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fix out-of-rame indel detection
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@Donaim
Donaim committed Jun 23, 2023
1 parent 61f9a66 commit 2b2fcaa
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Showing 5 changed files with 226 additions and 227 deletions.
13 changes: 9 additions & 4 deletions intact/intact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -591,10 +591,12 @@ def small_frames(
"No ORFs >" + str(length) + " bases found.")]

import util.coordinates as coords
coordinates_mapping = coords.map_positions(alignment[0], alignment[1])
reverse_coordinates_mapping = coords.map_positions(alignment[1], alignment[0])
coordinates_mapping = coords.map_positions(alignment[0], alignment[1].seq)
reverse_coordinates_mapping = coords.map_positions(alignment[1], alignment[0].seq)

reference = alignment[0].seq.replace("-", "")
reference_aligned_mapping = coords.map_nonaligned_to_aligned_positions(reference, alignment[0].seq)
query_aligned_mapping = coords.map_nonaligned_to_aligned_positions(sequence, alignment[1].seq)

def translate(seq, frame = 0):
for_translation = seq[frame:]
Expand Down Expand Up @@ -654,8 +656,11 @@ def find_real_correspondence(e):
for e in expected:
best_match = find_real_correspondence(e)

insertions = len(re.findall(r"-", str(alignment[0].seq[e.start:e.end])))
deletions = len(re.findall(r"-", str(alignment[1].seq[e.start:e.end])))
aligned_start = query_aligned_mapping[best_match.start]
aligned_end = query_aligned_mapping[best_match.end - 1] + 1

insertions = len(re.findall(r"-", str(alignment[0].seq[aligned_start:aligned_end])))
deletions = len(re.findall(r"-", str(alignment[1].seq[aligned_start:aligned_end])))
translated = best_match.aminoseq.split("*")[0]
adeletions = (len(best_match.expectedaminoseq) - (len(translated) + 1)) * 3

Expand Down
83 changes: 36 additions & 47 deletions tests/expected-results-large/errors.json
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,11 @@
"error": "InternalStopInOrf",
"message": "Smaller ORF vif at 5040-5619 contains an internal stop codon"
},
{
"sequence_name": "KX505501.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vif at 5040-5619 contains an out of frame indel: insertions 1 deletions 7182."
},
{
"sequence_name": "KX505501.1",
"error": "InternalStopInOrf",
Expand All @@ -20,36 +25,41 @@
"error": "DeletionInOrf",
"message": "Smaller ORF tat_exon1 at 5829-6044 can have maximum deletions 30, got 210"
},
{
"sequence_name": "KX505501.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF tat_exon1 at 5829-6044 contains an out of frame indel: insertions 0 deletions 215."
},
{
"sequence_name": "KX505501.1",
"error": "DeletionInOrf",
"message": "Smaller ORF rev_exon1 at 5968-6044 can have maximum deletions 30, got 72"
},
{
"sequence_name": "KX505501.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF rev_exon1 at 5968-6044 contains an out of frame indel: insertions 0 deletions 76."
"error": "InternalStopInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an internal stop codon"
},
{
"sequence_name": "KX505501.1",
"error": "InternalStopInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an internal stop codon"
"error": "FrameshiftInOrf",
"message": "Smaller ORF tat_exon2 at 8375-8468 contains an out of frame indel: insertions 1 deletions 0."
},
{
"sequence_name": "KX505501.1",
"error": "DeletionInOrf",
"message": "Smaller ORF rev_exon2 at 8376-8652 can have maximum deletions 30, got 96"
},
{
"sequence_name": "KX505501.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF rev_exon2 at 8376-8652 contains an out of frame indel: insertions 1 deletions 0."
},
{
"sequence_name": "KX505501.1",
"error": "InternalStopInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an internal stop codon"
},
{
"sequence_name": "KX505501.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 1 deletions 7182."
},
{
"sequence_name": "KX505501.1",
"error": "RevResponseElementDeletion",
Expand Down Expand Up @@ -97,12 +107,12 @@
{
"sequence_name": "MN692074",
"error": "FrameshiftInOrf",
"message": "Smaller ORF tat_exon1 at 5829-6044 contains an out of frame indel: insertions 0 deletions 215."
"message": "Smaller ORF tat_exon1 at 5829-6044 contains an out of frame indel: insertions 0 deletions 5236."
},
{
"sequence_name": "MN692074",
"error": "FrameshiftInOrf",
"message": "Smaller ORF rev_exon1 at 5968-6044 contains an out of frame indel: insertions 0 deletions 76."
"message": "Smaller ORF rev_exon1 at 5968-6044 contains an out of frame indel: insertions 0 deletions 5236."
},
{
"sequence_name": "MN692074",
Expand All @@ -114,11 +124,6 @@
"error": "DeletionInOrf",
"message": "Smaller ORF nef at 8795-9416 can have maximum deletions 30, got 123"
},
{
"sequence_name": "MN692074",
"error": "FrameshiftInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 0 deletions 617."
},
{
"sequence_name": "MN692074",
"error": "RevResponseElementDeletion",
Expand Down Expand Up @@ -200,14 +205,13 @@
"message": "Sequence contains an internal inversion."
}
],
"MK115581.1": [
"MK115581.1": [],
"MK115690.1": [
{
"sequence_name": "MK115581.1",
"sequence_name": "MK115690.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an out of frame indel: insertions 9 deletions 5."
}
],
"MK115690.1": [
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 16 deletions 6."
},
{
"sequence_name": "MK115690.1",
"error": "PackagingSignalDeletion",
Expand All @@ -220,11 +224,6 @@
}
],
"MK115571.1": [
{
"sequence_name": "MK115571.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an out of frame indel: insertions 9 deletions 1."
},
{
"sequence_name": "MK115571.1",
"error": "PackagingSignalDeletion",
Expand All @@ -237,11 +236,6 @@
}
],
"MK115514.1": [
{
"sequence_name": "MK115514.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an out of frame indel: insertions 9 deletions 7."
},
{
"sequence_name": "MK115514.1",
"error": "MajorSpliceDonorSiteMutated",
Expand Down Expand Up @@ -333,6 +327,11 @@
"error": "InternalStopInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an internal stop codon"
},
{
"sequence_name": "MK114705.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 7 deletions 69."
},
{
"sequence_name": "MK114705.1",
"error": "Scramble",
Expand Down Expand Up @@ -540,6 +539,11 @@
"error": "InternalStopInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an internal stop codon"
},
{
"sequence_name": "MK115464.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 0 deletions 13."
},
{
"sequence_name": "MK115464.1",
"error": "APOBECHypermutationDetected",
Expand All @@ -566,11 +570,6 @@
],
"MK115503.1": [],
"MK115570.1": [
{
"sequence_name": "MK115570.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an out of frame indel: insertions 9 deletions 7."
},
{
"sequence_name": "MK115570.1",
"error": "PackagingSignalDeletion",
Expand Down Expand Up @@ -599,11 +598,6 @@
"error": "FrameshiftInOrf",
"message": "ORF env at 6199-8764 contains an out of frame indel, deletions 50 insertions 37."
},
{
"sequence_name": "MK115702.1",
"error": "FrameshiftInOrf",
"message": "Smaller ORF nef at 8795-9416 contains an out of frame indel: insertions 0 deletions 19."
},
{
"sequence_name": "MK115702.1",
"error": "PackagingSignalDeletion",
Expand Down Expand Up @@ -684,11 +678,6 @@
}
],
"OQ092465": [
{
"sequence_name": "OQ092465",
"error": "FrameshiftInOrf",
"message": "Smaller ORF vpu at 6060-6309 contains an out of frame indel: insertions 5 deletions 0."
},
{
"sequence_name": "OQ092465",
"error": "MajorSpliceDonorSiteMutated",
Expand Down
160 changes: 160 additions & 0 deletions tests/expected-results-large/intact.fasta
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Original file line number Diff line number Diff line change
Expand Up @@ -161,6 +161,166 @@ CATATAAGCAGCTGCTTCTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTG
GGAGCTCTCTGGCTGACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGT
GCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACC
CTTTTAGTCAGTGTGGAAAATCTCTAGCA
>MK115581.1
AAATTGGGACGTTCGCCTACGCAAGCGAAAATTTCTCTACGTAGCCACCTTTCCCGATTA
ACGTCAGAACCCTAAAATTAAAATAAATCCTAGCGGCCGACCGACTCTGGTAACTAGAGA
TCCCTCAAAGATAAATCTCTAGCAGTGGCGCCCGAACAGACTCTGGTAACTAGAGATCCC
TCAGATTAAATCTCTAGCAGTGGCGCCCGAACAGAAATCTCTAGCAGTGGCGCCCGAACA
GACTCTGGTAACTAGAGATCCCTCAGATTAAATCTCTAGCAGTGGCGCCCGAATCATCTT
AGAGTGGCGCCCGAACGACTCTGGTAACTAGAGATCCCTCAAAGATAAATCTCTAGCAGT
GGCGCCCGCGACTCTGGTAACTAGAGATCCCTCAGATTAAATCTCTAGCAGTGGCGCCCG
AGACTCTGGTAACTAGAGATCCCTCAGATTAAATCTCTAGCAGTGGCGCCCGAACAGACT
CTGGTAACTAGAGATCCCTCAAAGATAAATCTCTAGCAGTGGCGCCCGACACAGGTACTA
GAGAAAGCGAAAGTAAAACCAGAGGAGCTCTCTCGGCGCAGGACTCGGCTTGCTGAAGCG
CGCACAGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCGAAAAAAATTTTTGACTAG
CGGAGGCTAGAAGGGGAGAGATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAG
ATGCATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATT
TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCCGTTAACCCTGGCCTGTTAGAAACAT
CAGAGGGATGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAG
AACTTAAATCATTATTTAATGCAGTAGCAGTCCTCTATTGTGTACATCAAAGGATACAGG
TACAAGACACCAAGGAAGCTTTAGAGAAGGTAGAGGAAGAGCAAAACAAAAGTAAGAAAA
AGGCACAGCAAGTAGCAGCAGCTGACACTGACACAGGAAACAGCAGCCAAAATTACCCCA
TAGTGCAGAACCTCCAGGGGCAAATGGTACATCAGCCCCTATCACCTAGAACTTTAAATG
CATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGCCCAGAAGTCATACCCATGTTTTCAG
CATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGAC
ATCAAGCAGCTATGCAAATGTTAAAAGAAACCATCAATGAGGAAGCTGCAGAATGGGATA
GATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAA
GTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGACGACAAATAATC
CACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCTTGGGATTAAATAAAATAG
TAAGGATGTATAGCCCTACCAGTATTCTGGATATAAAACAAGGACCAAAGGAACCCTTTA
GAGACTATGTAGACCGGTTCTATAGAACTTTAAGAGCTGAGCAAGCTTCACAGGAGGTAA
AAAATTGGATGACAGAAACCTTGTTGGTCCAAAATTCGAATCCAGATTGTAAGACTATTT
TAAAAGCATTAGGACCAGCAGCAACACTAGAGGAAATGATGACAGCATGTCAAGGAGTGG
GGGGACCAGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAAATTCAGCTA
ATGTAATGATGCAGAGAGGCAATTTTAGAAACCAAAGAAAGATTGTTAAGTGTTTCAATT
GTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGA
AATGTGGAAAGGAAGGACATCAAATGAAAGACTGTACAGAGAGACAGGCTAATTTTTTAG
GGAAAATCTGGCCTTCCCACAAAGGAAGGCCAGGGAACTTCCTTCAGAGCAGACCAGAGC
CAACAGCCCCACCAGAAGAGAGCTTCAGGTTTGGGGAAGAGACAATAACTCCCTCTCAGA
AGCAGGAGCCAAGAGACAAGGAACTGTATCCCTTGTCTTCCCTCAAATCACTCTTTGGCA
GCGACCCCTCGTCAGAATAAAGATAGGGGGGCAATTTAAAGAAGCTTTATTAGATACAGG
AGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAAATGGAAACCAAAAATGAT
AGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACCCATAGAAATCTG
TGGACACAAAGCTATAGGTACAGTATTAATAGGACCTACACCTGTCAACATAATTGGAAG
AAATCTGTTGACTCAGCTTGGTTGTACCTTAAATTTTCCCATTAGTCCTATTGAAACTGT
ACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGA
AGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTC
AAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCTATAAAGAAAAAAGACAG
TACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTCAATAAGAGAACTCAAGACTTTTG
GGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAAAAATCAGTAACAGT
ACTGGATGTGGGTGATGCATATTTTTCAATTCCCTTAGATAAAGAATTCAGGAAGTATAC
TGCATTTACCATACCTAGTACAAATAATGAGACACCAGGGATTAGGTATGAGTACAATGT
GCTGCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTT
AGAGCCTTTTAGAAAGCAAAATCCAGATATAGTTATCTATCAATACATGGATGATTTGTA
TGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACA
TCTGTTAAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCT
TTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGCCTATAATACTGCCAGA
AAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAG
TCAGATTTACGCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGGGGAACCAAAGC
ACTAACAGAGGTAGTACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGA
AATTTTAAGAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGA
AGTACAGAAGCAGGGCAATGGACAGTGGACATATCAAATTTATCAAGAGCCATTTAAAAA
TCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATT
AACAGAGGCAGTACAAAAGATAGCCACAGAAAGCATAGTAATATGGGGAAAAACTCCTAA
ATTTAGACTACCTATACAAAAAGAAACATGGGAGACATGGTGGGCAGAGTACTGGCAAGC
CACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAATTATGGTACCA
ATTAGAGAAAGAACCCATAGTAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCTAATAG
AGAAACTAAATTAGGCAAAGCAGGATATGTCACTGACAGAGGAAGACAAAAGGTTATCTC
CCTAACGGACACAACAAATCAAAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGA
TTCGGGATCAGAAGTAAACATAGTAACAGACTCACAATATACATTAGGAATCATTCAAGC
ACAACCAGATAAGAGTGAATCAGAGTTAGTCAATCAGATAATAGAGCAGTTAATAAAAAA
GGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGT
AGACAAACTAGTCAGTACTGGAGTCAGGAGAGTACTATTTCTAGATGGAATAGATAAGGC
CCAAGAAGACCATGAGAAATATCACAGTAATTGGAGAGCAATGGCTGGTGATTTTAATAT
ACCCCCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCAAAAAGGAGA
GGCCATGCATGGACAAGTAGATTGTAGTCCAGGAATATGGCAACTAGATTGTACACATCT
AGAAGGGAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGT
TATTCCAGCAGAGACAGGGCAGGAAACAGCATACTTTCTCCTGAAACTAGCAGGGAGATG
GCCAGTAAAAACAATACATACAGACAATGGCAGCAATTTCACCAGTAATGTGGTTAAGGC
CGCCTGTTGGTGGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCA
AGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCA
GGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAA
AGGGGGGATTGGGGGGTATAGTGCAGGGGAAAGAATAGTAGATATAATAGCAACAGACCT
ACAAACTAAAGAATTACAGAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAG
GGACAGCAGAGATCCACTTTGGAAAGGACCAGCAAAGCTTCTCTGGAAAGGTGAAGGGGC
AGTAGTAATACAAGATAATAGTGATATAAAAGTAGTGCCAAGGAGAAAAGCAAAAATCAT
TAGGGATTATGGCAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGA
TTAGAACATGGAACAGTTTAGTAAAACACCATATGCATGTTTCAAAGAAAACTAAAGGAT
GGTTTTATAGACATCACTATGAAAGCACTCATCCAAGAATAAGTTCAGAAGTACACATCC
CACTAGGGGATGCTAGATTGGTAGTAACAACATATTGGGGCCTGAATACAGGAGAAAGAG
AATGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGAAAAAGGAAATATAGCACACAAG
TTGACCCTAACCTAGCAGACCAACTAATTCATCTGTATTACTTTGATTGTTTTTCAGAAT
CTGCTATAAGAAATGCCATATTAGGACATATAGTTAGTCCTAGGTGTGAATATCAAGCAG
GACATAACAAGGTAGGCTCTCTACAATACTTGGCACTAAAAGCATTAACAACACCAAAGA
GAAGAAAGCCACCTTTACCTAGTGTTAGGAAACTGACAGAGGATAGATGGAACGAGCACC
AGAAGACCAAGGGCCACAGAGGGAGCCATACAATGAATGGACATTAGAGCTTTTAGAGGA
ACTTAAGAATGAAGCGGTTAGACATTTTCCTAGGCCGTGGCTCCATGGCTTAGGACAACA
TATCTATGAAACTTATGGGGACACTTGGACAGGAGTGGAGGCCATAATAAGAACCCTGCA
ACAACTGCTGTTTATTCATTTCAGACTTGGGTGTCGACATAGCAGAATAGGCATTGTGCC
ACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCACCCAG
GAAGTCAGCCTAAAACTCCTTGTACTAACTGCTATTGTAAAAAGTGTTGCTTTCATTGCC
AAGTTTGTTTCATAAAAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGC
GACGAAGAGCTCCTCAAGGCAGTCAGACTGATCAAGATTCTCTATCAAAGCAGTAAGTAG
TATATGTAATGCAACCTCTGCACATAGCAGCAATAGTAGGATTAGTAGTAGCAGCAATAA
TAGCAATAGTTGTGTGGACCATAGTGTTAATAGAATATAGGAAAATATTAAGACAAAAAA
GGATAGACAGGTTAATTGATAGAATAAGAGAAAGAGCAAAAGACAGTGGCAATGAGAGTG
AAGGGGATCAGGAAGAATTGTCAGCGCTTATGGAGATGGGGCACCATGCTCCTGGGGATG
TTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTGACAGTCTATTATGGGGTACCTGTA
TGGAAAGAAGCAAACACCACTCTATTTTGTGCATCGGATGCTAAAGCATATACCACAGAG
GCACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTA
GGATTGGAAAATGTGACAGAAAATTTTAACATGTGGAAAAATAACATGGTAGAACAGATG
CATGAGGATGTAATCAATTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCA
CTCTGTGTTACTTTAAATTGCACTAATCTGAATGTTACTAATACCAATAGCAGTAGTGAG
GAGGGAAAGATGGCGGAAGAAATGAGAAACTGCTCTTTCAATATCACCACAAAAATAAGA
AATAAGATGCAGAAGGAATATGCACTTTTTTATAAACTTGATGTAGTACCAATAGATAAT
GATAATACAAGTTATACATTGATAAATTGTAACACCTCAGTCATTACACAGGCCTGTCCA
AAGGTATCCTTTGAGCCAATTCCTATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTA
AAGTGTAAGGATAAGAAGTTCAATGGATCAGGACCATGTAAAAATGTCAGCACAGTACAA
TGTACACATGGAATTAAGCCAGTAGTGTCAACTCAACTACTGTTAAATGGCAGTTTAGCA
GAAGAAGAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAACCATAATAGTA
CATCTGAAGGAACCTATACAAATTAATTGTACAAGACCCAACAACAATACAATGAAAAGT
ATCCCTCTAGGACCAGGAAGAGCATTCTATGCAACAGGAGCCATAATAGGAGATATAAGA
CAAGCACATTGTAACCTTAGTAGAAAAGCATGGAATAATACTTTAAAACAGGTAGTTGAA
AAATTAAAAGAACAATATGAGAATAAAACAATAATCTTTAATCACTCCTCAGGAGGGGAC
CCAGAAATTATAATGCATACTTTTAATTGTGGAGGGGAATTTTTCTATTGTAATACAACA
CAGCTGTTTAATAGTACTTGGAATAGTACTTGGACTGGGAATGCTACCGAATTAGATGGA
AACATCACACTCCCATGCAGAATAAAACAGATTATAAACAGGTGGCAAGAAGTAGGAAAA
GCAATGTATGCCCCTCCCATTAGAGGAAAAATTAGATGTTCATCAAATATTACAGGGTTA
CTATTAGTAAGAGATGGTGGTAACACGAGCGAGACTGAGACCTTCAGACCTGGAGGAGGA
GATATGAAGGACAATTGGAGGAGTGAATTATATAAATATAAAGTAGAAAAAATTGAGCCA
TTAGGAGTAGCACCCACCAGGGCAAAGAGAAGAGTGGTGCAAAGAGAAAAAAGAGCAGTG
GGAATAGGAGCTGTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCG
TCAGTGACGCTGACGGTACAAGCCAGGCTGTTATTGTCTGGTATAGTGCAACAGCAAAAC
AATTTGCTGAGAGCTATTGAGGCGCAACAACATCTGTTGCAACTCACAGTCTGGGGCATC
AAGCAGCTCCAGGCAAGAGTCCTGGCTGTGGAAAGATACCTACAGGATCAACAGCGCCTG
GGAATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCCTGGAATGCTAGT
TGGAGTAATAAATCTCTGAATCAGATTTGGGATAACATGACCTGGATGGAGTGGGAAAGA
GAAATTAACAATTACACAGACACAATATACACCTTAATTGAAAAGGCGCAGAACCAGCAG
GAAAAAAATGAACAAGAATTATTGGAATTGGATAAATGGGCAAGTTTGTGGAATTGGTTT
AACATAACAAAATGGCTGTGGTACATAAAATTATTCATAATGATAGTAGGAGGATTGATA
GGTTTAAGAATAGTTTTTGCTGTACTTGCTATAGTAAATAGAGTTAGGCAGGGATATTCA
CCATTATCGTTTCAGACCCACCTCCCAGCCCCGAGGGGACCCGACAGGCCCGAAGGAATC
GAAGAAGAAGGTGGAGAAAGAGACAGAGACAGATCAGTTCGATTAGTGAACGGATTCTTG
GCACTTTTCTGGGACGACCTGCGGAGCCTGTGCCTCTTCCTCTGCCACCGCTTGAGAGAC
TTACTCTTGATTGTAACAAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAATCCTC
AAACATTGGTGGAGTCTCCTGCAGTATTGGATTCAGGAGCTAAAGAGTAGTGCTATTAGC
TTATTCAATGTCACAGCCATCGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTA
CAAAGAGCTTGTAGAGCTCTTCTCCACATACCTACAAGAATAAGACAGGGCTTGGAAAGG
GCATTGTTATAAAATGGGGGGCAAGTGGTCAAAAAGTAGTGGGGGTGGATGGCCTGCTGT
AAGGGAAAGAATGAGACGAACTGAGCCAGCAGCAGAAGGGGTGGGAGCAGTATCTCGAGA
CCTGGAAAGACATGGAGCAGTCACAAGTAGCAATACAGCAGCTACCAATGCTGATTGCGC
CTGGCTGGAAGCACAAGAAGAGGACAGTGAAGTGGGTTTTCCAGTCAGACCTCAGGTGCC
TTTAAGACCAATGACTTTCAAAGGAGCTCTCGATCTTAGCCACTTTTTAAAAGAAAAGGG
GGGACTGGAAGGGCTAATTTACTCCCAAAAAAGACAAGATATCCTTGACCTGTGGGTCTA
CAACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGACCAGATA
TCCACTGACCTTTGGGTGGTGTTTCAAGCTAGTACCAGTGGAGCCAGAAGAGGCCAATCA
AGGAGAGAACAACTGCTTGTTACACCCTATGAGCCTGCATGGGATGGAGGACCCGGAAAA
AGAAGTATTAATGTGGAAGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGAA
GCATCCGGAGTACTACAAAGACTGCTGACATTGAGCTTTCTACAAAGGGACTTTCCGCTG
GGGACTTTCCAGGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGC
TGCATATAAGCAGCTGCGTTCTGCCTGTAAGGGGTCTCTCTGGTTAGACCAGATCTGAGC
CTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTG
CACTCAAGGCAAGCT
>MK115498.1
AACACGGAATGGGAGATAAGCAGCATCTCTATCGGCGCGGCGAGATCTGACACTGGTAAC
TAGAGATCCCTCCTAAATCTCTAGCAGTGGCGCCCGAACAGACTCTGGTAACTAGAGATC
Expand Down
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