--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/39614.fna.aln	Mon Oct 30 09:52:00 2017 -0400
@@ -0,0 +1,99 @@
+>gnl_Orysa6.0_PACid_16878968
+ATG---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---TCACATATGGAAGCCTTCCAAAATGTTGTGCTCCTGCATAAAGCAAATTCAAATTCT
+ACACTAGAGGATATATCATCCCTATCTGCTGCAAGCTGTTGCAGCCTTGATCAGCTTCTA
+GCTTGTGTCGAGGGAGAGGCACAGAAGATATTTGGTGATATCCAGAATTTGCTAGCTGAT
+CATCGAAGCGAAGTGGCACATTTCACTCAAGAGTTGCGGGAGAGTTTCCGCATTAGCTTG
+GATAGGACGAAGGACATGTCTAGTTTCATCCTTGGGTTGTTCGATAAGTATGTGGAGGAA
+ACTTCGAAGTTGCAGAGCCACTCCAATCACACACATGAAGCACAAGTCAAAAGCCTTGAA
+GATTTCCAGAAGGCTTATGAGGAGCAATCAAAATCAGAAGAACAAAAGCTTCTGGCGGAC
+ATCACCAGTTTGGTTTCTAAACACGTTACTCGACAACGAGAACTGGTGGGTGGTAGACTA
+AACTCTCTTGGTGACGCCGCTCGTGGAAACAAAGCATTTTTGGATGAGCACACGTCCGCC
+ATGGAGGTGGTCACGAAGGACGCCAAGAGAAAGTGGGAAATGTTTGCAGAGCAGGCAGAG
+AATGACTGCAAAGTTGGGTCCAACTTCTCTGCAGCTAAGCATTGTCGCATGGAAACCATT
+CTGCAGGAATGTGCATGCACCGTCGACACTGCTGCTCAACAATGGAAAGCATCACATGCA
+ACTGTTAACGATCTATGCAGAAAACAAATAGCTGAAGTTGAAGCACTCGTCAGGAGTGCA
+ATCGAAACCAACGAGCAGCACGAAGCAGAGATTGCATCTTCCCGTGCCACGGCCGAGGAG
+CATGCGTCCAACAGCAGCAAGGACCTACTCCAAGATGTTGACAATATGCTGCAGGAGGCG
+CGCAATTCGTCGTCGAGAGTGGTGTCGACGGTGGAAGCTCATTTGGGAGAGAGCCAGCAT
+CTACAGGAGAGCCACTCCAGCCATACCGCCGGCATCAACACCCACGCCGACAACGCTTTC
+CAGAGCAGCTACAAGGACTACGAGCCGACCGGCGAAACTCCGGTGAGGTCGGAGCCGGAG
+GTGCCGAGCAAAGACGCGATCGAGTCGCTGCGAGCGATGCCGATGGAGTCCCTGATGGAC
+GAGTTCCGCGAGAACCACCCCTACGAGCCGAGC---------AAGGACCGCAGGCCATCG
+CTCATCCCTCGCTCGCCGCTCGCCACCATCAACAAC
+>gnl_Phoda3.0_PDK_30s1023721g001
+GTAAACCAAAAAATGATGAAATGTACATTAATCAAAGATCTCTATGGAGAAATTGAGCGT
+CTAAAAGCAGAGGTGTATGCTGCTCGTGAGAAAGTTGGAGTTTACATACCAAAAGAACGC
+TACCATCAAGAAGAGAGCGAACGGAAGGCAATGGCAGAACAAATTGAACAAATGGGGGTC
+TTGCTCGAAAACAATCAAAAGCAAATTGAGGATCTACAAGAAAGGTATAATACTCAACTT
+CAACAGTCTGATGACCTGAGCAAAAAGCTTGATGCCACCGAGATTCTCTGTGTTTCTCTG
+AGCAAAAAGCTTGATGCCACCGAGAAAAGTTTGGAGCACACTAGCAAGTTATTGGCTGCT
+GCCAGAGAAGATCTGAAGCAAGCTCAGTATACTCTGAAGGAGAAAGATTTTGTTATATCA
+GAGCAGAGGAAAGCAGCTAGAGAAGACAAACTGAATACTGCCAACAGATCTATTGTGAAC
+AATTTTCGGGCTGATCTTGCAACAAGGGTTGGAACACTTTGTAATACTGTTGTTGCATCC
+TTGGATCGGCAAAATGAACACCTTCAGTCTGTTGAGAAACTATGTCAATCTAGCCTTGAT
+TTCCATGACAAGGCAGTATCAGAGCTGAAAAGGAAAGTGTCAGCTTCAAGAGCTTTGTAT
+ACTTCCCATATGGAAGCACTACAAAATGTAGTGCGTTTGCATAAGGCAAGCAGCAATGCC
+AGCTTAGAAGAGATGTCATCCATGATTTCTGCCAATACCTGCTCTCTTGATCAGTTACTT
+GCCTTGGGGCAAAGCGAAGCAGATCTGATTTTTAGTGATCTGCAAAGCATATTGTCAATT
+CACCGAGGAGAGATTGCAAATTTCACCCGTGAACTTCGTGAGAAATTTCAAGTTAATTTG
+GATCGGACAAAGGAGATGTCCAATTTTATTCTTGAGCTGCTTGAAAAGATAGGGAAGGGA
+ACAAAAGAATTTCAGAATGACTCAACTTTGGTACATGAGGCTCAGGTGAAGAGCATTGGT
+GATTTCCAAAAGGCATATGAG---------------------------------------
+---------------------------------------------GTGGAAGTGAGGCTC
+ACTGGACTGGGAGATGCTGCTCGAGATAGCAAAGCAATTATGGATAACCATGCATCATCA
+ATGGACATCGTCACAACTGATGCTAAGAGGAAGTGGGAAGAATATTCCAAGCAGGCAGAG
+CAAGATTCAGAGGACGGTTCTAACTTTTCAGCAGCAAAACATTGTCGCATGGAACTCATG
+CTCCAACAGTGTGTAAACTCTGTTGATGCTACTTCTCAACAGTGGAAGAAGACACATGCA
+TCTGTTAGTGAGATGAGCAGCAAACACGTTGCTGAAATTGAAGCACTTGTAAGGAGTGCC
+ATTGAGAGCAATGATCAGCATGATGCTGAGGTTGCTTCAGCAAGAATGGCAGCAGAAGAG
+GATGTAGCGAAAAATAGCAAAGATGTTCTTCAGCATTTTGATACTGTGATTGATCATGAG
+CGCAACTCAGCCGCTGGAGTGATGGCAGCAGTCGAAGCTCACTCAGCAACCCTGCATAAA
+CTGCAAGAGGAACAATCAAGCCAGGCAACAGAGATTAATAGCCATGCGGAGGACACATTC
+CAAAACACCTACATGGACTATGAACCAACGGGAGAAACCCCAACAAGGTCGGAACCAGAT
+ATACCAAGCAGGGGAACAATCGAATCTCTTCGAGCCATGCCGATAGAAGCCCTCCTTGAA
+GAGTTCCGGGAGAACCATCCATACGAGTCC------------AAGGAGCCCAAACCGTCT
+CTCATACCACGCTCTCCACTCGTCCAGCTCAAC---
+>contig_3
+NNT---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------GTGGAT---------------------------------
+---------------------------------------GAAGGAGTTGTT---------
+------------------------------------------------------------
+------------------------------------GTTGCTGGCTTGTCAGAGCAGGAG
+AAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAAC
+CTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTC
+AGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGAT
+ATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAA
+GAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCT
+GTTACGACTCGTGCACCATTTTCACAGATCAAC---