changeset 1:7334f6d0ac17

Uploaded emboss functional test input and output data files.
author devteam
date Wed, 21 Mar 2012 16:30:01 -0400
parents b94ca591877b
children a52e6cbbb469
files test-data/1.fasta test-data/2.fasta test-data/3.fasta test-data/emboss_antigenic_out.tabular test-data/emboss_backtranseq_out.fasta test-data/emboss_banana_out.txt test-data/emboss_biosed_out.fasta test-data/emboss_btwisted_out.btwisted test-data/emboss_cai_out.cai test-data/emboss_charge_out.charge test-data/emboss_chips_out.chips test-data/emboss_codcmp_out.codcmp test-data/emboss_coderet_out.coderet test-data/emboss_compseq_out.compseq test-data/emboss_cpgreport_out1.gff test-data/emboss_cpgreport_out2.cpgreport test-data/emboss_cusp_out.cusp test-data/emboss_cutseq_out.fasta test-data/emboss_dan_out.png test-data/emboss_degapseq_out.fasta test-data/emboss_descseq_out.fasta test-data/emboss_einverted_out.einverted test-data/emboss_epestfind_out.epestfind test-data/emboss_equicktandem_out.equicktandem test-data/emboss_est2genome_out.est2genome test-data/emboss_etandem_out.table test-data/emboss_extractseq_out.fasta test-data/emboss_freak_out.freak test-data/emboss_fuzznuc_out.tabular test-data/emboss_fuzzpro_out.tabular test-data/emboss_fuzztran_out.tabular test-data/emboss_garnier_out.tabular test-data/emboss_geecee_out.geecee test-data/emboss_getorf_out.fasta test-data/emboss_helixturnhelix_out.tabular test-data/emboss_hmoment_out.hmoment test-data/emboss_iep_out.iep test-data/emboss_isochore_out.isochore test-data/emboss_marscan_out.tabular test-data/emboss_maskfeat_out.fasta test-data/emboss_maskseq_out.fasta test-data/emboss_matcher_out.fasta test-data/emboss_msbar_out.fasta test-data/emboss_needle_out.score test-data/emboss_newcpgreport_out.newcpgreport test-data/emboss_newcpgseek_out.newcpgseek test-data/emboss_newseq_out.fasta test-data/emboss_noreturn_out.noreturn test-data/emboss_notseq_out.fasta test-data/emboss_nthseq_out.fasta test-data/emboss_palindrome_out.palindrome test-data/emboss_pasteseq_out.fasta test-data/emboss_patmatdb_out.tabular test-data/emboss_pepcoil_out.pepcoil test-data/emboss_pepstats_out.pepstats test-data/emboss_plotorf_out.png test-data/emboss_plotorf_out1.png test-data/emboss_polydot_out.png test-data/emboss_prettyseq_out.prettyseq test-data/emboss_primersearch.fasta test-data/emboss_primersearch_out.primersearch test-data/emboss_revseq_out.fasta test-data/emboss_seqmatchall_out.fasta test-data/emboss_seqret_out.fasta test-data/emboss_sigcleave_out.tabular test-data/emboss_sirna_out.fasta test-data/emboss_sixpack_out2.sixpack test-data/emboss_skipseq_out.fasta test-data/emboss_splitter_out.fasta test-data/emboss_supermatcher_out.fasta test-data/emboss_syco_out.syco test-data/emboss_tranalign_out.fasta test-data/emboss_transeq_out.fasta test-data/emboss_trimest_out.fasta test-data/emboss_trimseq_out.fasta test-data/emboss_union_out.fasta test-data/emboss_water_out.fasta test-data/emboss_water_out.score test-data/emboss_wobble_out.png test-data/emboss_wobble_out.wobble test-data/emboss_wordcount_out.wordcount
diffstat 81 files changed, 4862 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,2 @@
+>hg17
+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtatagactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-cagaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtcatgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt----------------aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatattgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaaactttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa--------------------------------------------------ctc-aaagaatgcacattctCTGGGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTTTAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTCAattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggactgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAAAGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGCTTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGATGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATCAATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatattacatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaattcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaactattcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctccctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccgtggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaaataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatcttcataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacagattgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcagaataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcggggtcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagtaggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaaggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgcaatggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggtggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactgttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagacccttatcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccctcaccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacagtactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtactctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaaatattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagcatgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgtagaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcaccaacgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-attgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcactgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctgggattacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttcaccatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcctcccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGGAGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg-------------------ggttcctagcccattgctattcctt----accagctgtggattctaaggaaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaacaaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATACAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACATCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGACCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGAGCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTCTCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGGAGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAGGGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAGGACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAcccccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC----------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTACCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCCGAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAGCAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGCCGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGGCATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTCCTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATCCCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAGCTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGATTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCAGGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATTGGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA---TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGACATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCCTGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAGTAGAGGTGGGGGGAAACAAGTGTCAGGAAGA--------------------------------------------CTCAAA---------ATCTTC--------------------------------------------------------------CAGAGAAATTGT-----GCAGGGTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATGAGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAACTTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTATAGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACACTCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACAGTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAGG----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAGAGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GTGCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGGTGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGATTGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAATGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGGCAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCCCAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCCTCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAATATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGACAGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGTCTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAGGAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGCACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCATCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCCTTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGCTTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTGACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTGTTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATTTCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGGG-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---GGGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCCAGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGATGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCACATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCATTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCAAAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTTACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagatatttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga----------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttctgagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaattgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaaggcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaaccccatctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagctacttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgagccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacacacacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-tatctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCTGTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTGGTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTGTGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTGAATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGAAAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCCTGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCTCACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTCTGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAATGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCCACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAGGAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGTAGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgtgtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCCTACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTCTACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttggcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagttcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTTTGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGTTGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAACTTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGAGTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCAAATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT-------CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTGGG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAAGAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCATCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTTGTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAGGGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAACTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGCAGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTATATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatcttttttggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtgatcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcccaagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggctcaagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacacccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTTCTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GCCAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AGGGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCTCCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC--------TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAATGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACAGCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACAGCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGACTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGGACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAGTTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TGCTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGATTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCCACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctctcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatctcctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gcattggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcagccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaaaactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATAGCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACCCAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaatgcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctgaggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatacaaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaaggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcctatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccagctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgagccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaagaaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggaggatgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaacactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaataaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGCACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAATCAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATCCCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTGGCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATTATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtggtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGAATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTTCTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTAATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtttggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtctctcacacacacccagcacaagtccaag-------------------------accagcatggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagttgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccatatctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacgacaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttagtcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatggccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaagatattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgtgtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GATTCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATAGGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAGCTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTGGTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATTTGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGGGGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTGGAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCACTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTAACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGGAAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAAATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGGA---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc--------------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctgagccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAACATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCCTACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAATATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATTGGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtctttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccatatttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgccttccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcccattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgttgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcagtaagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAGTGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATGGGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACACCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagatagatatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatgcagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AGCATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAGCTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCTAAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGATGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTGGTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCTGTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCACTGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctgaatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTCTGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG--------------------------------------------------------TTCTAATTCTAAACCACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggctgggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcattcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaataataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggctgagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgccaccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaataaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttaggaggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggcaagacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGATTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCGATTAGCTGAGC----------CACATGCAGGCACAG------------------------CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCCTCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCTTG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------CTCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tgtagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccctttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtcttttctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaattaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaagttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacacacta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCCCCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGATAGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaaaaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCCCACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGTCAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACTGGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTACGGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCGGCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGAGGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGTTCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAGGGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTGGCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAGGAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCGA--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGTCTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGACCTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTCCAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCTGGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCTGGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCAGGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGAAGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCCAGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGACTCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAAGATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGGCTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCCTCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCAGGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGGTTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTCCC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATGGATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCTCCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTTGAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCAGTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTGCAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTTTTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGGGAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAGTGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA------------TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTTCTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTCCGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGATCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCTGGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTCTTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTTTACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACTGCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGGTCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTTTTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagctcacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCAAACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCAAATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCAGGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggcatcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaatttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
+tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
+cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
+aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
+gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
+tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
+ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
+ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
+tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
+aacaattcta atggtcaaaa a
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,50 @@
+>HSFAU1
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggccccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU2
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU3
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU4
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
+>HSFAU5
+ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
+agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
+cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
+tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
+tgactaccctggaagtaggccgcatgctttttggaggtaaagttcatggttccctggccc
+gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
+agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
+cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
+tctaataaaaaagccacttagttcagtcaaaaaaaaaa
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_antigenic_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,23 @@
+SeqName	Start	End	Score	Strand	Max_score_pos
+Sequence	196	225	1.340	+	221
+Sequence	253	283	1.263	+	266
+Sequence	27	45	1.241	+	32
+Sequence	60	72	1.236	+	66
+Sequence	357	368	1.214	+	360
+Sequence	130	159	1.191	+	148
+Sequence	83	93	1.186	+	87
+Sequence	165	175	1.147	+	173
+Sequence	6	22	1.147	+	20
+Sequence	293	301	1.147	+	299
+Sequence	324	343	1.147	+	330
+Sequence	473	481	1.142	+	479
+Sequence	540	551	1.119	+	545
+Sequence	501	510	1.114	+	504
+Sequence	409	415	1.097	+	412
+Sequence	48	56	1.097	+	51
+Sequence	553	558	1.092	+	558
+Sequence	106	112	1.087	+	110
+Sequence	488	494	1.075	+	490
+Sequence	423	429	1.075	+	426
+Sequence	118	123	1.070	+	118
+Sequence	239	247	1.042	+	245
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_backtranseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,30 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC
+ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC
+TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC
+ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC
+GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC
+TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC
+TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC
+GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC
+GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC
+GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC
+GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC
+TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC
+GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC
+TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC
+ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC
+ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC
+ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC
+GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC
+TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC
+GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC
+GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC
+ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC
+TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC
+GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC
+ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC
+GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC
+ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC
+GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC
+GCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_banana_out.txt	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,562 @@
+Base   Bend      Curve
+g       0.0      0.0
+t      10.8      0.0
+t      18.5      0.0
+c      26.9      0.0
+g      22.1      0.0
+a      19.5      0.0
+t      20.7      0.0
+g      26.2      0.0
+c      25.2      0.0
+c      12.5      0.0
+t       6.8      0.0
+a       3.4      0.0
+a       0.0      0.0
+a       1.3      0.0
+a       5.9      0.0
+t      10.6      0.0
+a      14.9      0.0
+c      17.7      0.0
+c      17.3      0.0
+t      13.3      0.0
+t      10.2     23.2
+c      13.9     22.5
+t       8.8     21.7
+t       0.0     20.6
+t       5.7     19.2
+t      13.9     17.7
+g      17.3     16.5
+t      15.1     15.5
+c      16.1     14.7
+c      18.7     13.9
+c      12.5     13.2
+t       9.7     12.5
+a      14.5     11.8
+c      19.1     11.1
+a      19.1     10.6
+c      15.3     10.0
+a      12.2      9.2
+g      14.3      7.9
+a      17.7      6.4
+c      17.7      5.0
+c      19.5      3.5
+a      19.1      2.9
+c      15.3      3.9
+a      16.3      5.5
+g      15.5      6.8
+t       6.3      7.8
+t       0.0      8.5
+t       5.0      9.3
+t      11.0     10.0
+c      15.1     10.8
+c      12.5     11.6
+t       6.8     12.5
+a       4.5     13.4
+a      12.4     14.3
+t      19.7     15.1
+g      25.2     15.7
+g      28.5     16.2
+c      20.7     16.6
+t       8.8     17.0
+t       3.4     17.5
+t       9.3     18.1
+a      14.5     18.5
+c      19.1     18.6
+a      19.5     18.5
+c      16.5     18.3
+c      21.1     18.0
+g      22.3     17.4
+a      18.3     16.3
+c      13.2     15.1
+t       7.2     13.8
+a       9.0     12.6
+g      10.2     11.4
+a       5.0     10.9
+a       1.3     11.0
+a       2.4     11.4
+t       6.1     11.9
+t      10.2     12.3
+c      13.9     12.5
+t      13.9     12.4
+t      13.9     12.4
+g      19.1     12.6
+t      20.5     12.9
+g      19.7     13.2
+c      15.3     13.1
+a      13.9     12.7
+a      20.7     12.2
+g      22.1     11.8
+c      20.5     11.5
+a      20.1     11.3
+c      13.2     10.9
+t       6.8     10.2
+a       4.5      9.6
+a       2.4      9.9
+t       6.7     10.9
+t      14.3     12.1
+g      13.7     13.2
+a       5.0     13.8
+a       8.8     13.6
+a      20.7     12.9
+g      24.5     12.1
+c      19.9     11.3
+g      16.5     10.3
+g      14.9      9.0
+t      11.4      7.5
+t      14.3      6.2
+g      25.2      5.2
+g      32.5      4.4
+c      25.2      4.0
+c      12.5      3.8
+t       7.2      3.4
+a       9.0      2.8
+g      14.3      2.4
+a      18.3      2.5
+g      20.1      2.8
+t      19.1      3.1
+g      14.5      3.2
+t       9.3      3.1
+t       9.3      2.6
+a      14.9      2.5
+c      16.5      2.7
+c      15.3      2.7
+g      16.5      2.6
+g      14.9      2.8
+t       6.3      2.9
+t       5.7      2.8
+t      13.9      2.3
+g      14.5      1.6
+t      10.6      0.6
+a       9.2      0.7
+t       8.2      1.8
+a      16.1      2.7
+g      24.5      3.7
+c      19.1      4.6
+t      15.7      5.6
+g      17.7      6.4
+a      21.1      7.1
+g      24.5      7.7
+c      24.5      8.1
+g      24.5      8.2
+c      21.1      8.0
+g      17.7      7.8
+t      14.3      7.7
+c      14.3      7.7
+t      14.3      7.9
+c      13.9      8.4
+t      13.9      9.1
+t      15.3     10.2
+g      26.2     11.3
+c      26.2     12.2
+c      18.7     12.7
+c      15.7     12.9
+t      15.7     12.9
+g      17.5     12.9
+a      17.3     13.0
+t      17.5     13.2
+c      14.3     13.3
+a       5.7     13.3
+a       8.8     13.2
+a      17.3     13.0
+g      17.7     12.9
+g      14.9     12.7
+t      10.8     12.6
+t      13.7     12.6
+c      19.7     12.6
+a      12.4     12.7
+t       1.3     12.9
+t       0.0     13.1
+t       5.0     13.1
+t      10.2     12.9
+c      14.3     12.6
+t      14.3     12.3
+c       9.0     11.9
+t       9.7     11.6
+a      15.5     11.2
+c      17.9     10.6
+t       8.8      9.9
+t       5.7      9.0
+t      14.3      8.1
+g      15.1      7.4
+g      11.0      6.8
+a      13.3      6.3
+a      13.9      5.9
+g      14.3      5.6
+a      17.7      5.3
+c      17.7      5.1
+g      14.9      5.0
+t      11.4      5.1
+t      13.9      5.2
+g      19.1      5.2
+t      19.5      5.0
+g      15.1      4.9
+g      11.0      4.9
+a      13.3      4.9
+a      13.9      4.9
+g      10.2      5.1
+a       6.1      5.5
+a       5.9      6.3
+t      10.6      7.0
+a      14.5      7.8
+c      13.9      8.4
+a      11.4      8.6
+a      14.5      8.7
+c      13.9      8.8
+a      13.9      8.9
+a      17.9      9.0
+g      15.5      9.0
+t      12.0      8.8
+a      14.9      8.9
+c      22.3      9.1
+g      22.3      9.3
+a      18.3      9.6
+g      18.3      9.9
+t      14.3     10.1
+c      14.3     10.2
+t      14.3     10.5
+c      14.3     11.2
+t      15.1     12.3
+c      16.1     13.4
+c      19.7     14.2
+c      19.7     14.9
+c      19.7     15.1
+c      18.7     15.0
+c      15.7     14.8
+t      15.7     14.4
+g      17.7     14.1
+g      14.9     13.5
+t       6.3     12.9
+t       5.7     12.4
+t      15.3     11.9
+g      22.1     11.5
+c      19.1     11.1
+t      15.7     10.4
+g      17.5      9.4
+a      10.1      8.3
+t       4.5      7.2
+t       9.3      6.2
+a      15.5      5.2
+c      16.3      4.2
+t      15.7      3.2
+g      15.1      2.5
+g      14.9      2.3
+a      13.3      2.9
+t      10.6      3.7
+a      14.5      4.5
+c      15.3      5.3
+a      16.3      6.1
+g      15.5      7.0
+t      11.4      7.5
+t      13.9      7.7
+g      14.5      7.9
+t       9.3      8.3
+a       4.5      8.6
+a       5.9      9.1
+t      10.6      9.7
+a      14.9     10.4
+c      18.7     11.1
+c      18.7     11.7
+c      17.3     12.1
+t      13.3     12.6
+t      18.5     12.9
+c      25.7     12.9
+g      22.1     12.6
+c      15.3     12.2
+a      11.4     11.7
+a      14.5     11.0
+c      19.1     10.3
+a      19.5      9.7
+c      16.5      9.0
+c      19.9      8.1
+g      24.5      7.2
+c      21.1      6.4
+g      14.9      5.5
+t       9.3      4.5
+a       9.3      3.5
+a      15.5      2.5
+c      13.2      1.7
+t       8.2      1.0
+a      13.3      0.8
+t      14.1      1.6
+c       9.0      2.9
+t       8.2      4.5
+a       9.2      6.0
+t       9.2      7.4
+a      15.6      8.8
+t      19.7     10.3
+g      13.7     11.7
+a       6.1     12.9
+a       2.4     14.1
+t       4.5     15.4
+t       7.8     16.6
+a       5.9     17.4
+t       1.3     17.8
+t       0.0     18.0
+t       5.0     18.0
+t      11.0     18.0
+c      16.1     17.9
+c      18.7     17.9
+c      17.3     17.6
+t       8.8     17.4
+t       3.4     17.4
+t       7.8     17.4
+a       5.9     17.5
+t       4.5     17.6
+t       7.8     17.6
+a       9.2     17.8
+t       9.2     18.3
+a      15.6     18.7
+t      19.3     18.8
+g      14.5     18.5
+t       9.7     17.9
+a      13.2     17.3
+g      15.5     16.7
+t       9.7     16.4
+a      12.5     16.0
+g      17.7     15.7
+g      14.9     15.6
+t      10.8     15.7
+t      18.5     15.7
+c      22.3     15.8
+g      17.7     15.6
+t      14.3     15.3
+c      13.9     15.2
+t       8.8     15.3
+t       3.4     15.6
+t       6.4     15.9
+a       4.5     16.4
+a      10.1     17.0
+t      14.1     18.0
+c      13.9     18.9
+t      13.3     19.6
+t      11.0     20.1
+c      15.1     20.5
+c      17.3     20.8
+t       8.8     21.1
+t       3.4     21.3
+t       6.8     21.4
+a      16.1     20.9
+g      22.1     19.9
+c      15.3     18.9
+a      13.9     18.1
+a      17.9     17.4
+g      18.3     16.9
+t      14.3     16.5
+c      13.9     16.5
+t       8.8     16.6
+t       0.0     16.6
+t       3.4     16.6
+t       9.3     16.7
+a      15.5     16.6
+c      16.3     16.4
+t      15.3     16.1
+g      14.5     15.8
+t       6.3     15.5
+t       0.0     15.3
+t       5.0     15.1
+t      18.5     15.2
+c      26.9     15.3
+g      22.3     15.6
+a      17.7     16.2
+c      17.7     16.7
+c      17.7     16.9
+t      17.7     17.1
+c      14.3     17.0
+a       6.7     16.9
+a      12.4     16.5
+t      19.3     16.1
+g      14.5     16.1
+t      10.8     16.2
+t      13.7     16.1
+c      19.7     16.0
+a      21.7     15.7
+t      19.3     15.3
+g      14.5     14.7
+t      10.8     14.3
+t      10.2     14.0
+c      13.9     13.8
+t      11.7     13.5
+t       6.8     12.9
+a      12.5     12.3
+g      17.7     11.7
+g      14.9     11.2
+t      11.4     10.6
+t      13.9     10.3
+g      14.5     10.2
+t       6.3     10.2
+t       0.0     10.2
+t       5.7     10.4
+t      14.3     11.0
+g      15.1     11.5
+g      14.9     11.9
+a      13.3     12.0
+t       7.8     12.0
+a       4.5     12.0
+a       5.9     12.0
+t       9.2     12.1
+a      15.6     12.2
+t      20.7     11.8
+g      22.1     11.3
+c      19.9     10.5
+g      16.5      9.8
+g      17.7      8.9
+t      17.7      7.9
+c      15.7      6.9
+a      16.3      5.8
+g      15.5      5.0
+t       6.3      4.5
+t       3.4      4.5
+t       6.4      5.1
+a       4.5      6.2
+a      10.1      7.8
+t      14.1      9.7
+c      13.9     11.7
+t      13.3     13.4
+t      18.5     14.9
+c      22.3     15.9
+g      14.9     16.5
+t      11.4     16.9
+t      13.9     17.0
+g      14.5     16.8
+t       6.3     16.2
+t       5.0     15.3
+t      10.2     14.0
+c      13.9     12.6
+t      13.3     11.1
+t      10.2      9.7
+c      13.9      8.5
+t      11.7      7.2
+t       6.4      6.1
+a       3.4      5.5
+a       0.0      5.7
+a       1.3      6.7
+a       5.9      7.9
+t       9.2      9.1
+a       5.9      9.8
+t       1.3     10.1
+t       3.4     10.3
+t       7.8     10.7
+a       5.9     11.0
+t       6.1     11.3
+t      13.7     11.4
+c      19.7     11.2
+a      21.7     10.8
+t      19.7     10.4
+g      17.7     10.4
+g      14.9     10.8
+t       6.3     11.3
+t       3.4     11.8
+t       6.4     12.2
+a       4.5     12.6
+a       2.4     12.9
+t       1.3     13.2
+t       0.0     13.3
+t       0.0     13.2
+t       5.7     12.8
+t      14.3     12.3
+g      17.7     12.1
+g      14.9     12.0
+t       6.3     12.0
+t       5.7     12.1
+t      13.9     12.2
+g      14.5     12.3
+t      12.0     12.4
+a      15.5     12.5
+c      17.9     12.9
+t      13.9     13.2
+t      13.9     12.8
+g      14.5     11.9
+t      10.8     10.9
+t      13.7     10.1
+c      15.7      9.7
+a      15.7      9.7
+g      18.7      9.8
+g      19.7      9.7
+g      26.2      9.2
+g      32.5      8.8
+c      25.2      8.6
+c      15.7      8.5
+a      16.3      8.4
+g      15.5      8.4
+t      10.8      8.4
+t      13.7      8.6
+c      19.7      8.8
+a      12.4      8.7
+t       4.5      8.5
+t       7.8      8.1
+a       5.9      7.9
+t       1.3      7.8
+t       3.4      7.8
+t       9.3      7.9
+a      15.5      8.2
+c      18.3      8.5
+t      14.3      8.8
+c      12.2      9.1
+t      15.3      9.2
+g      14.5      9.0
+t       6.3      8.4
+t       5.7      7.5
+t      13.9      6.4
+g      14.5      5.5
+t      10.6      4.9
+a       9.2      4.5
+t      10.6      4.1
+a      14.5      3.8
+c      15.3      3.7
+a      19.1      3.8
+g      22.1      3.9
+c      16.7      4.2
+a      16.3      4.8
+g      15.5      5.6
+t      10.8      6.6
+t      10.2      7.6
+c      13.9      8.6
+t       8.8      9.7
+t       0.0     10.8
+t       3.4     11.8
+t       7.8     12.6
+a       5.9     12.8
+t       1.3     12.4
+t       0.0     11.8
+t       0.0     11.2
+t       3.4     10.6
+t       6.8      9.8
+a      13.2      9.0
+g      15.5      8.2
+t      10.6      7.8
+a      15.6      7.8
+t      19.7      8.2
+g      17.5      8.8
+a      10.1      9.2
+t       1.3      9.3
+t       0.0      9.0
+t       3.4      8.5
+t       6.4      7.9
+a       4.5      7.1
+a       2.4      6.1
+t       1.3      5.0
+t       3.4      3.8
+t       6.4      2.6
+a       3.4      2.4
+a       0.0     90.8
+a       6.3      0.0
+a      14.5      0.0
+c      13.9      0.0
+a       6.7      0.0
+a       2.4      0.0
+t       6.1      0.0
+t      10.2      0.0
+c       9.0      0.0
+t       6.8      0.0
+a       4.5      0.0
+a      12.4      0.0
+t      19.7      0.0
+g      17.7      0.0
+g      17.7      0.0
+t      17.7      0.0
+c      14.3      0.0
+a       5.7      0.0
+a       0.0      0.0
+a       0.0      0.0
+a       0.0      0.0
+a       0.0      0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_biosed_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GTTCGAGTCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAAGTGCTT
+TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC
+CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG
+AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG
+GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATAGTAATTATTTTCCCTT
+TATTATAGTTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC
+CTCAAGTTTCAGTTTCTTAGGTTGTTTTGGATAATAGTCGGTCAGTTTAATCTTCGTTGT
+TTCTTCTTAAAATATTTATTCAGTGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT
+TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTAGTATTTTAATTTAA
+AACAATTCTAAGTGTCAAAAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_btwisted_out.btwisted	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,7 @@
+# Output from BTWISTED
+# Twisting calculated from 1 to 561 of Sequence
+Total twist (degrees): 19085.5
+Total turns : 53.02
+Average bases per turn: 10.58
+Total stacking energy : -4107.68
+Average stacking energy per dinucleotide: -7.34
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_cai_out.cai	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,1 @@
+Sequence: Sequence CAI: 0.188
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_charge_out.charge	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,560 @@
+CHARGE of Sequence from 1 to 561: window 5
+
+Position	Residue	Charge
+1		G	0.000
+2		T	0.000
+3		T	0.000
+4		C	0.000
+5		G	0.000
+6		A	0.000
+7		T	0.000
+8		G	0.000
+9		C	0.000
+10		C	0.000
+11		T	0.000
+12		A	0.000
+13		A	0.000
+14		A	0.000
+15		A	0.000
+16		T	0.000
+17		A	0.000
+18		C	0.000
+19		C	0.000
+20		T	0.000
+21		T	0.000
+22		C	0.000
+23		T	0.000
+24		T	0.000
+25		T	0.000
+26		T	0.000
+27		G	0.000
+28		T	0.000
+29		C	0.000
+30		C	0.000
+31		C	0.000
+32		T	0.000
+33		A	0.000
+34		C	0.000
+35		A	0.000
+36		C	0.000
+37		A	0.000
+38		G	0.000
+39		A	0.000
+40		C	0.000
+41		C	0.000
+42		A	0.000
+43		C	0.000
+44		A	0.000
+45		G	0.000
+46		T	0.000
+47		T	0.000
+48		T	0.000
+49		T	0.000
+50		C	0.000
+51		C	0.000
+52		T	0.000
+53		A	0.000
+54		A	0.000
+55		T	0.000
+56		G	0.000
+57		G	0.000
+58		C	0.000
+59		T	0.000
+60		T	0.000
+61		T	0.000
+62		A	0.000
+63		C	0.000
+64		A	0.000
+65		C	0.000
+66		C	0.000
+67		G	0.000
+68		A	0.000
+69		C	0.000
+70		T	0.000
+71		A	0.000
+72		G	0.000
+73		A	0.000
+74		A	0.000
+75		A	0.000
+76		T	0.000
+77		T	0.000
+78		C	0.000
+79		T	0.000
+80		T	0.000
+81		G	0.000
+82		T	0.000
+83		G	0.000
+84		C	0.000
+85		A	0.000
+86		A	0.000
+87		G	0.000
+88		C	0.000
+89		A	0.000
+90		C	0.000
+91		T	0.000
+92		A	0.000
+93		A	0.000
+94		T	0.000
+95		T	0.000
+96		G	0.000
+97		A	0.000
+98		A	0.000
+99		A	0.000
+100		G	0.000
+101		C	0.000
+102		G	0.000
+103		G	0.000
+104		T	0.000
+105		T	0.000
+106		G	0.000
+107		G	0.000
+108		C	0.000
+109		C	0.000
+110		T	0.000
+111		A	0.000
+112		G	0.000
+113		A	0.000
+114		G	0.000
+115		T	0.000
+116		G	0.000
+117		T	0.000
+118		T	0.000
+119		A	0.000
+120		C	0.000
+121		C	0.000
+122		G	0.000
+123		G	0.000
+124		T	0.000
+125		T	0.000
+126		T	0.000
+127		G	0.000
+128		T	0.000
+129		A	0.000
+130		T	0.000
+131		A	0.000
+132		G	0.000
+133		C	0.000
+134		T	0.000
+135		G	0.000
+136		A	0.000
+137		G	0.000
+138		C	0.000
+139		G	0.000
+140		C	0.000
+141		G	0.000
+142		T	0.000
+143		C	0.000
+144		T	0.000
+145		C	0.000
+146		T	0.000
+147		T	0.000
+148		G	0.000
+149		C	0.000
+150		C	0.000
+151		C	0.000
+152		T	0.000
+153		G	0.000
+154		A	0.000
+155		T	0.000
+156		C	0.000
+157		A	0.000
+158		A	0.000
+159		A	0.000
+160		G	0.000
+161		G	0.000
+162		T	0.000
+163		T	0.000
+164		C	0.000
+165		A	0.000
+166		T	0.000
+167		T	0.000
+168		T	0.000
+169		T	0.000
+170		C	0.000
+171		T	0.000
+172		C	0.000
+173		T	0.000
+174		A	0.000
+175		C	0.000
+176		T	0.000
+177		T	0.000
+178		T	0.000
+179		G	0.000
+180		G	0.000
+181		A	0.000
+182		A	0.000
+183		G	0.000
+184		A	0.000
+185		C	0.000
+186		G	0.000
+187		T	0.000
+188		T	0.000
+189		G	0.000
+190		T	0.000
+191		G	0.000
+192		G	0.000
+193		A	0.000
+194		A	0.000
+195		G	0.000
+196		A	0.000
+197		A	0.000
+198		T	0.000
+199		A	0.000
+200		C	0.000
+201		A	0.000
+202		A	0.000
+203		C	0.000
+204		A	0.000
+205		A	0.000
+206		G	0.000
+207		T	0.000
+208		A	0.000
+209		C	0.000
+210		G	0.000
+211		A	0.000
+212		G	0.000
+213		T	0.000
+214		C	0.000
+215		T	0.000
+216		C	0.000
+217		T	0.000
+218		C	0.000
+219		C	0.000
+220		C	0.000
+221		C	0.000
+222		C	0.000
+223		C	0.000
+224		T	0.000
+225		G	0.000
+226		G	0.000
+227		T	0.000
+228		T	0.000
+229		T	0.000
+230		G	0.000
+231		C	0.000
+232		T	0.000
+233		G	0.000
+234		A	0.000
+235		T	0.000
+236		T	0.000
+237		A	0.000
+238		C	0.000
+239		T	0.000
+240		G	0.000
+241		G	0.000
+242		A	0.000
+243		T	0.000
+244		A	0.000
+245		C	0.000
+246		A	0.000
+247		G	0.000
+248		T	0.000
+249		T	0.000
+250		G	0.000
+251		T	0.000
+252		A	0.000
+253		A	0.000
+254		T	0.000
+255		A	0.000
+256		C	0.000
+257		C	0.000
+258		C	0.000
+259		T	0.000
+260		T	0.000
+261		C	0.000
+262		G	0.000
+263		C	0.000
+264		A	0.000
+265		A	0.000
+266		C	0.000
+267		A	0.000
+268		C	0.000
+269		C	0.000
+270		G	0.000
+271		C	0.000
+272		G	0.000
+273		T	0.000
+274		A	0.000
+275		A	0.000
+276		C	0.000
+277		T	0.000
+278		A	0.000
+279		T	0.000
+280		C	0.000
+281		T	0.000
+282		A	0.000
+283		T	0.000
+284		A	0.000
+285		T	0.000
+286		G	0.000
+287		A	0.000
+288		A	0.000
+289		T	0.000
+290		T	0.000
+291		A	0.000
+292		T	0.000
+293		T	0.000
+294		T	0.000
+295		T	0.000
+296		C	0.000
+297		C	0.000
+298		C	0.000
+299		T	0.000
+300		T	0.000
+301		T	0.000
+302		A	0.000
+303		T	0.000
+304		T	0.000
+305		A	0.000
+306		T	0.000
+307		A	0.000
+308		T	0.000
+309		G	0.000
+310		T	0.000
+311		A	0.000
+312		G	0.000
+313		T	0.000
+314		A	0.000
+315		G	0.000
+316		G	0.000
+317		T	0.000
+318		T	0.000
+319		C	0.000
+320		G	0.000
+321		T	0.000
+322		C	0.000
+323		T	0.000
+324		T	0.000
+325		T	0.000
+326		A	0.000
+327		A	0.000
+328		T	0.000
+329		C	0.000
+330		T	0.000
+331		T	0.000
+332		C	0.000
+333		C	0.000
+334		T	0.000
+335		T	0.000
+336		T	0.000
+337		A	0.000
+338		G	0.000
+339		C	0.000
+340		A	0.000
+341		A	0.000
+342		G	0.000
+343		T	0.000
+344		C	0.000
+345		T	0.000
+346		T	0.000
+347		T	0.000
+348		T	0.000
+349		A	0.000
+350		C	0.000
+351		T	0.000
+352		G	0.000
+353		T	0.000
+354		T	0.000
+355		T	0.000
+356		T	0.000
+357		C	0.000
+358		G	0.000
+359		A	0.000
+360		C	0.000
+361		C	0.000
+362		T	0.000
+363		C	0.000
+364		A	0.000
+365		A	0.000
+366		T	0.000
+367		G	0.000
+368		T	0.000
+369		T	0.000
+370		C	0.000
+371		A	0.000
+372		T	0.000
+373		G	0.000
+374		T	0.000
+375		T	0.000
+376		C	0.000
+377		T	0.000
+378		T	0.000
+379		A	0.000
+380		G	0.000
+381		G	0.000
+382		T	0.000
+383		T	0.000
+384		G	0.000
+385		T	0.000
+386		T	0.000
+387		T	0.000
+388		T	0.000
+389		G	0.000
+390		G	0.000
+391		A	0.000
+392		T	0.000
+393		A	0.000
+394		A	0.000
+395		T	0.000
+396		A	0.000
+397		T	0.000
+398		G	0.000
+399		C	0.000
+400		G	0.000
+401		G	0.000
+402		T	0.000
+403		C	0.000
+404		A	0.000
+405		G	0.000
+406		T	0.000
+407		T	0.000
+408		T	0.000
+409		A	0.000
+410		A	0.000
+411		T	0.000
+412		C	0.000
+413		T	0.000
+414		T	0.000
+415		C	0.000
+416		G	0.000
+417		T	0.000
+418		T	0.000
+419		G	0.000
+420		T	0.000
+421		T	0.000
+422		T	0.000
+423		C	0.000
+424		T	0.000
+425		T	0.000
+426		C	0.000
+427		T	0.000
+428		T	0.000
+429		A	0.000
+430		A	0.000
+431		A	0.000
+432		A	0.000
+433		T	0.000
+434		A	0.000
+435		T	0.000
+436		T	0.000
+437		T	0.000
+438		A	0.000
+439		T	0.000
+440		T	0.000
+441		C	0.000
+442		A	0.000
+443		T	0.000
+444		G	0.000
+445		G	0.000
+446		T	0.000
+447		T	0.000
+448		T	0.000
+449		A	0.000
+450		A	0.000
+451		T	0.000
+452		T	0.000
+453		T	0.000
+454		T	0.000
+455		T	0.000
+456		G	0.000
+457		G	0.000
+458		T	0.000
+459		T	0.000
+460		T	0.000
+461		G	0.000
+462		T	0.000
+463		A	0.000
+464		C	0.000
+465		T	0.000
+466		T	0.000
+467		G	0.000
+468		T	0.000
+469		T	0.000
+470		C	0.000
+471		A	0.000
+472		G	0.000
+473		G	0.000
+474		G	0.000
+475		G	0.000
+476		C	0.000
+477		C	0.000
+478		A	0.000
+479		G	0.000
+480		T	0.000
+481		T	0.000
+482		C	0.000
+483		A	0.000
+484		T	0.000
+485		T	0.000
+486		A	0.000
+487		T	0.000
+488		T	0.000
+489		T	0.000
+490		A	0.000
+491		C	0.000
+492		T	0.000
+493		C	0.000
+494		T	0.000
+495		G	0.000
+496		T	0.000
+497		T	0.000
+498		T	0.000
+499		G	0.000
+500		T	0.000
+501		A	0.000
+502		T	0.000
+503		A	0.000
+504		C	0.000
+505		A	0.000
+506		G	0.000
+507		C	0.000
+508		A	0.000
+509		G	0.000
+510		T	0.000
+511		T	0.000
+512		C	0.000
+513		T	0.000
+514		T	0.000
+515		T	0.000
+516		T	0.000
+517		A	0.000
+518		T	0.000
+519		T	0.000
+520		T	0.000
+521		T	0.000
+522		T	0.000
+523		A	0.000
+524		G	0.000
+525		T	0.000
+526		A	0.000
+527		T	0.000
+528		G	0.000
+529		A	0.000
+530		T	0.000
+531		T	0.000
+532		T	0.000
+533		T	0.000
+534		A	0.000
+535		A	0.000
+536		T	0.000
+537		T	0.000
+538		T	0.000
+539		A	0.000
+540		A	0.000
+541		A	0.000
+542		A	0.000
+543		C	0.000
+544		A	0.000
+545		A	0.000
+546		T	0.000
+547		T	0.000
+548		C	0.000
+549		T	0.000
+550		A	0.000
+551		A	0.000
+552		T	0.000
+553		G	0.000
+554		G	0.000
+555		T	0.000
+556		C	0.000
+557		A	0.000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_chips_out.chips	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,3 @@
+# CHIPS codon usage statistics
+
+Nc = 61.000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_codcmp_out.codcmp	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,9 @@
+# CODCMP codon usage table comparison
+# Ehum.cut vs Eacc.cut
+
+Sum Squared Difference = 3.044
+Mean Squared Difference = 0.048
+Root Mean Squared Difference = 0.218
+Sum Difference         = 11.470
+Mean Difference         = 0.179
+Codons not appearing   = 0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_coderet_out.coderet	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,3 @@
+   CDS  mRNA non-c Trans Total Sequence
+ ===== ===== ===== ===== ===== ========
+     0     0     0     0     0 Sequence
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_compseq_out.compseq	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,34 @@
+#
+# Output from 'compseq'
+#
+# The Expected frequencies are calculated on the (false) assumption that every
+# word has equal frequency.
+#
+# The input sequences are:
+#	Sequence
+
+
+Word size	2
+Total count	560
+
+#
+# Word	Obs Count	Obs Frequency	Exp Frequency	Obs/Exp Frequency
+#
+AA	40		0.0714286	0.0625000	1.1428571
+AC	27		0.0482143	0.0625000	0.7714286
+AG	26		0.0464286	0.0625000	0.7428571
+AT	41		0.0732143	0.0625000	1.1714286
+CA	26		0.0464286	0.0625000	0.7428571
+CC	24		0.0428571	0.0625000	0.6857143
+CG	15		0.0267857	0.0625000	0.4285714
+CT	41		0.0732143	0.0625000	1.1714286
+GA	19		0.0339286	0.0625000	0.5428571
+GC	17		0.0303571	0.0625000	0.4857143
+GG	19		0.0339286	0.0625000	0.5428571
+GT	43		0.0767857	0.0625000	1.2285714
+TA	50		0.0892857	0.0625000	1.4285714
+TC	38		0.0678571	0.0625000	1.0857143
+TG	37		0.0660714	0.0625000	1.0571429
+TT	97		0.1732143	0.0625000	2.7714286
+
+Other	0		0.0000000	0.0000000	10000000000.0000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_cpgreport_out1.gff	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,13 @@
+##gff-version 2.0
+##date 2007-10-15
+##Type DNA Sequence
+Sequence	cpgreport	misc_feature	4	5	17.000	+	.	Sequence "Sequence.1"
+Sequence	cpgreport	misc_feature	66	67	17.000	+	.	Sequence "Sequence.2"
+Sequence	cpgreport	misc_feature	101	102	17.000	+	.	Sequence "Sequence.3"
+Sequence	cpgreport	misc_feature	121	141	34.000	+	.	Sequence "Sequence.4"
+Sequence	cpgreport	misc_feature	185	186	17.000	+	.	Sequence "Sequence.5"
+Sequence	cpgreport	misc_feature	209	210	17.000	+	.	Sequence "Sequence.6"
+Sequence	cpgreport	misc_feature	261	272	43.000	+	.	Sequence "Sequence.7"
+Sequence	cpgreport	misc_feature	319	320	17.000	+	.	Sequence "Sequence.8"
+Sequence	cpgreport	misc_feature	357	358	17.000	+	.	Sequence "Sequence.9"
+Sequence	cpgreport	misc_feature	399	416	19.000	+	.	Sequence "Sequence.10"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_cpgreport_out2.cpgreport	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,15 @@
+
+
+CPGREPORT of Sequence from 1 to 561
+
+Sequence              Begin    End Score        CpG   %CG  CG/GC
+Sequence                  4      5    17          1 100.0    -
+Sequence                 66     67    17          1 100.0    -
+Sequence                101    102    17          1 100.0    -
+Sequence                121    141    34          3  57.1   1.00
+Sequence                185    186    17          1 100.0    -
+Sequence                209    210    17          1 100.0    -
+Sequence                261    272    43          3  75.0   1.00
+Sequence                319    320    17          1 100.0    -
+Sequence                357    358    17          1 100.0    -
+Sequence                399    416    19          2  44.4    -
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_cusp_out.cusp	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,72 @@
+#CdsCount: 10
+
+#Coding GC 36.36%
+#1st letter GC 34.22%
+#2nd letter GC 35.29%
+#3rd letter GC 39.57%
+
+#Codon AA Fraction Frequency Number
+GCA    A     0.200     5.348      1
+GCC    A     0.400    10.695      2
+GCG    A     0.400    10.695      2
+GCT    A     0.000     0.000      0
+TGC    C     0.500    21.390      4
+TGT    C     0.500    21.390      4
+GAC    D     0.667    10.695      2
+GAT    D     0.333     5.348      1
+GAA    E     0.500     5.348      1
+GAG    E     0.500     5.348      1
+TTC    F     0.316    32.086      6
+TTT    F     0.684    69.519     13
+GGA    G     0.000     0.000      0
+GGC    G     0.200     5.348      1
+GGG    G     0.200     5.348      1
+GGT    G     0.600    16.043      3
+CAC    H     0.667    10.695      2
+CAT    H     0.333     5.348      1
+ATA    I     0.429    16.043      3
+ATC    I     0.143     5.348      1
+ATT    I     0.429    16.043      3
+AAA    K     0.600    32.086      6
+AAG    K     0.400    21.390      4
+CTA    L     0.152    26.738      5
+CTC    L     0.061    10.695      2
+CTG    L     0.152    26.738      5
+CTT    L     0.273    48.128      9
+TTA    L     0.182    32.086      6
+TTG    L     0.182    32.086      6
+ATG    M     1.000    16.043      3
+AAC    N     0.286    10.695      2
+AAT    N     0.714    26.738      5
+CCA    P     0.250     5.348      1
+CCC    P     0.500    10.695      2
+CCG    P     0.250     5.348      1
+CCT    P     0.000     0.000      0
+CAA    Q     0.333     5.348      1
+CAG    Q     0.667    10.695      2
+AGA    R     0.143     5.348      1
+AGG    R     0.143     5.348      1
+CGA    R     0.143     5.348      1
+CGC    R     0.000     0.000      0
+CGG    R     0.143     5.348      1
+CGT    R     0.429    16.043      3
+AGC    S     0.136    16.043      3
+AGT    S     0.227    26.738      5
+TCA    S     0.136    16.043      3
+TCC    S     0.227    26.738      5
+TCG    S     0.000     0.000      0
+TCT    S     0.273    32.086      6
+ACA    T     0.400    21.390      4
+ACC    T     0.100     5.348      1
+ACG    T     0.200    10.695      2
+ACT    T     0.300    16.043      3
+GTA    V     0.231    16.043      3
+GTC    V     0.000     0.000      0
+GTG    V     0.000     0.000      0
+GTT    V     0.769    53.476     10
+TGG    W     1.000    21.390      4
+TAC    Y     0.444    21.390      4
+TAT    Y     0.556    26.738      5
+TAA    *     0.500    26.738      5
+TAG    *     0.400    21.390      4
+TGA    *     0.100     5.348      1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_cutseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggcttt
+acaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttacc
+ggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgga
+agacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactgg
+atacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttcccttt
+attatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgacc
+tcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgtt
+tcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagtt
+cattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaaa
+acaattctaatggtcaaaaa
Binary file test-data/emboss_dan_out.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_degapseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_descseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequencetest 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;test
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_einverted_out.einverted	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,20 @@
+
+hg17: Score 97: 63/77 ( 81%) matches, 3 gaps
+    2684 gtggcaggctcggttcaccaacgtcatttgcagttccccgctttatgttatggg-t--tttgttttgttttgtttttttt 2760    
+         |||| ||||  | ||||||    || |||| ||||||||||||||  | ||||| |  |||||||||||||||||| |||
+    3298 caccatccgtacaaagtggacatagcaaacatcaaggggcgaaatgtactacccaaccaaacaaaacaaaacaaaacaaa 3219    
+
+hg17: Score 94: 34/36 ( 94%) matches, 0 gaps
+    7058 gacacacacacacacacacacacacacacacacaca 7093    
+         |||||||| ||||||||||| |||||||||||||||
+    7888 ctgtgtgtatgtgtgtgtgtctgtgtgtgtgtgtgt 7853    
+
+hg17: Score 139: 213/305 ( 69%) matches, 11 gaps
+    8604 ggtggctcatgcctgtaatcccagcattttgggaggccgaggcgggtggatcac--gaggtcaggagtttgagaccagcctggccaagatggtgaagcctcgtctctactaaaaatacaaa-aattagccaggt-gcggtg-gtgggcgcctgtatttccagctacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggttgcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtcaaaaaaaaaataaaaaaataaaaaaataaaaaaa 8914    
+         ||||||||| |||| |||||||||   ||||||||||| |||| || ||||| |  |||  ||||||||  |||||||||||| | | |  |  |  || | ||||||  ||||||| ||| ||  |   |  | || | | ||||  ||      ||   | | |||  |   ||  ||||||  |||  ||||  | || ||| ||| ||| |  |||| |||||||||    | ||||  || ||||||| |||||| |  ||| |||||||| || ||     ||||| ||||    ||||| ||||  |||
+    9563 ccaccgagt-cggatattagggtcccgaaaccctccggttccgtcctcctagcgaactcgggtcctcaagttctggtcggacccgctgtgtcgttctggggtagagattttttttatttttatttttatttttatcgactcacaccaccgtttgcgaa-cacca-ggg-tcgatgaaccctccggttccaccctccaaacggactcgggtcctacagctccgacgtcactccatactagtg-tgtcacgtgaggtcggacacactgtgtcgttctggggtag-agaatttttgttttcggttttttctattacttt 9254    
+
+hg17: Score 202: 70/72 ( 97%) matches, 0 gaps
+   18075 tgcattttattctggatggatttgaagcaaagcaccagcttctccaggctctttggggtcagccagggccag 18146   
+         ||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
+   18677 acgcaaaataagacctacctaaacttcgtttcgtagtcgaagaggtccgagaaaccccagtcggtcccggtc 18606   
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_epestfind_out.epestfind	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,41 @@
+PEST-find: Finds PEST motifs as potential proteolytic cleavage sites.
+
+    No PEST motif was identified in Sequence from 1 to 561.
+
+
+       ---------+---------+---------+---------+---------+---------+
+
+     1 GTTCGATGCCTAAAATACCTTCTTTTGTCCCTACACAGACCACAGTTTTCCTAATGGCTT 60
+                                                                   
+
+    61 TACACCGACTAGAAATTCTTGTGCAAGCACTAATTGAAAGCGGTTGGCCTAGAGTGTTAC 120
+                                                                   
+
+   121 CGGTTTGTATAGCTGAGCGCGTCTCTTGCCCTGATCAAAGGTTCATTTTCTCTACTTTGG 180
+                                                                   
+
+   181 AAGACGTTGTGGAAGAATACAACAAGTACGAGTCTCTCCCCCCTGGTTTGCTGATTACTG 240
+                                                                   
+
+   241 GATACAGTTGTAATACCCTTCGCAACACCGCGTAACTATCTATATGAATTATTTTCCCTT 300
+                                                                   
+
+   301 TATTATATGTAGTAGGTTCGTCTTTAATCTTCCTTTAGCAAGTCTTTTACTGTTTTCGAC 360
+                                                                   
+
+   361 CTCAATGTTCATGTTCTTAGGTTGTTTTGGATAATATGCGGTCAGTTTAATCTTCGTTGT 420
+                                                                   
+
+   421 TTCTTCTTAAAATATTTATTCATGGTTTAATTTTTGGTTTGTACTTGTTCAGGGGCCAGT 480
+                                                                   
+
+   481 TCATTATTTACTCTGTTTGTATACAGCAGTTCTTTTATTTTTAGTATGATTTTAATTTAA 540
+                                                                   
+
+   541 AACAATTCTAATGGTCAAAAA 561
+                            
+
+       Symbols   PEST motifs
+       +++++++   potential
+       OOOOOOO   poor     
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_equicktandem_out.equicktandem	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,16 @@
+    22       8881       8915  1  35
+    33       7059       7093  2  17
+    29       7847       7891  2  22
+    27       3213       3248  5   7
+    20       9430       9457  6   4
+    39      19631      19709 36   2
+    39      19851      19927 36   2
+    37      20067      20141 36   2
+    21      19550      19630 60   1
+    21      19770      19850 60   1
+    79      19928      20066 60   2
+    24       8595       8793 133   1
+    26       2844       3045 134   1
+    35      10945      11179 136   1
+    22      15264      15435 138   1
+    29      11181      11429 168   1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_est2genome_out.est2genome	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,1 @@
+Note Best alignment is between reversed est and forward genome, and splice sites imply forward gene
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_etandem_out.table	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,2 @@
+    24       7847       7886 10   4  92.5 tgtgtgtgtg
+    22       7059       7098 10   4  90.0 acacacacac
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_extractseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_freak_out.freak	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,534 @@
+FREAK of Sequence from 1 to 561 Window 30 Step 1
+
+1          0.400000
+2          0.400000
+3          0.400000
+4          0.400000
+5          0.400000
+6          0.366667
+7          0.400000
+8          0.400000
+9          0.400000
+10         0.366667
+11         0.366667
+12         0.400000
+13         0.400000
+14         0.433333
+15         0.433333
+16         0.466667
+17         0.466667
+18         0.466667
+19         0.433333
+20         0.400000
+21         0.433333
+22         0.466667
+23         0.433333
+24         0.433333
+25         0.433333
+26         0.433333
+27         0.466667
+28         0.466667
+29         0.500000
+30         0.466667
+31         0.433333
+32         0.400000
+33         0.400000
+34         0.433333
+35         0.400000
+36         0.433333
+37         0.433333
+38         0.466667
+39         0.433333
+40         0.466667
+41         0.433333
+42         0.400000
+43         0.433333
+44         0.400000
+45         0.400000
+46         0.366667
+47         0.366667
+48         0.366667
+49         0.400000
+50         0.400000
+51         0.366667
+52         0.366667
+53         0.366667
+54         0.400000
+55         0.433333
+56         0.433333
+57         0.400000
+58         0.400000
+59         0.400000
+60         0.400000
+61         0.433333
+62         0.433333
+63         0.433333
+64         0.400000
+65         0.400000
+66         0.366667
+67         0.366667
+68         0.333333
+69         0.333333
+70         0.300000
+71         0.333333
+72         0.366667
+73         0.366667
+74         0.400000
+75         0.400000
+76         0.400000
+77         0.433333
+78         0.466667
+79         0.466667
+80         0.500000
+81         0.500000
+82         0.466667
+83         0.500000
+84         0.466667
+85         0.466667
+86         0.466667
+87         0.500000
+88         0.466667
+89         0.433333
+90         0.433333
+91         0.433333
+92         0.466667
+93         0.500000
+94         0.533333
+95         0.533333
+96         0.533333
+97         0.500000
+98         0.533333
+99         0.533333
+100        0.533333
+101        0.500000
+102        0.466667
+103        0.466667
+104        0.466667
+105        0.466667
+106        0.500000
+107        0.466667
+108        0.466667
+109        0.466667
+110        0.466667
+111        0.500000
+112        0.533333
+113        0.500000
+114        0.533333
+115        0.500000
+116        0.533333
+117        0.500000
+118        0.500000
+119        0.533333
+120        0.566667
+121        0.566667
+122        0.566667
+123        0.533333
+124        0.533333
+125        0.533333
+126        0.533333
+127        0.566667
+128        0.533333
+129        0.533333
+130        0.533333
+131        0.566667
+132        0.600000
+133        0.566667
+134        0.533333
+135        0.566667
+136        0.533333
+137        0.533333
+138        0.500000
+139        0.466667
+140        0.433333
+141        0.433333
+142        0.400000
+143        0.433333
+144        0.400000
+145        0.400000
+146        0.400000
+147        0.400000
+148        0.400000
+149        0.366667
+150        0.366667
+151        0.366667
+152        0.333333
+153        0.333333
+154        0.333333
+155        0.333333
+156        0.366667
+157        0.366667
+158        0.366667
+159        0.366667
+160        0.400000
+161        0.366667
+162        0.366667
+163        0.400000
+164        0.400000
+165        0.366667
+166        0.400000
+167        0.400000
+168        0.400000
+169        0.400000
+170        0.400000
+171        0.400000
+172        0.400000
+173        0.366667
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_fuzznuc_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,41 @@
+SeqName	Start	End	Score	Strand	Pattern_name	Mismatch
+Sequence	12	13	2	+	pattern1	.
+Sequence	13	14	2	+	pattern1	.
+Sequence	14	15	2	+	pattern1	.
+Sequence	53	54	2	+	pattern1	.
+Sequence	73	74	2	+	pattern1	.
+Sequence	74	75	2	+	pattern1	.
+Sequence	85	86	2	+	pattern1	.
+Sequence	92	93	2	+	pattern1	.
+Sequence	97	98	2	+	pattern1	.
+Sequence	98	99	2	+	pattern1	.
+Sequence	157	158	2	+	pattern1	.
+Sequence	158	159	2	+	pattern1	.
+Sequence	181	182	2	+	pattern1	.
+Sequence	193	194	2	+	pattern1	.
+Sequence	196	197	2	+	pattern1	.
+Sequence	201	202	2	+	pattern1	.
+Sequence	204	205	2	+	pattern1	.
+Sequence	252	253	2	+	pattern1	.
+Sequence	264	265	2	+	pattern1	.
+Sequence	274	275	2	+	pattern1	.
+Sequence	287	288	2	+	pattern1	.
+Sequence	326	327	2	+	pattern1	.
+Sequence	340	341	2	+	pattern1	.
+Sequence	364	365	2	+	pattern1	.
+Sequence	393	394	2	+	pattern1	.
+Sequence	409	410	2	+	pattern1	.
+Sequence	429	430	2	+	pattern1	.
+Sequence	430	431	2	+	pattern1	.
+Sequence	431	432	2	+	pattern1	.
+Sequence	449	450	2	+	pattern1	.
+Sequence	534	535	2	+	pattern1	.
+Sequence	539	540	2	+	pattern1	.
+Sequence	540	541	2	+	pattern1	.
+Sequence	541	542	2	+	pattern1	.
+Sequence	544	545	2	+	pattern1	.
+Sequence	550	551	2	+	pattern1	.
+Sequence	557	558	2	+	pattern1	.
+Sequence	558	559	2	+	pattern1	.
+Sequence	559	560	2	+	pattern1	.
+Sequence	560	561	2	+	pattern1	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_fuzzpro_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,41 @@
+SeqName	Start	End	Score	Strand	Pattern_name	Mismatch
+Sequence	12	13	2	+	pattern1	.
+Sequence	13	14	2	+	pattern1	.
+Sequence	14	15	2	+	pattern1	.
+Sequence	53	54	2	+	pattern1	.
+Sequence	73	74	2	+	pattern1	.
+Sequence	74	75	2	+	pattern1	.
+Sequence	85	86	2	+	pattern1	.
+Sequence	92	93	2	+	pattern1	.
+Sequence	97	98	2	+	pattern1	.
+Sequence	98	99	2	+	pattern1	.
+Sequence	157	158	2	+	pattern1	.
+Sequence	158	159	2	+	pattern1	.
+Sequence	181	182	2	+	pattern1	.
+Sequence	193	194	2	+	pattern1	.
+Sequence	196	197	2	+	pattern1	.
+Sequence	201	202	2	+	pattern1	.
+Sequence	204	205	2	+	pattern1	.
+Sequence	252	253	2	+	pattern1	.
+Sequence	264	265	2	+	pattern1	.
+Sequence	274	275	2	+	pattern1	.
+Sequence	287	288	2	+	pattern1	.
+Sequence	326	327	2	+	pattern1	.
+Sequence	340	341	2	+	pattern1	.
+Sequence	364	365	2	+	pattern1	.
+Sequence	393	394	2	+	pattern1	.
+Sequence	409	410	2	+	pattern1	.
+Sequence	429	430	2	+	pattern1	.
+Sequence	430	431	2	+	pattern1	.
+Sequence	431	432	2	+	pattern1	.
+Sequence	449	450	2	+	pattern1	.
+Sequence	534	535	2	+	pattern1	.
+Sequence	539	540	2	+	pattern1	.
+Sequence	540	541	2	+	pattern1	.
+Sequence	541	542	2	+	pattern1	.
+Sequence	544	545	2	+	pattern1	.
+Sequence	550	551	2	+	pattern1	.
+Sequence	557	558	2	+	pattern1	.
+Sequence	558	559	2	+	pattern1	.
+Sequence	559	560	2	+	pattern1	.
+Sequence	560	561	2	+	pattern1	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_fuzztran_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,133 @@
+SeqName	Start	End	Score	Strand	Pattern_name	Mismatch	Frame	PStart	PEnd	Translation
+hg17	3958	3963	2	+	pattern1	.	1	1320	1321	AA
+hg17	3961	3966	2	+	pattern1	.	1	1321	1322	AA
+hg17	4099	4104	2	+	pattern1	.	1	1367	1368	AA
+hg17	4315	4320	2	+	pattern1	.	1	1439	1440	AA
+hg17	5194	5199	2	+	pattern1	.	1	1732	1733	AA
+hg17	8584	8589	2	+	pattern1	.	1	2862	2863	AA
+hg17	9232	9237	2	+	pattern1	.	1	3078	3079	AA
+hg17	9343	9348	2	+	pattern1	.	1	3115	3116	AA
+hg17	9715	9720	2	+	pattern1	.	1	3239	3240	AA
+hg17	9769	9774	2	+	pattern1	.	1	3257	3258	AA
+hg17	9841	9846	2	+	pattern1	.	1	3281	3282	AA
+hg17	9994	9999	2	+	pattern1	.	1	3332	3333	AA
+hg17	10045	10050	2	+	pattern1	.	1	3349	3350	AA
+hg17	10048	10053	2	+	pattern1	.	1	3350	3351	AA
+hg17	12157	12162	2	+	pattern1	.	1	4053	4054	AA
+hg17	12487	12492	2	+	pattern1	.	1	4163	4164	AA
+hg17	12688	12693	2	+	pattern1	.	1	4230	4231	AA
+hg17	12691	12696	2	+	pattern1	.	1	4231	4232	AA
+hg17	15010	15015	2	+	pattern1	.	1	5004	5005	AA
+hg17	17521	17526	2	+	pattern1	.	1	5841	5842	AA
+hg17	17551	17556	2	+	pattern1	.	1	5851	5852	AA
+hg17	1148	1153	2	+	pattern1	.	2	383	384	AA
+hg17	2078	2083	2	+	pattern1	.	2	693	694	AA
+hg17	2432	2437	2	+	pattern1	.	2	811	812	AA
+hg17	3080	3085	2	+	pattern1	.	2	1027	1028	AA
+hg17	3593	3598	2	+	pattern1	.	2	1198	1199	AA
+hg17	3692	3697	2	+	pattern1	.	2	1231	1232	AA
+hg17	4055	4060	2	+	pattern1	.	2	1352	1353	AA
+hg17	5018	5023	2	+	pattern1	.	2	1673	1674	AA
+hg17	5147	5152	2	+	pattern1	.	2	1716	1717	AA
+hg17	8276	8281	2	+	pattern1	.	2	2759	2760	AA
+hg17	9587	9592	2	+	pattern1	.	2	3196	3197	AA
+hg17	9668	9673	2	+	pattern1	.	2	3223	3224	AA
+hg17	9920	9925	2	+	pattern1	.	2	3307	3308	AA
+hg17	9971	9976	2	+	pattern1	.	2	3324	3325	AA
+hg17	10112	10117	2	+	pattern1	.	2	3371	3372	AA
+hg17	10115	10120	2	+	pattern1	.	2	3372	3373	AA
+hg17	11837	11842	2	+	pattern1	.	2	3946	3947	AA
+hg17	12026	12031	2	+	pattern1	.	2	4009	4010	AA
+hg17	12944	12949	2	+	pattern1	.	2	4315	4316	AA
+hg17	12953	12958	2	+	pattern1	.	2	4318	4319	AA
+hg17	13229	13234	2	+	pattern1	.	2	4410	4411	AA
+hg17	13232	13237	2	+	pattern1	.	2	4411	4412	AA
+hg17	15356	15361	2	+	pattern1	.	2	5119	5120	AA
+hg17	15482	15487	2	+	pattern1	.	2	5161	5162	AA
+hg17	16061	16066	2	+	pattern1	.	2	5354	5355	AA
+hg17	17822	17827	2	+	pattern1	.	2	5941	5942	AA
+hg17	15	20	2	+	pattern1	.	3	5	6	AA
+hg17	33	38	2	+	pattern1	.	3	11	12	AA
+hg17	3669	3674	2	+	pattern1	.	3	1223	1224	AA
+hg17	3759	3764	2	+	pattern1	.	3	1253	1254	AA
+hg17	5646	5651	2	+	pattern1	.	3	1882	1883	AA
+hg17	5847	5852	2	+	pattern1	.	3	1949	1950	AA
+hg17	5850	5855	2	+	pattern1	.	3	1950	1951	AA
+hg17	5853	5858	2	+	pattern1	.	3	1951	1952	AA
+hg17	7674	7679	2	+	pattern1	.	3	2558	2559	AA
+hg17	9699	9704	2	+	pattern1	.	3	3233	3234	AA
+hg17	9891	9896	2	+	pattern1	.	3	3297	3298	AA
+hg17	10074	10079	2	+	pattern1	.	3	3358	3359	AA
+hg17	10407	10412	2	+	pattern1	.	3	3469	3470	AA
+hg17	12675	12680	2	+	pattern1	.	3	4225	4226	AA
+hg17	13746	13751	2	+	pattern1	.	3	4582	4583	AA
+hg17	17115	17120	2	+	pattern1	.	3	5705	5706	AA
+hg17	17421	17426	2	+	pattern1	.	3	5807	5808	AA
+hg17	19122	19127	2	+	pattern1	.	3	6374	6375	AA
+hg17	19353	19358	2	+	pattern1	.	3	6451	6452	AA
+hg17	-2312	-2317	2	-	pattern1	.	1	772	773	AA
+hg17	-4073	-4078	2	-	pattern1	.	1	1359	1360	AA
+hg17	-4652	-4657	2	-	pattern1	.	1	1552	1553	AA
+hg17	-4778	-4783	2	-	pattern1	.	1	1594	1595	AA
+hg17	-6902	-6907	2	-	pattern1	.	1	2302	2303	AA
+hg17	-6905	-6910	2	-	pattern1	.	1	2303	2304	AA
+hg17	-7181	-7186	2	-	pattern1	.	1	2395	2396	AA
+hg17	-7190	-7195	2	-	pattern1	.	1	2398	2399	AA
+hg17	-8108	-8113	2	-	pattern1	.	1	2704	2705	AA
+hg17	-8297	-8302	2	-	pattern1	.	1	2767	2768	AA
+hg17	-10019	-10024	2	-	pattern1	.	1	3341	3342	AA
+hg17	-10022	-10027	2	-	pattern1	.	1	3342	3343	AA
+hg17	-10163	-10168	2	-	pattern1	.	1	3389	3390	AA
+hg17	-10214	-10219	2	-	pattern1	.	1	3406	3407	AA
+hg17	-10466	-10471	2	-	pattern1	.	1	3490	3491	AA
+hg17	-10547	-10552	2	-	pattern1	.	1	3517	3518	AA
+hg17	-11858	-11863	2	-	pattern1	.	1	3954	3955	AA
+hg17	-14987	-14992	2	-	pattern1	.	1	4997	4998	AA
+hg17	-15116	-15121	2	-	pattern1	.	1	5040	5041	AA
+hg17	-16079	-16084	2	-	pattern1	.	1	5361	5362	AA
+hg17	-16442	-16447	2	-	pattern1	.	1	5482	5483	AA
+hg17	-16541	-16546	2	-	pattern1	.	1	5515	5516	AA
+hg17	-17054	-17059	2	-	pattern1	.	1	5686	5687	AA
+hg17	-17702	-17707	2	-	pattern1	.	1	5902	5903	AA
+hg17	-18056	-18061	2	-	pattern1	.	1	6020	6021	AA
+hg17	-18986	-18991	2	-	pattern1	.	1	6330	6331	AA
+hg17	-783	-788	2	-	pattern1	.	2	262	263	AA
+hg17	-1014	-1019	2	-	pattern1	.	2	339	340	AA
+hg17	-2715	-2720	2	-	pattern1	.	2	906	907	AA
+hg17	-3021	-3026	2	-	pattern1	.	2	1008	1009	AA
+hg17	-6390	-6395	2	-	pattern1	.	2	2131	2132	AA
+hg17	-7461	-7466	2	-	pattern1	.	2	2488	2489	AA
+hg17	-9729	-9734	2	-	pattern1	.	2	3244	3245	AA
+hg17	-10062	-10067	2	-	pattern1	.	2	3355	3356	AA
+hg17	-10245	-10250	2	-	pattern1	.	2	3416	3417	AA
+hg17	-10437	-10442	2	-	pattern1	.	2	3480	3481	AA
+hg17	-12462	-12467	2	-	pattern1	.	2	4155	4156	AA
+hg17	-14283	-14288	2	-	pattern1	.	2	4762	4763	AA
+hg17	-14286	-14291	2	-	pattern1	.	2	4763	4764	AA
+hg17	-14289	-14294	2	-	pattern1	.	2	4764	4765	AA
+hg17	-14490	-14495	2	-	pattern1	.	2	4831	4832	AA
+hg17	-16377	-16382	2	-	pattern1	.	2	5460	5461	AA
+hg17	-16467	-16472	2	-	pattern1	.	2	5490	5491	AA
+hg17	-20103	-20108	2	-	pattern1	.	2	6702	6703	AA
+hg17	-20121	-20126	2	-	pattern1	.	2	6708	6709	AA
+hg17	17553	17548	2	-	pattern1	.	3	863	864	AA
+hg17	17523	17518	2	-	pattern1	.	3	873	874	AA
+hg17	15012	15007	2	-	pattern1	.	3	1710	1711	AA
+hg17	12693	12688	2	-	pattern1	.	3	2483	2484	AA
+hg17	12690	12685	2	-	pattern1	.	3	2484	2485	AA
+hg17	12489	12484	2	-	pattern1	.	3	2551	2552	AA
+hg17	12159	12154	2	-	pattern1	.	3	2661	2662	AA
+hg17	10050	10045	2	-	pattern1	.	3	3364	3365	AA
+hg17	10047	10042	2	-	pattern1	.	3	3365	3366	AA
+hg17	9996	9991	2	-	pattern1	.	3	3382	3383	AA
+hg17	9843	9838	2	-	pattern1	.	3	3433	3434	AA
+hg17	9771	9766	2	-	pattern1	.	3	3457	3458	AA
+hg17	9717	9712	2	-	pattern1	.	3	3475	3476	AA
+hg17	9345	9340	2	-	pattern1	.	3	3599	3600	AA
+hg17	9234	9229	2	-	pattern1	.	3	3636	3637	AA
+hg17	8586	8581	2	-	pattern1	.	3	3852	3853	AA
+hg17	5196	5191	2	-	pattern1	.	3	4982	4983	AA
+hg17	4317	4312	2	-	pattern1	.	3	5275	5276	AA
+hg17	4101	4096	2	-	pattern1	.	3	5347	5348	AA
+hg17	3963	3958	2	-	pattern1	.	3	5393	5394	AA
+hg17	3960	3955	2	-	pattern1	.	3	5394	5395	AA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_garnier_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,102 @@
+SeqName	Start	End	Score	Strand	helix	sheet	turns	coil
+Sequence	1	9	0.000	+	.	.	T	.
+Sequence	10	10	0.000	+	.	E	.	.
+Sequence	11	16	0.000	+	H	.	.	.
+Sequence	17	39	0.000	+	.	.	T	.
+Sequence	40	40	0.000	+	H	.	.	.
+Sequence	41	42	0.000	+	.	E	.	.
+Sequence	43	48	0.000	+	.	.	T	.
+Sequence	49	52	0.000	+	.	E	.	.
+Sequence	53	68	0.000	+	.	.	T	.
+Sequence	69	75	0.000	+	H	.	.	.
+Sequence	76	78	0.000	+	.	E	.	.
+Sequence	79	87	0.000	+	.	.	T	.
+Sequence	88	90	0.000	+	.	E	.	.
+Sequence	91	96	0.000	+	H	.	.	.
+Sequence	97	98	0.000	+	.	E	.	.
+Sequence	99	99	0.000	+	.	.	.	C
+Sequence	100	107	0.000	+	.	.	T	.
+Sequence	108	111	0.000	+	.	E	.	.
+Sequence	112	116	0.000	+	.	.	T	.
+Sequence	117	120	0.000	+	.	E	.	.
+Sequence	121	123	0.000	+	.	.	T	.
+Sequence	124	126	0.000	+	.	.	.	C
+Sequence	127	131	0.000	+	.	E	.	.
+Sequence	132	153	0.000	+	.	.	T	.
+Sequence	154	157	0.000	+	.	E	.	.
+Sequence	158	161	0.000	+	.	.	T	.
+Sequence	162	162	0.000	+	.	.	.	C
+Sequence	163	164	0.000	+	.	E	.	.
+Sequence	165	172	0.000	+	.	.	T	.
+Sequence	173	176	0.000	+	.	E	.	.
+Sequence	177	180	0.000	+	.	.	T	.
+Sequence	181	183	0.000	+	.	.	.	C
+Sequence	184	187	0.000	+	.	E	.	.
+Sequence	188	194	0.000	+	.	.	.	C
+Sequence	195	206	0.000	+	H	.	.	.
+Sequence	207	234	0.000	+	.	.	T	.
+Sequence	235	237	0.000	+	.	E	.	.
+Sequence	238	241	0.000	+	.	.	T	.
+Sequence	242	242	0.000	+	.	.	.	C
+Sequence	243	246	0.000	+	.	E	.	.
+Sequence	247	247	0.000	+	.	.	T	.
+Sequence	248	249	0.000	+	.	.	.	C
+Sequence	250	275	0.000	+	.	.	T	.
+Sequence	276	282	0.000	+	.	E	.	.
+Sequence	283	283	0.000	+	H	.	.	.
+Sequence	284	289	0.000	+	.	.	.	C
+Sequence	290	301	0.000	+	.	.	T	.
+Sequence	302	307	0.000	+	.	E	.	.
+Sequence	308	313	0.000	+	.	.	.	C
+Sequence	314	321	0.000	+	.	.	T	.
+Sequence	322	322	0.000	+	.	E	.	.
+Sequence	323	344	0.000	+	.	.	T	.
+Sequence	345	348	0.000	+	.	E	.	.
+Sequence	349	360	0.000	+	.	.	T	.
+Sequence	361	363	0.000	+	.	E	.	.
+Sequence	364	374	0.000	+	.	.	T	.
+Sequence	375	378	0.000	+	.	E	.	.
+Sequence	379	381	0.000	+	.	.	T	.
+Sequence	382	384	0.000	+	.	.	.	C
+Sequence	385	386	0.000	+	.	E	.	.
+Sequence	387	392	0.000	+	.	.	.	C
+Sequence	393	396	0.000	+	.	E	.	.
+Sequence	397	401	0.000	+	.	.	T	.
+Sequence	402	402	0.000	+	.	.	.	C
+Sequence	403	403	0.000	+	.	E	.	.
+Sequence	404	406	0.000	+	.	.	T	.
+Sequence	407	407	0.000	+	.	.	.	C
+Sequence	408	409	0.000	+	.	.	T	.
+Sequence	410	412	0.000	+	.	E	.	.
+Sequence	413	422	0.000	+	.	.	T	.
+Sequence	423	427	0.000	+	.	E	.	.
+Sequence	428	436	0.000	+	H	.	.	.
+Sequence	437	441	0.000	+	.	E	.	.
+Sequence	442	444	0.000	+	.	.	T	.
+Sequence	445	447	0.000	+	.	.	.	C
+Sequence	448	452	0.000	+	.	E	.	.
+Sequence	453	455	0.000	+	.	.	.	C
+Sequence	456	457	0.000	+	.	.	T	.
+Sequence	458	460	0.000	+	.	.	.	C
+Sequence	461	463	0.000	+	.	E	.	.
+Sequence	464	467	0.000	+	.	.	T	.
+Sequence	468	469	0.000	+	.	E	.	.
+Sequence	470	480	0.000	+	.	.	T	.
+Sequence	481	484	0.000	+	.	E	.	.
+Sequence	485	490	0.000	+	.	.	T	.
+Sequence	491	491	0.000	+	.	E	.	.
+Sequence	492	496	0.000	+	.	.	T	.
+Sequence	497	497	0.000	+	.	.	.	C
+Sequence	498	500	0.000	+	.	.	T	.
+Sequence	501	504	0.000	+	.	E	.	.
+Sequence	505	510	0.000	+	.	.	T	.
+Sequence	511	514	0.000	+	.	E	.	.
+Sequence	515	517	0.000	+	.	.	.	C
+Sequence	518	520	0.000	+	.	E	.	.
+Sequence	521	532	0.000	+	.	.	.	C
+Sequence	533	534	0.000	+	.	E	.	.
+Sequence	535	547	0.000	+	H	.	.	.
+Sequence	548	549	0.000	+	.	E	.	.
+Sequence	550	554	0.000	+	.	.	T	.
+Sequence	555	555	0.000	+	.	.	.	C
+Sequence	556	561	0.000	+	H	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_geecee_out.geecee	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,2 @@
+#Sequence   GC content
+Sequence      0.36
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_getorf_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,65 @@
+>Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+VRCLKYLLLSLHRPQFS
+>Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+NTFFCPYTDHSFPNGFTPTRNSCASTN
+>Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+LKAVGLECYRFV
+>Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC
+>Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL
+>Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE
+DVVEEYNKYESLPPGLLITGYSCNTLRNTA
+>Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+LLDTVVIPFATPRNYLYELFSLYYM
+>Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+IIFPLLYVVGSSLIFL
+>Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+QVFYCFRPQCSCS
+>Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG
+>Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+YAVSLIFVVSS
+>Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV
+>Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF
+>Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV
+>Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+FLVCTCSGASSLFTLFVYSSSFIFSMILI
+>Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+NHTKNKRTAVYKQSK
+>Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+IKIILKIKELLYTNRVNNELAPEQVQTKN
+>Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+IMNWPLNKYKPKIKP
+>Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TSTNQKLNHE
+>Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+INILRRNNED
+>Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TMNKYFKKKQRRLN
+>Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+PHIIQNNLRT
+>Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TLRSKTVKDLLKED
+>Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+EETTKIKLTAYYPKQPKNMNIEVENSKRLAKGRLKTNLLHIIKGK
+>Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+IVTRCCEGYYNCIQ
+>Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SANQGGETRTCCILPQRLPK
+>Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+RKIKDEPTTYNKGKIIHIDSYAVLRRVLQLYPVISKPGGRDSYLLYSSTTSSKVEKMNL
+>Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+LRGVAKGITTVSSNQQTRGERLVLVVFFHNVFQSRENEPLIRARDALSYTNR
+>Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TFDQGKRRAQLYKPVTL
+>Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ANRFQLVLAQEFLVGVKPLGKLWSV
+>Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ENCGLCRDKRRYFRHR
+>Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+SGQETRSAIQTGNTLGQPLSISACTRISSRCKAIRKTVVCVGTKEGILGIE
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_helixturnhelix_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,1 @@
+SeqName	Start	End	Score	Strand	Maximum_score_at	Standard_deviations
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_hmoment_out.hmoment	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,556 @@
+HMOMENT of Sequence from 1 to 561
+
+Window: 10 Angle: 100 Max uH: 0.205
+Position	uH
+1		0.100
+2		0.071
+3		0.127
+4		0.152
+5		0.127
+6		0.056
+7		0.049
+8		0.032
+9		0.066
+10		0.041
+11		0.019
+12		0.020
+13		0.081
+14		0.125
+15		0.092
+16		0.044
+17		0.040
+18		0.051
+19		0.063
+20		0.038
+21		0.063
+22		0.052
+23		0.065
+24		0.086
+25		0.106
+26		0.073
+27		0.048
+28		0.088
+29		0.082
+30		0.044
+31		0.007
+32		0.035
+33		0.041
+34		0.094
+35		0.035
+36		0.045
+37		0.073
+38		0.069
+39		0.024
+40		0.055
+41		0.040
+42		0.007
+43		0.066
+44		0.009
+45		0.071
+46		0.111
+47		0.095
+48		0.144
+49		0.138
+50		0.143
+51		0.113
+52		0.120
+53		0.078
+54		0.051
+55		0.042
+56		0.035
+57		0.055
+58		0.027
+59		0.037
+60		0.029
+61		0.032
+62		0.077
+63		0.148
+64		0.108
+65		0.035
+66		0.098
+67		0.128
+68		0.118
+69		0.083
+70		0.108
+71		0.112
+72		0.076
+73		0.116
+74		0.102
+75		0.043
+76		0.090
+77		0.073
+78		0.025
+79		0.031
+80		0.058
+81		0.043
+82		0.066
+83		0.075
+84		0.146
+85		0.173
+86		0.140
+87		0.142
+88		0.200
+89		0.154
+90		0.089
+91		0.140
+92		0.121
+93		0.063
+94		0.055
+95		0.051
+96		0.057
+97		0.075
+98		0.136
+99		0.132
+100		0.068
+101		0.067
+102		0.076
+103		0.055
+104		0.019
+105		0.043
+106		0.041
+107		0.022
+108		0.064
+109		0.060
+110		0.085
+111		0.090
+112		0.111
+113		0.049
+114		0.083
+115		0.131
+116		0.137
+117		0.099
+118		0.119
+119		0.120
+120		0.054
+121		0.064
+122		0.059
+123		0.042
+124		0.026
+125		0.032
+126		0.078
+127		0.104
+128		0.117
+129		0.096
+130		0.116
+131		0.108
+132		0.084
+133		0.056
+134		0.063
+135		0.058
+136		0.050
+137		0.048
+138		0.025
+139		0.047
+140		0.093
+141		0.072
+142		0.027
+143		0.021
+144		0.053
+145		0.022
+146		0.049
+147		0.040
+148		0.103
+149		0.154
+150		0.105
+151		0.076
+152		0.127
+153		0.126
+154		0.105
+155		0.088
+156		0.107
+157		0.131
+158		0.095
+159		0.052
+160		0.114
+161		0.088
+162		0.041
+163		0.071
+164		0.067
+165		0.008
+166		0.056
+167		0.060
+168		0.064
+169		0.059
+170		0.055
+171		0.046
+172		0.030
+173		0.092
+174		0.062
+175		0.036
+176		0.019
+177		0.038
+178		0.032
+179		0.037
+180		0.051
+181		0.100
+182		0.051
+183		0.036
+184		0.088
+185		0.090
+186		0.039
+187		0.080
+188		0.076
+189		0.079
+190		0.061
+191		0.074
+192		0.090
+193		0.042
+194		0.024
+195		0.063
+196		0.065
+197		0.050
+198		0.061
+199		0.077
+200		0.136
+201		0.116
+202		0.037
+203		0.092
+204		0.120
+205		0.066
+206		0.026
+207		0.070
+208		0.075
+209		0.041
+210		0.075
+211		0.082
+212		0.034
+213		0.031
+214		0.023
+215		0.048
+216		0.047
+217		0.098
+218		0.098
+219		0.083
+220		0.059
+221		0.103
+222		0.099
+223		0.085
+224		0.110
+225		0.127
+226		0.163
+227		0.132
+228		0.190
+229		0.194
+230		0.197
+231		0.154
+232		0.205
+233		0.171
+234		0.166
+235		0.148
+236		0.161
+237		0.106
+238		0.035
+239		0.026
+240		0.026
+241		0.038
+242		0.084
+243		0.016
+244		0.060
+245		0.121
+246		0.061
+247		0.028
+248		0.076
+249		0.046
+250		0.050
+251		0.072
+252		0.042
+253		0.033
+254		0.083
+255		0.031
+256		0.093
+257		0.106
+258		0.042
+259		0.055
+260		0.053
+261		0.008
+262		0.030
+263		0.062
+264		0.078
+265		0.037
+266		0.114
+267		0.108
+268		0.078
+269		0.107
+270		0.134
+271		0.117
+272		0.091
+273		0.150
+274		0.147
+275		0.071
+276		0.025
+277		0.064
+278		0.022
+279		0.069
+280		0.072
+281		0.044
+282		0.107
+283		0.170
+284		0.176
+285		0.116
+286		0.110
+287		0.128
+288		0.078
+289		0.059
+290		0.055
+291		0.061
+292		0.020
+293		0.051
+294		0.048
+295		0.055
+296		0.112
+297		0.139
+298		0.083
+299		0.055
+300		0.105
+301		0.100
+302		0.049
+303		0.087
+304		0.086
+305		0.069
+306		0.131
+307		0.096
+308		0.090
+309		0.095
+310		0.134
+311		0.102
+312		0.098
+313		0.062
+314		0.055
+315		0.111
+316		0.098
+317		0.106
+318		0.131
+319		0.132
+320		0.098
+321		0.097
+322		0.096
+323		0.059
+324		0.089
+325		0.083
+326		0.088
+327		0.025
+328		0.103
+329		0.065
+330		0.028
+331		0.086
+332		0.109
+333		0.100
+334		0.094
+335		0.116
+336		0.109
+337		0.111
+338		0.063
+339		0.043
+340		0.074
+341		0.099
+342		0.090
+343		0.073
+344		0.067
+345		0.086
+346		0.092
+347		0.089
+348		0.092
+349		0.044
+350		0.045
+351		0.066
+352		0.039
+353		0.019
+354		0.013
+355		0.059
+356		0.069
+357		0.070
+358		0.045
+359		0.079
+360		0.117
+361		0.081
+362		0.138
+363		0.135
+364		0.083
+365		0.034
+366		0.096
+367		0.071
+368		0.034
+369		0.029
+370		0.038
+371		0.083
+372		0.105
+373		0.112
+374		0.070
+375		0.096
+376		0.096
+377		0.079
+378		0.078
+379		0.072
+380		0.088
+381		0.036
+382		0.059
+383		0.056
+384		0.043
+385		0.114
+386		0.114
+387		0.107
+388		0.101
+389		0.089
+390		0.079
+391		0.029
+392		0.098
+393		0.100
+394		0.036
+395		0.106
+396		0.075
+397		0.085
+398		0.090
+399		0.091
+400		0.096
+401		0.048
+402		0.032
+403		0.049
+404		0.070
+405		0.110
+406		0.059
+407		0.107
+408		0.102
+409		0.106
+410		0.081
+411		0.138
+412		0.143
+413		0.112
+414		0.138
+415		0.136
+416		0.127
+417		0.113
+418		0.107
+419		0.111
+420		0.092
+421		0.134
+422		0.098
+423		0.055
+424		0.044
+425		0.055
+426		0.056
+427		0.040
+428		0.041
+429		0.095
+430		0.158
+431		0.153
+432		0.106
+433		0.186
+434		0.187
+435		0.118
+436		0.167
+437		0.162
+438		0.168
+439		0.108
+440		0.155
+441		0.121
+442		0.121
+443		0.059
+444		0.053
+445		0.098
+446		0.087
+447		0.119
+448		0.149
+449		0.149
+450		0.113
+451		0.069
+452		0.083
+453		0.084
+454		0.095
+455		0.119
+456		0.117
+457		0.100
+458		0.102
+459		0.096
+460		0.100
+461		0.116
+462		0.187
+463		0.150
+464		0.080
+465		0.106
+466		0.115
+467		0.085
+468		0.036
+469		0.098
+470		0.095
+471		0.112
+472		0.061
+473		0.077
+474		0.119
+475		0.141
+476		0.099
+477		0.154
+478		0.184
+479		0.185
+480		0.136
+481		0.194
+482		0.178
+483		0.177
+484		0.138
+485		0.132
+486		0.087
+487		0.055
+488		0.057
+489		0.051
+490		0.037
+491		0.087
+492		0.035
+493		0.031
+494		0.080
+495		0.053
+496		0.023
+497		0.045
+498		0.033
+499		0.030
+500		0.087
+501		0.089
+502		0.035
+503		0.064
+504		0.125
+505		0.132
+506		0.069
+507		0.085
+508		0.072
+509		0.088
+510		0.050
+511		0.049
+512		0.043
+513		0.064
+514		0.071
+515		0.111
+516		0.109
+517		0.082
+518		0.089
+519		0.054
+520		0.038
+521		0.032
+522		0.032
+523		0.038
+524		0.054
+525		0.059
+526		0.015
+527		0.068
+528		0.073
+529		0.026
+530		0.106
+531		0.055
+532		0.047
+533		0.103
+534		0.091
+535		0.049
+536		0.031
+537		0.032
+538		0.038
+539		0.068
+540		0.130
+541		0.077
+542		0.043
+543		0.104
+544		0.058
+545		0.045
+546		0.108
+547		0.084
+548		0.139
+549		0.189
+550		0.130
+551		0.062
+552		0.136
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_iep_out.iep	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,31 @@
+IEP of Sequence from 1 to 561
+Isoelectric Point = 5.0278
+
+   pH     Bound    Charge
+  1.00   108.00     1.00
+  1.50   107.99     0.99
+  2.00   107.98     0.98
+  2.50   107.93     0.93
+  3.00   107.80     0.80
+  3.50   107.56     0.56
+  4.00   107.28     0.28
+  4.50   107.10     0.10
+  5.00   107.00     0.00
+  5.50   106.91    -0.09
+  6.00   106.67    -0.33
+  6.50   105.94    -1.06
+  7.00   103.73    -3.27
+  7.50    97.29    -9.71
+  8.00    81.33   -25.67
+  8.50    53.56   -53.44
+  9.00    25.75   -81.25
+  9.50     9.75   -97.25
+ 10.00     3.29   -103.71
+ 10.50     1.06   -105.94
+ 11.00     0.34   -106.66
+ 11.50     0.11   -106.89
+ 12.00     0.03   -106.97
+ 12.50     0.01   -106.99
+ 13.00     0.00   -107.00
+ 13.50     0.00   -107.00
+ 14.00     0.00   -107.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_isochore_out.isochore	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,7 @@
+Position	Percent G+C 1 .. 561
+140	0.446
+196	0.414
+252	0.396
+308	0.357
+364	0.332
+420	0.282
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_marscan_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,4 @@
+SeqName	Start	End	Score	Strand	type	start8bp	end8bp	start16bp	end16bp
+hg17	440	492	0.000	+	MAR/SAR recognition site (MRS)	440	447	477	492
+hg17	13640	13750	0.000	+	MAR/SAR recognition site (MRS)	13640	13647	13735	13750
+hg17	15229	15392	0.000	+	MAR/SAR recognition site (MRS)	15385	15392	15229	15244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_maskfeat_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_maskseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+NNNcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_matcher_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,6 @@
+>Sequence
+CTTTAGCAAGTCTTTTACTGTTTTCGACCTCAATGTTCATGTTCTTAGGTTGTTTTGGAT
+A
+>hg17
+CTTCAGCAAGTTCCTTACTGTCTTTAAGCCTTGTTTTCATCATCT--GGATAATGGGGAT
+A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_msbar_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_needle_out.score	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,4 @@
+Sequence hg17 20190 (604.5)
+
+#---------------------------------------
+#---------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_newcpgreport_out.newcpgreport	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+ID   Sequence  561 BP.
+XX
+DE   CpG Island report.
+XX
+CC   Obs/Exp ratio > 0.60.
+CC   % C + % G > 50.00.
+CC   Length > 200.
+XX
+FH   Key              Location/Qualifiers
+FT   no islands detected
+//
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_newcpgseek_out.newcpgseek	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,9 @@
+
+
+NEWCPGSEEK of Sequence from 1 to 561
+with score > 17 
+
+ Begin    End  Score        CpG  %CG  CG/GC
+   121    141    34          3  57.1   1.00
+   261    272    43          3  75.0   1.00
+-------------------------------------------
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_newseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,2 @@
+>cytoc fragment of cytochrome c
+KKKEERADLIAY
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_noreturn_out.noreturn	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcc taaaatacct tcttttgtcc ctacacagac cacagttttc ctaatggctt
+tacaccgact agaaattctt gtgcaagcac taattgaaag cggttggcct agagtgttac
+cggtttgtat agctgagcgc gtctcttgcc ctgatcaaag gttcattttc tctactttgg
+aagacgttgt ggaagaatac aacaagtacg agtctctccc ccctggtttg ctgattactg
+gatacagttg taataccctt cgcaacaccg cgtaactatc tatatgaatt attttccctt
+tattatatgt agtaggttcg tctttaatct tcctttagca agtcttttac tgttttcgac
+ctcaatgttc atgttcttag gttgttttgg ataatatgcg gtcagtttaa tcttcgttgt
+ttcttcttaa aatatttatt catggtttaa tttttggttt gtacttgttc aggggccagt
+tcattattta ctctgtttgt atacagcagt tcttttattt ttagtatgat tttaatttaa
+aacaattcta atggtcaaaa a
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_notseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_nthseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_palindrome_out.palindrome	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,15 @@
+Palindromes of:  Sequence 
+Sequence length is: 561 
+Start at position: 1
+End at position: 561
+Minimum length of Palindromes is: 10 
+Maximum length of Palindromes is: 100 
+Maximum gap between elements is: 100 
+Number of mismatches allowed in Palindrome: 0
+
+
+
+Palindromes:
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_pasteseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,371 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccag
+gctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagt
+caggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagcca
+ctaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTG
+ACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC----------------
+---------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------T
+GAA-------------------AACATCCACTAAAATTTGTGGTTTATTCATTTTTCATT
+ATTTTGTTTAAGGAGGTCTATAGTGGAAGAGGGAGATATTTGGggaaatt---ttgtata
+gactagctttcacgatgttagggaattattattgtgtgataatggtcttgcagttaca-c
+agaaattcttccttattttttgggaa---gcaccaaag----tagggat---aaaatgtc
+atgatgtgtgcaatacactttaaaatgtttttg-----ccaaaataatt-----------
+-----aatgaagc--aaatatggaaa-ataataattattaaatctaggtgatgggtatat
+tgtagttcactatagtattgcacacttttctgtatgtttaaatttttcatttaaaaaaaa
+actttgagc-----tagacaccaggctatgagctaggagcatagcaatgaccaa------
+------------------------------------------------------------
+----------------------------atagactcctaccaa-----------------
+---------------------------------ctc-aaagaatgcacattctCTGGGAA
+ACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTG
+ATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAGTTT
+TAAACATTTA------CCTTCCCAGTGGCCTTGCGTCTAGAGGAATCCCTGTATAGTGGT
+-ACATGAATATAACACATAACAAA-AATCATCTCTATGGTGTGTGTTGTTCCTGGGGTTC
+Aattcagcaaattttccctg-ggcacccatgtgttcttggcactggaaaagtaccgggac
+tgaaacagttgatggccca-atccctgtcctct---taaaacctaagggaggagaTGGAA
+AGGGG-CACCCAACCCAGACTGAGAGACAGGAATTAGCTGCAAGGGGAACTAGGAAAAGC
+TTCTTTA---AGGATGGAGAGGCCCTAGTGGAAT-GGGGAGATTCTTCCGGGAGAAGCGA
+TGGATGCACAGTTGGGCATCCCCACAGACGGACTGGAAAGAAAAAAGGCCTGGAGGAATC
+AATGTG-------CAATGTATGTGTGTTCCCTGGTTcaagggctgg-gaactttctcta-
+aagggccaggtagaaaacattttaggctttctaagccaag--gcaaaat-tgaggatatt
+acatgggtacttatacaacaagaataaacaatt---tacacaattttttgttgacagaat
+tcaaaactttat----agacacagaaatgcaaatttcctgtaattttcccat-gagaact
+attcttct--tttgttttgttttgcgacAGGGTTGCGCtgatcctcccgcctcagtctcc
+ctaagtgctgagatgttgcaggaagtcagggaccccgaacagagagatcggctggagccg
+tggcagaggaacataaattttgaagatttcattttaatatggacacttatcagttcccaa
+ataatacttttataattttttatgcctgtctttgctttaatctcttaatcctgttatctt
+cataagctaaggatgtacgtcacctcaggaccactgtgataattgtgttaactgtacaga
+ttgattgcaaaacatgtgtgtttgaacaatatgaaatcagtgcaccttgaaaaagagcag
+aataacagcaatttttagggaacaagggaagacaactataaggtctgactgcctgcgggg
+tcgggcaaagggagccatatttttcttcttgcagagagcctataaatagacctgcaagta
+ggagagatattgctaatttcttttgctagcatggaatattaatattaacaccctgggaaa
+ggaatgcattcctggggggaggtctataaatggccgctctgggaatgtctatcctacgca
+atggagataaggactgagatacgccctggtctcctgcagtaccctcaggcttactagggt
+ggtgaaaaactccgccctggtaaatttgtggtcagaccagttttctgctctcgaacactg
+ttttctgttgtttaagatgtttatcaagacaatacgtgcaccgctgaacacagaccctta
+tcagtagttctcctttttgccctttgaagcatgtgatctactccctgttttacaccccct
+caccttttgaaacccttaataaaaaacttgctggttt-gaggctcaggtgggcatcacag
+tactaccgatatgtgatgtcacccccggcggcccagctgtaaaattcctctctttgtact
+ctctctctttatttctcagccagctgacacttatggaaaatagaaagaacctacgttgaa
+atattgggggcaggttcccccaataTCTGGTGCCCAACGTGGGAtactgagattacaagc
+atgagccactgcatctggcctcttcttttgatttttttttttcaaacttttacaaatgta
+gaaaccattcttagcttttgggcattaccaaacccggcagtgg-caggctcggttcacca
+acgtcatttgcagttccccgCTTTATGTTATGGgttttgttttgttttgtttttttt-at
+tgagacagagtttcactcttgttgcccaggctgtagtgcaatggtctgatcttggctcac
+tgcaacctccacttcccaggttcaagccattctcctgcctcagcctctcaagtagctggg
+attacagacactcaccaccacacctggctaattttgtatttttagtagagatgaggtttc
+accatgttggccaggctggtctcgaaatcctgacctcaggtgatccacccaccttggcct
+cccaaagtgctgggattacaggcttgagctaccacgcctggctGGGTTGGTTCTCAATGG
+AGTGGTTTGTTTTTGGAGCTGCTCT-GCGCAGtggggaccagaataggcctg--------
+-----------ggttcctagcccattgctattcctt----accagctgtggattctaagg
+aaagtcatttaacctcgctggaccttag-attcctcatccctgaaGCCCAAGGGTaaaac
+aaaacaaaacaaaacaaaacaaaccaaCCCATCATGTAAAGCGGGGAACTACAAACGATA
+CAGGTGAAACATGCCTACCACACCACTCACAGGCT--ATGATGACAAAAACGTGGCTACA
+TCTGGGACCACCCCCCAACCCCCACTTTGTACGTAGGAAATACGGAGTTGAGGATGGAGA
+CCCACAGTATGTCCAGAGTGTCCCCAAAGGCCACAGTGCCCGCCTGGAGCCCTCCAGAGA
+GCGTGCACTCCCTGGGGTGCCAGCCAGAGACAACTTGCCCTGAGGCTTGGAACTCGATTC
+TCCGCGTGCCAGAGAAGGGGTGGGACTTCAGAACCCCCAACCCCGCAATCTGGGTCGGGG
+AGCCTGGCGCACTGCGGGCCGCTCCCTCTAACCCTGGGCTTCCCTG------GCGTCCAG
+GGCCGTCGG-----------GGCCGAGTCCCGATTCGCTCCCACCCCGAAGCCGCGCCAG
+GACCAACGAGGGCGCAGCCGTATGCCCCAGCCCGCTCCGCGGAGCCCCTCACAGCCAccc
+ccgccccgaccgcgccccgcgcggcTCGAAGCACCTTCCCAAGGGGCTGGTCCTTGC---
+-------GCCATAGTCGCGCCGGAGCCTCTGGAGGGACATCAAGGATTTCTC-GCTCCTA
+CCAGCCACCCCCAAATTTTTGGGAGGTACCCAAGGGTGCGCGCGTGGCTCCTGGCGCGCC
+GAGGCCCTCCCTCGAGGCCCCGCGAGGTGCACACTGC---------GGGCCCAGGGCTAG
+CAGCCGCCCGGCACGTCGCTACCCTGAGGGGCGGGGCGGGAGCTGGCGCTAGAAATGCGC
+CGGGGCCTGCGGGGCAGTTGCGCAAGTTGTGATCGGGCCGCTATAAGAGGGGCGGGCAGG
+CATGGAGCCCCGTAGGAATCGCAGCGCCAGCGGTTGCAAGGTAAGGCCC-CGGCGCGCTC
+CTTCCTCCTTCTCTGCTGGTCTTTCTTGGCAGGCCACAGGGCCCCACACAACTCTGGATC
+CCGGGGAAACTGAGTCAGG-AGGGATGCAGGGCGGATGGCTTAGTTCTGGACTATGATAG
+CTTTGTACCGAG-----TTCTAGCCAGATAGAAGGTTACCGGGAGCTGGGGAGCGTTGGA
+TTTGCTGCTGGGCTGTGCCGGTGCCCAGAAGGCA------GGACCTTGCAGAACCAGCCA
+GGTCCCTGGGAGACTGTCAGACCCACCAACCTGGTGGCATTCGCAGAGCTGAGATGCATT
+GGAAATTGCCTTGGGCACATCCCCAAAGATCAGGATGTCCCACCCCAGTCTGAAGGAGA-
+--TAAAGTTGGGGGTAGGAGAGACGCAG-ATGCAAGTGATCAGTCTC---AGTCCCAGAC
+ATTGCCTTGCTCTGCGGGTAGGAATTCAGGATTCATTTTCCAGGGAAG--------TTCC
+TGACCTCTGAATGAGAGGGGCTGTGTAAGGCCAATGCCTGGG-AGGAAGGCAAGGATGAG
+TAGAGGTGGGGGGAAACAAGTGTCAGGAAGA-----------------------------
+---------------CTCAAA---------ATCTTC------------------------
+--------------------------------------CAGAGAAATTGT-----GCAGG
+GTCTTACCAGATCTGTCCTCAAAGCCATGCAAATTGCCTTCTTTGCAATGCAT-ACAATG
+AGGTGTCTCTGGGGGTCAGAACTGG-----------------------TTATTAGGGAAC
+TTCTAGCCAGGACTGCTAAATACGCGCTGTTGG---------CCCACCAGGCTCACCTAT
+AGCCT-TCCTTCAGTCTGGGCTTGGTTTGGATTTCACTGTGGGTGCCATCGCCTTTACAC
+TCCTGTTTCTATAGTTTAAAGATAGTGGTGCTTTGGGAAAG---TGACTCCTTAAATACA
+GTTAGGTCCAAGTGA-GACAAGTGGCCTGGCTGTCATTTCAGAATAGCAGCTTCCAAGAG
+G----------TGATTAATTTCTGTTGGAAGGGTGAT-CTTTGGGGAGGT--GGGTGAAG
+AGCAGAGACTTGGTGGTACCGTTCCAGGAGCACAGGCTCTCT-----TCCTTTGCA--GT
+GCAGAATGACCTCTGGCAGCCGGAGTTGTGTTTGTT--------CTGTAGGATTCTGAGG
+TGGGCCATGGGCAGCTGGAACTGGG-----GAATTTTGCCAATCTCTTTCATATTAGGAT
+TGTCTGCAGAACCAGATATGGAGG------CTTCTAGCAACGTGAGTGCTCCTGTTCTAA
+TGCCCTTAGAAACAAGAAGGCCACACTGATCATTTCTCTCACTTAGGCAGGGAGACAAGG
+CAAGAGAGAAACAGT-----------------GGATGC--TTTTAGGTTCTTTCCCTTCC
+CAAGCAGTTGTGGACATTGGGCTGA-GGGGAACATTTCCACATTGGCTAAAGGAGCGTCC
+TCCTCATATTTTGTACATTTTATACCCAA--AATAA-CTCTTCTTGGTATTT-GGGGAAA
+TATTTTCCTCCCCGTCC------------ATTCCAGGAAATGGCTCCAAGTGCCAAGGAC
+AGAGCCAGGGAAGTTGCAATGAATTCCTGCCCGTCAGCCCCAGGCAGATGCCTTGCACGT
+CTGAGTGGCCCATGCAGAGCGTGGAGGTGGCCGCC----------------ACGGAACC-
+TGGGTCAATGT-CCCACCCCCG----CTTAGATGCCA-CCAGGGG--CGTGGGAGCCAAG
+GAG--AGAAGAGGGGCTCCAGGAAGGTAGAGTCCTTGTGTCTTGTGCATCTGTGAACAGC
+ACTGGTATGATTTAAAGGAAAATTGAGCCAAATTTTCCGGCAGTCAGTT-----ACCCCA
+TCCCCACCGGGGTAGGAGTCTGGCAGCCGCAGCTCCATTCTGGCCAGTCGGCAGAGAGCC
+TTGAAATTCTTCTTTGTCCACACAGTTGTCTCAGAGAAACAG--AGAGGTT-GTTTCTGC
+TTAAAAACAACACACTTGGTGTCTGGGCCCACAGACTCCTTTGCACTTATTCCACGTGTG
+ACAGCCAATGTGCCTCGTTGCTTAGCAGACAGCATGTTACCGTCTTTCCTGCTCAGTTTG
+TTAG--------------CTCTATGGAATGGAATTTATAATCAATGCCCATACCAACATT
+TCACTAATATCATAGGAGATTTAGTCTCCATCTGGGTGTACATTACATTTGC--TCTGGG
+G-TGCTCCAGGC--TGGGGGGTTGCCAAGGAAGAGAAGAGAAACCGCAGAGAAGAC---G
+GGAGGGCAGGGCAGGGGTCTCTGAGAAGGGGAGGGGTCCCAGAGTGCAGGAGCAGGAGCC
+AGGCTC---------ATGAAAGGGGCCACGGGCGGGAGTATCCAGGGACGGCAGTCAAGA
+TGGAGCACAGCTTAGG--AAGCTGAAGGGAATCCTGGCCCACCTGGGTGCTAGAGGGCAC
+ATAGGAAGTGCAGGAAGCAGACCAAGGTCCCCAAGAGAGGGAGACCTGGACGCTGAAGCA
+TTTTCTGTCTTTATTAAG-------------ACAACTCCGTAAGAATTCCTGCTGGGCCA
+AAGTGAATTCTAGGATGCGACTTTAAGATGGGAGCAAGCGAACCATTGAGGAGGCAGGTT
+ACCCTAGTTAGCCAATGCAGATCGAGAATGGGAAATCTTTCatttattcatgcaacagat
+atttaacgaagccctgccgtgttccaggcctgtgatagatgctggaacaggtacagaga-
+---------tAc-------aggtgtcattaattgatcaggg--caacctctc---cttct
+gagt--cttgctggagcttcagatgc-ccctcacacagagctcgagggagcctc-aacaa
+ttgatcagaagtcaggcaccatggctcacgcatataatcccagcactttgggaggccaag
+gcaggtggatcactggagcccaggagttccagatcagctggggcaacatggcaaaacccc
+atctctattaaaaaaaaaaaaagtaactggatgtgatggtacacacctgtagtcccagct
+acttgggaggctgagaggtgggagaattgcttgagcccgggaagtcgggggtccagtgag
+ccttgatcacaccactgcactccagcctgagtgacagagcaagaccctgacacacacaca
+cacacacacacacacacacacacagattagagctgaaacaggagtagaaacctatctg-t
+atctctgATGA-GATCAGATC---------TTTCTGATGAACAGAAAGAATGTAACCCCT
+GTACTCACACCCTCTCTGCTGGTTACATATGTTAACACGATTTCTCAAATGAGGCTTTTG
+GTTGCAAATAAGAGAAAATCACTCACGCT-GGCCCTGTG--TTTTTCAAATTGTTTATTG
+TGATCAACATTTGAAAAAAGAGCCGAGACTCTCAAGAGTGCATTACCCACGGTAAGGGTG
+AATTTT-ACTTCTTGACACTTATTTCTCTTACATGTATCTATCTGTCTC-----AAATGA
+AAAATATATTTAGAAAGTTGAAAGCTATCCAAGTGAGTATAAGAAAAGAGTATCTCACCC
+TGAAGGCTAAGGACAGGGAGGGC---------------------------CACCAGGCCT
+CACGAGGACCCAGGAACCACAAAGAAGGCT-AGGAAGGAGCACAGGCGGTGACCATACTC
+TGGCTCAGTGGCTATGTGGGCTCTGGTCTCTCTCAGCTGTTCCATGCATATGAGGCCAAA
+TGTGGCTACCCTAGAGCTTCTGAGCCCTCAACAGAGATGAACTGGACTCTCTGCAGCCCC
+ACTCTAAATTCCTAAGAGAGAAGTTGATTGACCCAATCAGGGTCAGGAGAAGGAAGGGAG
+GAGGAAAGGGAGGAGAGAAGAGCCTCTTCGTCTCTTGCCTACCACTGGCCAGGCAATTGT
+AGCCAAGGGGGCTGGAGTGTAAATGCAAACATAGCCATCAAGGGTtgtgtatgtgtgtgt
+gtgtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGA-TCTCCCAGGAGGTCCC
+TACTAAACAGACTTAAGCCCGCAAAATTTTAGCTCTCCAGCCTCACACACTCCACCCCTC
+TACCATATTGAATCTTCCCAAACCAACTATGGCTTTCCCTAACTCCGGAGc------ttg
+gcctggaatgccctgcttcccctctttcccctggggaacgcctgtccttcaggcctcagt
+tcacacactgcctcccttgcaaagctctccTCCCATCCCCGGAGTCCCT--CTTCCCCTT
+TGTTCTTTGGGTTCTATGCTTCTTCCCTCATAACTCCCACCAGGTTGTGTTAAAATGAGT
+TGTTCAAGGTCCTGTCTGTTCCACTAGATTCTGAGCAACTTGGAGAACGAAGATCCAAAC
+TTCGCTGCCTTTATTTCCTCCTTTGTTCTTTTCTCATCCCCAAGTCCCTTCCAACTTGGA
+GTTATgaagaaaggaaggaaggaagggtgggagggaagaaCAGGAGGGGATCCCACAGG-
+AGAATGTGTATAGGGAGAGGACTCAGACTAGCTAAAGCTTTTCCCTCATAATTAATAGCA
+AATACCATGTTACCTGAATTTAATTCACAGTAGCATACAAAAGACTCGCTTTGTTCT---
+----CCCCA---------TTGATGTCATCAGAGG--------------------GCTGTG
+GG--------------CAGGCCTAATCTTGGCTCAGGAGGCCCTCCAGCCTGGATCTAAA
+GAGCAGCAGATGggccaggctcggtggctcatgcctgtaatcccagcattttgggaggcc
+gaggcgggtggatcacgaggtcaggagtttgagaccagcctggccaagatggtgaagcct
+cgtctctactaaaaatacaaaaattagccaggtgcggtggtgggcgcctgtatttccagc
+tacccgggaggctgaggaggctgaggcaggagaatcgcttgaacccgggaggcggaggtt
+gcagtgagccgaggtcacgccactgcactctagcctgggcaacagagcaagactccgtca
+aaaaaaaaataaaaaaataaaaaaataaaaaaaataaaGAGGAGCACACATCTCTGCCCA
+TCCTAACTCCCACTTTGACATTGAGGTCCCCAGGATGGAGGGTCTGCCTCCATCTGCCTT
+GTCCCCTG-CAATGGTGGGAAGGTGATGGAGCTCAAGTCTAGAGGCCACCAGCTTCTTAG
+GGAGG--TAGGAGGTG---------------GAGGGTGGGGTGC-GGGCCCTGCACACAA
+CTGCCAAGTGAGGATGGGGGTGGG-GTCCACCTGAGGATAAGTAACAGTGAGGCTGGTGC
+AGAGGACCCAGGTGGAGGTAGACAGCAGAATTTGTGGTGGGGT--GGATGGCAC-ATTAT
+ATAAGCCTCTCTTGC------TGCCCTGT---TTACTGAGATTGTTTCAttatctttttt
+ggcttttgtttttaagagatggggtcttgctgtgtcacacaggctggagtgcactgtgtg
+atcatacctcactgcagcctcgacatcctgggctcaggcaaacctcccaccttggcctcc
+caagtagctgggaccacaagcgtttgccaccacactcagctatttttatttttattttta
+--ttttttttagagatggggtcttgctgtgtcgcccaggctggtcttgaactcctgggct
+caagcgatcctcctgccttggcctcccaaagccctgggattataggctgagccaccacac
+ccagccACATTTCATCTGTGCAGCTCCAGGGGCTCCACATTCT-ACTCTTCTCATTTCTT
+CTCCAGGGTACCC----------ATGGCAAGGGATGAGGGT--AGAAGATGGGGCA--GC
+CAGGCCTTGATTAAAGGAGAAGGAAGGCAGCCTGTGGAGAGG---GCAGCC---C---AG
+GGAG---TGCAGAGAGAAGTGGGCCATGAGGGAGA---CAGCAGAGTGCAGGCTGCGTCC
+---CAAATGAGCATACAGCCCACTGTGAGCCCACC--ATCTTCCTAGA-GA--CCCCTCT
+CCTCTCC-AGGAGCTGCTTCAGTAGCACTCA---------GAGGAAAGAATGATGC----
+----TGTATCAACATTTCAGCAGCTCATCTTTTAACTCTAAGAAAATGGCAGCTCCTAAA
+TGTTCAA--AACTGCTTTGGAAACTTCT---GGAGAGAGGTTTTGCAGCTCAGGCAGACA
+GCTGATCGCGGCCTTTCTTCCACCCCAACCCATGCTCTCCCCATGCT--CTCCTGCCACA
+GCTGCAGCGGGCCCCTGGGTCCTACATTTGCAG-CCCTTTGTCTCTGAGCT-----CAGA
+CTTCCAATTCCAAGCGGCAGCTGGGCAGGCTCACCAGCATGT---CCAGCCAGTACTAGG
+ACATCAGCAGGAGC----CCAACCACCTCTTTCCAAAATCTCTCCTCATGTCTCTCCTAG
+TTTCCATCTCCATCCTTCTAGTCAGCCAGGCTGAAAACATT-----------------TG
+CTCCTCAGGGTGCAGAAGGGAAAGCTTTGCCTCCCTTCCTGGTGCTCACTGCCCCTGCGA
+TTCCAGCCCAAGCCCTCCCCGGCTCCTCACC----------CTGGTGTCAGCTGGAAGCC
+ACCATCTCCTAAACCCACCTGtgttcttccacctctgc--------cagggctgc-cctc
+tcctccaccttcacaaactcaattcctacccattctcaggtcccttatcaaatgccatct
+cctccatgatgcctccctgattccccTGCTGGAaataatggtgataacagctaag--gca
+ttggggttggctacgtgccaggcaaggagttggcactttacatgctttatctcatttcag
+ccacataacatcgacaggt-ggcattatgattcatatcatccccatctgatagccaggaa
+aactgagtcccagagaggttagc-cactttcctagggccCTGTGCTCTGACTCAAGCATA
+GCTCTGAGGAACTCTAGCATTCATCAGTTTAAGCACCATGACTTTCTTTGCTGAGTCACC
+CAAGGCAT-TTCTTCATTTAAATGTTCTTCCTTGGCCAGGCGCAGTGGCTCAggcccaat
+gcggtggctcacgcctgtaatctcaacactttgggaggccgaggtgggcagataatctga
+ggtcaggagttcaagaccagcctggccaacatggtgaaaccccatctctactaaaaatac
+aaaaaaatgaggctgggcgtgatgactcacacctgtaatcccagcactttgggaggccaa
+ggcaggtggattacatgaggtcaggagttcgagaccagcctggccaacatggtgaaatcc
+tatctctattaaaaatacaaaaaattagccaggcatggtggcaggcacctgtaatcccag
+ctacttgggaggctgaggcaggaaaatggcttgaacccgggaggtggaggttgcagtgag
+ccaaggttgcaccattgcactccagcctgggcaaaaagagggaaacatcgtctaaaaaag
+aaaaaaaaaaaattagccaggctgggtggtgcatgcccgtaattccagctactcaggagg
+atgaagcaagagaattgcttgaacccaggaggcagagattacagtgagctgagatcacaa
+cactgcactccagcctaggtaaagaacaagactccatctcaaaaataaataaataaaaat
+aaaTGTTCTTCCTTGCAATGAAGTTAAATATGTAAATTCTCAAACCAGTTGCTTAAGGGC
+ACAGTTTTGTTCTTTACCTATATTTTTAACAAATATTTTATGTAAGTAGTTGAC-AAAAT
+CAAATACTGT-GTACACTACCGAGGCTTCCCTGGGAAAGCCATCAG-CCTCTGCCCCATC
+CCTTCCCACTCCTGATT-CCACTTTCCTGTGTTTCCATATCTTTTTCATGTCTGTTTCTG
+GCCCACAGTGGGCGATCAATACATGTTAGCCACCAACCATCAAACCTATATTGAGTAATT
+ATGGTATGTCAGGCACTATGCTCAATGAAATTGTAttaggcttgtacaaaagtaattgtg
+gtttttaagagtaatggcaaaaacggcagttactttcgcaccaacTATTTGCTGCCTTGA
+ATTATTCCTCCTCTC-CTCATCCCTAAACCCTGCTCCTCCCAGCCATTCTTCCTCCCCTT
+CTTGGGCCATGGCCAGGCCCCACCCAGGTACTAAGACTCAGGTGAACCAAGGAAGACTTA
+ATGCCCACTCTTTTCTGATGCCCATGTT--GGCATGTGTTAAGtcggttagcattaagtt
+tggctgcatttagcagagacccaaaagaacagtgccttttaaaaggcagaggttatgtct
+ctcacacacacccagcacaagtccaag-------------------------accagcat
+ggcatctcagctccatcaa--cctcaggaaccgagctcctgcagctccctgccctgcagt
+tgataaggtgaggtctttgtcctcctggttcaagatggtgctagaatgttggctaccata
+tctatagtccaggcatcagaatggagcaagggatgaaaaaggaagagatgaaggcacacg
+acaggttcctgagagctggcacaggacacttctgcttatatttcactggccagaacttag
+tcacatggtcacacctagttgggagactctgagaagtaa----agtatttattctagatg
+gccatatccctacc-taagacttggagttttctatgactggggaagaacggaagacaaga
+tattgggaaagactagcagcctctactaAAAGGGTGATCtgtgttgatgtgcgtgtgtgt
+gtgatgtttgtatg---agcatgtgtgt-tatgtgttgt--gtgtTGGTGGGGCA--GAT
+TCTTGCGAGCACTTTGGTCTCAGATGGACCTGCTACCAGTTCTCTCTGCAGACCCCCATA
+GGTTTCTCCTAAACCTGGCCT-CTCCTATTAGGCAGCCTTACTCAGCGGCAGCTTCTCAG
+CTCCATGTTTTCAAGGAACCACAATTTATTTCCAGCATCCACTGAAGCATATTATCAGTG
+GTGATAGAGGGGGCTTGTAAAACTGTTTTTCCACTTAGGTATTAGAGGGTGGCCATTATT
+TGAGAGTGAC-----TATGACCACAGTTAATCTGGTAATAAATTCTCTTGGGTAGGAGGG
+GGAAAGGAAAGGATGCTTTAAGGAAGCATCTTGCCAGGAGACACAAAGCTAACAAGAGTG
+GAGCCTGCAG----------------------------CTGGAGCCGCAGAGCCTAATCA
+CTACACCCGCCCATCTCTGCTAGGGTTTCATGACTTCGTATCGGGGATTAGCAGTATTTA
+ACTCTGTTGCACAAACATTTGGTGTA-----TTATTCAGGTAACAAGTAGCTAATAGAGG
+AAGTTTTACTTTTTTAAGACATAA--------------------ATTTGCCTTTTCCCAA
+ATTACTTGGTACATAGTAC-TTTTCATGTTTGAAGTTGAGATGTGGGTACAATACCATAG
+CTTTATTCCAGAGCAGGGTATTTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGAC
+TGGGAATTGGGGTG-----TGATTTGGGCTTTTCCTTAAATCCTTGA-----GGAGCTGG
+A---GGGGTGGGTGGCTCGCACTCCTGCTTTctgg---------atctgaatc-------
+-------ctgactctgtcatggacctgtt-tgactttgggcaagttgactcctattcctg
+agccccatat-ttttctcttctgtgaaattcagattaaaaA-AACATGGCTTTGATCAAA
+CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAG-AAATGAATCC
+TACTAATATTGCCATCTATGGACAGAAAATGTATTACCTGTCTTCATCAAGACCCAGACG
+AGGAAGAACACGAAAAGCGGAGATTAATTTTACTGCCATCTCCAGAACCGTCATCCTAAT
+ATTTACTTACAT-TTTATTATTATTTCAGGCTCATGCACATATACTTAGCATGGATCATT
+GGCCACAGACTCGCATACATTTAACTTTATTACCTTT-TGCCTCATGTATCTCATTAAAA
+TTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCAAGA
+CTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgc--tctctcccgccaccatgtc
+tttataccccctgatttctcagccact-atggcaaccactttctactcttagtagcccat
+atttag--tccaatccccagctcaggagacacttcttccaggg--agccccctgtgcctt
+ccagtagtatcttgtacctgccctttttgcaaagctctttcctcctggcttagaatggcc
+cattgacctgtttgtttctcctattaaactgtaagccactcgagggtagagagcatctgt
+tgttcaccattgcatcctcggtgctgagcactgcgtctgacatattatttagaaggtcag
+taagtgctagtgggatTCAGGCTCCCAGTGGGTGGGAGAGAAAGGACGTAAGGAAGCAAG
+TGGTAAAGGCCCTCACAGA-GTATCAGCAGGCTGGTGTGA-GGGAGAAATGCAGAGGATG
+GGTGAGTAGCA-----TAATCGCTAATGAT-AGGGTAATGATAGAGCACATTTCACAACA
+CCTTt-aagccctttcacgtgcatcagataatttgatcctcataaaagcctagagataga
+tatattacagg-gatgaaggtggagtattttgtggttatgtgatatg-tttaaaattatg
+cagtgagtaaatgactgggttcaaaccagaccttaaaagtctgttatctttccCTCG-AG
+CATGCAATGAAGTCTACATCATCCCTACCATGTCCATTTGATCACACCCTGGCCTCACAG
+CTCTGTGGTCTACAGGATACCTCATGGTGGTTTTATTGACCAGACAATAATCCTCTTTCT
+AAGGGGATGCATTTCATTAATACATATGTAGATCATGAATTGTCTTTGACTTTGAGGGGA
+TGGTAGC----CAGAGCAGAAAGCAAAGCTGATTTTCATCCCCGTCTGGTAATGTGGTTG
+GTAATGTGAAGA-TGGGTGTATTCTGAGATACCGGCTCCTTGCAGTGTGTGGTTCCTTCT
+GTTTTCAGGCCC------AAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTG
+TGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAA
+GTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCA
+CACACGGTAAGGAG---AGTATGCGGGGACAAA---GTAGAACTGCAGCCAGCCCAGCAC
+TGGCTCCTAGTGGCACT-GGACC-CAGATAGtccaagaaacatttattgaacgcctcctg
+aatgccaggcacctactggaagctgagaaGGATTTGAAAGCACAGGGC-TCCACTCTTTC
+TGGTTGTTTCTTTTGGCCCCTCTGCCTGCTGAGATTCCAGGGGTTAGTGG----------
+----------------------------------------------TTCTAATTCTAAAC
+CACTCCAAGAACATTTGATTTTGCTACATGTTTCCATTTAAAAATCATAGGATTTGggct
+gggtgtggtggcttgtacctgtcatcccagcactttgggaggccaaagcaggaggatcat
+tcgagcccaagagttcgagaccagcctgggcagcatagggagaccccatctctacaaaaa
+taataaaaaatgttagctgggcatggtggtgtgtacctgtggtcccagctaggggaggct
+gagatggaaggatcacctgagcctgggaggttgaggctgcagtgggccctgatcatgcca
+ccgtgctccagcctgggtgacagagtgagaccttgtctcaaaataaataaataaataaat
+aaaAGTCATAGGATTTgatcaggcatgatgggtcacatctgtaagcccattgctttagga
+ggccaaggtaggaggatcagttgaggccaggagttcaagaccagcctgggcaacatggca
+agacctctctctctaatttttaaaaaaataaaaaTTAAAGATAAGAAAAAAATCATAGGA
+TTCTCATGAGGCCTCACGTGCTTATTTTCAACCTACCAAGGGGAAACCCAGGCCTCAGCG
+ATTAGCTGAGC----------CACATGCAGGCACAG------------------------
+CCACTG-----TCTCTTTCCTTCCTGTCCCCTCTGTCCCCACCTTCTGCGCTCGCCTTCC
+TCCCTGACTTCACTTCCTTGAATCTTAGTGCCTACGACCAGAGGGAGCTGTGAAGTTCCT
+TG----TGTCCCATTGGCAGGAA-CAAGACCCCCAGAAGCATCTCCTCAGGGC------C
+TCTA-----TCCCATCTC-TAGATGTGCTTGTCATTAGG-Gttct-------------tg
+tagttccagctgatctctggccctgccgctcaaagatacccaaaagagcgagtctaccct
+ttttcacattcaaccctctactgatttgcaaatagcagtcagtgcccaccctggtctttt
+ctctggggtccagcaggcctagaccttcagccattttcctgatgaGGTCTGTAtttgaaa
+ttaggaagattaagtttgaatcttcacacttctgat----gtctgtgagatcttcagcaa
+gttccttact--gtctttaagccttgt-tttcatcatctggataatggggatatcacaca
+cta-ttcacaaggttgttatgaggcctaaattagctaaagcaATTGAATCCTCCTTACCC
+CCTGCATGGAGCTCTCTGGAGACTTCCACGTCTCCTGGTCATTGTGGGTGTCTTATGGTA
+-GTCTTGGGCAGTTAGGGAGAAGTTAGGTGTCTGGAAGCAAAGATGGCTCAGAACTAGAT
+AGAGTC-TTGGGCATTTTATA-GATAAAAACTCTT--GTCTCCtttaaaaataataaaaa
+aaaattaGCTGGGCATATTAGCCACTCAGCAAGACTGCACGTGATAGATCCCGAGTGCCC
+CACCTTGGGTGGTGTAATACACAATATCACGGGAGCCCCGGGTAGTAACCACGGAGGTGT
+CAGCCTCAGTGCTGTGGGCAGATG-GATGGGGAGAGCC--TCCCGG-AACTGGAGTCACT
+GGAGCA----------------------------GGGTTGGGGGGCCTCACTGAGGGTAC
+GGCCTTGATCTCTAAGGAGGAGGGACTGCCTGGAAAAGC-TGACTGGGAGGGAGGACTCG
+GCTGGGGGTAGAAGGGA----------CTAGGGAAGGCTGGGGGTGGGGGTGCTTATGGA
+GGACCTCAGATGCCTGGGGAACAGACTCCACTAAATAAAACATATGAAACCATGGCTGGT
+TCTTCAGCAGAGGCCATGTAGAGAAAGGAATGACCTAGGAAAGTTGGCCTGGAAGTGGAG
+GGAAGGATGGTGTGGGAAAAGCAGGAA--------TCTCGGAGACCAGCTTAGAGGCTTG
+GCAGTCACCTGGGTGCAGG-ATACAAGGGCCTGAGCCAAAGTGGTGAGGGAGGGTGGAAG
+GAGGCAGCCCAGAGAATGACCCTCCATGCCCACGGGGAAGGCAGAGGGCTCT-GAGAGCG
+A--TTCCTCCCACATG-CT-GAGCACTTGTTCTCCCTCTTCCTCCTGCATAGCAGTCAGT
+CTCCTCCAAACAGAAAGTCACCGGTTTGGACTTCATTCCTGGGCTCCACCCCATCCTGAC
+CTTATCCAAGATGGACCAGACACTGGCAGTCTACCAACAGATCCTCACCAGTATGCCTTC
+CAGAAACGTGATCCAAATATCCAACGACCTGGAGAACCTCCGGGATCTTCTTCACGTGCT
+GGCCTTCTCTAAGAGCTGCCACTTGCCCTGGGCCAGTGGCCTGGAGACCTTGGACAGCCT
+GGGGGGTGTCCTGGAAGCTTCAGGCTACTCCACAGAGGTGGTGGCCCTGAGCAGGCTGCA
+GGGGTCTCTGCAGGACATGCTGTGGCAGCTGGACCTCAGCCCTGGGTGCTGAGGCCTTGA
+AGGTCACTCTTCCTGCAAGGACTACGTTAAGGGAAGGAACTCTGGCTTCCAGGTATCTCC
+AGGATTGAAGAGCATTGCATGGACACCCCTTATCCAGGACTCTGTCAATT--TCCCTGAC
+TCCTCTAAGCCACTCTTCCAAAGGCATAAGACCCTAAGCCTCCTTTTGCTTGAAACCAAA
+GATATATACACAGGATCCTATTCTCACCAGGAAGGGGG-TCCACCC-AGCAAAGAGTGGG
+CTGCATCTGGGATTCCCACCAAGGTCTTCAGCCATCA---ACAAGAGTTGTCTTGTCCCC
+TCT-TGACCCATCT-----------------CCCCCTCACTGAATGCCTCAATGTGACCA
+GGGGTGATTTCAGAGAGGGCAGAGGGGTAGGCAGAGCCTTTGGATGACCA--GAACAAGG
+TTCCCTCTGAGAATTCCAAGGAGTTCCATGAAGACCACATCCACACACG--CAGGAACTC
+CC--AGCAACACAAGCTGGAA---GCACATGTTTATTTATTCTGCATTTTATTCTGGATG
+GATTTGAAGCAAAGCACCAGCTTCTCCAGGCTCTTTGGGGTCAGCCAGGGCCAGGGGTCT
+CCCTGGAGTGCAGTTTCCAATCCCATAGATGGGTC-TGGCTGAGCTGAACCCA---TTTT
+GAGTGACT----CGAGGGTTGGG-TTCATCTGAGCAAGAGCTGGCAAAGGTGGCTCTCCA
+GTTAGTTCTCTCGTAACTGGTTTCATTTCTACTGTGACTGATGTTACATCACAGTGTTTG
+CAATGGTGTTGCCCTGAGTGGATCTCCAAGGACCAGGTTATTTTAAAA---AGATTTGTT
+TTGTCAAGTGTCATATGTAGGTGTCTGCACCCAGGGGTGGG-GAATGTTTGGGCAGAAGG
+GAGAAGGATCTAGAATGTGTTTTCTGAATAACATTTGTGTGGTGGGTTCTTTGGAAGGAG
+TGAGA-TCATTTTCTTATCTTCTGCAATTGCTTAGGATGTTTTTCATGAAAA--------
+----TAGCTCTTTCAG-GGGGGTTGTGAGGCCTGGCCAGGCACCCCCTGGAGAGAAGTTT
+CTGGCCCTGGCTGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCA
+GAATAAAACGCAAAGGGCTGAAAGCCATTTGTTGGGGCAGTGGTAAGCTCTGGCTTTCTC
+CGACTGCTAGGGAGTGGTCTTTCCTATCATGGAGTGACGGTCCCACACTGGTGACTGCGA
+TCTTCAGAGCAGGGGTCCTTGGTGT-GACCCTCTGAATGGTCCAGGGTTGATCACACTCT
+GGGTTTATTACATGGCAG-----TGTTCCTATTTGGGGCTTGCATGCCAAATTGTAGTTC
+TTGTCTGATTGGCTCACCC-AAGCAAGGCCAAAATTACCAAAAATCTTGGGGGG--TTTT
+TACTC-CAGTGGTGAAGAAAACTCCTTTAGCAGG-TGGTCCTGAGACCT-GACAAGCACT
+GCTAGGCGAGTGCCAGGACTCCCCAGGCCAGGCCACCAGGATGGCCCTTCCCACTGGAGG
+TCACATTCAGGAAGATGAAAGAGGAGGTTTGGGGTCTGCCACCATCCTGCTGCTGTGTTT
+TTGCTATCACACAGTGGGTGGTGGATCTGTCCAAGGAAACTTGAATCAAAGCAGTTAAC-
+TTTAAGactgagcacctgcttcatgctcagccctgactggtgctataggctggagaagct
+cacccaataaacattaagatt-gaggcctgccctcagggatcttgcattcccagtggTCA
+AACC-GCACTCACCCATGTGCCAAGGTGGGGTA-TTTACCACAGCAG--CTGAACAGCCA
+AATGCATGGTGCAGTTGACAGCAGGTGGGAAATGGTATGAGCTGAGGGGGGCCGTGCCCA
+GGGGCCCACAGG-GAACCCTGCTTGCACTTTGTAACATGTTTA-----CTTTTCagggca
+tcttagctt---ctatta-----tagccacatccctttga---aacaagataactgagaa
+tttaaaaataagaa-----aata--TGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC
+TTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGC
+TTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACG
+CAAATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAA
+ACGCATGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA
+AACGCAGACCCCAAAGAGCCTGGAGAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAA
+AACGCAGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGACCCCAAAGAGCCTGGA
+GAAGCTGATGCTTTGCTTCAAATCCATCCAGAATAAAACGCAGATGCTTTGCTTCAAATC
+CATCCAGAATAAAACGCAgttcgatgcctaaaataccttcttttgtccctacacagacca
+cagttttcctaatggctttacaccgactagaaattcttgtgcaagcactaattgaaagcg
+gttggcctagagtgttaccggtttgtatagctgagcgcgtctcttgccctgatcaaaggt
+tcattttctctactttggaagacgttgtggaagaatacaacaagtacgagtctctccccc
+ctggtttgctgattactggatacagttgtaatacccttcgcaacaccgcgtaactatcta
+tatgaattattttccctttattatatgtagtaggttcgtctttaatcttcctttagcaag
+tcttttactgttttcgacctcaatgttcatgttcttaggttgttttggataatatgcggt
+cagtttaatcttcgttgtttcttcttaaaatatttattcatggtttaatttttggtttgt
+acttgttcaggggccagttcattatttactctgtttgtatacagcagttcttttattttt
+agtatgattttaatttaaaacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_patmatdb_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,41 @@
+SeqName	Start	End	Score	Strand
+Sequence	560	561	2	+
+Sequence	559	560	2	+
+Sequence	558	559	2	+
+Sequence	557	558	2	+
+Sequence	550	551	2	+
+Sequence	544	545	2	+
+Sequence	541	542	2	+
+Sequence	540	541	2	+
+Sequence	539	540	2	+
+Sequence	534	535	2	+
+Sequence	449	450	2	+
+Sequence	431	432	2	+
+Sequence	430	431	2	+
+Sequence	429	430	2	+
+Sequence	409	410	2	+
+Sequence	393	394	2	+
+Sequence	364	365	2	+
+Sequence	340	341	2	+
+Sequence	326	327	2	+
+Sequence	287	288	2	+
+Sequence	274	275	2	+
+Sequence	264	265	2	+
+Sequence	252	253	2	+
+Sequence	204	205	2	+
+Sequence	201	202	2	+
+Sequence	196	197	2	+
+Sequence	193	194	2	+
+Sequence	181	182	2	+
+Sequence	158	159	2	+
+Sequence	157	158	2	+
+Sequence	98	99	2	+
+Sequence	97	98	2	+
+Sequence	92	93	2	+
+Sequence	85	86	2	+
+Sequence	74	75	2	+
+Sequence	73	74	2	+
+Sequence	53	54	2	+
+Sequence	14	15	2	+
+Sequence	13	14	2	+
+Sequence	12	13	2	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_pepcoil_out.pepcoil	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,6 @@
+PEPCOIL of Sequence
+   using a window of 28 residues
+
+
+Other structures from 1 to 561 (561 residues)
+   Max score: 0.827 (probability 0.00)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_pepstats_out.pepstats	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,48 @@
+PEPSTATS of Sequence from 1 to 561
+
+Molecular weight = 48582.66  		Residues = 561   
+Average Residue Weight  = 86.600  	Charge   = 0.0   
+Isoelectric Point = 5.0278
+A280 Molar Extinction Coefficient  = 0       
+A280 Extinction Coefficient 1mg/ml = 0.00      
+Improbability of expression in inclusion bodies = 0.520
+
+Residue		Number		Mole%		DayhoffStat
+A = Ala		135		24.064 		2.798  	
+B = Asx		0		0.000  		0.000  	
+C = Cys		106		18.895 		6.515  	
+D = Asp		0		0.000  		0.000  	
+E = Glu		0		0.000  		0.000  	
+F = Phe		0		0.000  		0.000  	
+G = Gly		98		17.469 		2.080  	
+H = His		0		0.000  		0.000  	
+I = Ile		0		0.000  		0.000  	
+J = ---		0		0.000  		0.000  	
+K = Lys		0		0.000  		0.000  	
+L = Leu		0		0.000  		0.000  	
+M = Met		0		0.000  		0.000  	
+N = Asn		0		0.000  		0.000  	
+O = ---		0		0.000  		0.000  	
+P = Pro		0		0.000  		0.000  	
+Q = Gln		0		0.000  		0.000  	
+R = Arg		0		0.000  		0.000  	
+S = Ser		0		0.000  		0.000  	
+T = Thr		222		39.572 		6.487  	
+U = ---		0		0.000  		0.000  	
+V = Val		0		0.000  		0.000  	
+W = Trp		0		0.000  		0.000  	
+X = Xaa		0		0.000  		0.000  	
+Y = Tyr		0		0.000  		0.000  	
+Z = Glx		0		0.000  		0.000  	
+
+Property	Residues		Number		Mole%
+Tiny		(A+C+G+S+T)		561		100.000
+Small		(A+B+C+D+G+N+P+S+T+V)	561		100.000
+Aliphatic	(A+I+L+V)		135		24.064
+Aromatic	(F+H+W+Y)		0		 0.000
+Non-polar	(A+C+F+G+I+L+M+P+V+W+Y)	339		60.428
+Polar		(D+E+H+K+N+Q+R+S+T+Z)	222		39.572
+Charged		(B+D+E+H+K+R+Z)		0		 0.000
+Basic		(H+K+R)			0		 0.000
+Acidic		(B+D+E+Z)		0		 0.000
+
Binary file test-data/emboss_plotorf_out.png has changed
Binary file test-data/emboss_plotorf_out1.png has changed
Binary file test-data/emboss_polydot_out.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_prettyseq_out.prettyseq	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,42 @@
+PRETTYSEQ of Sequence from 1 to 561
+
+           ---------|---------|---------|---------|---------|---------|
+         1 gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 60
+         1 V  R  C  L  K  Y  L  L  L  S  L  H  R  P  Q  F  S  *  W  L   2
+
+           ---------|---------|---------|---------|---------|---------|
+        61 tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 120
+         3 Y  T  D  *  K  F  L  C  K  H  *  L  K  A  V  G  L  E  C  Y   9
+
+           ---------|---------|---------|---------|---------|---------|
+       121 cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 180
+        10 R  F  V  *  L  S  A  S  L  A  L  I  K  G  S  F  S  L  L  W   16
+
+           ---------|---------|---------|---------|---------|---------|
+       181 aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 240
+        17 K  T  L  W  K  N  T  T  S  T  S  L  S  P  L  V  C  *  L  L   2
+
+           ---------|---------|---------|---------|---------|---------|
+       241 gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 300
+         3 D  T  V  V  I  P  F  A  T  P  R  N  Y  L  Y  E  L  F  S  L   22
+
+           ---------|---------|---------|---------|---------|---------|
+       301 tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 360
+        23 Y  Y  M  *  *  V  R  L  *  S  S  F  S  K  S  F  T  V  F  D   11
+
+           ---------|---------|---------|---------|---------|---------|
+       361 ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 420
+        12 L  N  V  H  V  L  R  L  F  W  I  I  C  G  Q  F  N  L  R  C   31
+
+           ---------|---------|---------|---------|---------|---------|
+       421 ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 480
+        32 F  F  L  K  Y  L  F  M  V  *  F  L  V  C  T  C  S  G  A  S   10
+
+           ---------|---------|---------|---------|---------|---------|
+       481 tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 540
+        11 S  L  F  T  L  F  V  Y  S  S  S  F  I  F  S  M  I  L  I  *   29
+
+           ---------|---------|-
+       541 aacaattctaatggtcaaaaa 561
+         1 N  N  S  N  G  Q  K   7
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_primersearch.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,7 @@
+# This is my primer file
+D1S243  cacacaggctcacatgcc      gctccagcgtcatggact
+D1S468 aattaaccgttttggtcct     gcgacacacacttccc 
+D1S2845 ccaaagggtgcttctc        gtggcattccaacctc
+D1S1608 gatggcttttggggactatt    cactgagccaagtgacacag
+D1S2893 aaaacatcaactctcccctg    ctcaaaccccaataagcctt
+D1S2660 cacacatgcacatgcac       agtgacaccagcaggg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_primersearch_out.primersearch	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,12 @@
+
+Primer name D1S243
+
+Primer name D1S468
+
+Primer name D1S2845
+
+Primer name D1S1608
+
+Primer name D1S2893
+
+Primer name D1S2660
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_revseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tttttgaccattagaattgttttaaattaaaatcatactaaaaataaaagaactgctgta
+tacaaacagagtaaataatgaactggcccctgaacaagtacaaaccaaaaattaaaccat
+gaataaatattttaagaagaaacaacgaagattaaactgaccgcatattatccaaaacaa
+cctaagaacatgaacattgaggtcgaaaacagtaaaagacttgctaaaggaagattaaag
+acgaacctactacatataataaagggaaaataattcatatagatagttacgcggtgttgc
+gaagggtattacaactgtatccagtaatcagcaaaccaggggggagagactcgtacttgt
+tgtattcttccacaacgtcttccaaagtagagaaaatgaacctttgatcagggcaagaga
+cgcgctcagctatacaaaccggtaacactctaggccaaccgctttcaattagtgcttgca
+caagaatttctagtcggtgtaaagccattaggaaaactgtggtctgtgtagggacaaaag
+aaggtattttaggcatcgaac
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_seqmatchall_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,3 @@
+
+#---------------------------------------
+#---------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_seqret_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_sigcleave_out.tabular	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,6 @@
+SeqName	Start	End	Score	Strand	mature_peptide
+Sequence	27	39	5.175	+	CCACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCA
+Sequence	253	265	4.809	+	CACCGCGTAACTATCTATATGAATTATTTTCCCTTTATTATATGTAGTAG
+Sequence	29	41	4.790	+	ACAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACT
+Sequence	541	553	3.820	+	GTCAAAAA
+Sequence	30	42	3.530	+	CAGTTTTCCTAATGGCTTTACACCGACTAGAAATTCTTGTGCAAGCACTA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_sirna_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,158 @@
+>Sequence_92 %GC 50.0 Score 9 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aattgaaagcggttggcctagag
+>Sequence_53 %GC 45.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatggctttacaccgactagaaa
+>Sequence_97 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaagcggttggcctagagtgtta
+>Sequence_98 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagcggttggcctagagtgttac
+>Sequence_201 %GC 55.0 Score 8 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aacaagtacgagtctctcccccc
+>Sequence_14 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aataccttcttttgtccctacac
+>Sequence_85 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagcactaattgaaagcggttgg
+>Sequence_181 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagacgttgtggaagaatacaac
+>Sequence_196 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatacaacaagtacgagtctctc
+>Sequence_204 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagtacgagtctctcccccctgg
+>Sequence_252 %GC 60.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatacccttcgcaacaccgcgta
+>Sequence_264 %GC 40.0 Score 7 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aacaccgcgtaactatctatatg
+>Sequence_38 %GC 45.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaccacagttttcctaatggctt
+>Sequence_73 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaattcttgtgcaagcactaatt
+>Sequence_96 %GC 55.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaaagcggttggcctagagtgtt
+>Sequence_118 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taccggtttgtatagctgagcgc
+>Sequence_200 %GC 50.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caacaagtacgagtctctccccc
+>Sequence_326 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatcttcctttagcaagtctttt
+>Sequence_364 %GC 35.0 Score 6 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatgttcatgttcttaggttgtt
+>Sequence_12 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaaataccttcttttgtccctac
+>Sequence_13 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaataccttcttttgtccctaca
+>Sequence_16 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taccttcttttgtccctacacag
+>Sequence_32 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacacagaccacagttttcctaa
+>Sequence_52 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taatggctttacaccgactagaa
+>Sequence_74 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aattcttgtgcaagcactaattg
+>Sequence_88 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cactaattgaaagcggttggcct
+>Sequence_91 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taattgaaagcggttggcctaga
+>Sequence_128 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tatagctgagcgcgtctcttgcc
+>Sequence_173 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tactttggaagacgttgtggaag
+>Sequence_193 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagaatacaacaagtacgagtct
+>Sequence_198 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacaacaagtacgagtctctccc
+>Sequence_243 %GC 45.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacagttgtaatacccttcgcaa
+>Sequence_251 %GC 55.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taatacccttcgcaacaccgcgt
+>Sequence_313 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taggttcgtctttaatcttcctt
+>Sequence_340 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aagtcttttactgttttcgacct
+>Sequence_393 %GC 35.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatatgcggtcagtttaatcttc
+>Sequence_489 %GC 40.0 Score 5 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tactctgtttgtatacagcagtt
+>Sequence_34 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cacagaccacagttttcctaatg
+>Sequence_36 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cagaccacagttttcctaatggc
+>Sequence_61 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacaccgactagaaattcttgtg
+>Sequence_63 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caccgactagaaattcttgtgca
+>Sequence_70 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tagaaattcttgtgcaagcacta
+>Sequence_84 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caagcactaattgaaagcggttg
+>Sequence_110 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tagagtgttaccggtttgtatag
+>Sequence_112 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gagtgttaccggtttgtatagct
+>Sequence_135 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gagcgcgtctcttgccctgatca
+>Sequence_180 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaagacgttgtggaagaatacaa
+>Sequence_183 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gacgttgtggaagaatacaacaa
+>Sequence_203 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caagtacgagtctctcccccctg
+>Sequence_210 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gagtctctcccccctggtttgct
+>Sequence_245 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cagttgtaatacccttcgcaaca
+>Sequence_254 %GC 60.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacccttcgcaacaccgcgtaac
+>Sequence_263 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caacaccgcgtaactatctatat
+>Sequence_266 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caccgcgtaactatctatatgaa
+>Sequence_348 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tactgttttcgacctcaatgttc
+>Sequence_395 %GC 40.0 Score 4 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tatgcggtcagtttaatcttcgt
+>Sequence_157 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaaggttcattttctctactttg
+>Sequence_158 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aaggttcattttctctactttgg
+>Sequence_207 %GC 65.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tacgagtctctcccccctggttt
+>Sequence_325 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taatcttcctttagcaagtcttt
+>Sequence_392 %GC 35.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taatatgcggtcagtttaatctt
+>Sequence_409 %GC 30.0 Score 3 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+aatcttcgttgtttcttcttaaa
+>Sequence_11 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+taaaataccttcttttgtcccta
+>Sequence_41 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cacagttttcctaatggctttac
+>Sequence_43 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cagttttcctaatggctttacac
+>Sequence_67 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gactagaaattcttgtgcaagca
+>Sequence_72 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaaattcttgtgcaagcactaat
+>Sequence_130 %GC 65.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tagctgagcgcgtctcttgccct
+>Sequence_192 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaagaatacaacaagtacgagtc
+>Sequence_195 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gaatacaacaagtacgagtctct
+>Sequence_236 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tactggatacagttgtaataccc
+>Sequence_241 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gatacagttgtaatacccttcgc
+>Sequence_304 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tatatgtagtaggttcgtcttta
+>Sequence_306 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tatgtagtaggttcgtctttaat
+>Sequence_310 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+tagtaggttcgtctttaatcttc
+>Sequence_358 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gacctcaatgttcatgttcttag
+>Sequence_370 %GC 35.0 Score 2 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+catgttcttaggttgttttggat
+>Sequence_156 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+caaaggttcattttctctacttt
+>Sequence_403 %GC 30.0 Score 1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+cagtttaatcttcgttgtttctt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_sixpack_out2.sixpack	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,134 @@
+
+
+          V  R  C  L  K  Y  L  L  L  S  L  H  R  P  Q  F  S  *  W  L     F1
+           F  D  A  *  N  T  F  F  C  P  Y  T  D  H  S  F  P  N  G  F    F2
+            S  M  P  K  I  P  S  F  V  P  T  Q  T  T  V  F  L  M  A  L   F3
+          gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+                   10        20        30        40        50        60        
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa
+           T  R  H  R  F  Y  R  R  K  D  R  C  L  G  C  N  E  *  H  S    F6
+          X  E  I  G  L  I  G  E  K  T  G  V  C  V  V  T  K  R  I  A     F5
+            N  S  A  *  F  V  K  K  Q  G  *  V  S  W  L  K  G  L  P  K   F4
+
+
+          Y  T  D  *  K  F  L  C  K  H  *  L  K  A  V  G  L  E  C  Y     F1
+           T  P  T  R  N  S  C  A  S  T  N  *  K  R  L  A  *  S  V  T    F2
+            H  R  L  E  I  L  V  Q  A  L  I  E  S  G  W  P  R  V  L  P   F3
+          tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+                   70        80        90        100       110       120       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg
+           *  V  S  *  F  N  K  H  L  C  *  N  F  A  T  P  R  S  H  *    F6
+          K  C  R  S  S  I  R  T  C  A  S  I  S  L  P  Q  G  L  T  N     F5
+            V  G  V  L  F  E  Q  A  L  V  L  Q  F  R  N  A  *  L  T  V   F4
+
+
+          R  F  V  *  L  S  A  S  L  A  L  I  K  G  S  F  S  L  L  W     F1
+           G  L  Y  S  *  A  R  L  L  P  *  S  K  V  H  F  L  Y  F  G    F2
+            V  C  I  A  E  R  V  S  C  P  D  Q  R  F  I  F  S  T  L  E   F3
+          cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+                   130       140       150       160       170       180       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc
+           R  N  T  Y  S  L  A  D  R  A  R  I  L  P  E  N  E  R  S  Q    F6
+          G  T  Q  I  A  S  R  T  E  Q  G  S  *  L  N  M  K  E  V  K     F5
+            P  K  Y  L  Q  A  R  R  K  G  Q  D  F  T  *  K  R  *  K  P   F4
+
+
+          K  T  L  W  K  N  T  T  S  T  S  L  S  P  L  V  C  *  L  L     F1
+           R  R  C  G  R  I  Q  Q  V  R  V  S  P  P  W  F  A  D  Y  W    F2
+            D  V  V  E  E  Y  N  K  Y  E  S  L  P  P  G  L  L  I  T  G   F3
+          aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+                   190       200       210       220       230       240       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac
+           F  V  N  H  F  F  V  V  L  V  L  R  E  G  R  T  Q  Q  N  S    F6
+          S  S  T  T  S  S  Y  L  L  Y  S  D  R  G  G  P  K  S  I  V     F5
+            L  R  Q  P  L  I  C  C  T  R  T  E  G  G  Q  N  A  S  *  Q   F4
+
+
+          D  T  V  V  I  P  F  A  T  P  R  N  Y  L  Y  E  L  F  S  L     F1
+           I  Q  L  *  Y  P  S  Q  H  R  V  T  I  Y  M  N  Y  F  P  F    F2
+            Y  S  C  N  T  L  R  N  T  A  *  L  S  I  *  I  I  F  P  L   F3
+          gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+                   250       260       270       280       290       300       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa
+           S  V  T  T  I  G  K  A  V  G  R  L  *  R  Y  S  N  N  E  R    F6
+          P  Y  L  Q  L  V  R  R  L  V  A  Y  S  D  I  H  I  I  K  G     F5
+            I  C  N  Y  Y  G  E  C  C  R  T  V  I  *  I  F  *  K  G  K   F4
+
+
+          Y  Y  M  *  *  V  R  L  *  S  S  F  S  K  S  F  T  V  F  D     F1
+           I  I  C  S  R  F  V  F  N  L  P  L  A  S  L  L  L  F  S  T    F2
+            L  Y  V  V  G  S  S  L  I  F  L  *  Q  V  F  Y  C  F  R  P   F3
+          tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+                   310       320       330       340       350       360       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg
+           *  *  I  Y  Y  T  R  R  *  D  E  K  L  L  D  K  V  T  K  S    F6
+          K  N  Y  T  T  P  E  D  K  I  K  R  *  C  T  K  *  Q  K  R     F5
+            I  I  H  L  L  N  T  K  L  R  G  K  A  L  R  K  S  N  E  V   F4
+
+
+          L  N  V  H  V  L  R  L  F  W  I  I  C  G  Q  F  N  L  R  C     F1
+           S  M  F  M  F  L  G  C  F  G  *  Y  A  V  S  L  I  F  V  V    F2
+            Q  C  S  C  S  *  V  V  L  D  N  M  R  S  V  *  S  S  L  F   F3
+          ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+                   370       380       390       400       410       420       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca
+           R  L  T  *  T  R  L  N  N  Q  I  I  H  P  *  N  L  R  R  Q    F6
+          G  *  H  E  H  E  *  T  T  K  S  L  I  R  D  T  *  D  E  N     F5
+            E  I  N  M  N  K  P  Q  K  P  Y  Y  A  T  L  K  I  K  T  T   F4
+
+
+          F  F  L  K  Y  L  F  M  V  *  F  L  V  C  T  C  S  G  A  S     F1
+           S  S  *  N  I  Y  S  W  F  N  F  W  F  V  L  V  Q  G  P  V    F2
+            L  L  K  I  F  I  H  G  L  I  F  G  L  Y  L  F  R  G  Q  F   F3
+          ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+                   430       440       450       460       470       480       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca
+           K  K  K  F  Y  K  N  M  T  *  N  K  T  Q  V  Q  E  P  A  L    F6
+          N  R  R  L  I  N  I  *  P  K  I  K  P  K  Y  K  N  L  P  W     F5
+            E  E  *  F  I  *  E  H  N  L  K  Q  N  T  S  T  *  P  G  T   F4
+
+
+          S  L  F  T  L  F  V  Y  S  S  S  F  I  F  S  M  I  L  I  *     F1
+           H  Y  L  L  C  L  Y  T  A  V  L  L  F  L  V  *  F  *  F  K    F2
+            I  I  Y  S  V  C  I  Q  Q  F  F  Y  F  *  Y  D  F  N  L  K   F3
+          tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+                   490       500       510       520       530       540       
+          ----:----|----:----|----:----|----:----|----:----|----:----|
+          agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt
+           E  N  N  V  R  N  T  Y  L  L  E  K  I  K  L  I  I  K  I  *    F6
+          N  M  I  *  E  T  Q  I  C  C  N  K  *  K  *  Y  S  K  L  K     F5
+            *  *  K  S  Q  K  Y  V  A  T  R  K  N  K  T  H  N  *  N  L   F4
+
+
+          N  N  S  N  G  Q  K                                            F1
+           T  I  L  M  V  K  X                                           F2
+            Q  F  *  W  S  K  X                                          F3
+          aacaattctaatggtcaaaaa
+                   550       560       
+          ----:----|----:----|-
+          ttgttaagattaccagttttt
+           F  L  E  L  P  *  F                                           F6
+          F  C  N  *  H  D  F                                            F5
+            V  I  R  I  T  L  F                                          F4
+
+##############################
+Minimum size of ORFs : 1
+
+Total ORFs in frame 1 :    10
+Total ORFs in frame 2 :    11
+Total ORFs in frame 3 :     8
+Total ORFs in frame 4 :    14
+Total ORFs in frame 5 :    12
+Total ORFs in frame 6 :    14
+
+Total ORFs :    69
+##############################
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_skipseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_splitter_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence_1-561 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_supermatcher_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,24 @@
+>hg17
+CCCTAGAGCTTCTGAGCCCTCAACAG--------AGATGAACTGGACTCTCTGCAGCCCC
+ACTCTAAATTC-----------CTAAGAGAGAAGTTGATTGACCCAATCAG-------GG
+TCAGGAGAAGGAAGGGAGGAGGAAAGGGAG---------GAGAGAAGAGCCTCTTCGTCT
+CTTGCCTACCAC--TGGCCAGGCAATTGTAG---------CCAAGGGGGCT-GGAGTGTA
+AATGCAAACATAGCC----------ATCAAGGGTt---gtgtatgtgtgtgtgt------
+----gtgtctgtgtgtgtgtatgtgtgtCTCTTGGGTAGGTTAGATCTCCC---------
+---AGGAGGTCCCTAC--TAAACAGACTTAAGCCCGCAAAA---TTTTA--GCTCTCCAG
+CCTCACACACTCCACCCCTCTAC-----CATA-------TTGAATCTTCCCAAACCAACT
+ATG-GCT---TTCCCTAA-CTCCGGAGcttggcctggaa--------tgccctgcttccc
+ct--ctttcccctgg---ggaacgcctgtccttcaggcctcagttca-----cacactgc
+ctcccttgca-----aagctct
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ccctaca----caga-----ccacagttttcctaa-------tgg---ctttaca--ccg
+actagaaattcttgtgcaagcactaattga-aag-cggttggccta--gagtgttaccgg
+tttgta------------tagctgagcgcgtctcttgccctgatcaaaggttcattttct
+ct--------actttgg--aagacgttgtggaagaatacaacaag-----tacgagtctc
+tcccc--------cctggtttgctgattactggatacagt-----------tgtaatacc
+cttcgcaacaccgcgtaactatctatat-------gaa--tta-ttttccctttattata
+tgtagtaggttcgt-ctttaatcttcctttagc------aagtcttttactgttttcga-
+cctca------------atgttcatgttcttaggttgttttggat------------aat
+atgcggtcagtt---taatcttcgttgtttcttcttaaaatatttatt--catggtt---
+-taatttt----tggtttgta---cttg---ttcaggggccagttcattatttactctg-
+----tttgtatacagcagttct
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_syco_out.syco	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,484 @@
+SYCO of Sequence from 1 to 561
+
+
+Frame 1
+Mid base	Gribskov value
+46      	1.007
+49      	1.014
+52      	1.012
+55      	1.002
+58      	1.003
+61      	0.997
+64      	0.998
+67      	0.996
+70      	1.005
+73      	1.006
+76      	1.007
+79      	1.020
+82      	1.008
+85      	1.000
+88      	0.995
+91      	1.005
+94      	1.023
+97      	1.011
+100     	1.008
+103     	1.003
+106     	1.017
+109     	1.028
+112     	1.029
+115     	1.019
+118     	1.013
+121     	1.014
+124     	1.003
+127     	1.003
+130     	0.990
+133     	0.981
+136     	0.975
+139     	0.981
+142     	0.983
+145     	0.981
+148     	0.987
+151     	1.000
+154     	0.989
+157     	0.997
+160     	0.995
+163     	0.998
+166     	0.988
+169     	0.981
+172     	0.993
+175     	1.007
+178     	1.016
+181     	1.016
+184     	0.994
+187     	1.006
+190     	1.017
+193     	1.008
+196     	1.016
+199     	0.995
+202     	0.987
+205     	0.982
+208     	0.983
+211     	0.978
+214     	0.989
+217     	1.000
+220     	1.006
+223     	1.013
+226     	1.008
+229     	0.992
+232     	1.002
+235     	1.002
+238     	0.996
+241     	0.987
+244     	0.988
+247     	0.972
+250     	0.966
+253     	0.973
+256     	0.972
+259     	0.968
+262     	0.956
+265     	0.951
+268     	0.942
+271     	0.923
+274     	0.923
+277     	0.907
+280     	0.897
+283     	0.908
+286     	0.888
+289     	0.896
+292     	0.891
+295     	0.911
+298     	0.923
+301     	0.924
+304     	0.914
+307     	0.904
+310     	0.896
+313     	0.901
+316     	0.910
+319     	0.928
+322     	0.918
+325     	0.914
+328     	0.915
+331     	0.911
+334     	0.910
+337     	0.927
+340     	0.926
+343     	0.917
+346     	0.922
+349     	0.920
+352     	0.917
+355     	0.923
+358     	0.917
+361     	0.926
+364     	0.931
+367     	0.937
+370     	0.937
+373     	0.929
+376     	0.930
+379     	0.931
+382     	0.940
+385     	0.915
+388     	0.908
+391     	0.908
+394     	0.899
+397     	0.909
+400     	0.918
+403     	0.904
+406     	0.896
+409     	0.885
+412     	0.884
+415     	0.884
+418     	0.885
+421     	0.889
+424     	0.889
+427     	0.884
+430     	0.892
+433     	0.903
+436     	0.902
+439     	0.906
+442     	0.900
+445     	0.890
+448     	0.893
+451     	0.903
+454     	0.903
+457     	0.899
+460     	0.910
+463     	0.932
+466     	0.935
+469     	0.925
+472     	0.915
+475     	0.926
+478     	0.925
+481     	0.929
+484     	0.943
+487     	0.934
+490     	0.920
+493     	0.925
+496     	0.925
+499     	0.935
+502     	0.936
+505     	0.939
+508     	0.940
+511     	0.936
+514     	0.932
+
+
+Frame 2
+Mid base	Gribskov value
+47      	1.003
+50      	0.992
+53      	1.002
+56      	0.997
+59      	1.006
+62      	1.005
+65      	1.007
+68      	0.997
+71      	1.001
+74      	0.996
+77      	0.997
+80      	0.982
+83      	0.975
+86      	0.965
+89      	0.971
+92      	0.977
+95      	0.975
+98      	0.968
+101     	0.979
+104     	0.968
+107     	0.978
+110     	0.982
+113     	0.984
+116     	0.994
+119     	0.984
+122     	0.983
+125     	0.984
+128     	0.996
+131     	1.004
+134     	0.986
+137     	0.992
+140     	0.997
+143     	0.980
+146     	0.972
+149     	0.966
+152     	0.971
+155     	0.956
+158     	0.950
+161     	0.943
+164     	0.944
+167     	0.933
+170     	0.944
+173     	0.944
+176     	0.955
+179     	0.949
+182     	0.944
+185     	0.945
+188     	0.952
+191     	0.941
+194     	0.952
+197     	0.946
+200     	0.934
+203     	0.943
+206     	0.935
+209     	0.940
+212     	0.952
+215     	0.953
+218     	0.937
+221     	0.923
+224     	0.934
+227     	0.938
+230     	0.930
+233     	0.936
+236     	0.949
+239     	0.943
+242     	0.944
+245     	0.946
+248     	0.950
+251     	0.954
+254     	0.968
+257     	0.968
+260     	0.962
+263     	0.960
+266     	0.949
+269     	0.943
+272     	0.946
+275     	0.956
+278     	0.963
+281     	0.963
+284     	0.952
+287     	0.947
+290     	0.950
+293     	0.930
+296     	0.934
+299     	0.936
+302     	0.925
+305     	0.915
+308     	0.939
+311     	0.943
+314     	0.928
+317     	0.930
+320     	0.936
+323     	0.941
+326     	0.938
+329     	0.943
+332     	0.949
+335     	0.939
+338     	0.935
+341     	0.934
+344     	0.924
+347     	0.929
+350     	0.929
+353     	0.932
+356     	0.930
+359     	0.934
+362     	0.930
+365     	0.911
+368     	0.916
+371     	0.925
+374     	0.921
+377     	0.917
+380     	0.916
+383     	0.924
+386     	0.922
+389     	0.919
+392     	0.921
+395     	0.930
+398     	0.912
+401     	0.916
+404     	0.920
+407     	0.909
+410     	0.908
+413     	0.908
+416     	0.898
+419     	0.890
+422     	0.880
+425     	0.885
+428     	0.899
+431     	0.907
+434     	0.912
+437     	0.904
+440     	0.901
+443     	0.901
+446     	0.893
+449     	0.897
+452     	0.894
+455     	0.903
+458     	0.890
+461     	0.886
+464     	0.894
+467     	0.894
+470     	0.894
+473     	0.885
+476     	0.884
+479     	0.875
+482     	0.870
+485     	0.879
+488     	0.878
+491     	0.875
+494     	0.875
+497     	0.876
+500     	0.881
+503     	0.878
+506     	0.876
+509     	0.883
+512     	0.891
+515     	0.896
+
+
+Frame 3
+Mid base	Gribskov value
+48      	0.929
+51      	0.933
+54      	0.930
+57      	0.946
+60      	0.940
+63      	0.947
+66      	0.947
+69      	0.953
+72      	0.968
+75      	0.950
+78      	0.949
+81      	0.939
+84      	0.929
+87      	0.915
+90      	0.910
+93      	0.922
+96      	0.921
+99      	0.931
+102     	0.925
+105     	0.935
+108     	0.945
+111     	0.935
+114     	0.930
+117     	0.940
+120     	0.949
+123     	0.949
+126     	0.960
+129     	0.944
+132     	0.947
+135     	0.943
+138     	0.946
+141     	0.955
+144     	0.949
+147     	0.948
+150     	0.953
+153     	0.950
+156     	0.960
+159     	0.965
+162     	0.958
+165     	0.979
+168     	0.987
+171     	0.991
+174     	1.003
+177     	1.017
+180     	1.018
+183     	1.004
+186     	0.994
+189     	1.008
+192     	1.010
+195     	0.998
+198     	1.002
+201     	1.013
+204     	1.021
+207     	1.012
+210     	1.002
+213     	1.013
+216     	1.001
+219     	1.012
+222     	1.024
+225     	1.037
+228     	1.035
+231     	1.025
+234     	1.028
+237     	1.011
+240     	1.007
+243     	1.016
+246     	1.006
+249     	0.997
+252     	0.999
+255     	0.989
+258     	0.971
+261     	0.962
+264     	0.950
+267     	0.936
+270     	0.931
+273     	0.931
+276     	0.928
+279     	0.907
+282     	0.897
+285     	0.910
+288     	0.915
+291     	0.904
+294     	0.902
+297     	0.899
+300     	0.905
+303     	0.895
+306     	0.905
+309     	0.896
+312     	0.887
+315     	0.877
+318     	0.879
+321     	0.874
+324     	0.875
+327     	0.878
+330     	0.880
+333     	0.871
+336     	0.871
+339     	0.866
+342     	0.853
+345     	0.851
+348     	0.861
+351     	0.870
+354     	0.874
+357     	0.887
+360     	0.892
+363     	0.892
+366     	0.897
+369     	0.897
+372     	0.903
+375     	0.891
+378     	0.881
+381     	0.881
+384     	0.879
+387     	0.884
+390     	0.875
+393     	0.875
+396     	0.866
+399     	0.865
+402     	0.861
+405     	0.852
+408     	0.852
+411     	0.856
+414     	0.852
+417     	0.850
+420     	0.859
+423     	0.859
+426     	0.867
+429     	0.879
+432     	0.893
+435     	0.903
+438     	0.912
+441     	0.913
+444     	0.910
+447     	0.910
+450     	0.908
+453     	0.908
+456     	0.906
+459     	0.905
+462     	0.918
+465     	0.929
+468     	0.939
+471     	0.940
+474     	0.940
+477     	0.939
+480     	0.943
+483     	0.943
+486     	0.942
+489     	0.943
+492     	0.948
+495     	0.948
+498     	0.948
+501     	0.943
+504     	0.958
+507     	0.960
+510     	0.954
+513     	0.956
+516     	0.947
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_tranalign_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,45 @@
+>HSFAU1
+cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
+ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
+cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
+ctcctggcaggc---cccctggaggatgaggccactctgggccagtgcggggtggaggcc
+ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
+gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
+aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
+cccacctttggcaagaagaagggccccaatgccaactct
+>HSFAU2
+cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
+ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
+cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
+ctcctggcaggcgcgcccctggaggatgcactctgggccagtgcggggtggaggccc---
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------
+>HSFAU3
+cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
+ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
+cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
+ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
+ctgactaccctggaagtagcaggccgcatgcttgga---ggtaaagttcatggttccctg
+gcccgtgctggaaaagtgagaggtcagactcctaagggggccaaacaggagaagaagaag
+aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
+cccacctttggcaagaagaagggccccaatgccaactct
+>HSFAU4
+cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
+ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
+cagatcaaggctcatgaaatagcctcactggagggcattgccccggaagatcaagtcgtg
+ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
+ctgactaccctggaagtagcaggccgcatgcttgcccgaggtaaagttcatggttccctg
+gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
+aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
+cccacctttggcaagaagaagggccccaatgccaactct
+>HSFAU5
+cctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcag
+ctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcc
+cagatcaaggctcatgtagcctca---ctggagggcattgccccggaagatcaagtcgtg
+ctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggcc
+ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg
+gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
+aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
+cccacctttggcaagaagaagggccccaatgccaactct
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_transeq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,5 @@
+>Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+VRCLKYLLLSLHRPQFS*WLYTD*KFLCKH*LKAVGLECYRFV*LSASLALIKGSFSLLW
+KTLWKNTTSTSLSPLVC*LLDTVVIPFATPRNYLYELFSLYYM**VRL*SSFSKSFTVFD
+LNVHVLRLFWIICGQFNLRCFFLKYLFMV*FLVCTCSGASSLFTLFVYSSSFIFSMILI*
+NNSNGQK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_trimest_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other; [poly-A tail removed]
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_trimseq_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_union_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,11 @@
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
+tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
+cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
+aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
+gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
+tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
+ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
+ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
+tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
+aacaattctaatggtcaaaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_water_out.fasta	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,32 @@
+>hg17
+GTTTGAAGTTGAGATGTGGGTACAATACCATAGCTTTATTC------CAGAGCAGGGTAT
+TTGTTTCCAAATGCCATGTTCCCAGCAGCTGCCCTTGACTGGGAATTGGGGTGTGATTTG
+GGCTTTT-----CCTTAAATCCTTGAGGAGCTGGAGGGGTGGGTGGCTCGCACTCCTGCT
+TTctggatctgaatcctgactctgtcatggacctgtttgactttgggcaagttgactcct
+attcctgagccccatatttttctcttctgtgaaattcagattaaaaAAACATGGCTTTGA
+TCAAA----CATTATAAATAATATATAGACAGACTGCTTGTTTTTATTGTATTGCCAGAA
+ATGAATCCTACTAATA-------------------TTGC-CATCTA-TGG--ACAGAAAA
+TGTATTACCTGTCTTCATCAAGACCCAGACGAGGAAGAACACGAAAAGCGGA--------
+---GATTAATTTTACTGCC-------ATCTCCAGAA---CCGTCATCCTAATATTTACTT
+A-CA----TTTTATTATTATTTCAGGCTC-ATGCACATATACTTAG-----CATGGATCA
+T-TGGCCACAGACTCGCATACATTTAA-CTTTATTACCTTTTGCCTCATGTATCTCATTA
+AAATTTTGCTGCTTAATCAAGGATCTGCATATTATTTTAATTTTAGAATTCACAGTTCCA
+AGACTTTGAAAGTTTCAAGCGTTCTGGGTGaatgtgttatgctctctcccgcca--ccat
+gtctttataccccctgatttct---cagccactatggcaaccactttctactcttagta-
+gcccat----atttagtccaatccccagctcaggagacacttct
+>Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+gttcga----------tgcctaaaatacctt--cttttgtccctacacagaccacagt--
+---tttcctaatggc---tttacacc----------gactagaaatt-------------
+--cttgtgcaagcactaa----ttga-aagc---------ggttggc-------------
+--ctaga--------------gtgt----taccggtttg--------------------t
+atagctgagcgc-------gtctctt---------------------------gccctga
+tcaaaggttcattttctctact---ttggaagac-----------gttgt-------gga
+a-gaatacaacaagtacgagtctctcccccctggtttgctgat-tactggatacag---t
+tgtaatacc---cttc-gcaacacc----------------------gcgtaactatcta
+tatgaattatttt----ccctttattatatgtagtaggttcgtctt--taatcttccttt
+agcaagtcttttactgt--tttcgacctcaatgttcatgttcttaggttgttttggataa
+tatgcggtcag-----------tttaatcttcgt--------------tgtttcttctta
+aaatat------ttattcatgg-------------tttaatttttggttt----gt----
+--actt--------------gttcaggg----------------------gccagttcat
+-tattta----ctctg-tttgtatacagc----------agttcttt-tatttttagtat
+g---attttaattta-------------------aaacaattct
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_water_out.score	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,4 @@
+Sequence hg17 884 (610.5)
+
+#---------------------------------------
+#---------------------------------------
Binary file test-data/emboss_wobble_out.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_wobble_out.wobble	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,1 @@
+Expected GC content in third position = 36.36
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_wordcount_out.wordcount	Wed Mar 21 16:30:01 2012 -0400
@@ -0,0 +1,202 @@
+ttta	13
+tttt	13
+tctt	11
+gttt	10
+ttgt	10
+taat	9
+ttct	8
+attt	8
+tttg	8
+gttc	8
+tgtt	8
+ggtt	8
+cttt	8
+aatt	6
+tatt	6
+ttaa	6
+ttat	6
+ttca	5
+ttcg	5
+tttc	5
+cagt	5
+gttg	5
+taca	5
+aata	5
+ccct	5
+agtt	5
+tgta	5
+tact	5
+cttc	5
+atac	5
+ttac	5
+aaaa	5
+atta	4
+tctc	4
+ctaa	4
+gtct	4
+ccta	4
+tata	4
+ctct	4
+cctt	4
+tatg	4
+ttgg	4
+acag	4
+tgga	4
+atat	4
+tcat	4
+tggt	4
+atct	3
+aaat	3
+ttcc	3
+taaa	3
+tcta	3
+attc	3
+tgat	3
+cggt	3
+agca	3
+aaca	3
+cccc	3
+agta	3
+tacc	3
+aatg	3
+caag	3
+cttg	3
+atgg	3
+atgt	3
+acaa	3
+acac	3
+tcaa	3
+aggt	3
+gcaa	3
+ttag	3
+ctga	3
+accg	3
+gtat	3
+acta	3
+tccc	3
+tgaa	2
+tcct	2
+actt	2
+ggaa	2
+gcct	2
+gtca	2
+ctac	2
+gaaa	2
+ctag	2
+gaag	2
+gctg	2
+ggat	2
+ctat	2
+gaat	2
+agcg	2
+tgcc	2
+agtc	2
+aatc	2
+cgac	2
+ggcc	2
+caaa	2
+caac	2
+gacc	2
+cctg	2
+tgtg	2
+caat	2
+ggtc	2
+ctta	2
+gata	2
+atga	2
+atgc	2
+tcga	2
+gatt	2
+gcgg	2
+tcgt	2
+ttgc	2
+gcgt	2
+cgcg	2
+caca	2
+cacc	2
+cgtc	2
+aaga	2
+catg	2
+aagc	2
+cgtt	2
+tcag	2
+catt	2
+aagt	2
+tggc	2
+taga	2
+tagc	2
+tagg	2
+gtaa	2
+ctgg	2
+gtac	2
+gtag	2
+tagt	2
+ctgt	2
+gagt	2
+agaa	2
+agac	2
+acct	2
+aaag	2
+actg	2
+gccc	1
+ccag	1
+tgag	1
+taac	1
+attg	1
+caga	1
+tctg	1
+cagc	1
+gtcc	1
+cagg	1
+gctt	1
+gtta	1
+agct	1
+tgca	1
+aact	1
+tgcg	1
+agtg	1
+tacg	1
+ctca	1
+cgag	1
+ctcc	1
+cctc	1
+tgct	1
+acga	1
+gacg	1
+tgtc	1
+cgat	1
+ggct	1
+tatc	1
+gact	1
+acgt	1
+gatc	1
+tcgc	1
+gatg	1
+gcgc	1
+ttga	1
+cgca	1
+gtgc	1
+gtgg	1
+cgta	1
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