--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/TestFiles/testC2S.fa	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,100 @@
+>chr1
+CAACATTAGCGCCATGCCCACTGTGGGGAATTTACCAGCAGCCCGCACAC
+TTAGCCGGCCTGCTGCAAAGCGGGATTTATTTAATTCATCCTCCAAGAGC
+CCAAACGAGCATCCTATGAGTTTCTCGGAAGTGGTAGCTGGAGCAGGTCC
+AGTTTCTATGGCACCCCCTAATCCGGCACCACTGACGAAAACCCCAGGAA
+AGCGGACAAACGACGATCTGGATTGCTCAAATTTTAAGACGCCCAATAAA
+AAATTATGCGCGACATCCAATTTTGTAACTCCCTGCATTTTTCCCCCGCT
+CATCACACCAGTTTTCAAAAGCAAGGCAGCTCAATCTGTTTATGAGGAAT
+CAAAAGCCAGAAACGGACCCACCCGCCAGCCGTTACCCTGTAGCATCAAT
+GTCTCTGCTTGCAGCGCAGCGGCGCCACCCGTTATCGCCCCCCTACCCCC
+TCAAAATACAGATGCACAGCTGCCTCCATGGAAAATCGTGCCCCAGAGCC
+GTAGAGCACCCCCTATACTCGTCAATGATGTGAAGGAAATTGTCCCTCTC
+CTGGAAAAGCTAAATTATACAGCAGGAGTATCCAGCTACACCACCAGAGC
+AATAGAAGGAAACGGGGTCAGGATCCAGGCCAAGGATATGACCGCCTACA
+ACAAAATTAAAGAAGTCCTGGTGGCCAACGGATTTCCTTTATTCACCAAC
+CAGCCCAAGTCTGAGAGAGGCTTCCGAGTCATCATCAGACACCTCCATCA
+TTCCACACCATGCTCGTGGATAGTCGAGGAGCTGCTGAAGCTCGGTCTCC
+AAGCGCGCTTCGTCAGAAACATGACGAATCCAGCTACAGGTGGCCCCATG
+CGAATGTTTGAAGTGGAGATCGTCATGGCCAAAGATGGCAGCCACGATAA
+AATTCTCTCACTCAAACAAATCGGTGGGCAAAAGGTGGATATTGAAAGGA
+AAAATAGGACACAGGAGCCGGTTCAGTGCTACAGATGCCAGGGCTTCAGA
+CATGCCAAAAATTCATGCATGAGGACGCCTAAATGCATGAAATGCGCTGG
+CGATCACCTGTCATCCTGCTGCACCAAGCCAAAATCCACCCCCGCCACCT
+GCATCAACTGCTCTGGGGAACATATCAGCGCTTATAAAGGATGCCCCGCC
+TACAAGGCCGAAAAACGAAAGCTGGCGGCTAACATTATTGACACAAACAA
+AATAAGGACAATCAAAGACGCAACTAATCACTTTTATAAACGACAAGGCC
+CCCCTCCACGTAATAATACCCCTCGACTACCGCACAGCTCAGCAATCCTG
+ACCAAGTCAATCGCTGAAGCTCGCCAGGAAGCCGCCAAAAAGTCGATGCT
+AAATCCTTATTGGCAAAGCTCGAACGACAGAAGGCCACGTTTCTCCTCCC
+ATGACACTGCCATTCAAAAACGGCTAAACAAATGGCGCCGAAACTCTAAT
+AAGATACCCAAAAAGGGTAGGATATCCTCAAAGGACAATGCAAAGCCAAG
+ACCGGCATCCAAGACAAGCAACCCAGCGCAAAGACATCTGGAAAAATACC
+AGGACATGCTCCGAAACGAAAGGAGTGAAGAAATTGACCATGAACCTGAA
+AAAGGTACTCCTAATCCCAGCCGAGTCGGCAACGACAGCCCTCCGACCAC
+CAGCAGAGCCGCCAGAGCTAACTTTAAGCCAAGAATTATCGATGAAGCTA
+CGCCATCGCCAAGAAACTCCAATCCTTACCTACAGAAGAGCTTCTCGGAC
+GACCCCACCATTAATCTAGCTAATAGAGTCGATAATTTAGAAAAGAAAAT
+TGACATTTTAATGGCTTTAATCATACAAGGAACCAATAACAATAATCTTG
+ACATTGATACATCAATCTAAATTTACATTACACTTATTTATATTTATACC
+TATTATAAATATATATATCCGACACAAAAGCGCACGTCTGCCCACCCTTA
+TAATGTTCTAATTATTATCACCTTCCTCGACGCAAAGCTTAAACCTCTGT
+TGAAAAACAAATCAATTAGATGGATGACATAAAAACGTAAATAAATAATC
+TTCTCACCTCAAGCATCCGGATAAAAAAGGCAATACGCACTCCAACTCCT
+GATGAAGCTATGTGAAGAAAACTACACCAGGATTCAAAAGTCGAATCGGA
+GGATGGACATGAGAAGAATCTGTGCGGCAGAAGCATGATGAATAGAGGCG
+ACTCGCTGCAGCAAAATATGCACTACGCCACTTACCTGAATCTTCTGCGG
+CGCAGTCTTTTTATGTACCATCATCTCCGCCGCAACCGCTTCACACAGCT
+CCACAACATAAGATGCGCCACCAAAGCTGCCTCCGTACTGAACTGGACAT
+CATGCGTTGCGCTGCAAATCCTATCCTATTGACGAGCGCCAACAGCGGGT
+CTGCGCTAAAAACCTAAAAACAAAACAAAACAAAACAATTAATCAACAAC
+AAATTGAACATAACAATCAAACAATAACAATCACTTACCTCCTTGACTGC
+ATCCAATCGCTGACCCAAATCCAACACAACCGACAACAGGAGACGGGCTT
+CGCAAATGCAAAACAAAATCGCCAACTTTTGCGATTATAAATACAAAAAA
+TTGACAATTTTCTGATGCCATCTCCATCCTTTGATCCCACTGCCCAAATA
+AGGATCATTAGCGCGGAGCTGAAGCCACATTAATAAGCTGTAAAATTGAT
+CCCCAAAATGTATATTTCTCCTCAATACCGTATCTTCAACGAACTTTCCG
+CCAACCTGCAATGAAAGGGAAATTAATAATAATGCTATACAGAATTAATC
+AGCGACACATAGAAAATAGCAAACCAGACAGGCAAAGTAGTAGATGCAAA
+CAGGCGACTCCATCCCGCCGACGACAAGCATTCAAATCCTTCATACTGAA
+ACAAGGAAGCACAAGCCAATACTGGGAATTATTTACTCAAACAAAATACT
+TATCTAATTACCAACTCGACGACTCCAAATACGCGGCACACCGGCTGCGA
+TAGCTCTTAAATAAAGGGCCTCCTAATTAACTACAAAACGTACCTGAAAA
+ATAAAACAATTAACGCAATCGTAAATAATTACAATTATAATACTCACCTC
+CAGATTAGCCTAATGTACCTGAAAAACAAAAACAAAAATTAATGCAATAA
+TTATAAAAACAAATAAATACAAACACAATACTTACCTCCAAATTACCTCC
+CAGCCAAAGCACCTGAAATACAAAAACAAAGAATTAATGCAATAAATAAA
+TCAAATAAATACAAATACAATACTCACCCCAAATAACCTCCCAGCTAATT
+TACCTGAAAAAACAAAAATTAATACAATATTAAAAACGAATAACAAATGT
+AATACTTACCAAATTTTAACTTTGTATTCATTTCCATGGCCCAAATCGTT
+GCGACGGTCCTCGGCAACAAATCATGTTCCGGCGGCTCCTAGCTGCCAAT
+CCCGACGCATTGGCCACAAGACGCGGCGCTCCTGGCAACTCTCGATGAAT
+AACCGAGCTCCAATTTCCACGACGACTCTTCTGCCAAACGAGTCAGATTA
+CACCAACATAATGCCAGCAGCTCCCAAACAATGCAATGACGGCTGCGCGG
+GATCCATCTTCAGATTTTCTTCTTCCTGACGACCGGCTAAGCTGCCCTGC
+AATTTAAGAAATTTTATTAAACAATTGCAAATATCTACCACTGAGGGTGG
+TAGAGACAACCACCAAATGACAGCGGCGCGGGATACACCCACCACGAATA
+GGCTTTCTGCAGCGCTGGCCGGACATGCATGTTGCGACGCGCATTCAGCG
+TCCACAACAAGCCCCAGCCAGAATACAACAAACACTCACCTGCAATGTTT
+CCTGAGGCTTCCAGCGACTCGGTGCTTCCGTCCTTCTGGCGGGGGTACCT
+GAAAAGAATTAATTCAAATTATGTTAGTCTTAAATTCCAATGTTTCTTGT
+TAAATAATTCAAATTATCAAATGTAAACATAACATACAATGTGATAATGT
+TACCAGTCCATGTTACTGCCAAAAACCTAAGTTTACAAAAAAATACTTAC
+CTCTTAATATTAATACTAAATCTATGTCCAATCCCCAAACTCACCCCACG
+TAATGTACACCTCAAAAATTCAAATAATTGTACCTACATATTGCATTCTA
+TGTAATCAAAGGCAAAATAAATTGTGGATGCGGAACAGAATTCATTCTGT
+CTCCGTACCTCCACCAGCAAAGTTAAAAATGAAATATCCCTCATCACCGC
+TGCAATCTACATACATGGATACAGCGCAAAAGACGGTCAACCACGTCGTC
+TCCGAGTCGTTCAGGACACCTTGCTGCTCTCAATAACCTCCAGCCTGACG
+AGCGCCAACAGCGAGTTGACGCTAAAACCTAAAAACAAACAACAACAAAT
+TAAATACAAACAAATAAAATAAAATCAAACAAAACACTTACTTCACTGAC
+AACAGCCAATTGCTGATCCACATTCAACGCAACAGACAACAGGAGACGGG
+CCCCGCAAACGCAAAACAAAATCGCCAATTTTTGCGATTTTAAATACAAA
+AAATCGACAATTTTACTAAGCCCTCTCCATCTCCTGATGCCACCGCCACA
+ATAAGGATCACTAGCGCGGCGCTGATGCCACATCAATAAACCGCAATATT
+TGTCCTCAAAACGTATACTTCTTCTCAGTATCGCAACTTCTACGAATTTC
+CCGCTAACCTACAATGAAAGGAAAATCAATAAGAATGTGATACAAAAAAT
+TAATCAAGGGCAAATAGAAAATAGCTTACCGGACAGGCATACTAGCAGAT
+GCTAATATGCAACTCCATCCTTCTGAGACAAATACGCAACTCCTTTTTTC
+CAAGATTGCAAATACTGAAACAAGGAAGCACAAGCCAATACTGGGAATTA
+TTTAATTAAACAAAATACTTATCTAATTGCCAATTCGACGACTCCAAATC