(): # is a mismatch
-					identity = read_seq[read_pos]
-					ref_pos += offset 
-					# check for position in mismatch dictionary from clustering
-					# only include these positions if they aren't registered mismatches between clusters, or if they are known modified sites (lowercase)
-					if (ref_pos not in mismatch_dict[reference]) or (ref_pos in mismatch_dict[reference] and identity.islower()):
-						modTable[reference][ref_pos+1][identity] += 1 # log the identity of the misincorporated base
-						# if interval == interval.lower():
-						# 	modTable[reference][ref_pos]['known'] = 1 # log if the mismatch was a known modified position by checking for lowercase letter in MD tag (see --md-lowercase-snp in GSNAP parameters)
-						# else:
-						# 	modTable[reference][ref_pos]['known'] = 0
-					elif ref_pos in mismatch_dict[reference]:
-						clusterMMTable[reference][ref_pos][identity] += 1 # here 0 based numbering used for pos as these positions will refer back to sequences positions and not used for referring to canonical numbering etc...
-					# move forward
-					read_pos += 1
-					ref_pos += 1
-
-			elif not interval.startswith('^'):
-				if interval.isdigit(): # stretch of matches
-					read_pos += int(interval)
-					ref_pos += int(interval)
-				elif interval.isalpha(): # is a mismatch
-					identity = read_seq[read_pos] # identity is misincorporated nucleotide
-					# check for position in mismatch dictionary from clustering
-					# only include these positions if they aren't registered mismatches between clusters, or if they are known modified sites (lowercase)
-					if (ref_pos not in mismatch_dict[reference]) or (ref_pos in mismatch_dict[reference] and identity.islower()):
-						modTable[reference][ref_pos+1][identity] += 1
-						# if interval == interval.lower():
-						# 	modTable[reference][ref_pos]['known'] = 1
-						# else:
-						# 	modTable[reference][ref_pos]['known'] = 0
-					elif ref_pos in mismatch_dict[reference]:
-						clusterMMTable[reference][ref_pos][identity] += 1
-					# move forward
-					read_pos += 1
-					ref_pos += 1
-			elif interval.startswith('^'):
-				insertion = len(interval) - 1
-				identity = "insertion"
-				clusterMMTable[reference][ref_pos][identity] += 1
-				ref_pos += insertion
+		temp = defaultdict()
+		temp, ref_pos, read_pos, reference = countMods(temp, ref_pos, read_pos, read_seq, offset, reference, md_list, unique_isodecoderMMs, mismatch_dict, remap)
+
+		# read counts, stops and coverage
+		counts[inputs][reference] += 1
+		geneCov[reference] += 1
+		# offset + 1 (0 to 1 based) is start of alignment - i.e. any start > 1 indicates a stop to RT at this position
+		stopTable[reference][offset+1] += 1
+		for i in range(offset+1, aln_end+1):
+			cov[reference][i] += 1
+
+		for pos, identity in temp.items():
+			modTable[reference][pos][identity] += 1
 
 		################
 		# CCA analysis #
@@ -168,7 +144,9 @@ def countMods_mp(out_dir, cov_table, min_cov, info, mismatch_dict, cca, filtered
 			dinuc = read.query_sequence[-2:]
 			dinuc_dict[dinuc] += 1
 
-			ref_length = bam_file.get_reference_length(reference)
+			mapped_ref = read.reference_name
+
+			ref_length = bam_file.get_reference_length(mapped_ref)
 			if ref_pos in [ref_length, ref_length - 1]:
 				cca_dict[reference][dinuc] += 1
 			elif ref_pos == ref_length - 2:
@@ -178,142 +156,164 @@ def countMods_mp(out_dir, cov_table, min_cov, info, mismatch_dict, cca, filtered
 				dinuc = "Absent"
 				cca_dict[reference][dinuc] += 1
 
-	if cca:
-		# write dinuc proportions for current bam
-		for dinuc, count in dinuc_dict.items():
-			dinuc_prop.write(dinuc + "\t" + str(count/aln_count) + "\t" + inputs.split("/")[-1] + "\n")
-
-		# add missing ends to dict to prevent issues with plotting in R
-		for end in ["CA", "CC", "C", "Absent"]:
-			for cluster, data in cca_dict.items():
-				if not end in data.keys():
-					cca_dict[cluster][end] = 0
-
-		# write CCA outputs for current bam
-		for cluster, data in cca_dict.items():
-			for dinuc, count in data.items():
-				if (dinuc.upper() == "CC") or (dinuc.upper() == "CA") or (dinuc.upper() == "C") or (dinuc == "Absent"):
-					CCAvsCC_counts.write(cluster + "\t" + dinuc + "\t" + inputs + "\t" + condition + "\t" + str(count) + "\n")
-
-		dinuc_prop.close()
-		CCAvsCC_counts.close()
-
 	## Edit misincorportation and stop data before writing
 
-	# build dictionaries for mismatches, isodecoder counts, and stops, normalizing to total coverage per nucleotide
-	modTable_prop = {cluster: {pos: {
-				group: count / cov_table[(cov_table.pos == pos) & (cov_table.condition == condition) & (cov_table.bam == inputs)].loc[cluster]['cov']
+	# build dictionaries for mismatches and stops, normalizing to total coverage per nucleotide
+	modTable_prop = {isodecoder: {pos: {
+				group: count / cov[isodecoder][pos]
 				  for group, count in data.items() if group in ['A','C','G','T']
 								}
 			for pos, data in values.items()
 							}
-		for cluster, values in modTable.items()
-					}
-
-	clusterMMTable_prop = {cluster: {pos: {
-				group: count / cov_table[(cov_table.pos == pos+1) & (cov_table.condition == condition) & (cov_table.bam == inputs)].loc[cluster]['cov']
-				  for group, count in data.items() if group in ['A','C','G','T', 'insertion']
-								}
-			for pos, data in values.items()
-							}
-		for cluster, values in clusterMMTable.items()
+		for isodecoder, values in modTable.items()
 					}
 
-	# knownTable = {cluster: {pos: test['known']
-	# 		for pos, test in values.items()
-	# 					}
-	# 	for cluster, values in modTable.items()
-	# 			}
-
-	stopTable_prop = {cluster: {
-			pos: count / geneCov[cluster]
+	stopTable_prop = {isodecoder: {
+			pos: count / geneCov[isodecoder]
 			for pos, count in values.items()
 						}
-		for cluster, values in stopTable.items()
+		for isodecoder, values in stopTable.items()
 				}
-
-	# if remapping is enabled, find uknown mod sites
-	if remap:
-		new_mods, new_Inosines = unknownMods(inputs, out_dir, knownTable, modTable_prop, misinc_thresh, cov_table, min_cov, tRNA_dict, cons_pos_dict)
-	else:
+				
+	# find unknown mod sites
+	new_mods, new_Inosines = unknownMods(inputs, out_dir, knownTable, cluster_dict, modTable_prop, misinc_thresh, cov, min_cov, tRNA_dict, remap)
+	
+	# format and output mods and stops if remap is disabled (i.e. also occurs after round 2 of mapping)
+	if not remap:
 		new_mods = {}
 		new_Inosines = {}
 
-	# reformat modTable, add gaps and structure, and save to temp file
-	reform = {(outerKey, innerKey): values for outerKey, innerDict in modTable_prop.items() for innerKey, values in innerDict.items()}
-	modTable_prop_df = pd.DataFrame.from_dict(reform)
-	modTable_prop_df['type'] = modTable_prop_df.index
-	modTable_prop_melt = modTable_prop_df.melt(id_vars=['type'], var_name=['cluster','pos'], value_name='proportion')
-	modTable_prop_melt['condition'] = condition
-	modTable_prop_melt['bam'] = inputs
-	modTable_prop_melt.pos = pd.to_numeric(modTable_prop_melt.pos)
-	# add coverage per nucelotide from cov_table
-	cov_merge = cov_table.loc[:, ('pos', 'cov', 'bam')]
-	cov_merge['cluster'] = cov_merge.index
-	#cov_merge.columns = ['canon_pos', 'cov', 'bam', 'cluster']
-	cov_merge['pos'] = cov_merge['pos'].astype(int)
-	modTable_prop_melt = pd.merge(modTable_prop_melt, cov_merge, on = ['cluster', 'pos', 'bam'], how = 'left')
-	
-	grouped = modTable_prop_melt.groupby('cluster')
-	for name, group in grouped:
-		for pos in tRNA_struct.loc[name].index:
-			if tRNA_struct.loc[name].iloc[pos-1].struct == 'gap':
-				modTable_prop_melt.loc[(modTable_prop_melt.cluster == name) & (modTable_prop_melt.pos >= pos), 'pos'] += 1
-				new = pd.DataFrame({'cluster':name, 'pos':pos, 'type':pd.Categorical(['A','C','G','T']), 'proportion':'NA', 'condition':group.condition.iloc[1], 'bam':group.bam.iloc[1], 'cov':'NA'})
-				modTable_prop_melt = modTable_prop_melt.append(new)
-			if not any(modTable_prop_melt.loc[modTable_prop_melt.cluster == name].pos == pos):
-				new = pd.DataFrame({'cluster':name, 'pos':pos, 'type':pd.Categorical(['A','C','G','T']), 'proportion':'NA', 'condition':group.condition.iloc[1], 'bam':group.bam.iloc[1], 'cov':'NA'})
-				modTable_prop_melt = modTable_prop_melt.append(new)
-
-
-	modTable_prop_melt = modTable_prop_melt[['cluster','pos', 'type','proportion','condition', 'bam', 'cov']]
-	modTable_prop_melt = modTable_prop_melt.join(tRNA_struct, on=['cluster', 'pos'])
-	modTable_prop_melt = modTable_prop_melt.dropna(subset=['struct'])
-
-	modTable_prop_melt.to_csv(inputs + "mismatchTable.csv", sep = "\t", index = False, na_rep = 'NA')
-
-	# reformat clusterMMTable and save to temp
-	reform = {(outerKey, innerKey): values for outerKey, innerDict in clusterMMTable_prop.items() for innerKey, values in innerDict.items()}
-	clusterMMTable_prop_df = pd.DataFrame.from_dict(reform)
-	clusterMMTable_prop_df['type'] = clusterMMTable_prop_df.index
-	clusterMMTable_prop_melt = clusterMMTable_prop_df.melt(id_vars=['type'], var_name=['cluster','pos'], value_name='proportion')
-	clusterMMTable_prop_melt['bam'] = inputs
-	clusterMMTable_prop_melt.pos = pd.to_numeric(clusterMMTable_prop_melt.pos)
-	clusterMMTable_prop_melt = clusterMMTable_prop_melt.dropna()
-	clusterMMTable_prop_melt.index = clusterMMTable_prop_melt['cluster']
-	clusterMMTable_prop_melt = clusterMMTable_prop_melt.drop(columns = ['cluster'])
-	clusterMMTable_prop_melt.to_csv(inputs + "clusterMMTable.csv", sep = "\t", index = True)
-
-	# reformat stopTable, add gaps and structure, and save to temp file
-	stopTable_prop_df = pd.DataFrame.from_dict(stopTable_prop)
-	stopTable_prop_df['pos'] = stopTable_prop_df.index
-	stopTable_prop_melt = stopTable_prop_df.melt(id_vars='pos', var_name='cluster', value_name='proportion')
-	stopTable_prop_melt['condition'] = condition
-	stopTable_prop_melt['bam'] = inputs
-	stopTable_prop_melt.pos = pd.to_numeric(stopTable_prop_melt.pos)
-
-	grouped = stopTable_prop_melt.groupby('cluster')
-	for name, group in grouped:
-		for pos in tRNA_struct.loc[name].index:
-			if tRNA_struct.loc[name].iloc[pos-1].struct == 'gap':
-				stopTable_prop_melt.loc[(stopTable_prop_melt.cluster == name) & (stopTable_prop_melt.pos >= pos), 'pos'] += 1
-				new = pd.DataFrame({'cluster':name, 'pos':pos, 'proportion':'NA', 'condition':group.condition.iloc[1], 'bam':group.bam.iloc[1]}, index=[0])
-				stopTable_prop_melt = stopTable_prop_melt.append(new)
-			if not any(stopTable_prop_melt.loc[stopTable_prop_melt.cluster == name].pos == pos):
-				new = pd.DataFrame({'cluster':name, 'pos':pos, 'proportion':'NA', 'condition':group.condition.iloc[1], 'bam':group.bam.iloc[1]}, index=[0])
-				stopTable_prop_melt = stopTable_prop_melt.append(new)
+		log.info('Building modification, stop and count data tables for {}'.format(inputs))
+
+		# reformat modTable, add gaps and structure, and save to temp file
+		reform = {(outerKey, innerKey): values for outerKey, innerDict in modTable_prop.items() for innerKey, values in innerDict.items()}
+		modTable_prop_df = pd.DataFrame.from_dict(reform)
+		modTable_prop_df['type'] = modTable_prop_df.index
+		modTable_prop_melt = modTable_prop_df.melt(id_vars=['type'], var_name=['isodecoder','pos'], value_name='proportion')
+		modTable_prop_melt['condition'] = condition
+		modTable_prop_melt['bam'] = inputs
+		modTable_prop_melt.pos = pd.to_numeric(modTable_prop_melt.pos)
+		# add coverage per nucelotide from cov
+		cov_table = pd.DataFrame.from_dict(cov)
+		cov_table['pos'] = cov_table.index
+		cov_table['pos'] = cov_table['pos'].astype(int)
+		cov_table_melt = cov_table.melt(id_vars='pos', var_name='isodecoder', value_name='cov')
+		cov_table_melt.dropna(inplace = True)
+		cov_table_melt['bam'] = inputs
+		cov_table_melt = cov_table_melt[['isodecoder', 'pos', 'bam', 'cov']]
+		cov_table_melt.to_csv(out_dir + inputs.split("/")[-1] + "_coverage.txt", sep = "\t", index = False)
+		modTable_prop_melt = pd.merge(modTable_prop_melt, cov_table_melt, on = ['isodecoder', 'pos', 'bam'], how = 'left')
+
+		modTable_prop_melt = addNA(modTable_prop_melt, tRNA_struct, cluster_dict, "mods")
+		modTable_prop_melt = modTable_prop_melt[['isodecoder','pos', 'type','proportion','condition', 'bam', 'cov']]
+
+		# reformat stopTable, add gaps and structure, and save to temp file
+		stopTable_prop_df = pd.DataFrame.from_dict(stopTable_prop)
+		stopTable_prop_df['pos'] = stopTable_prop_df.index
+		stopTable_prop_melt = stopTable_prop_df.melt(id_vars='pos', var_name='isodecoder', value_name='proportion')
+		stopTable_prop_melt['condition'] = condition
+		stopTable_prop_melt['bam'] = inputs
+		stopTable_prop_melt.pos = pd.to_numeric(stopTable_prop_melt.pos)
+		
+		stopTable_prop_melt.dropna(inplace = True)
+		stopTable_prop_melt = addNA(stopTable_prop_melt, tRNA_struct, cluster_dict, "stops")
+		stopTable_prop_melt = stopTable_prop_melt[['isodecoder', 'pos', 'proportion', 'condition', 'bam']]
+
+		# build temp counts DataFrame
+		counts_table = pd.DataFrame.from_dict(counts)
+		counts_table['isodecoder'] = counts_table.index
+		counts_table = counts_table[['isodecoder', inputs]]
+		# add 0 count isodecoders to table
+		temp_add = pd.DataFrame(columns = ['isodecoder', inputs])
+		for isodecoder in isodecoder_sizes.keys():
+			if not isodecoder in counts_table['isodecoder']:
+				temp_add = temp_add.append({'isodecoder':isodecoder, inputs:0}, ignore_index = True)
+		counts_table = counts_table.append(temp_add)
+
+		counts_table.to_csv(inputs + "countTable.csv", sep = "\t", index = False, na_rep = "NA")
+		modTable_prop_melt.to_csv(inputs + "mismatchTable.csv", sep = "\t", index = False, na_rep = 'NA')
+		stopTable_prop_melt.to_csv(inputs + "RTstopTable.csv", sep = "\t", index = False, na_rep = 'NA')
 
-	stopTable_prop_melt = stopTable_prop_melt[['cluster', 'pos', 'proportion', 'condition', 'bam']]
-	stopTable_prop_melt = stopTable_prop_melt.join(tRNA_struct, on = ['cluster', 'pos'])
-	stopTable_prop_melt = stopTable_prop_melt.dropna(subset=['struct'])
+		if cca:
+			# write dinuc proportions for current bam
+			for dinuc, count in dinuc_dict.items():
+				dinuc_prop.write(dinuc + "\t" + str(count/aln_count) + "\t" + inputs.split("/")[-1] + "\n")
+
+			# add missing ends to dict to prevent issues with plotting in R
+			for end in ["CA", "CC", "C", "Absent"]:
+				for cluster, data in cca_dict.items():
+					if not end in data.keys():
+						cca_dict[cluster][end] = 0
+
+			# write CCA outputs for current bam
+			for cluster, data in cca_dict.items():
+					for dinuc, count in data.items():
+						if (dinuc.upper() == "CC") or (dinuc.upper() == "CA") or (dinuc.upper() == "C") or (dinuc == "Absent"):
+							CCAvsCC_counts.write(cluster + "\t" + dinuc + "\t" + inputs + "\t" + condition + "\t" + str(count) + "\n")
 
-	stopTable_prop_melt.to_csv(inputs + "RTstopTable.csv", sep = "\t", index = False, na_rep = 'NA')
+			dinuc_prop.close()
+			CCAvsCC_counts.close()
 
 	log.info('Analysis complete for {}...'.format(inputs))
 
 	return(new_mods, new_Inosines)
 
-def generateModsTable(sampleGroups, out_dir, threads, cov_table, min_cov, mismatch_dict, filtered_list, cca, remap, misinc_thresh, knownTable, tRNA_dict, Inosine_clusters):
+def countMods(temp, ref_pos, read_pos, read_seq, offset, reference, md_list, unique_isodecoderMMs, mismatch_dict, remap):
+# Loop though mismatches in read and return new reference for splitting reads and/or count mods
+	
+	old_reference = reference
+	for index, interval in enumerate(md_list):
+		if not index == 0:
+			new_offset = 0
+		else:
+			new_offset = offset
+		if not interval.startswith('^'): 
+			if interval.isdigit(): # stretch of matches
+				read_pos += int(interval)
+				interval = int(interval) + new_offset
+				ref_pos += interval
+			elif interval.isalpha(): # is a mismatch
+				identity = read_seq[read_pos]
+				ref_pos += new_offset 
+				# update reference for isodecoder splitting if cluster_id not 1 and remap is disabed or this is round 2 of alignment (avoid errors in adding new mods for clusters)
+				if (unique_isodecoderMMs) and (identity in unique_isodecoderMMs[old_reference][ref_pos]) and (not remap):
+					reference = unique_isodecoderMMs[old_reference][ref_pos][identity]
+				# only include these positions if they aren't registered mismatches between clusters, or if they are known modified sites (lowercase)
+				elif (ref_pos not in mismatch_dict[old_reference]): #or (ref_pos in mismatch_dict[old_reference] and interval.islower()):
+					temp[ref_pos+1] = identity
+				# move forward
+				read_pos += 1
+				ref_pos += 1
+		elif interval.startswith('^'):
+			identity = 'insertion'
+			if (unique_isodecoderMMs) and (identity in unique_isodecoderMMs[old_reference][ref_pos]) and (not remap):
+				reference = unique_isodecoderMMs[old_reference][ref_pos][identity]
+			insertion = len(interval) - 1
+			ref_pos += insertion
+
+	return(temp, ref_pos, read_pos, reference)
+
+def addNA(table, tRNA_struct, cluster_dict, data_type):
+# fill mods and stops tables with 'NA' for gapped alignment
+	
+	grouped = table.groupby('isodecoder')
+	for name, group in grouped:
+		#cluster = [parent for parent, child in cluster_dict.items() if name in child][0]
+		for pos in tRNA_struct.loc[name].index:
+			if data_type == 'mods':
+				new = pd.DataFrame({'isodecoder':name, 'pos':pos, 'type':pd.Categorical(['A','C','G','T']), 'proportion':'NA', 'condition':group.condition.iloc[1], 'bam':group.bam.iloc[1], 'cov':'NA'})
+			elif data_type == 'stops':
+				new = pd.DataFrame({'isodecoder':name, 'pos':pos, 'proportion':'NA', 'condition':group.condition.iloc[0], 'bam':group.bam.iloc[0]}, index=[0])
+			if tRNA_struct.loc[name].iloc[pos-1].struct == 'gap':
+				if not pos == max(tRNA_struct.loc[name].index):
+					table.loc[(table.isodecoder == name) & (table.pos >= pos), 'pos'] += 1
+				table = table.append(new)
+			if not any(table.loc[table.isodecoder == name].pos == pos):
+				table = table.append(new)
+
+	return(table)
+
+def generateModsTable(sampleGroups, out_dir, threads, min_cov, mismatch_dict, cluster_dict, cca, remap, misinc_thresh, knownTable, tRNA_dict, Inosine_clusters, unique_isodecoderMMs, splitBool, isodecoder_sizes):
 # Wrapper function to call countMods_mp with multiprocessing
 
 	if cca:
@@ -351,71 +351,117 @@ def generateModsTable(sampleGroups, out_dir, threads, cov_table, min_cov, mismat
 		multi = len(baminfo)
 
 	# get tRNA struct info from ssAlign
-	tRNA_struct, cons_pos_list, cons_pos_dict = ssAlign.tRNAclassifier(out_dir)
+	tRNA_struct, tRNA_ungap2canon, cons_pos_list, cons_pos_dict = ssAlign.tRNAclassifier(out_dir)
 	tRNA_struct_df = pd.DataFrame(tRNA_struct).unstack().rename_axis(('cluster', 'pos')).rename('struct')
 	tRNA_struct_df = pd.DataFrame(tRNA_struct_df)
 
 	# initiate multiprocessing pool and run with bam names
 	pool = Pool(multi)
-	func = partial(countMods_mp, out_dir, cov_table, min_cov, baminfo, mismatch_dict, cca, filtered_list, tRNA_struct_df, remap, misinc_thresh, knownTable, tRNA_dict, cons_pos_dict)
+	func = partial(bamMods_mp, out_dir, min_cov, baminfo, mismatch_dict, cluster_dict, cca, tRNA_struct_df, remap, misinc_thresh, knownTable, tRNA_dict, unique_isodecoderMMs, splitBool, isodecoder_sizes)
 	new_mods, new_Inosines = zip(*pool.map(func, bamlist))
 	pool.close()
 	pool.join()
 
-	modTable_total = pd.DataFrame()
-	clusterMMTable_total = pd.DataFrame()
-	#knownTable_total = pd.DataFrame()
-	stopTable_total = pd.DataFrame()
-
-	dinuc_table = pd.DataFrame()
-	CCAvsCC_table = pd.DataFrame()
-
-	for bam in bamlist:
-		# read in temp files and then delete
-		modTable = pd.read_csv(bam + "mismatchTable.csv", header = 0, sep = "\t")
-		modTable['canon_pos'] = modTable['pos'].map(cons_pos_dict)
-		for cluster in Inosine_clusters:
-			modTable.at[(modTable.canon_pos == '34') & (modTable['type'] == 'G') & (modTable.cluster == cluster), 'proportion'] = 1 - sum(modTable[(modTable.canon_pos == '34') & (modTable['type'] != 'G') & (modTable.cluster == cluster)]['proportion'].dropna())
-		os.remove(bam + "mismatchTable.csv")
-
-		clusterMMTable = pd.read_csv(bam + "clusterMMTable.csv", header = 0, sep = "\t", index_col = 0)
-		os.remove(bam + "clusterMMTable.csv")
-
-		stopTable = pd.read_csv(bam + "RTstopTable.csv", header = 0, sep = "\t")
-		stopTable['canon_pos'] = stopTable['pos'].map(cons_pos_dict)
-		os.remove(bam + "RTstopTable.csv")
-
-		# add individual temp files to main big table and save
-		modTable_total = modTable_total.append(modTable)
-		clusterMMTable_total = clusterMMTable_total.append(clusterMMTable)
-		stopTable_total = stopTable_total.append(stopTable)
+	filtered = list()
+	
+	if not remap:
+
+		modTable_total = pd.DataFrame()
+		countsTable_total = pd.DataFrame()
+		stopTable_total = pd.DataFrame()
+		newMods_total = pd.DataFrame()
+
+		dinuc_table = pd.DataFrame()
+		CCAvsCC_table = pd.DataFrame()
+
+		for bam in bamlist:
+			# read in temp files and then delete
+			modTable = pd.read_csv(bam + "mismatchTable.csv", header = 0, sep = "\t")
+			modTable['canon_pos'] = modTable['pos'].map(cons_pos_dict)
+			for cluster in Inosine_clusters:
+				modTable.at[(modTable.canon_pos == '34') & (modTable['type'] == 'G') & (modTable.isodecoder == cluster), 'proportion'] = 1 - sum(modTable[(modTable.canon_pos == '34') & (modTable['type'] != 'G') & (modTable.isodecoder == cluster)]['proportion'].dropna())
+			os.remove(bam + "mismatchTable.csv")
+
+			stopTable = pd.read_csv(bam + "RTstopTable.csv", header = 0, sep = "\t")
+			stopTable['canon_pos'] = stopTable['pos'].map(cons_pos_dict)
+			os.remove(bam + "RTstopTable.csv")
+
+			countsTable = pd.read_csv(bam + "countTable.csv", header = 0, sep = "\t")
+			os.remove(bam + "countTable.csv")
+
+			newModsTable = pd.read_csv(bam + "_predictedModstemp.csv", header = None, names = ['isodecoder', 'pos', 'identity', 'bam'], sep = "\t")
+			os.remove(bam + "_predictedModstemp.csv")
+
+			# add individual temp files to main big table
+			modTable_total = modTable_total.append(modTable)
+			stopTable_total = stopTable_total.append(stopTable)
+			if countsTable_total.empty:
+				countsTable_total = countsTable_total.append(countsTable)
+			else:
+				countsTable_total = pd.merge(countsTable_total, countsTable, on = "isodecoder", how = "left")
+			newMods_total = newMods_total.append(newModsTable)
+
+			if cca:
+				# same for CCA analysis files
+				dinuc = pd.read_csv(bam + "_dinuc.csv", header = None, keep_default_na=False, sep = "\t")
+				os.remove(bam + "_dinuc.csv")
+				CCA = pd.read_table(bam + "_CCAcounts.csv", header = None)
+				os.remove(bam + "_CCAcounts.csv")
+
+				dinuc_table = dinuc_table.append(dinuc)
+				CCAvsCC_table = CCAvsCC_table.append(CCA)
+
+		# plot coverage and get isodecoders to filter from mods and stops
+		countsTable_total.index = countsTable_total.isodecoder
+		countsTable_total.drop(columns = ['isodecoder'], inplace = True)
+		filtered = filterCoverage(countsTable_total, min_cov)
+
+		# filter and output tables
+		modTable_total = modTable_total[~modTable_total.isodecoder.isin(filtered)]
+		#modTable_total.drop(modTable_total[modTable_total['isodecoder'] in filtered].index, inplace = True)
+		modTable_total.to_csv(out_dir + "mods/mismatchTable.csv", sep = "\t", index = False, na_rep = 'NA')
+		with open(out_dir + "mods/knownModsTable.csv", "w") as known:
+			known.write("cluster\tpos\n")
+			for cluster, data in knownTable.items():
+				for pos in data:
+					known.write(cluster + "\t" + str(pos) + "\n")
+
+		stopTable_total = stopTable_total[~stopTable_total.isodecoder.isin(filtered)]
+		stopTable_total.to_csv(out_dir + "mods/RTstopTable.csv", sep = "\t", index = False, na_rep = 'NA')	
+		
+		# add column to counts to indicate complete isodecoder split or not
+		countsTable_total['Single_isodecoder'] = "NA"
+		for cluster in countsTable_total.index:
+			if cluster in splitBool:
+				countsTable_total.at[cluster, 'Single_isodecoder'] = "False"
+			else:
+				countsTable_total.at[cluster, 'Single_isodecoder'] = "True"
+		countsTable_total.to_csv(out_dir + "Isodecoder_counts.txt", sep = "\t", index = True)
+
+		# map canon_pos for each isodecoder ungapped pos to newMods
+		tRNA_ungap2canon_table = pd.DataFrame.from_dict(tRNA_ungap2canon, orient = "index")
+		tRNA_ungap2canon_table = tRNA_ungap2canon_table.reset_index()
+		tRNA_ungap2canon_table = tRNA_ungap2canon_table.melt(var_name='pos', value_name='canon_pos', id_vars='index')
+		tRNA_ungap2canon_table.columns = ['isodecoder', 'pos', 'canon_pos']
+		newMods_total = pd.merge(newMods_total, tRNA_ungap2canon_table, on = ['isodecoder', 'pos'], how = "left")
+		# make pivot table from mods and add A, C, G, T misinc. proportions for new mods
+		pivot = modTable_total.pivot_table(index = ['isodecoder', 'bam', 'canon_pos'], columns = 'type', values = 'proportion')
+		pivot = pivot.reset_index()
+		pivot['bam'].replace(out_dir, "", regex = True, inplace = True)
+		newMods_total = pd.merge(newMods_total, pivot, on = ['isodecoder', 'canon_pos', 'bam'], how = "left")
+		newMods_total.drop(columns = ['pos'], inplace = True)
+		newMods_total.to_csv(out_dir + 'mods/predictedMods.csv', sep = "\t", index = False, na_rep = "NA")
 
 		if cca:
-			# same for CCA analysis files
-			dinuc = pd.read_csv(bam + "_dinuc.csv", header = None, keep_default_na=False, sep = "\t")
-			os.remove(bam + "_dinuc.csv")
-			CCA = pd.read_table(bam + "_CCAcounts.csv", header = None)
-			os.remove(bam + "_CCAcounts.csv")
-
-			dinuc_table = dinuc_table.append(dinuc)
-			CCAvsCC_table = CCAvsCC_table.append(CCA)
-
-	modTable_total.to_csv(out_dir + "mods/mismatchTable.csv", sep = "\t", index = False, na_rep = 'NA')
-	with open(out_dir + "mods/knownModsTable.csv", "w") as known:
-		known.write("cluster\tpos\n")
-		for cluster, data in knownTable.items():
-			for pos in data:
-				known.write(cluster + "\t" + str(pos) + "\n")
-	#knownTable_total.to_csv(out_dir + "mods/knownModsTable.csv", sep = "\t", index = False, na_rep = 'NA')
-	stopTable_total.to_csv(out_dir + "mods/RTstopTable.csv", sep = "\t", index = False, na_rep = 'NA')	
+			dinuc_table.columns = ['dinuc', 'proportion', 'sample']
+			dinuc_table.to_csv(out_dir + "CCAanalysis/AlignedDinucProportions.csv", sep = "\t", index = False, na_rep = 'NA')
+			CCAvsCC_table.columns = ['gene', 'end', 'sample', 'condition', 'count']
+			CCAvsCC_table = CCAvsCC_table[~CCAvsCC_table.gene.isin(filtered)]
+			CCAvsCC_table.to_csv(out_dir + "CCAanalysis/CCAcounts.csv", sep = "\t", index = False)
 
-	if cca:
-		dinuc_table.columns = ['dinuc', 'proportion', 'sample']
-		dinuc_table.to_csv(out_dir + "CCAanalysis/AlignedDinucProportions.csv", sep = "\t", index = False, na_rep = 'NA')
-		CCAvsCC_table.columns = ['gene', 'end', 'sample', 'condition', 'count']
-		#CCAvsCC_table = CCAvsCC_table.pivot_table(index = 'gene', columns = 'sample', values = 'count', fill_value = 0)
-		CCAvsCC_table.to_csv(out_dir + "CCAanalysis/CCAcounts.csv", sep = "\t", index = False)
+		# Anticodon counts
+		tRNAtools.countReadsAnticodon(out_dir + "Isodecoder_counts.txt", out_dir)
 
-	return(new_mods, new_Inosines, clusterMMTable_total)
+		log.info("** Read counts per isodecoder saved to " + out_dir + "counts/Isodecoder_counts.txt **")
 
-			
\ No newline at end of file
+	return(new_mods, new_Inosines, filtered)
diff --git a/scripts/modPlot.R b/scripts/modPlot.R
index 61b8da8..71959ca 100644
--- a/scripts/modPlot.R
+++ b/scripts/modPlot.R
@@ -31,57 +31,56 @@ misinc_thresh = as.numeric(args[4])
 mods = read.table(paste(out, "mods/mismatchTable.csv", sep = ''), header=T, sep = "\t", quote = '')
 mods$proportion[is.na(mods$proportion)] = 0
 mods$proportion[is.infinite(mods$proportion)] = 0
-mods$cluster = sub(".*_mito_tRNA-","mito",mods$cluster)
-mods$cluster = sub(".*_nmt_tRNA-","nmt",mods$cluster)
-mods$cluster = sub(".*_tRNA-","",mods$cluster)
-mods$cluster = ifelse(mods$cluster == 'eColiLys-TTT-1-1', 'eColiLys', mods$cluster)
-mods_agg = aggregate(mods$proportion, by = list(cluster=mods$cluster, pos=mods$pos, bam=mods$bam, struct=mods$struct, condition=mods$condition, canon_pos=mods$canon_pos), FUN = sum)
-mods_agg = aggregate(mods_agg$x, by = list(cluster=mods_agg$cluster, pos=mods_agg$pos, struct=mods_agg$struct, condition=mods_agg$condition, canon_pos=mods_agg$canon_pos), FUN = mean)
+mods$isodecoder = sub(".*_mito_tRNA-","mito",mods$isodecoder)
+mods$isodecoder = sub(".*_nmt_tRNA-","nmt",mods$isodecoder)
+mods$isodecoder = sub(".*_tRNA-","",mods$isodecoder)
+mods$isodecoder = ifelse(mods$isodecoder == 'eColiLys-TTT-1-1', 'eColiLys', mods$isodecoder)
+mods_agg = aggregate(mods$proportion, by = list(isodecoder=mods$isodecoder, pos=mods$pos, bam=mods$bam, condition=mods$condition, canon_pos=mods$canon_pos), FUN = sum)
+mods_agg = aggregate(mods_agg$x, by = list(isodecoder=mods_agg$isodecoder, pos=mods_agg$pos, condition=mods_agg$condition, canon_pos=mods_agg$canon_pos), FUN = mean)
 
 # read in stops table and process as above for mods
 stops = read.table(paste(out, "mods/RTstopTable.csv", sep = ''), header = T, sep = "\t", quote = '')
 stops$proportion[is.na(stops$proportion)] = 0
 stops$proportion[is.infinite(stops$proportion)] = 0
-stops$cluster = sub(".*_mito_tRNA-","mito",stops$cluster)
-stops$cluster = sub(".*_nmt_tRNA-","nmt",stops$cluster)
-stops$cluster = sub(".*_tRNA-","",stops$cluster)
-stops$cluster = ifelse(stops$cluster == 'eColiLys-TTT-1-1', 'eColiLys', stops$cluster)
-
-#stops = stops[-5396, ] ## NB!! This cluster had info for pos 122 which doesn't exist - removed manually. Must be changed for other libraries ##
-stops_agg = aggregate(stops$proportion, by = list(cluster=stops$cluster, pos=stops$pos, condition=stops$condition, struct=stops$struct, canon_pos=stops$canon_pos), FUN = mean)
+stops$isodecoder = sub(".*_mito_tRNA-","mito",stops$isodecoder)
+stops$isodecoder = sub(".*_nmt_tRNA-","nmt",stops$isodecoder)
+stops$isodecoder = sub(".*_tRNA-","",stops$isodecoder)
+stops$isodecoder = ifelse(stops$isodecoder == 'eColiLys-TTT-1-1', 'eColiLys', stops$isodecoder)
+stops_agg = aggregate(stops$proportion, by = list(isodecoder=stops$isodecoder, pos=stops$pos, condition=stops$condition, canon_pos=stops$canon_pos), FUN = mean)
 
 # read in context info created by ssAlign module
 context_info = read.table(paste(out, "mods/modContext.txt", sep = ''), header = TRUE)
-context_info$cluster = sub(".*_mito_tRNA-","mito", context_info$cluster)
-context_info$cluster = sub(".*_nmt_tRNA-","nmt", context_info$cluster)
-context_info$cluster = sub(".*_tRNA-","", context_info$cluster)
-context_info$cluster = ifelse(context_info$cluster == 'eColiLys-TTT-1-1', 'eColiLys', context_info$cluster)
+colnames(context_info) = c("isodecoder", "pos", "identity", "upstream", "downstream")
+context_info$isodecoder = sub(".*_mito_tRNA-","mito", context_info$isodecoder)
+context_info$isodecoder = sub(".*_nmt_tRNA-","nmt", context_info$isodecoder)
+context_info$isodecoder = sub(".*_tRNA-","", context_info$isodecoder)
+context_info$isodecoder = ifelse(context_info$isodecoder == 'eColiLys-TTT-1-1', 'eColiLys', context_info$isodecoder)
 
 # for each condition make a misincorporation and stops heatmap as a combined figure using ComplexHeatmap
 # ... make a scatter plot of misincorporation rates faceted by positions in cons_mods (selected known mod sites of interest) and by identity of nucleotide
 for (i in unique(mods_agg$condition)) {
   
   # cyto mods
-  sub_mods_agg = mods_agg[mods_agg$condition == i & !grepl("mito", mods_agg$cluster) & !grepl("nmt", mods_agg$cluster),]
-  sub_mods_wide = dcast(sub_mods_agg[,c('cluster','pos', 'x')], list(.(cluster), .(pos)), value.var = 'x', fun.aggregate = mean)
+  sub_mods_agg = mods_agg[mods_agg$condition == i & !grepl("mito", mods_agg$isodecoder) & !grepl("nmt", mods_agg$isodecoder),]
+  sub_mods_wide = dcast(sub_mods_agg[,c('isodecoder','pos', 'x')], list(.(isodecoder), .(pos)), value.var = 'x', fun.aggregate = mean)
   sub_mods_wide[is.na(sub_mods_wide)] = 0
-  rownames(sub_mods_wide) = sub_mods_wide$cluster
+  rownames(sub_mods_wide) = sub_mods_wide$isodecoder
   sub_mods_wide = sub_mods_wide[, -1]
   sub_mods_mat = as.matrix(sub_mods_wide)
   col_anno = HeatmapAnnotation(Mean = anno_barplot(aggregate(sub_mods_agg$x, by = list(pos = sub_mods_agg$pos), FUN = mean)$x, height = unit(1.5, 'cm'),  gp = gpar(fill = '#C8553D')))
-  count_mods = sub_mods_agg %>% group_by(cluster) %>% summarise(count = sum(x > 0.1))
+  count_mods = sub_mods_agg %>% group_by(isodecoder) %>% summarise(count = sum(x > 0.1))
   row_anno = rowAnnotation(Count = row_anno_barplot(count_mods$count, width = unit(1, 'cm'),  gp = gpar(fill = '#C8553D')))
   cyto_mods_hm = Heatmap(sub_mods_mat, column_labels = cons_pos, row_title = "Misincorporations", column_title = as.character(i), column_title_side = "top", cluster_columns = FALSE, cluster_rows = TRUE, col = col_fun, top_annotation = col_anno, right_annotation = row_anno, heatmap_legend_param = list(title = "Misincorporation proportion", direction = "horizontal"))
   
   # cyto stops
-  sub_stops_agg = stops_agg[stops_agg$condition == i & !grepl("mito", stops_agg$cluster) & !grepl("nmt", stops_agg$cluster),]
-  sub_stops_wide = dcast(sub_stops_agg[,c('cluster','pos', 'x')], list(.(cluster), .(pos)), value.var = 'x', fun.aggregate = mean)
+  sub_stops_agg = stops_agg[stops_agg$condition == i & !grepl("mito", stops_agg$isodecoder) & !grepl("nmt", stops_agg$isodecoder),]
+  sub_stops_wide = dcast(sub_stops_agg[,c('isodecoder','pos', 'x')], list(.(isodecoder), .(pos)), value.var = 'x', fun.aggregate = mean)
   sub_stops_wide[is.na(sub_stops_wide)] = 0
-  rownames(sub_stops_wide) = sub_stops_wide$cluster
+  rownames(sub_stops_wide) = sub_stops_wide$isodecoder
   sub_stops_wide = sub_stops_wide[, -1]
   sub_stops_mat = as.matrix(sub_stops_wide)
   col_anno = HeatmapAnnotation(Mean = anno_barplot(aggregate(sub_stops_agg$x, by = list(pos = sub_stops_agg$pos), FUN = mean)$x, height = unit(1.5, 'cm'),  gp = gpar(fill = '#C8553D')))
-  count_stops = sub_stops_agg %>% group_by(cluster) %>% summarise(count = sum(x > 0.1))
+  count_stops = sub_stops_agg %>% group_by(isodecoder) %>% summarise(count = sum(x > 0.1))
   row_anno = rowAnnotation(Count = row_anno_barplot(count_stops$count, width = unit(1, 'cm'),  gp = gpar(fill = '#C8553D')))
   cyto_stops_hm = Heatmap(sub_stops_mat, column_labels = cons_pos, row_title = "RT stops", cluster_columns = FALSE, cluster_rows = TRUE, col = col_fun, top_annotation = col_anno, right_annotation = row_anno, heatmap_legend_param = list(title = "RT stop proportion", direction = "horizontal"))
   
@@ -92,26 +91,26 @@ for (i in unique(mods_agg$condition)) {
   
   if (!is.na(mito_trnas)){
     # mito mods
-    sub_mods_agg = mods_agg[mods_agg$condition == i & (grepl("mito", mods_agg$cluster) | grepl("nmt", mods_agg$cluster)),]
-    sub_mods_wide = dcast(sub_mods_agg[,c('cluster','pos', 'x')], list(.(cluster), .(pos)), value.var = 'x', fun.aggregate = mean)
+    sub_mods_agg = mods_agg[mods_agg$condition == i & (grepl("mito", mods_agg$isodecoder) | grepl("nmt", mods_agg$isodecoder)),]
+    sub_mods_wide = dcast(sub_mods_agg[,c('isodecoder','pos', 'x')], list(.(isodecoder), .(pos)), value.var = 'x', fun.aggregate = mean)
     sub_mods_wide[is.na(sub_mods_wide)] = 0
-    rownames(sub_mods_wide) = sub_mods_wide$cluster
+    rownames(sub_mods_wide) = sub_mods_wide$isodecoder
     sub_mods_wide = sub_mods_wide[, -1]
     sub_mods_mat = as.matrix(sub_mods_wide)
     col_anno = HeatmapAnnotation(Mean = anno_barplot(aggregate(sub_mods_agg$x, by = list(pos = sub_mods_agg$pos), FUN = mean)$x, height = unit(1.5, 'cm'),  gp = gpar(fill = '#C8553D')))
-    count_mods = sub_mods_agg %>% group_by(cluster) %>% summarise(count = sum(x > 0.1))
+    count_mods = sub_mods_agg %>% group_by(isodecoder) %>% summarise(count = sum(x > 0.1))
     row_anno = rowAnnotation(Count = row_anno_barplot(count_mods$count, width = unit(1, 'cm'),  gp = gpar(fill = '#C8553D')))
     mito_mods_hm = Heatmap(sub_mods_mat, column_labels = cons_pos, row_title = "Misincorporations", column_title = as.character(i), column_title_side = "top", cluster_columns = FALSE, cluster_rows = TRUE, col = col_fun, top_annotation = col_anno, right_annotation = row_anno, heatmap_legend_param = list(title = "Misincorporation proportion", direction = "horizontal"))
     
     # mito stops
-    sub_stops_agg = stops_agg[stops_agg$condition == i & (grepl("mito", stops_agg$cluster) | grepl("nmt", stops_agg$cluster)),]
-    sub_stops_wide = dcast(sub_stops_agg[,c('cluster','pos', 'x')], list(.(cluster), .(pos)), value.var = 'x', fun.aggregate = mean)
+    sub_stops_agg = stops_agg[stops_agg$condition == i & (grepl("mito", stops_agg$isodecoder) | grepl("nmt", stops_agg$isodecoder)),]
+    sub_stops_wide = dcast(sub_stops_agg[,c('isodecoder','pos', 'x')], list(.(isodecoder), .(pos)), value.var = 'x', fun.aggregate = mean)
     sub_stops_wide[is.na(sub_stops_wide)] = 0
-    rownames(sub_stops_wide) = sub_stops_wide$cluster
+    rownames(sub_stops_wide) = sub_stops_wide$isodecoder
     sub_stops_wide = sub_stops_wide[, -1]
     sub_stops_mat = as.matrix(sub_stops_wide)
     col_anno = HeatmapAnnotation(Mean = anno_barplot(aggregate(sub_stops_agg$x, by = list(pos = sub_stops_agg$pos), FUN = mean)$x, height = unit(1.5, 'cm'),  gp = gpar(fill = '#C8553D')))
-    count_stops = sub_stops_agg %>% group_by(cluster) %>% summarise(count = sum(x > 0.1))
+    count_stops = sub_stops_agg %>% group_by(isodecoder) %>% summarise(count = sum(x > 0.1))
     row_anno = rowAnnotation(Count = row_anno_barplot(count_stops$count, width = unit(1, 'cm'),  gp = gpar(fill = '#C8553D')))
     mito_stops_hm = Heatmap(sub_stops_mat, column_labels = cons_pos, row_title = "RT stops", cluster_columns = FALSE, cluster_rows = TRUE, col = col_fun, top_annotation = col_anno, right_annotation = row_anno, heatmap_legend_param = list(title = "RT stop proportion", direction = "horizontal"))
     
@@ -127,19 +126,19 @@ for (i in unique(mods_agg$condition)) {
   }
   
   # scatter plots
-  temp_mods = merge(mods, context_info, by = c('cluster', 'pos'))
-  temp_mods = temp_mods %>% group_by(cluster, pos, bam, identity) %>% mutate(new_prop = proportion/sum(proportion))
-  filter_proportions = temp_mods %>% group_by(cluster, pos, bam, identity) %>% filter((any(max(new_prop) > 0.95) & any(canon_pos != 34)) | (any(max(new_prop) > 0.95) & any(identity != 'A') & any(canon_pos == 34) & any(type != 'G')))
+  temp_mods = merge(mods, context_info, by = c('isodecoder', 'pos'))
+  temp_mods = temp_mods %>% group_by(isodecoder, pos, bam, identity) %>% mutate(new_prop = proportion/sum(proportion))
+  filter_proportions = temp_mods %>% group_by(isodecoder, pos, bam, identity) %>% filter((any(max(new_prop) > 0.95) & any(canon_pos != 34)) | (any(max(new_prop) > 0.95) & any(identity != 'A') & any(canon_pos == 34) & any(type != 'G')))
   sub_mods_agg = mods_agg[mods_agg$condition == i,]
   sub_mods_pos = sub_mods_agg[sub_mods_agg$canon_pos %in% mod_sites,]
   sub_mods_pos[which(sub_mods_pos$x > 1), 'x'] = 1
-  sub_mods_pos = merge(sub_mods_pos, context_info, by = c('cluster', 'pos'))
-  sub_mods_pos = anti_join(sub_mods_pos, filter_proportions, by = c('cluster', 'pos', 'identity'))
+  sub_mods_pos = merge(sub_mods_pos, context_info, by = c('isodecoder', 'pos'))
+  sub_mods_pos = anti_join(sub_mods_pos, filter_proportions, by = c('isodecoder', 'pos', 'identity'))
   names(sub_mods_pos)[names(sub_mods_pos) == 'x'] = 'Proportion'
   
   sub_mods_pos$canon_pos = factor(sub_mods_pos$canon_pos, levels = c('9','20', '20a', '26', '32','34','37','58'))
   
-  mods_scatter = ggplot(sub_mods_pos[!grepl("mito", sub_mods_pos$cluster) & !grepl("nmt", sub_mods_pos$cluster), ], aes(x=as.character(canon_pos), y = Proportion, color = Proportion)) + geom_jitter(width = 0.1, size = 3) +
+  mods_scatter = ggplot(sub_mods_pos[!grepl("mito", sub_mods_pos$isodecoder) & !grepl("nmt", sub_mods_pos$isodecoder), ], aes(x=as.character(canon_pos), y = Proportion, color = Proportion)) + geom_jitter(width = 0.1, size = 3) +
     theme_bw() + facet_grid(identity~canon_pos, scales = "free_x", labeller = label_both) + scale_color_gradientn(breaks = c(0.0, 0.25, 0.50, 0.75, 1.0), colours = cols) +
     geom_hline(yintercept = 0.1, linetype = "dashed", alpha = 0.4) + 
     theme(
@@ -151,7 +150,7 @@ for (i in unique(mods_agg$condition)) {
   ggsave(paste(out, "mods/", paste(i, 'misincProps.pdf', sep = '_'), sep = ''), mods_scatter, height=10, width=14)
   
   if (!is.na(mito_trnas)){
-    mito_mods_scatter = ggplot(sub_mods_pos[grepl("mito", sub_mods_pos$cluster) | grepl("nmt", sub_mods_pos$cluster), ], aes(x=as.character(canon_pos), y = Proportion, color = Proportion)) + geom_jitter(width = 0.1, size = 3) +
+    mito_mods_scatter = ggplot(sub_mods_pos[grepl("mito", sub_mods_pos$isodecoder) | grepl("nmt", sub_mods_pos$isodecoder), ], aes(x=as.character(canon_pos), y = Proportion, color = Proportion)) + geom_jitter(width = 0.1, size = 3) +
       theme_bw() + facet_grid(identity~canon_pos, scales = "free_x", labeller = label_both) + scale_color_gradientn(breaks = c(0.0, 0.25, 0.50, 0.75, 1.0), colours = cols) +
       geom_hline(yintercept = 0.1, linetype = "dashed", alpha = 0.4) + 
       theme(
@@ -170,13 +169,13 @@ for (i in unique(mods_agg$condition)) {
   # subset mods table for condition
   sub_mods_aggtype = mods[mods$condition == i, ]
   # use filter to filter rows from this table
-  sub_mods_aggtype = anti_join(sub_mods_aggtype, filter_misincthresh, by=c("cluster","pos"))
+  sub_mods_aggtype = anti_join(sub_mods_aggtype, filter_misincthresh, by=c("isodecoder","pos"))
   # add in context info
-  sub_mods_aggtype = merge(sub_mods_aggtype, context_info, by = c("cluster","pos"))
+  sub_mods_aggtype = merge(sub_mods_aggtype, context_info, by = c("isodecoder","pos"))
   sub_mods_aggtype$bam = sub(out, "", sub_mods_aggtype$bam)
-  sub_mods_aggtype_cyt = sub_mods_aggtype[!grepl("mito", sub_mods_aggtype$cluster) & !grepl("nmt", sub_mods_aggtype$cluster), ]
-  # renormalise by sum of misinc at each site for each cluster in each bam file - this makes sum all misinc types = 1, additionally filter all clusters at each pos where misinc of highest nucle > 0.95
-  sub_mods_aggtype_cyt = sub_mods_aggtype_cyt %>% group_by(cluster, pos, bam, identity) %>% mutate(new_prop = proportion/sum(proportion)) %>% filter(any(max(new_prop) < 0.95) | (any(max(new_prop) >= 0.95 & any(identity == 'A') & any(canon_pos == 34) & any(type == 'G'))))
+  sub_mods_aggtype_cyt = sub_mods_aggtype[!grepl("mito", sub_mods_aggtype$isodecoder) & !grepl("nmt", sub_mods_aggtype$isodecoder), ]
+  # renormalise by sum of misinc at each site for each isodecoder in each bam file - this makes sum all misinc types = 1, additionally filter all clusters at each pos where misinc of highest nucle > 0.95
+  sub_mods_aggtype_cyt = sub_mods_aggtype_cyt %>% group_by(isodecoder, pos, bam, identity) %>% mutate(new_prop = proportion/sum(proportion)) %>% filter(any(max(new_prop) < 0.95) | (any(max(new_prop) >= 0.95 & any(identity == 'A') & any(canon_pos == 34) & any(type == 'G'))))
                                                                                                                                                                                   
   #sub_mods_aggtype_cyt_up = aggregate(sub_mods_aggtype_cyt$proportion, by = list(identity = sub_mods_aggtype_cyt$identity, type = sub_mods_aggtype_cyt$type, upstream = sub_mods_aggtype_cyt$upstream, pos = sub_mods_aggtype_cyt$pos, canon_pos=sub_mods_aggtype_cyt$canon_pos), FUN = function(x) c(mean=mean(x), sd=sd(x)))
   #sub_mods_aggtype_cyt_up = do.call("data.frame", sub_mods_aggtype_cyt_up)
@@ -224,9 +223,9 @@ for (i in unique(mods_agg$condition)) {
   ggsave(paste(out, "mods/", paste(i, 'misincSignatures_downstreamContext.pdf', sep = '_'), sep = ''), signature_plot_downstream, height=10, width=14, useDingbats=FALSE)
   
   if (!is.na(mito_trnas)){
-    sub_mods_aggtype_mito = sub_mods_aggtype[grepl("mito", sub_mods_aggtype$cluster) | grepl("nmt", sub_mods_aggtype$cluster), ]
-    # renormalise by sum of misinc at each site for each cluster in each bam file - this makes sum all misinc types = 1
-    sub_mods_aggtype_mito = sub_mods_aggtype_mito %>% group_by(cluster, pos, bam) %>% mutate(new_prop = proportion/sum(proportion)) %>% filter(any(max(new_prop) < 0.95))
+    sub_mods_aggtype_mito = sub_mods_aggtype[grepl("mito", sub_mods_aggtype$isodecoder) | grepl("nmt", sub_mods_aggtype$isodecoder), ]
+    # renormalise by sum of misinc at each site for each isodecoder in each bam file - this makes sum all misinc types = 1
+    sub_mods_aggtype_mito = sub_mods_aggtype_mito %>% group_by(isodecoder, pos, bam) %>% mutate(new_prop = proportion/sum(proportion)) %>% filter(any(max(new_prop) < 0.95))
     #sub_mods_aggtype_mito = aggregate(sub_mods_aggtype_mito$proportion, by = list(identity = sub_mods_aggtype_mito$identity, type = sub_mods_aggtype_mito$type, upstream = sub_mods_aggtype_mito$upstream, downstream = sub_mods_aggtype_mito$downstream, pos = sub_mods_aggtype_mito$pos, canon_pos=sub_mods_aggtype_mito$canon_pos), FUN = function(x) c(mean=mean(x), sd=sd(x)))
     #sub_mods_aggtype_mito = do.call("data.frame", sub_mods_aggtype_mito)
     sub_mods_aggtype_mito$canon_pos = factor(sub_mods_aggtype_mito$canon_pos, levels = c('9', '20', '20a', '26','32','34','37','58'))
diff --git a/scripts/splitReads.py b/scripts/splitReads.py
index a188b2b..1790c3a 100755
--- a/scripts/splitReads.py
+++ b/scripts/splitReads.py
@@ -3,6 +3,7 @@
 import pandas as pd
 import numpy as np
 import logging
+import ssAlign
 from collections import defaultdict
 
 #########################################################
@@ -11,23 +12,29 @@
 
 log = logging.getLogger(__name__)
 
-def splitReadsIsodecoder(isodecoder_counts, clusterMMprops, tRNA_dict, cluster_dict, mismatch_dict, insert_dict, cluster_perPos_mismatchMembers, out_dir, experiment_name):
+def dd():
+	return(defaultdict(dict))
 
-	log.info("\n+--------------------------------------+\
-		\n| Splitting read counts by isodecoders |\
-		\n+--------------------------------------+")
+def splitReadsIsodecoder(isodecoder_count, tRNA_dict, cluster_dict, mismatch_dict, insert_dict, cluster_perPos_mismatchMembers, out_dir, experiment_name):
+
+	log.info("\n+------------------------------------------------------------------------------+\
+		\n| Characterizing cluster mismatches for read splitting by unique tRNA sequence |\
+		\n+------------------------------------------------------------------------------+")
 
 	# read in counts from featureCounts
-	counts = pd.read_csv(out_dir + "counts.txt", header = 0, sep = "\t", comment='#', quotechar="'")
-	counts.index = counts['Geneid']
-	counts = counts.drop(columns=['Geneid', 'Chr','Start','End','Strand','Length'])
+	#counts = pd.read_csv(out_dir + "counts.txt", header = 0, sep = "\t", comment='#', quotechar="'")
+	#counts.index = counts['Geneid']
+	#counts = counts.drop(columns=['Geneid', 'Chr','Start','End','Strand','Length'])
 
 	isodecoder_sizes = defaultdict(int)
+	unique_isodecoderMMs = defaultdict(dd)
 	total_isodecoders = 0
 
+	log.info("** Assessing mismatches between cluster members and parent... **")
+
 	for cluster, mismatches in mismatch_dict.items():
 		mismatches = sorted(mismatches, reverse = True)
-		isodecoder_num = isodecoder_counts[cluster] 
+		isodecoder_num = isodecoder_count[cluster] 
 		total_isodecoders += isodecoder_num
 		curr_isodecoders = 1 # automatically start at 1 which is the cluster parent
 		detected_seqs = defaultdict(list)
@@ -59,23 +66,12 @@ def splitReadsIsodecoder(isodecoder_counts, clusterMMprops, tRNA_dict, cluster_d
 						new_cluster_counts = list()
 						detected_clusters.append(tRNAs[0])
 						isodecoder_items = [tRNA for tRNA, sequence in cluster_members.items() if sequence == tRNA_dict[tRNAs[0]]['sequence']]
-						isodecoder_size = len(isodecoder_items)
-						isodecoder_sizes[tRNAs[0]] = isodecoder_size
+						isodecoder_sizes[tRNAs[0]] = len(isodecoder_items)
 						# update cluster_dict by keeping only tRNAs not in current isodecoder group
 						cluster_dict[cluster] = [tRNA for tRNA in cluster_dict[cluster] if not tRNA in isodecoder_items]
 						curr_isodecoders += 1
-						for bam in clusterMMprops['bam'].unique().tolist():
-							try:
-								fraction = clusterMMprops[(clusterMMprops.bam == bam) & (clusterMMprops.pos == pos) & (clusterMMprops.type == identity)].loc[cluster]['proportion']
-							except KeyError:
-								fraction = 0 
-							
-							new_read_count = round(int(counts[bam].loc[cluster]) * fraction)
-							new_cluster_counts.append(new_read_count)
-							remaining_read_count = int(counts[bam].loc[cluster]) - new_read_count
-							counts.at[cluster, bam] = remaining_read_count
-						
-						counts.loc[tRNAs[0]] = new_cluster_counts
+						unique_isodecoderMMs[cluster][pos][identity] = tRNAs[0]
+
 					# Otherwise remove the sequence from detected_seqs so that it can be processed again for another mismatch position at which it might be unique
 					elif len(tRNAs) > 1:
 						for tRNA in tRNAs:
@@ -102,51 +98,38 @@ def splitReadsIsodecoder(isodecoder_counts, clusterMMprops, tRNA_dict, cluster_d
 						# update cluster_dict by keeping only tRNAs not in current isodecoder group
 						cluster_dict[cluster] = [tRNA for tRNA in cluster_dict[cluster] if not tRNA in isodecoder_items]
 						curr_isodecoders += 1
-						for bam in clusterMMprops['bam'].unique().tolist():
-							try:
-								fraction = clusterMMprops[(clusterMMprops.bam == bam) & (clusterMMprops.pos == insertion) & (clusterMMprops.type == identity)].loc[cluster]['proportion']
-							except KeyError:
-								fraction = 0 
-							
-							new_read_count = round(int(counts[bam].loc[cluster]) * fraction)
-							new_cluster_counts.append(new_read_count)
-							remaining_read_count = int(counts[bam].loc[cluster]) - new_read_count
-							counts.at[cluster, bam] = remaining_read_count
-						
-						counts.loc[tRNAs[0]] = new_cluster_counts
+						unique_isodecoderMMs[cluster][insertion][identity] = tRNAs[0]
+
 					# Otherwise remove the sequence from detected_seqs so that it can be processed again for a mismatch position at which it is unique
 					elif len(tRNAs) > 1:
 						for tRNA in tRNAs:
 							sequence = tRNA_dict[tRNA]['sequence'].upper()
 							detected_seqs.remove(sequence)
 
-	
-	counts['Single_isodecoder'] = "NA"
 	# for all clusters in cluster_dict, isdecoder size is number of members remaining after updating in above code
 	# these include clusters with only one isodecoder - i.e. not in mismatch_dict, and clusters that could not be separated into isodecoders because no unique mismatch distinguishes them
+	splitBool = list()
 	for cluster, members in cluster_dict.items():
 		cluster_size = len(members)
 		isodecoder_sizes[cluster] = cluster_size
 		remaining_isodecoders = set([data['sequence'].upper() for member, data in tRNA_dict.items() if member in members])
 		if len(remaining_isodecoders) > 1:
-			counts.at[cluster, 'Single_isodecoder'] = "False"
-		# if cluster not in mismatch_dict:
-		# 	cluster_members = [gene for gene, data in tRNA_dict.items() if gene in cluster_dict[cluster]]
-		# 	parent_size = len(cluster_members)
-		# 	isodecoder_sizes[cluster] = parent_size
-		# else:
-		# 	#for member in cluster_dict[cluster]:
-		# 	#	cluster_uniqeseqs.add(tRNA_dict[member]['sequence'].upper())
-		# 	cluster_size = len(cluster_dict)
-		# 	isodecoder_sizes[cluster] = cluster_size
+			splitBool.append(cluster)
 
 	# save isodecoder info for DESeq2
+	total_detected_isodecoders = 0
 	with open(out_dir + experiment_name + "isodecoderInfo.txt", "w") as isodecoderInfo:
 		isodecoderInfo.write("Isodecoder\tsize\n")
 		for isodecoder, size in isodecoder_sizes.items():
 			isodecoderInfo.write(isodecoder + "\t" + str(size) + "\n")
+			total_detected_isodecoders += 1
 
-	counts.to_csv(out_dir + "Isodecoder_counts.txt", sep = "\t", na_rep = "NA")
-	log.info("Read counts per isodecoder saved to " + out_dir + "counts/Isodecoder_counts.txt")
+	# write isodecoder fasta for alignment and context analysis
+	with open(out_dir + experiment_name + '_isodecoderTranscripts.fa', 'w') as tempSeqs:
+		for seq in isodecoder_sizes.keys():
+			tempSeqs.write(">" + seq + "\n" + tRNA_dict[seq]['sequence'] + "\n")
+	ssAlign.aligntRNA(tempSeqs.name, out_dir)
 
+	log.info(" Total deconvoluted unique tRNA sequences: {}".format(total_detected_isodecoders))
 
+	return(unique_isodecoderMMs, splitBool, isodecoder_sizes)
diff --git a/scripts/ssAlign.py b/scripts/ssAlign.py
index 958387b..bfc4d51 100755
--- a/scripts/ssAlign.py
+++ b/scripts/ssAlign.py
@@ -25,7 +25,7 @@ def extraCCA():
 	extra_cca = list()
 	stk = AlignIO.read(stkname, "stockholm", alphabet=generic_rna)
 	for record in stk:
-		if record.seq[-3:] == 'cca':
+		if record.seq[-3:] == 'cca': #lowercase here indicates alignment issue to other clusters
 			extra_cca.append(record.name)
 
 	os.remove(stkname)
@@ -35,20 +35,7 @@ def extraCCA():
 def tRNAclassifier(out):
 
 	struct_dict = structureParser()
-	tRNA_struct = defaultdict(dict)
-
-	# Loop thorugh every tRNA in alignment and create dictionary entry for pos - structure information (1-based to match to mismatchTable from mmQuant)
 	stk = AlignIO.read(stkname, "stockholm", alphabet=generic_rna)
-	for record in stk:
-		tRNA = record.id
-		seq = record.seq
-		bases = ["A", "C", "G", "U"]
-
-		for i, letter in enumerate(seq, 1):
-			if letter.upper() in bases:
-				tRNA_struct[tRNA][i] = struct_dict[i]
-			else:
-				tRNA_struct[tRNA][i] = 'gap'
 
 	# Get canonical tRNA position numbering (cons_pos_list). Useful to retain cononical numbering of tRNA positions (i.e. anticodon at 34 - 36, m1A 58 etc...)
 	# Return list of characters with pos or '-'. To be used in all plots with positional data such as heatmaps for stops or modifications.
@@ -116,7 +103,25 @@ def tRNAclassifier(out):
 
 	cons_pos_list = "_".join(cons_pos_list)
 
-	return(tRNA_struct, cons_pos_list, cons_pos_dict)
+	# Loop thorugh every tRNA in alignment and create dictionary entry for pos-structure and pos-canonpos information (1-based to match to mismatchTable from mmQuant)
+	tRNA_struct = defaultdict(dict)
+	tRNA_ungap2canon = defaultdict(dict)
+
+	for record in stk:
+		tRNA = record.id
+		seq = record.seq
+		ungapped_pos = 0
+		bases = ["A", "C", "G", "U"]
+
+		for i, letter in enumerate(seq, 1):
+			if letter.upper() in bases:
+				tRNA_ungap2canon[tRNA][ungapped_pos] = cons_pos_dict[i]
+				ungapped_pos += 1
+				tRNA_struct[tRNA][i] = struct_dict[i]
+			else:
+				tRNA_struct[tRNA][i] = 'gap'
+
+	return(tRNA_struct, tRNA_ungap2canon, cons_pos_list, cons_pos_dict)
 
 def tRNAclassifier_nogaps():
 
@@ -182,7 +187,7 @@ def clusterAnticodon(cons_anticodon, cluster):
 def modContext(out):
 # outputs file of defined mods of interest pos, identity and context sequence for each cluster
 
-	tRNA_struct, cons_pos_list, cons_pos_dict = tRNAclassifier(out)
+	tRNA_struct, tRNA_ungap2canon, cons_pos_list, cons_pos_dict = tRNAclassifier(out)
 	anticodon = getAnticodon_1base()
 
 	# Define positions of conserved mod sites in gapped alignment for each tRNA
diff --git a/scripts/tRNAmap.py b/scripts/tRNAmap.py
index 56ea776..c52c8ad 100755
--- a/scripts/tRNAmap.py
+++ b/scripts/tRNAmap.py
@@ -269,57 +269,6 @@ def mapReads(fq, genome_index_path, genome_index_name, snp_index_path, snp_index
 
 	return(unique_bam, unique_count, alignstats_dict)
 
-def countReads(unique_bam_list, mode, threads, out_dir):
-
-	log.info('\n+-----------------------------------+\
-		\n| Counting reads with featureCounts |\
-		\n+-----------------------------------+')
-
-	# Counts per cluster
-
-	# Find tRNA gff produced earlier...
-	gff_file = glob.glob(out_dir + '*.gff')[0]
-
-	cmd = ["featureCounts", "-T", str(threads)] 
-
-	if mode == "none":
-		cmd.extend(["-a", gff_file, "-o", out_dir + "counts.txt"])
-		cmd.extend(unique_bam_list)
-	elif mode == "all":
-		cmd.extend(["-O", "-a", gff_file, "-o", out_dir + "counts.txt"])
-		cmd.extend(unique_bam_list)
-	elif mode == "fraction":
-		cmd.extend(["-O", "--fraction", "-a", gff_file, "-o", out_dir + "counts.txt"])
-		cmd.extend(unique_bam_list)
-
-	subprocess.check_call(cmd, stderr = open(out_dir + "featureCounts.log", "a"))
-
-	log.info("Read counts per tRNA/cluster saved to " + out_dir + "counts/counts.txt")
-
-	# Counts per anticodon
-
-	count_dict = defaultdict(lambda: defaultdict(int))
-
-	with open(out_dir + "counts.txt", "r") as counts_file:
-		for line in counts_file:
-			line = line.strip()
-			if not line.startswith("#"):
-				if line.startswith("Geneid"):
-					sample_list = [samples for samples in line.split("\t")[6:]]
-				else:
-					cluster = line.split("\t")[1]
-					isodecoder = '-'.join(cluster.split("-")[:-2])
-					col = 6
-					for sample in sample_list:
-						count_dict[isodecoder][sample] += int(line.split("\t")[col])
-						col += 1
-
-	count_pd = pd.DataFrame.from_dict(count_dict, orient='index')
-	count_pd.index.name = 'Geneid'
-	count_pd.to_csv(out_dir + 'Anticodon_counts.txt', sep = '\t')
-
-	log.info("Read counts per anticodon saved to " + out_dir + "counts/Anticodon_counts.txt")
-
 if __name__ == '__main__':
 	mainAlign(sys.argv[1:])
 
diff --git a/scripts/tRNAtools.py b/scripts/tRNAtools.py
index 4b438ce..483135c 100755
--- a/scripts/tRNAtools.py
+++ b/scripts/tRNAtools.py
@@ -14,6 +14,7 @@
 from pathlib import Path
 import urllib.request
 from collections import defaultdict
+import pandas as pd
 import ssAlign
 
 log = logging.getLogger(__name__)
@@ -98,7 +99,7 @@ def tRNAparser (gtRNAdb, tRNAscan_out, mitotRNAs, modifications_table, posttrans
 	modomics_file = getModomics()
 	modomics_dict = {}
 	perSpecies_count = defaultdict(int)
-	for line in modomics_file.splitlines():
+	for line in modomics_file:
 		line = line.strip()
 		sameIDcount = 0
 
@@ -152,20 +153,6 @@ def tRNAparser (gtRNAdb, tRNAscan_out, mitotRNAs, modifications_table, posttrans
 				modomics_dict[curr_id]['unmod_sequence'] = unmod_sequence
 				modomics_dict[curr_id]["InosinePos"] = inosinePos
 
-				# If 'N' in anticodon then duplicate entry 4 times for each possibility
-				# anticodon = curr_id.split('-')[2]
-				# if 'N' in anticodon:
-				# 	for rep in ['A','C','G','T']:
-				# 		duplicate_item = str(curr_id.split('-')[0]) + '-' + str(curr_id.split('-')[1]) + '-' + str(anticodon.replace('N', rep))
-				# 		duplicate_unmod_seq = modomics_dict[curr_id]['unmod_sequence'].replace('N',rep)
-				# 		duplicate_anticodon = modomics_dict[curr_id]['anticodon'].replace('N', rep)
-				# 		modomics_dict[duplicate_item] = copy.deepcopy(modomics_dict[curr_id])
-				# 		modomics_dict[duplicate_item]['unmod_sequence'] = duplicate_unmod_seq
-				# 		modomics_dict[duplicate_item]['anticodon'] = duplicate_anticodon
-				# 	del modomics_dict[curr_id]
-				# else:
-				# 	duplicate_item = curr_id
-
 	for species in perSpecies_count:
 		log.info('Number of Modomics entries for {}: {}'.format(species, perSpecies_count[species]))
 
@@ -176,10 +163,11 @@ def getModomics():
 
 	try:
 		with urllib.request.urlopen('http://modomics.genesilico.pl/sequences/list/?type_field=tRNA&subtype=all&species=all&display_ascii=Display+as+ASCII&nomenclature=abbrev') as response:
-			modomics = response.read().decode()
+			modomics = response.read().decode().splitlines()
 	except Exception as e:
-		logging.error("Error in {}".format("fetching modomics"), exc_info=e)
-		raise
+		logging.error("Error in {}".format("fetching modomics. Using local files..."))
+		modomics = open("./data/modomics", "r")
+		
 
 	return modomics
 
@@ -509,7 +497,7 @@ def modsToSNPIndex(gtRNAdb, tRNAscan_out, mitotRNAs, modifications_table, experi
 							member_Inosines = tRNA_dict[member_name]["InosinePos"]
 							mod_lists[cluster_name] = list(set(mod_lists[cluster_name] + member_mods))
 							Inosine_lists[cluster_name] = list(set(Inosine_lists[cluster_name] + member_Inosines))
-							cluster_dict[cluster_name].append(member_name)			
+							cluster_dict[cluster_name].append(member_name)	
 
 		clusterbed.close()
 
@@ -594,7 +582,7 @@ def newModsParser(out_dir, experiment_name, new_mods_list, new_Inosines, mod_lis
 		\n| Parsing new mods |\
 		\n+------------------+")	
 
-	new_snps = 0
+	new_snps_num = 0
 	new_inosines = 0
 	newInosine_lists = defaultdict(list)
 
@@ -618,19 +606,9 @@ def newModsParser(out_dir, experiment_name, new_mods_list, new_Inosines, mod_lis
 			tRNA_dict[cluster]['modified'] = list(set(tRNA_dict[cluster]['modified'] + l[cluster]))
 			old_mods = len(mod_lists[cluster])
 			mod_lists[cluster] = list(set(mod_lists[cluster] + l[cluster]))
-			new_snps += len(mod_lists[cluster]) - old_mods
+			new_snps_num += len(mod_lists[cluster]) - old_mods
 
-	log.info("{} new predicted modifications".format(new_snps))
-
-	# write file of new predicted mods
-	predictedMods = open(out_dir + "mods/predictedMods.csv", "w")
-	predictedMods.write("cluster\tpos\tidentity\tmisinc\n")
-	with open(out_dir + "mods/predictedModstemp.csv", "r") as predictedTemp:
-		for line in predictedTemp:
-			cluster, pos, misinc = line.split("\t")
-			identity = str(tRNA_dict[cluster]['sequence'][int(pos)])
-			predictedMods.write(cluster + "\t" + str(pos) + "\t" + identity + "\t" + str(misinc) + "\n")
-	os.remove(out_dir + "mods/predictedModstemp.csv")
+	log.info("{} new predicted modifications".format(new_snps_num))
 
 	# rewrite SNP index
 	total_snps = 0
@@ -652,11 +630,6 @@ def newModsParser(out_dir, experiment_name, new_mods_list, new_Inosines, mod_lis
 	
 	tRNA_seqs = SeqIO.to_dict(SeqIO.parse(tRNA_ref, 'fasta'))	
 
-	# edit A to G for updated inosines list
-	# for cluster in Inosine_lists:
-	# 	for pos in Inosine_lists[cluster]:
-	# 		tRNA_seqs[cluster].seq = tRNA_seqs[cluster].seq[0:pos] + "G" + tRNA_seqs[cluster].seq[pos+1:]
-
 	# rewrite tRNA transcript reference
 	with open(tRNA_ref, "w") as transcript_fasta:
 		SeqIO.write(tRNA_seqs.values(), transcript_fasta, "fasta")
@@ -681,7 +654,7 @@ def additionalModsParser(input_species, out_dir):
 			additionalMods[tRNA]['species'] = species
 
 	# initialise dictionaries of structure (with and without gapped numbering) and anticodon positions to define canonical mod sites
-	tRNA_struct, cons_pos_list, cons_pos_dict = ssAlign.tRNAclassifier(out_dir)
+	tRNA_struct, tRNA_ungap2canon, cons_pos_list, cons_pos_dict = ssAlign.tRNAclassifier(out_dir)
 	tRNA_struct_nogap = ssAlign.tRNAclassifier_nogaps()
 	cons_anticodon = ssAlign.getAnticodon()
 
@@ -940,6 +913,31 @@ def intronRemover (Intron_dict, seqIO_dict, seqIO_record, posttrans_mod_off):
 
 	return(seq)
 
+def countReadsAnticodon(input_counts, out_dir):
+
+	# Counts per anticodon
+	count_dict = defaultdict(lambda: defaultdict(int))
+
+	with open(input_counts, "r") as counts_file:
+		for line in counts_file:
+			line = line.strip()
+			if not line.startswith("#"):
+				if line.startswith("isodecoder"):
+					sample_list = [samples for samples in line.split("\t")[1:-1]]
+				else:
+					anticodon = line.split("\t")[0]
+					anticodon = '-'.join(anticodon.split("-")[:-2])
+					col = 1
+					for sample in sample_list:
+						count_dict[anticodon][sample] += float(line.split("\t")[col])
+						col += 1
+
+	count_pd = pd.DataFrame.from_dict(count_dict, orient='index')
+	count_pd.index.name = 'Anticodon'
+	count_pd.to_csv(out_dir + 'Anticodon_counts.txt', sep = '\t')
+
+	log.info("** Read counts per anticodon saved to " + out_dir + "counts/Anticodon_counts.txt **")
+
 def tidyFiles (out_dir, cca):
 	
 	os.mkdir(out_dir + "annotation/")