diff --git a/msyd/pyxfiles/io.pyx b/msyd/pyxfiles/io.pyx
index d5c3071..1cb7342 100644
--- a/msyd/pyxfiles/io.pyx
+++ b/msyd/pyxfiles/io.pyx
@@ -691,7 +691,7 @@ cpdef save_df_to_psf(df, buf, save_cigars=True, emit_header=True, force_ref_pos=
             else:
                 buf.write('\t'.join(['.', '.', '.', f"PRIVATE{privcounter}", priv.ref.org, priv.ref.chr, str(priv.ref.start), str(priv.ref.end), '']))
 
-            write_multisyns([priv], buf, orgs, save_cigars=save_cigars)
+            write_multisyn(priv, buf, orgs, save_cigars=save_cigars)
             privcounter += 1
 
         # write mesyn regions that have a position on reference at their appropriate position
diff --git a/msyd/pyxfiles/priv.pyx b/msyd/pyxfiles/priv.pyx
index 6a1d908..6d8ade6 100644
--- a/msyd/pyxfiles/priv.pyx
+++ b/msyd/pyxfiles/priv.pyx
@@ -8,9 +8,6 @@
 import sys
 import logging
 
-logger = util.CustomFormatter.getlogger(__name__)
-logger.setLevel(logging.INFO)
-
 from collections import deque, defaultdict
 from multiprocessing import Pool
 
@@ -22,6 +19,10 @@ import msyd.util as util
 from msyd.multisyn import Multisyn, Private
 from msyd.coords import Range
 
+logger = util.CustomFormatter.getlogger(__name__)
+logger.setLevel(logging.INFO)
+
+
 cdef int MIN_PRIV_THRESH = intersection.get_min_syn_thresh()
 
 
diff --git a/msyd/pyxfiles/realignment.pyx b/msyd/pyxfiles/realignment.pyx
index d7c7cf8..52b205b 100644
--- a/msyd/pyxfiles/realignment.pyx
+++ b/msyd/pyxfiles/realignment.pyx
@@ -74,6 +74,12 @@ cpdef construct_mts(merasyns, old, syn):
     offsetdict = {org:rng.end for org, rng in old.ranges_dict.items()} # stores the current offset in each org
 
     for merasyn in merasyns:
+        # mark private regions as covered, if they are 
+        if merasyn.is_private():
+            if merasyn.ref.org != 'ref':
+                offsetdict[merasyn.ref.org] = merasyn.ref.end
+            continue
+
         # iterate through all multisyns found so far
         for org, rng in merasyn.ranges_dict.items():
             #print(f"{offsetdict[org]}, {posdict[org]}, {rng}, {mappingtrees[org]}")
@@ -129,7 +135,7 @@ cpdef mt_to_privates(mt, org, chrom):
     :chrom: chromosome we are working on
     """
     cdef ret = deque()
-    for entry in mappingtree:
+    for entry in mt:
         if entry.end - entry.start >= priv.MIN_PRIV_THRESH:
             ret.append(Private(org, chrom, entry.data, entry.data + entry.end - entry.start))
 
@@ -645,20 +651,27 @@ cdef process_gaps(df, qrynames, fastas, mp_preset='asm20', ncores=1, annotate_pr
                 logger.debug("Running syri")
                 syns = syri_get_syntenic(ref, alns)
 
+                # no synteny found; can be genuine, or an issue with alignment
                 if len(syns) == 0:
                     logger.info(f"No synteny to {ref} was found!")
                     # debug: emit non-aligning sequences
                     #if refend - refstart > 1000:
                     #    print(f"\n===\n>{ref} {list(reftree)}\n{refseq}")
                     #    print('\n'.join([f">{id} {list(mappingtrees[id])}\n{seq}" for id, seq in seqdict.items()]))
+                    # draw out remaining sequences as private from the mappingtree
+                    # if there is none, there wouldn't have been any to call as large enough anyway
+                    if annotate_private and ref in mappingtrees:
+                        merasyns[ref] = mt_to_privates(mappingtrees[ref], ref, syn.ranges_dict[org].chr)
                     continue
 
                 ## Find merasyn in the syri calls
-                multisyns = intersection.reduce_find_overlaps(list(syns.values()), cores=ncores, annotate_private=annotate_private)
+                multisyns = intersection.reduce_find_overlaps(list(syns.values()), cores=ncores)
 
                 # no need to recalculate the tree if no multisynteny was found
                 if multisyns is None or multisyns.empty:
                     logger.info("No multisynteny was found in this round!")
+                    if annotate_private and ref in mappingtrees:
+                        merasyns[ref] = mt_to_privates(mappingtrees[ref], ref, syn.ranges_dict[org].chr)
                     continue
 
                 # Add all merasyns with alphabetical sorting by reference name