--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ecoli.mira4_de_novo.fasta	Fri Nov 21 06:42:56 2014 -0500
@@ -0,0 +1,86 @@
+>MIRA_c1
+gccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacat
+ctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+aaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcgg
+caggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
+ttcgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgggtaagaac
+tacctgcaaaatcaggaaggttttgttcatatttgccggctggatacggcgggcgcacga
+gtactggaaaactaaatgaaactctacaatctgaaagatcacaacgagcaggtcagcttt
+gcgcaagccgtaacccaggggttgggcaaaaatcaggggctgttttttccgcacgacctg
+ccggaattcagcctgactgaaattgatgagatgctgaagctggattttgtcacccgcagt
+gcgaagatcctctcggcgtttattggtgatgaaatcccacaggaaatcctggaagagcgc
+gtgcgcgcggcgtttgccttcccggctccggtcgccaatgttgaaagcgatgtcggttgt
+ctggaattgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggca
+caaatgctgacccatattgcgggtgataagccagtgaccattctgaccgcgacctccggt
+gataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatc
+ctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattgggcggc
+aatatcgaaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagcag
+gcgtttgatgatgaagaactgaaagtggcgctagggttaaactcggctaactcgattaac
+atcagccgtttgctggcgcagatttgctactactttgaagctgttgcgcagctgccgcag
+gagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgatttgacggcg
+ggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaacgtg
+aacgataccgtgccacgtttcctgcacgacggtcagtggtcacccaaagcgactcaggcg
+acgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaagagttg
+ttccgccgcaaaatctggcaactgaaagagctgggttatgcagccgtggatgatgaaacc
+acgcaacagacaatgcgtgagttaaaagaactgggctacacttcggagccgcacgctgcc
+gtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggc
+accgcgcatccggcgaaatttaaagagagcgtggaagcgattctcggtgaaacgttggat
+ctgccaaaagagctggcagaacgtgctgatttacccttgctttcacataatctgcccgcc
+gattttgctgcgttgcgtaaattgatgatgaatcatcagtaaaatctattcattatctca
+atagcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtg
+tctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgactta
+ggtcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagt
+acacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaa
+cggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggct
+ttttttttcgaccaaaggtaacgaggtaacaaccatgcgagagttgaagttcggcggtac
+atcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccag
+gcaggggcaggtggccaccgtcctctctgcccccgccaaaacaccaaccacctggtggcg
+atgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgccgaacgt
+atttttgccgaacttttgacgggactcgccgccgcccagccggggttcccgctggcgacg
+tcaattgaaaactttcgtcgatcaggaatttgcccaaataaaacatgtcctgcatggcat
+tagtttgttggggcagtgcccggatagcatcaacgctgcgctgatttgccgtggcgagaa
+aatgtcgatcgccgttatggccggcgtattagaagcgcgcggtcacaacgttactgttat
+cgatccggtcgaaaaactgctggcagtggggcattacctcgaatctaccgtcgatattgc
+tgagtccacccgccgtattgcggcaagccgcattccggctgatcacatggtgctgatggc
+aggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgcaacggttccga
+ctactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacgga
+cgttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtc
+gatgtcctaccaggaagcgatggagctttcctacttcggcgctaaagttcttcacccccg
+caccattacccccatcgcccagttccagatcccttgcctgattaaaaataccggaaatcc
+tcaagcaccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaaggg
+catttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaagggat
+ggtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgct
+gattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgt
+gcgagctgaacgggcaatgcaggaagagttctacctggaactgaaagaaggcttactgga
+gccgctggcagtgacggaacggctggccattatctcggtggtaggtgatggtatgcgcac
+cttgcgtgggatctcggcgaaattctttgccgcactggcccgcgccaatatcaacattgt
+cgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgc
+gaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagt
+gtttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagca
+aagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggc
+tctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagc
+caaagagccgtttaatctcgggcgcttaattcgcctcgtgaaagaatatcatctgctgaa
+cccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcct
+gcgcgaaggtttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgatggatta
+ctaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaa
+cgttggggctggattaccggttattgagaacctgcaaaatctgctcaatgcaggtgatga
+attgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttaga
+cgaaggcatgagtttctccgaggcgaccacgctggcgcgggaaatgggttataccgaacc
+ggacccgcgagatgatctttctggtatggatgtggcgcgtaaactattgattctcgctcg
+tgaaacgggacgtgaactggagctggcggatattgaaattgaacctgtgctgcccgcaga
+gtttaacgccgagggtgatgttgccgcttttatggcgaatctgtcacaactcgacgatct
+ctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttggcaa
+tattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgct
+gttcaaagtgaaaaatggcgaaaacgccctggccttctatagccactattatcagccgct
+gccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgc
+tgatctgctacgtaccctctcatggaagttaggagtctgacatggttaaagtttatgccc
+cggcttccagtgccaatatgagcgtcgggtttgatgtgctcggggcggcggtgacacctg
+ttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctca
+acaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatc
+agtgctgggagcgtttttgccaggaactgggtaagcaaattccagtggcgatgaccctgg
+aaaagaatatgccgatcggttcgggcttaggctccagtgcctgttcggtggtcgcggcgc
+tgatggcgatgaatgaacactgcggcaagccgcttaatgacactcgtttgctggctttga
+tgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgtt
+ttctcggtggtatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccag
+ggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaag
+ccagggctattttaccggcgcagtatcgccgcca