--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mature_ref_other_species.fa	Tue Jan 27 09:06:24 2015 -0500
@@ -0,0 +1,490 @@
+>cbr-let-7
+TGAGGTAGTAGGTTGTATAGTT
+>cbr-lin-4
+TCCCTGAGACCTCAAGTGTGA
+>cbr-miR-1
+TGGAATGTAAAGAAGTATGTA
+>cbr-miR-34
+AGGCAGTGTGGTTAGCTGGTTG
+>cbr-miR-42
+CACCGGGTTAACATCTACAG
+>cbr-miR-43
+TATCACAGTTTACTTGCTGTCGC
+>cbr-miR-44
+TGACTAGAGACACATTCAGCT
+>cbr-miR-45
+TGACTAGAGACACATTCAGCT
+>cbr-miR-46
+TGTCATGGAGTCGCTCTCTTCA
+>cbr-miR-47
+TGTCATGGAGGCGCTCTCTTCA
+>cbr-miR-48
+TGAGGTAGGCTCAGTAGATGCGA
+>cbr-miR-49
+AAGCACCACGAGAAGCTGCAGA
+>cbr-miR-50
+TGATATGTCTGATATTCTTGGGTT
+>cbr-miR-52
+CACCCGTACATATGTTTCCGTGCT
+>cbr-miR-57
+TACCCTGTAGATCGAGCTGTGTGT
+>cbr-miR-58
+TGAGATCGTTCAGTACGGCAAT
+>cbr-miR-60
+TATTATGCACATTTTCTAGTCCA
+>cbr-miR-67
+TCACAACCTCCTAGAAAGAGTAGA
+>cbr-miR-71
+TGAAAGACATGGGTAGTGA
+>cbr-miR-73
+TGGCAAGATGTTGGCAGTTCAGT
+>cbr-miR-74
+TGGCAAGAAATGGCAGTCTAGA
+>cbr-miR-75
+TTAAAGCTACCAACCGCCTTCA
+>cbr-miR-77
+TTCATCAGGCCATAGCTGTCCA
+>cbr-miR-79
+ATAAAGCTAGGTTACCAAAGCT
+>cbr-miR-80
+TGAGATCATTAGTTGAAAGCCGA
+>cbr-miR-81
+TGAGATCATCGTGAAAGCTAGT
+>cbr-miR-82
+TGAGATCATCGTGAAAGCCAGT
+>cbr-miR-85
+TACAAAGTATTTGAAAAGGCGTGC
+>cbr-miR-86
+TAAGTGAATGCTTTGCCACAGTC
+>cbr-miR-87
+GTGAGCAAAGTTTCAGGTGT
+>cbr-miR-90
+TGATATGTTGTTTGAATGCCCC
+>cbr-miR-124
+TAAGGCACGCGGTGAATGCCA
+>cbr-miR-228
+AATGGCACTGCATGAATTCACGG
+>cbr-miR-230
+GTATTAGTTGTGCGACCAGGAAA
+>cbr-miR-232
+TAAATGCATCTTAACTGCGGTGA
+>cbr-miR-233
+TTGAGCAATGCGCATGTGCGGGA
+>cbr-miR-234
+TTATTGCTCGAGAATACCCTT
+>cbr-miR-236
+TAATACTGTCAGGTAATGACGCT
+>cbr-miR-241
+TGAGGTAGGTGTGAGAAATGA
+>cbr-miR-244
+TCTTTGGTTGTACAAAGTGGTATG
+>cbr-miR-245
+ATTGGTCCCCTCCAAGTAGCTC
+>cbr-miR-248
+TACACGTGCTCGGATAACGCTCA
+>cbr-miR-250
+TCACAGTCAACTGTTGGCACGG
+>cbr-miR-251
+TTAAGTAGTGGTGCCGCTCTTATT
+>cbr-miR-252
+TAAGTAGTAGTGCCGCAGGTAAC
+>cbr-miR-259
+AAATCTCATCCTAATCTGGTT
+>cbr-miR-268
+GGCAAGAATTAGAAGCAGTTTTGGT
+>cbr-miR-72
+AGGCAGATGTTGGCATAGC
+>cbr-lsy-6
+TTTTGTATGAGACGCATTCCG
+>cbr-miR-353
+CAAGTATCATGTGTTGGTATC
+>cbr-miR-64
+CATGACACTGAAGCGTGTACGGA
+>cbr-miR-231
+TAAGCTCGTGAACAACAGGCAGGA
+>cbr-miR-356
+ATGAGCAACGCGAACAAATCC
+>cbr-miR-83
+TAGCACCATATAAATTCAGTGT
+>cbr-miR-246
+TTACATGTATTGGGTAGGAGCT
+>cbr-miR-51
+TACCCGTAGCTCCTTGCCATGTT
+>cbr-miR-357
+AAAATGCCAGTCATTGACGGA
+>cbr-miR-253
+CACACCTCACTAACACTAACT
+>cbr-miR-70
+TAATACGTGATTGGTGTTCCCAG
+>cbr-miR-358
+CAATTGGTATCCTTAGTCGTGG
+>cbr-miR-61
+TGACTAGAACCTTGACTCTGCTC
+>cbr-miR-360
+TGACCGTAATCCCGTTCACAA
+>cbr-miR-239a
+TTTGTACTACAATTAGGTACTGG
+>cbr-miR-249
+TCACAGGATTTTTGAGTGTTGC
+>cbr-miR-240
+TACTGGCCTCCAAATTTTCGCT
+>cbr-miR-254
+TGCAAATCTTTTGCAACTGTATA
+>cbr-miR-239b
+TTGTACTGCACAAAAGTACTG
+>cbr-miR-62
+TGATATGTAATCTAGCTTACAG
+>cbr-miR-55
+TACCCGTATATTTTTCTGCCGAG
+>cbr-miR-84
+TGAGGTAGTTTGCAATGCTGTC
+>cbr-miR-354
+ACCTTGTTTGTTGCTGCTCCT
+>cbr-miR-35
+TCACCGGGTGAAAACTTGCAAG
+>cbr-miR-36
+TCACCGGGTGAAAATTCGCAAT
+>cbr-miR-38
+TCACCGGGAGACAACCTGGTAT
+>cbr-miR-39
+TCACCGGGTGAAAAACGGTTAG
+>cbr-miR-40
+TCACCGGGTGTCAATCAGCTAG
+>cbr-miR-41
+TCACCGGGTGAAAAACTCCCA
+>cbr-miR-355
+TTTGTTTTAGCCTGAGCTATG
+>cbr-miR-784
+TGGCACAATACCTGTATGTAGA
+>cbr-miR-785
+TAAGTGAATACTCTGTGTTGA
+>cbr-miR-786
+TAATGCCCTGTACGAGATTTGGT
+>cbr-miR-787
+TAAGCTCGTCTTAGTTTTCCTCT
+>cbr-miR-788
+TCCGCTTCTCAATGCTCCATTTGCAA
+>cbr-miR-789a
+TCCCTGCCTGGGTCAAATGTTTT
+>cbr-miR-789b
+GCCCTGCCTGGGTCACCATGTGA
+>cbr-miR-790
+CTTGGCACTCGCGAACACCGCG
+>cbr-miR-791
+ATTGGCACTCCGCTGATTTGGTG
+>cbr-miR-792
+TTGAAATTTTTTCTATTTTCGGT
+>cbr-miR-235
+TATTGCACTTTCCCTGGCCAGA
+>cbr-miR-242
+TTGCGTAGGCCTTTGTTTCGA
+>cbr-miR-255
+AAACTGAAGAGATTTTTTACAG
+>cbr-miR-359
+TCACTGGTTATCCTCTGTCGAA
+>cbr-miR-392
+TATCATCGATCATGTGAGCTGT
+>dme-miR-1
+TGGAATGTAAAGAAGTATGGAG
+>dme-miR-2a
+TATCACAGCCAGCTTTGATGAGC
+>dme-miR-2b
+TATCACAGCCAGCTTTGAGGAGC
+>dme-miR-3
+TCACTGGGCAAAGTGTGTCTCA
+>dme-miR-4
+ATAAAGCTAGACAACCATTGA
+>dme-miR-5
+AAAGGAACGATCGTTGTGATATG
+>dme-miR-6
+TATCACAGTGGCTGTTCTTTTT
+>dme-miR-7
+TGGAAGACTAGTGATTTTGTTGT
+>dme-miR-8
+TAATACTGTCAGGTAAAGATGTC
+>dme-miR-9a
+TCTTTGGTTATCTAGCTGTATGA
+>dme-miR-10
+CAAATTCGGTTCTAGAGAGGTTT
+>dme-miR-11
+CATCACAGTCTGAGTTCTTGC
+>dme-miR-12
+TGAGTATTACATCAGGTACTGGT
+>dme-miR-13a
+TATCACAGCCATTTTGATGAGT
+>dme-miR-13b
+TATCACAGCCATTTTGACGAGT
+>dme-miR-14
+TCAGTCTTTTTCTCTCTCCTA
+>dme-miR-263a
+GTTAATGGCACTGGAAGAATTCAC
+>dme-miR-184
+TGGACGGAGAACTGATAAGGGC
+>dme-miR-274
+TTTTGTGACCGACACTAACGGGTAAT
+>dme-miR-275
+TCAGGTACCTGAAGTAGCGCGCG
+>dme-miR-92a
+CATTGCACTTGTCCCGGCCTAT
+>dme-miR-219
+TGATTGTCCAAACGCAATTCTTG
+>dme-miR-276a
+TAGGAACTTCATACCGTGCTCT
+>dme-miR-277
+TAAATGCACTATCTGGTACGACA
+>dme-miR-278
+TCGGTGGGACTTTCGTCCGTTT
+>dme-miR-133
+TTGGTCCCCTTCAACCAGCTGT
+>dme-miR-279
+TGACTAGATCCACACTCATTAA
+>dme-miR-33
+AGGTGCATTGTAGTCGCATTG
+>dme-miR-280
+TGTATTTACGTTGCATATGAAATGATA
+>dme-miR-281
+TGTCATGGAATTGCTCTCTTTGT
+>dme-miR-282
+AATCTAGCCTCTACTAGGCTTTGTCTGT
+>dme-miR-283
+TAAATATCAGCTGGTAATTCT
+>dme-miR-284
+TGAAGTCAGCAACTTGATTCCAGCAATTG
+>dme-miR-34
+TGGCAGTGTGGTTAGCTGGTTGTG
+>dme-miR-124
+TAAGGCACGCGGTGAATGCCAAG
+>dme-miR-79
+TAAAGCTAGATTACCAAAGCAT
+>dme-miR-276b
+TAGGAACTTAATACCGTGCTCT
+>dme-miR-210
+TTGTGCGTGTGACAGCGGCTA
+>dme-miR-285
+TAGCACCATTCGAAATCAGTGC
+>dme-miR-100
+AACCCGTAAATCCGAACTTGTG
+>dme-miR-92b
+AATTGCACTAGTCCCGGCCTGC
+>dme-miR-286
+TGACTAGACCGAACACTCGTGCT
+>dme-miR-287
+TGTGTTGAAAATCGTTTGCAC
+>dme-miR-87
+TTGAGCAAAATTTCAGGTGTG
+>dme-miR-263b
+CTTGGCACTGGGAGAATTCAC
+>dme-miR-288
+TTTCATGTCGATTTCATTTCATG
+>dme-miR-289
+TAAATATTTAAGTGGAGCCTGCGACT
+>dme-bantam
+TGAGATCATTTTGAAAGCTGATT
+>dme-miR-303
+TTTAGGTTTCACAGGAAACTGGT
+>dme-miR-31b
+TGGCAAGATGTCGGAATAGCTG
+>dme-miR-304
+TAATCTCAATTTGTAAATGTGAG
+>dme-miR-305
+ATTGTACTTCATCAGGTGCTCTG
+>dme-miR-9c
+TCTTTGGTATTCTAGCTGTAGA
+>dme-miR-306
+TCAGGTACTTAGTGACTCTCAA
+>dme-miR-9b
+TCTTTGGTGATTTTAGCTGTATG
+>dme-let-7
+TGAGGTAGTAGGTTGTATAGT
+>dme-miR-125
+TCCCTGAGACCCTAACTTGTGA
+>dme-miR-307
+TCACAACCTCCTTGAGTGAG
+>dme-miR-308
+AATCACAGGATTATACTGTGAG
+>dme-miR-31a
+TGGCAAGATGTCGGCATAGCTGA
+>dme-miR-309
+GCACTGGGTAAAGTTTGTCCTA
+>dme-miR-310
+TATTGCACACTTCCCGGCCTTT
+>dme-miR-311
+TATTGCACATTCACCGGCCTGA
+>dme-miR-312
+TATTGCACTTGAGACGGCCTGA
+>dme-miR-313
+TATTGCACTTTTCACAGCCCGA
+>dme-miR-314
+TATTCGAGCCAATAAGTTCGG
+>dme-miR-315
+TTTTGATTGTTGCTCAGAAAGC
+>dme-miR-316
+TGTCTTTTTCCGCTTACTGGCG
+>dme-miR-317
+TGAACACAGCTGGTGGTATCCAGT
+>dme-miR-318
+TCACTGGGCTTTGTTTATCTCA
+>dme-miR-2c
+TATCACAGCCAGCTTTGATGGGC
+>dme-miR-iab-4-5p
+ACGTATACTGAATGTATCCTGA
+>dme-miR-iab-4-3p
+CGGTATACCTTCAGTATACGTAAC
+>dme-miR-iab-4as-5p
+TTACGTATACTGAAGGTATACCG
+>dme-miR-iab-4as-3p
+GGATACATTCAGTATACGTTTA
+>dme-miR-954
+TCTGGGTGTTGCGTTGTGTGT
+>dme-miR-955
+CATCGTGCAGAGGTTTGAGTGTC
+>dme-miR-190
+AGATATGTTTGATATTCTTGGTTG
+>dme-miR-193
+TACTGGCCTACTAAGTCCCAAC
+>dme-miR-956
+TTTCGAGACCACTCTAATCCATT
+>dme-miR-957
+TGAAACCGTCCAAAACTGAGGC
+>dme-miR-958
+TGAGATTCTTCTATTCTACTTT
+>dme-miR-375
+TTTGTTCGTTTGGCTTAAGTTA
+>dme-miR-959
+TTGTCATCGGGGGTATTATGAA
+>dme-miR-960
+TGAGTATTCCAGATTGCATAGC
+>dme-miR-961
+TTTGATCACCAGTAACTGAGAT
+>dme-miR-962
+ATAAGGTAGAGAAATTGATGCTGTC
+>dme-miR-963
+ACAAGGTAAATATCAGGTTGTTTC
+>dme-miR-964
+TTAGAATAGGGGAGCTTAACTT
+>dme-miR-932
+TCAATTCCGTAGTGCATTGCAG
+>dme-miR-965
+TAAGCGTATAGCTTTTCCCCTT
+>dme-miR-966
+TGTGGGTTGTGGGCTGTGTGG
+>dme-miR-967
+AGAGATACCTCTGGAGAAGCG
+>dme-miR-1002
+TTAAGTAGTGGATACAAAGGGCGA
+>dme-miR-968
+TAAGTAGTATCCATTAAAGGGTTG
+>dme-miR-969
+GAGTTCCACTAAGCAAGTTTT
+>dme-miR-970
+TCATAAGACACACGCGGCTAT
+>dme-miR-971
+TTGGTGTTACTTCTTACAGTGA
+>dme-miR-972
+TGTACAATACGAATATTTAGGC
+>dme-miR-973
+TGGTTGGTGGTTGAACTTCGATTTT
+>dme-miR-974
+AAGCGAGCAAAGAAGTAGTATT
+>dme-miR-975
+TAAACACTTCCTACATCCTGTAT
+>dme-miR-976
+TTGGATTAGTTATCATCAATGC
+>dme-miR-977
+TGAGATATTCACGTTGTCTAA
+>dme-miR-978
+TGTCCAGTGCCGTAAATTGCAG
+>dme-miR-979
+TTCTTCCCGAACTCAGGCTAA
+>dme-miR-980
+TAGCTGCCTTGTGAAGGGCTTA
+>dme-miR-981
+TTCGTTGTCGACGAAACCTGCA
+>dme-miR-982
+TCCTGGACAAATATGAAGTAAAT
+>dme-miR-983
+ATAATACGTTTCGAACTAATGA
+>dme-miR-984
+TGAGGTAAATACGGTTGGAATTT
+>dme-miR-927
+TTTAGAATTCCTACGCTTTACC
+>dme-miR-985
+CAAATGTTCCAATGGTCGGGCA
+>dme-miR-986
+TCTCGAATAGCGTTGTGACTGA
+>dme-miR-987
+TAAAGTAAATAGTCTGGATTGATG
+>dme-miR-988
+CCCCTTGTTGCAAACCTCACGC
+>dme-miR-989
+TGTGATGTGACGTAGTGGAAC
+>dme-miR-137
+TATTGCTTGAGAATACACGTAG
+>dme-miR-990
+ATTCACCGTTCTGAGTTGGCC
+>dme-miR-991
+TTAAAGTTGTAGTTTGGAAAGT
+>dme-miR-992
+AGTACACGTTTCTGGTACTAAG
+>dme-miR-929
+CTCCCTAACGGAGTCAGATTG
+>dme-miR-993
+GAAGCTCGTCTCTACAGGTATCT
+>dme-miR-994
+CTAAGGAAATAGTAGCCGTGAT
+>dme-miR-995
+TAGCACCACATGATTCGGCTT
+>dme-miR-996
+TGACTAGATTTCATGCTCGTCT
+>dme-miR-252
+CTAAGTACTAGTGCCGCAGGAG
+>dme-miR-997
+CCCAAACTCGAAGGAGTTTCA
+>dme-miR-998
+TAGCACCATGAGATTCAGCTC
+>dme-miR-999
+TGTTAACTGTAAGACTGTGTCT
+>dme-miR-1000
+ATATTGTCCTGTCACAGCAGT
+>dme-miR-1001
+TGGGTAAACTCCCAAGGATCA
+>dme-miR-1003
+TCTCACATTTACATATTCACAG
+>dme-miR-1004
+TCTCACATCACTTCCCTCACAG
+>dme-miR-1005
+TCTGGAATCTTTAATTCGCAG
+>dme-miR-1006
+TAAATTCGATTTCTTATTCATAG
+>dme-miR-1007
+TAAGCTCAATTAACTGTTTGCA
+>dme-miR-1008
+TCACAGCTTTTTGTGTTTACA
+>dme-miR-1009
+TCTCAAAAATTGTTACATTTCAG
+>dme-miR-1010
+TTTCACCTATCGTTCCATTTGCAG
+>dme-miR-1011
+TTATTGGTTCAAATCGCTCGCAG
+>dme-miR-1012
+TTAGTCAAAGATTTTCCCCATAG
+>dme-miR-1013
+ATAAAAGTATGCCGAACTCG
+>dme-miR-1014
+AAAATTCATTTTCATTTGCAG
+>dme-miR-1015
+TCCTGGGACATCTCTCTTGCAG
+>dme-miR-1016
+TTCACCTCTCTCCATACTTAG
+>dme-miR-1017
+GAAAGCTCTACCCAAACTCATCC
+>dme-miR-2279
+TTTCACGCGAAGATATTTATTT
+>dme-miR-2280
+TCTTAGCTTGGCAATAAAATAT
+>dme-miR-2281
+TATCTGTATCTGCAGTATTGC
+>dme-miR-2282
+ATCGGTGAGCTAAAAATAGAAT
+>dme-miR-2283
+GAAAATATCATGAATACGACAAT