--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fa	Sun Jun 21 14:30:20 2015 -0400
@@ -0,0 +1,159 @@
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_4/7_Confidence_0.286_Length_409_hit1_IdMatch=96.58,AligLength=409,E-val=0.0
+TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTTCTGGCTGCA
+GTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTGTCCTGCAAT
+GTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCATCTCCAGTA
+GTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCTCCAACTTTA
+TCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTAACGACGGCT
+TGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATCCGAACTACT
+TTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTTTAAGAG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0
+ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA
+GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT
+TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA
+TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA
+TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG
+AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC
+CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG
+AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA
+AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC
+TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA
+TATTCAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113
+ATAGAAGCACTGTGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTG
+CCTATCTCCAGGAGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTC
+TCCATGAGTCGGAAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTG
+ACACTAAGAAAGTTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0
+GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA
+CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA
+TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC
+TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC
+TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG
+ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC
+ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA
+GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_2/7_Confidence_0.143_Length_224_hit1_IdMatch=97.77,AligLength=224,E-val=3e-104
+ACATCCTGGGTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTT
+GGCCGTACCTCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGG
+ACATATGCCATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGAT
+ACTCCTGCAACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTGGTTGTCAAAGAGGGAA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98
+TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA
+GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT
+AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG
+ACTCGCCCAACAGATGGGCCGGACAACGGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_1/7_Confidence_0.286_Length_199_hit1_IdMatch=98.48,AligLength=197,E-val=2e-92
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_1/2_Confidence_0.667_Length_506_hit1_IdMatch=97.04,AligLength=506,E-val=0.0
+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC
+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA
+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA
+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA
+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC
+CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC
+TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT
+GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG
+GATGAAGAGACAAGGCTTAGTTGTCA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139
+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG
+TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG
+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG
+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG
+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118
+TGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCACC
+GAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACAAT
+TTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTCGT
+TCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCAAC
+AGTTCTTGTTA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_7/7_Confidence_0.000_Length_627_hit1_IdMatch=97.93,AligLength=627,E-val=0.0
+GTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCCTCAAACACTTTGTACTCATCATTCA
+GATTCGCCTCAGGAGGAGGAGGGCATCCTACAACCTCCTTGACATCATAGTCGTTGGATT
+GGACTGTCAAATTTATCTGCCTCACAGCCACTCTCTGCTCCCTCTTAAACTCGTCCAGGA
+ATCCTGACAATGTGGGGAACAGATTAATCCATCCCGCTTTGTCATCCTCTCCATCTGAAT
+AGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCTGACGAATCTGGATATTCAAAGTCCT
+GGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGCTCTTGCGTTTGCATGACAATAATCT
+CGCCGGGGATTGTGTTAACCACAGCGTGTATTGTCTCTTCGATCCGAGGTATGCTGAATC
+CCATTGTTATCATTAAACCCCTCATACGGTCATACAGAGTTCTTTGGCGTGCCGTTCTAG
+ATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAGAGCATCATCTCAAGAGCATCGCTCT
+CAGGCATTGTGGGGACATGTATCACACGGTGTCTGTGGTACACTCCCATAATTTGTACGC
+CAAGAAATTTGTGGTCCGTAATTAGAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129
+ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT
+GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA
+GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG
+CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG
+TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0
+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG
+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG
+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG
+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC
+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC
+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA
+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT
+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG
+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA
+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT
+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA
+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC
+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC
+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC
+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC
+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC
+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT
+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC
+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC
+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC
+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG
+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG
+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128
+GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG
+GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT
+ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC
+CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG
+CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_5/7_Confidence_0.286_Length_421_hit1_IdMatch=96.67,AligLength=421,E-val=0.0
+TACTCCTGCAACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAA
+AGCTGACGTTCTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTC
+TCTTTGACTGTCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTC
+TCCAAGTTCATCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTA
+GGCACTAGCTCCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGT
+AAGCCATCTAACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACT
+TTCTGTGATCCGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGG
+T
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118
+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA
+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA
+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC
+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA
+ACAGTTCTTGTTA
+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171
+GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG
+ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA
+CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA
+TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG
+AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT
+GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC