diff --git a/test/input/TestOrderAndOrient/contigs.ebov.ambig.fasta.gz b/test/input/TestOrderAndOrient/contigs.ebov.ambig.fasta.gz
new file mode 100644
index 000000000..a53fd24da
Binary files /dev/null and b/test/input/TestOrderAndOrient/contigs.ebov.ambig.fasta.gz differ
diff --git a/test/input/TestOrderAndOrient/expected.ebov.ambig.fasta b/test/input/TestOrderAndOrient/expected.ebov.ambig.fasta
new file mode 100644
index 000000000..39bd9e9fa
--- /dev/null
+++ b/test/input/TestOrderAndOrient/expected.ebov.ambig.fasta
@@ -0,0 +1,311 @@
+>KJ660346.2_contigs_ordered_and_oriented
+GAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGT
+TACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGG
+TCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGG
+CCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGC
+AACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAAC
+TTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGT
+AAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGAT
+TCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCAC
+AAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCA
+GTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCT
+GGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCG
+TACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCAC
+GGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCA
+GCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACG
+ACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTA
+GTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAA
+GGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGT
+TTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTT
+GCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCA
+GGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTT
+CGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCT
+GCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTT
+TCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGA
+GTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAG
+CTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAA
+CTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAA
+AAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTG
+GCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGAT
+GATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAA
+GATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGAT
+GATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGAC
+TTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCG
+ACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACA
+CAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCT
+CCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTG
+ACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTT
+CCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCC
+ACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAA
+GATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACC
+CAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTT
+GATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGAT
+GGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAA
+AAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGG
+CCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGC
+ATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAA
+ACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAG
+TTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTT
+AATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAG
+CGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACA
+TTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCAT
+CCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAG
+CTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCA
+AAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGG
+AAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGC
+ATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGA
+CCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGT
+TGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAA
+TGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGC
+TGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGC
+TGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTA
+TGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGT
+TAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAA
+ACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGG
+AACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATT
+GGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGC
+CCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCA
+CATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACC
+ATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACT
+TGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGC
+TTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTA
+GATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTA
+AAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAA
+CCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTC
+ATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATT
+GCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAAT
+TGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACAC
+TCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACC
+AGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAA
+AGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTA
+CAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGG
+CAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCC
+CCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGT
+CCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACT
+GCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGG
+AATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGG
+GAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGA
+CTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAAC
+TCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCC
+TGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGT
+AATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAA
+GTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAAC
+ATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGT
+GCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATA
+TACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCC
+TACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCC
+TTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAG
+ATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGC
+TCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCAT
+CTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAAC
+CAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAAT
+ATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCT
+TTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAG
+TGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGT
+TGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGANNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGT
+CTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCA
+CAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATT
+CAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATA
+AAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCA
+ATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGA
+CTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAA
+TGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGT
+GGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAAT
+ATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTA
+ATGCGGAGGTTTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTT
+CATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCT
+GTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTAC
+ACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTT
+AGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACC
+TACAACGAACATTACTTTGAGCACCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAA
+TCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCC
+AGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAA
+TATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAG
+TTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTC
+ACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAA
+TGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGC
+TGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTT
+TGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACA
+CTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGT
+CGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGA
+ACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAA
+CTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACC
+GCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTA
+CACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTA
+TCTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAA
+CTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTC
+TTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACC
+CTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAA
+TTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAAT
+TGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTC
+CATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAA
+AAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGAT
+ATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTAT
+TGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATC
+CGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTG
+TTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAA
+TTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGT
+TCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCA
+AAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTT
+CAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAA
+CTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATT
+TAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTAC
+CACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCA
+AAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAA
+TGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGG
+TTGAGGACCCATTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGA
+GCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCG
+AACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGAT
+TCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTG
+CACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGG
+AGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTG
+TGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCAT
+TACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATT
+ATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTC
+TTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTAT
+GGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAA
+GTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCG
+AGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAAC
+AATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCG
+AGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATG
+TAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAG
+CTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAAC
+GTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCG
+GTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTG
+CATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTA
+AGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATT
+ATTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTA
+GTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTA
+TTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTG
+TGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAG
+GCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAG
+TTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTA
+TCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGG
+CTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTA
+GTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAA
+TAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGAT
+TTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAA
+TATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGA
+AATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTT
+ATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGA
+ACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAG
+ACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACA
+AACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGT
+GGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGC
+CGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCT
+CTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATACATT
+GCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGC
+TTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGC
+ACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATT
+CAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACC
+TGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAA
+TGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGA
+AGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGC
+CATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCT
+AATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGAC
+CCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTC
+TTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTT
+AGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGT
+TATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATAT
+CCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCA
+GTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATT
+GATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCC
+ATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTT
+ATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTC
+GTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTA
+TCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATAC
+AATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAAT
+TCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGT
+TATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGG
+TGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCT
+TACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATA
+TCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACT
+GCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACA
+TCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTC
+ATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTC
+TTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAAC
+CACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAAT
+AAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCT
+AAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAA
+TGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACA
+TCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAA
+TGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGA
+TACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGA
+GGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGC
+TGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGC
+TACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCT
+ACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAG
+CCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAG
+GCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATT
+GTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTGTTGAAAGCAGT
+GGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGC
+CCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGA
+GTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCA
+TCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATA
+CTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCT
+TGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAG
+AGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATT
+GACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTAC
+TGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACA
+AGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAG
+TGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCA
+AACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATTGAAAGGCTGACAGG
+GCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTAT
+TTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTC
+TCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTT
+ACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAG
+CATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTT
+TATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTA
+TCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAAC
+TTAATCTTAAAGATCAGTTTT
diff --git a/test/input/TestOrderAndOrient/expected.lasv.ambig.fasta b/test/input/TestOrderAndOrient/expected.lasv.ambig.fasta
index f811a8e53..bcca56396 100644
--- a/test/input/TestOrderAndOrient/expected.lasv.ambig.fasta
+++ b/test/input/TestOrderAndOrient/expected.lasv.ambig.fasta
@@ -101,10 +101,10 @@ CTGTCTTTAGCTCTCTTCCTACTGTCTATCCACCGTTTNNNNNNNNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-NNNNNNNNNTCAGTTTTAACAAATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTA
+NNNCAACACTGCATCTGCTCACTTTGAGAGTCAGCAGCCCTTTCTTCACCAGAATCTAAA
+TCTGCATATAAGAACTTAAGGACTGGAGAGGCTCTTCGGAACTGGTATGTTAACTGCTCA
+ATATTGTCATCACAAGTGTCTATTTTATCACTATATAGCTTTCTGAAATCCCCTAACAGC
+TTCATCTTATCAGTTTTAACAAATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTA
 AAGATTTGATACTCCTCTTCAATTAAACTCTTGACTTCATGAGAGGTGAGCTTGTTATTA
 ATGCCCTGATGACAACAAGAAATTATTTCCTCAAAGTGTTTTGCACGCTTGTCAGTTAGA
 ACATTAATGCTTTCAATCCCGGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGT
diff --git a/test/input/TestOrderAndOrient/ref.ebov.makona_C15.fasta b/test/input/TestOrderAndOrient/ref.ebov.makona_C15.fasta
new file mode 100644
index 000000000..3ec1a60e7
--- /dev/null
+++ b/test/input/TestOrderAndOrient/ref.ebov.makona_C15.fasta
@@ -0,0 +1,273 @@
+>KJ660346.2 Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Makona-Kissidougou-C15, complete genome
+CGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA
+TTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTT
+CAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGT
+TGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCC
+AACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAA
+TTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAAC
+ATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA
+GTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG
+TTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCA
+ACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT
+TGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG
+GGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT
+ATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCC
+GGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA
+AGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT
+AGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAA
+GGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT
+TTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT
+CCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTG
+GCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG
+GTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGT
+AAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATAT
+GCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATC
+AGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA
+GCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT
+CCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG
+ATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGA
+AAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCA
+GTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGAC
+AGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACT
+CACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAA
+GAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAG
+AACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA
+CTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAA
+GACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGC
+CATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAA
+AGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAAT
+GATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAAT
+TCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCT
+AACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT
+AAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA
+GTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATT
+TATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT
+TATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC
+ACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCA
+GGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA
+GCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC
+TACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAA
+TTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC
+CATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG
+GCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA
+CAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACC
+TGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAA
+AGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG
+ACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA
+ATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAG
+GCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC
+AAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTT
+GCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA
+ACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAA
+CTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAA
+TTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATAC
+CTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCT
+ACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT
+GAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCA
+ACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCAT
+CGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC
+AGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT
+TGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG
+CTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGG
+AATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCA
+CCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTG
+CTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC
+AAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG
+GAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA
+TCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGG
+ACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC
+ATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAAT
+TGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATC
+CGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTC
+TCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCA
+TGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGC
+ACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGAT
+TGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTC
+TAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT
+TGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATA
+TTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT
+CATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAG
+TACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA
+TCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCT
+TCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT
+TGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG
+TGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTG
+CTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT
+TGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT
+GCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTA
+ATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA
+GTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATT
+TGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC
+TAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAG
+AGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAG
+AAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT
+TGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACA
+CCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACA
+GCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAG
+TAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAAC
+AACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA
+CTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCA
+ACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG
+ATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAA
+TCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGA
+GCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGC
+CACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC
+AGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG
+GAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATA
+TGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTA
+GGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTC
+AAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT
+AGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTC
+TTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTG
+TAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGT
+CAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCG
+AGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT
+TATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA
+GAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG
+TGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATC
+GCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA
+ATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGC
+AGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGT
+GCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAG
+GGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG
+TTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT
+ATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT
+CAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG
+CTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC
+AAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAA
+TTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC
+TCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTA
+CAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATA
+TTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTAT
+TGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGA
+AAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCC
+CCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT
+TAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATC
+TCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGG
+GCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCGCC
+CTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGT
+CTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGG
+GACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT
+CTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA
+GGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTAT
+TTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGC
+AGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC
+TCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA
+GCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT
+CGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA
+ACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGC
+CGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCA
+AAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAAC
+TCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAAT
+AAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG
+ACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCT
+TTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGC
+AGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAA
+GTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA
+AGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTAT
+CATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCT
+TAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACC
+AAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCAC
+TATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACAC
+AATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAC
+CACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG
+ACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGA
+TGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTG
+AACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG
+GGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCG
+ATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTT
+AAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA
+TCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGG
+CCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTA
+AAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC
+AACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA
+AAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTT
+TTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAA
+ATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT
+GCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT
+TTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGG
+GATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC
+TATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTC
+TCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC
+AAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC
+GGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAG
+CATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAGT
+TTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA
+TACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAAT
+CGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA
+AACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTC
+AGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAG
+CAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG
+GAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT
+GAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT
+GATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA
+TCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCT
+CGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA
+TTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA
+ATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA
+TTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC
+GGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCC
+TAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTG
+TAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGC
+GGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA
+ATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAG
+TTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA
+CAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCAT
+GTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAA
+GCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCA
+TCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGC
+AACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC
+ATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA
+AGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATC
+AATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAA
+CACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATA
+AATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTG
+CTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATACACATCTACATT
+GGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTC
+AATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTA
+TTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAA
+TAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC
+AAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA
+AGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATT
+GCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTT
+TCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT
+CCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT
+AGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTG
+GTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATC
+TTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCA
+CAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT
+CATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGC
+AAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTC
+ATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTG
+AAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTAC
+CTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGAT
+ATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTC
+TCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGG
+CAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACAC
+GCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT
+GTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA
+TAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGA
+TGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCAT
+GTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGC
+TAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTC
+TAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC
+AGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATT
+TAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT
+ACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCA
+CATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT
+ATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT
+TGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG
+TGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC
+ATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGG
+TCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACA
+GATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGAT
+AACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACA
+ATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATA
+ATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCA
+GATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTA
+TAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGAT
+TAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAA
+AAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAA
+TGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGG
+AAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA
+
diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py
index a32e0af5e..71be96d51 100644
--- a/test/unit/test_assembly.py
+++ b/test/unit/test_assembly.py
@@ -401,6 +401,23 @@ def get_seqs(fasta):
             return [str(s.seq) for s in Bio.SeqIO.parse(fasta, 'fasta')]
         self.assertEqual(get_seqs(outFasta), get_seqs(expected))
 
+    def test_ambig_align_ebov(self):
+        inDir = util.file.get_test_input_path(self)
+        contigs_gz = os.path.join(inDir, 'contigs.ebov.ambig.fasta.gz')
+        contigs = util.file.mkstempfname('.fasta')
+        with util.file.open_or_gzopen(contigs_gz, 'rb') as f_in:
+            with open(contigs, 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
+        expected = os.path.join(inDir, 'expected.ebov.ambig.fasta')
+        outFasta = util.file.mkstempfname('.fasta')
+        assembly.order_and_orient(
+            contigs,
+            os.path.join(inDir, 'ref.ebov.makona_C15.fasta'),
+            outFasta)
+        def get_seqs(fasta):
+            return [str(s.seq) for s in Bio.SeqIO.parse(fasta, 'fasta')]
+        self.assertEqual(get_seqs(outFasta), get_seqs(expected))
+
     def test_obscure_mummer3_bug(self):
         inDir = util.file.get_test_input_path(self)
         outFasta = util.file.mkstempfname('.fasta')
diff --git a/tools/mummer.py b/tools/mummer.py
index 4129f4bdc..3ac678f92 100644
--- a/tools/mummer.py
+++ b/tools/mummer.py
@@ -209,7 +209,8 @@ def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,
             aligner='nucmer', extend=None, breaklen=None,
             maxgap=None, minmatch=None, mincluster=None,
             min_contig_coverage_diff=0.0,
-            min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200):
+            min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200,
+            ambig_max_aligns=2, ambig_max_lens=1, ambig_max_frac=.01):
         ''' Re-implement a less buggy version of MUMmer's pseudomolecule
             feature to scaffold contigs onto a reference genome.
         '''
@@ -282,17 +283,35 @@ def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,
                     # (# assembled segments)
                     continue
 
+                def n_diff_vals(*vals): return len(set(vals))
+                def n_diff_lens(seqs): return n_diff_vals(*map(len, seqs))
+                def frac_unambig(seqs):
+                    """Given a list of seqs of the same length, return the fraction of positions on which they all agree"""
+                    util.misc.chk(n_diff_lens(alt_seqs_f) == 1, 'ambig_max_lens>1 not currently supported')
+                    n_tot = len(seqs[0])
+                    n_unambig = list(map(n_diff_vals, *seqs)).count(1)
+                    return float(n_unambig) / float(n_tot or 1.0)
+
                 # construct scaffolded sequence for this chromosome
                 seq = []
                 for _, left, right, n_features, features in fs.get_intervals(c):
                     # get all proposed sequences for this specific region
                     alt_seqs = []
-                    for f in features:
-                        try:
-                            alt_seqs.append(alnReaders[(c, f[-1][0])].retrieve_alt_by_ref(left, right, aln_start=f[1], aln_stop=f[2]))
-                        except AmbiguousAlignmentException:
-                            log.warn("dropping ambiguous alignment to ref seq {} at [{},{}]".format(c, f[1], f[2]))
-                            pass
+                    for consider_ambig_aligns in (False, True):
+                        for f in features:
+                            alt_seqs_f = alnReaders[(c, f[-1][0])].retrieve_alts_by_ref(left, right, aln_start=f[1], aln_stop=f[2])
+                            if len(alt_seqs_f) == 1:
+                                alt_seqs.append(alt_seqs_f[0])
+                            elif consider_ambig_aligns:
+                                if len(alt_seqs_f) <= ambig_max_aligns and n_diff_lens(alt_seqs_f) <= ambig_max_lens and \
+                                   frac_unambig(alt_seqs_f) > (1.0 - ambig_max_frac):
+                                    alt_seqs.append(alt_seqs_f[0])
+                                    log.info("using ambiguous alignment to ref seq {} at [{},{}]".format(c, f[1], f[2]))
+                                else:
+                                    log.warning("dropping ambiguous alignment to ref seq {} at [{},{}]".format(c, f[1], f[2]))
+                        if alt_seqs:
+                            # if have a non-unambiguous alignment, don't consider ambiguous ones
+                            break
 
                     # pick the "right" one and glue together into a chromosome
                     ranked_unique_seqs = contig_chooser(alt_seqs, right-left+1, "%s:%d-%d" % (c, left, right))
@@ -541,8 +560,8 @@ def get_ref_seq(self, start, stop):
         '''
         return str(self.reference_seq.seq[start-1:stop])
 
-    def retrieve_alt_by_ref(self, start, stop, aln_start=None, aln_stop=None):
-        ''' Retrieve a sub-sequence from the alternate (2nd) sequence in the
+    def retrieve_alts_by_ref(self, start, stop, aln_start=None, aln_stop=None):
+        ''' Retrieve sub-sequence(s) from the alternate (2nd) sequence in the
             alignment using coordinates relative to the reference sequence.
             No gaps will be emitted.
             Required: start-stop interval must be wholly contained within
@@ -550,49 +569,52 @@ def retrieve_alt_by_ref(self, start, stop, aln_start=None, aln_stop=None):
         '''
 
         # grab the one alignment that contains this window
-        aln = list(a for a in self.alignments if a[1]<=start and a[2]>=stop)
+        alns = list(a for a in self.alignments if a[1]<=start and a[2]>=stop)
         if aln_start is not None and aln_stop is not None:
             # if specified, restrict to a specific alignment that comes from show-tiling
             # (sometimes show-aligns is more promiscuous than show-tiling)
-            new_aln = []
-            for a in aln:
+            new_alns = []
+            for a in alns:
                 if a[1] > aln_start or a[2] < aln_stop:
                     log.debug("dropping undesired alignment: %s(%s):%s-%s to %s(%s):%s-%s (%s:%s-%s requested)",
                         self.seq_ids[0], a[0], a[1], a[2],
                         self.seq_ids[1], a[3], a[4], a[5],
                         self.seq_ids[0], aln_start, aln_stop)
                 else:
-                    new_aln.append(a)
-            aln = new_aln
-        if len(aln) != 1:
-            log.error("invalid %s:%d-%d -> %s specified, %d alignments found that contain it",
-                self.seq_ids[0], start, stop, self.seq_ids[1], len(aln))
-            for x in aln:
-                log.debug("alignment: %s", str(x[:6]))
-            raise AmbiguousAlignmentException()
-        aln = aln[0]
+                    new_alns.append(a)
+            alns = new_alns
+        if len(alns) != 1:
+            log.warning("invalid %s:%d-%d -> %s specified, %d alignments found that contain it",
+                self.seq_ids[0], start, stop, self.seq_ids[1], len(alns))
+            for aln in alns:
+                log.debug("alignment: %s", str(aln[:6]))
+
+        return [self._aln_to_alt_seq(aln, start, stop) for aln in alns]
+
+    def _aln_to_alt_seq(self, aln, start, stop):
+        """Given an alignment of a contig to ref, return the contig sequence aligned to a given stretch of ref"""
         ref_l, ref_r, ref_seq, alt_seq = (aln[1], aln[2], aln[-2], aln[-1])
 
         # convert desired start/stop relative to this reference window
         #  such that 0 <= start <= stop <= ref_r-ref_l+1
-        start = start - ref_l
-        stop = stop - ref_l
+        aln_start = start - ref_l
+        aln_stop = stop - ref_l
 
         # travel down alignment until we've reached the left edge
         #  (because of gaps, you must check each position one by one)
-        #  end loop when ref_seq[:i_left] contains {start} bases
+        #  end loop when ref_seq[:i_left] contains {aln_start} bases
         n_ref_bases = 0
         i_left = 0
-        while n_ref_bases < start:
+        while n_ref_bases < aln_start:
             if ref_seq[i_left] != '-':
                 n_ref_bases += 1
             i_left += 1
 
         # travel down alignment until we've reached the right edge
         #  (because of gaps, you must check each position one by one)
-        #  end loop when ref_seq[:i_right] contains {stop} bases
+        #  end loop when ref_seq[:i_right] contains {aln_stop} bases
         i_right = i_left
-        while n_ref_bases < stop:
+        while n_ref_bases < aln_stop:
             if ref_seq[i_right] != '-':
                 n_ref_bases += 1
             i_right += 1
@@ -601,6 +623,6 @@ def retrieve_alt_by_ref(self, start, stop, aln_start=None, aln_stop=None):
             i_right += 1
 
         # grab the alternate sequence and strip gaps
-        alt_seq = alt_seq[i_left:i_right+1].replace('-','')
-        return alt_seq
+        return alt_seq[i_left:i_right+1].replace('-','')
+