bio-alignment 0.0.1.alpha → 0.0.2

data/test/data/regression/aa-aln.fa

@@ -0,0 +1,24 @@
+>ZK909.2e
+MPTRLDIVGNLQFSSSTDNGDEDQEADVTACFVLPSPSSFSKLSILDDPVEDFKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2j
+-------MGNAASGGSSGGGGSARRGNGGGNNGSDYNNAMVFSNGRLAAAETIKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2l
+MPTRLDIVGNLQFSSSTDNGDEDQEADVTACFVLPSPSSFSKLSILDDPVEDFKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF
+>ZK909.2k
+-----MLSSSFFRGSMKERKNEALKNHKSKYISGGYLE-------------TVKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2h
+-------MGNAASGGSSGGGGSARRGNGGGNNGSDYNNAMVFSNGRLAAAETIKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF
+>ZK909.2b
+-------MLKFLKPKSSDEGSSKDNKNSA----------------------SLKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2f
+-----MLSSSFFRGSMKERKNEALKNHKSKYISGGYLE-------------TVKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF
+>ZK909.2d
+-------MSSSSNKKVQVK--------------------------------FFKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2a
+-------MLKFLKPKSSDEGSSKDNKNSA----------------------SLKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF
+>ZK909.2i
+-------MGSMVF--------------------------------------IVKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKITPPSFSKGESNGRLFEALYPRVDGPADTRHFVEEVQEPTEFVIAATPQLEELFVEF
+>ZK909.2m
+-------MSSSSNKKVQVK--------------------------------FFKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF
+>ZK909.2g
+-------MGSMVF--------------------------------------IVKEFLDKAREDFKQRWENPAQNTACLDDFDRIKTLGTGSFGRVMLVKHKQSGNYYAMKILDKQKVVKLKQVEHTLNEKRILQAIDFPFLVNMTFSFKDNSNLYMVLEFISGGEMFSHLRRIGRFSEPHSRFYAAQIVLAFEYLHSLDLIYRDLKPENLLIDSTGYLKITDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVKFPSHFSNELKDLLKNLLQVDLTKRYGNLKNGVADIKNHKWFGSTDWIAIYQKKIEAP--------------FLPKCRGPGDASNFDDYEEEP--LRISGTEKCAKEFAEF

data/test/data/regression/nt-aln.fa

@@ -0,0 +1,24 @@
+>ZK909.2e
+[atg, ccc, act, cga, ttg, gat, att, gtt, gga, aac, ctt, cag, ttc, tct, agc, tca, act, gat, aac, gga, gat, gaa, gac, cag, gaa, gct, gac, gtg, aca, gcc, tgc, ttt, gtg, ctt, cct, tct, cca, tcg, agt, ttt, tct, aaa, ttg, agc, atc, ttg, gat, gat, cct, gtg, gag, gat, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2j
+[---, ---, ---, ---, ---, ---, ---, atg, gga, aat, gcg, gca, tct, ggc, gga, tct, tct, gga, ggt, ggg, gga, tcg, gca, cga, cgt, gga, aac, ggt, ggc, gga, aac, aac, ggt, agt, gac, tat, aac, aat, gcg, atg, gtt, ttc, tcg, aat, gga, cgt, tta, gcc, gcg, gca, gag, aca, atc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2l
+[atg, ccc, act, cga, ttg, gat, att, gtt, gga, aac, ctt, cag, ttc, tct, agc, tca, act, gat, aac, gga, gat, gaa, gac, cag, gaa, gct, gac, gtg, aca, gcc, tgc, ttt, gtg, ctt, cct, tct, cca, tcg, agt, ttt, tct, aaa, ttg, agc, atc, ttg, gat, gat, cct, gtg, gag, gat, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+>ZK909.2k
+[---, ---, ---, ---, ---, atg, ctg, tcc, tcg, tcg, ttt, ttc, cgc, ggc, agt, atg, aaa, gaa, cgg, aag, aat, gag, gcg, ttg, aag, aat, cac, aaa, agt, aaa, tac, ata, tca, gga, ggt, tat, tta, gaa, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, act, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2h
+[---, ---, ---, ---, ---, ---, ---, atg, gga, aat, gcg, gca, tct, ggc, gga, tct, tct, gga, ggt, ggg, gga, tcg, gca, cga, cgt, gga, aac, ggt, ggc, gga, aac, aac, ggt, agt, gac, tat, aac, aat, gcg, atg, gtt, ttc, tcg, aat, gga, cgt, tta, gcc, gcg, gca, gag, aca, atc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+>ZK909.2b
+[---, ---, ---, ---, ---, ---, ---, atg, ctc, aag, ttt, ctg, aaa, cca, aaa, tcg, tcg, gac, gag, gga, agc, tcg, aag, gac, aac, aag, aac, tcg, gcg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, tcg, ctc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2f
+[---, ---, ---, ---, ---, atg, ctg, tcc, tcg, tcg, ttt, ttc, cgc, ggc, agt, atg, aaa, gaa, cgg, aag, aat, gag, gcg, ttg, aag, aat, cac, aaa, agt, aaa, tac, ata, tca, gga, ggt, tat, tta, gaa, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, act, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+>ZK909.2d
+[---, ---, ---, ---, ---, ---, ---, atg, tcg, tcc, agt, agc, aat, aaa, aaa, gtg, caa, gtc, aag, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttt, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2a
+[---, ---, ---, ---, ---, ---, ---, atg, ctc, aag, ttt, ctg, aaa, cca, aaa, tcg, tcg, gac, gag, gga, agc, tcg, aag, gac, aac, aag, aac, tcg, gcg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, tcg, ctc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+>ZK909.2i
+[---, ---, ---, ---, ---, ---, ---, atg, gga, tcc, atg, gtg, ttc, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, att, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+>ZK909.2m
+[---, ---, ---, ---, ---, ---, ---, atg, tcg, tcc, agt, agc, aat, aaa, aaa, gtg, caa, gtc, aag, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttt, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+>ZK909.2g
+[---, ---, ---, ---, ---, ---, ---, atg, gga, tcc, atg, gtg, ttc, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, att, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]

data/test/data/regression/pal2nal.fa

@@ -0,0 +1,24 @@
+>ZK909.2e
+atgcccactcgattggatattgttggaaaccttcagttctctagctcaactgataacggagatgaagaccaggaagctgacgtgacagcctgctttgtgcttccttctccatcgagtttttctaaattgagcatcttggatgatcctgtggaggatttcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2j
+---------------------atgggaaatgcggcatctggcggatcttctggaggtgggggatcggcacgacgtggaaacggtggcggaaacaacggtagtgactataacaatgcgatggttttctcgaatggacgtttagccgcggcagagacaatcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2l
+atgcccactcgattggatattgttggaaaccttcagttctctagctcaactgataacggagatgaagaccaggaagctgacgtgacagcctgctttgtgcttccttctccatcgagtttttctaaattgagcatcttggatgatcctgtggaggatttcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt
+>ZK909.2k
+---------------atgctgtcctcgtcgtttttccgcggcagtatgaaagaacggaagaatgaggcgttgaagaatcacaaaagtaaatacatatcaggaggttatttagaa---------------------------------------actgtcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2h
+---------------------atgggaaatgcggcatctggcggatcttctggaggtgggggatcggcacgacgtggaaacggtggcggaaacaacggtagtgactataacaatgcgatggttttctcgaatggacgtttagccgcggcagagacaatcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt
+>ZK909.2b
+---------------------atgctcaagtttctgaaaccaaaatcgtcggacgagggaagctcgaaggacaacaagaactcggcg------------------------------------------------------------------tcgctcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2f
+---------------atgctgtcctcgtcgtttttccgcggcagtatgaaagaacggaagaatgaggcgttgaagaatcacaaaagtaaatacatatcaggaggttatttagaa---------------------------------------actgtcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt
+>ZK909.2d
+---------------------atgtcgtccagtagcaataaaaaagtgcaagtcaag------------------------------------------------------------------------------------------------tttttcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2a
+---------------------atgctcaagtttctgaaaccaaaatcgtcggacgagggaagctcgaaggacaacaagaactcggcg------------------------------------------------------------------tcgctcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt
+>ZK909.2i
+---------------------atgggatccatggtgttc------------------------------------------------------------------------------------------------------------------attgtcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcacaccgccctcgttctccaaaggagaatccaatggtcgactgttcgaggctctgtatccacgtgtcgatggtcccgccgacacacgtcattttgtggaagaggtgcaagagccgactgagtttgtgatcgccgcgactccacagttggaagagctgttcgtcgagttt
+>ZK909.2m
+---------------------atgtcgtccagtagcaataaaaaagtgcaagtcaag------------------------------------------------------------------------------------------------tttttcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt
+>ZK909.2g
+---------------------atgggatccatggtgttc------------------------------------------------------------------------------------------------------------------attgtcaaagaattcctggacaaggcacgcgaagacttcaaacaacgatgggagaatccggctcagaacacggcgtgtcttgacgactttgataggataaaaacccttggaaccggatcattcgggcgcgtgatgcttgtgaagcataagcagtcgggcaactattatgccatgaaaattctagacaaacaaaaggttgtaaaactcaagcaagtggagcacacgttgaacgaaaagcgcattctccaggctatcgattttccgtttttggtgaacatgacgttctctttcaaggacaactccaacttgtacatggtgctcgaattcatctcgggaggtgagatgttctcacatttacgccgaatcggacgtttctccgagccccactcgcgtttctacgccgctcaaattgtgcttgcctttgagtaccttcactccttagatctcatctatcgtgatctgaaacccgagaacttgcttatcgattccactggatatctaaagatcaccgatttcggatttgcgaaacgtgtcaaaggacgaacgtggacattgtgcggcacaccagaatacttggcacccgagattattttgtcaaaaggatacaataaggctgtcgattggtgggcacttggtgtgttgatctacgaaatggccgccggttatccgccgttctttgccgatcagccgattcaaatttatgagaagattgtgtcaggaaaagtgaaattcccgtcgcacttctcgaatgagttgaaagacttgctgaagaatttgctccaagttgatcttacaaagcgatacggtaacctgaaaaatggagttgccgatatcaaaaatcacaagtggtttggaagtaccgactggattgccatctatcagaagaagatcgaagcaccg------------------------------------------ttccttccaaaatgccgtggccctggcgacgcatctaactttgacgactacgaggaagagccg------cttcgtatctcgggcaccgagaaatgcgccaaagagtttgccgagttt

metadata

@@ -1,19 +1,63 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.1.alpha
-  prerelease: 6
+  version: 0.0.2
+  prerelease: 
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-25 00:00:00.000000000Z
+date: 2012-02-03 00:00:00.000000000Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: &13944060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *13944060
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &13932960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *13932960
+- !ruby/object:Gem::Dependency
+  name: bio-bigbio
+  requirement: &13932060 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 0.1.3
+  type: :development
+  prerelease: false
+  version_requirements: *13932060
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: &13930840 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *13930840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &18984620 !ruby/object:Gem::Requirement
+  requirement: &13929020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +65,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *18984620
+  version_requirements: *13929020
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &18984040 !ruby/object:Gem::Requirement
+  requirement: &13927920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +76,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *18984040
+  version_requirements: *13927920
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &18983460 !ruby/object:Gem::Requirement
+  requirement: &13926060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,21 +87,8 @@ dependencies:
         version: 1.7.0
   type: :development
   prerelease: false
-  version_requirements: *18983460
-- !ruby/object:Gem::Dependency
-  name: bio
-  requirement: &18982860 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.4.2
-  type: :development
-  prerelease: false
-  version_requirements: *18982860
-description: Alignment handler for multiple sequence alignments. Support for any nucleotide,
-  amino acid and codon sequences that are lists. I.e. any list with payload can be
-  used, as long as it can be indexed
+  version_requirements: *13926060
+description: Alignment handler for multiple sequence alignments (MSA)
 email: pjotr.public01@thebird.nl
 executables:
 - bio-alignment
@@ -75,9 +106,22 @@ files:
 - VERSION
 - bin/bio-alignment
 - doc/bio-alignment-design.md
+- features/codon-feature.rb
+- features/codon.feature
+- features/pal2nal-feature.rb
+- features/pal2nal.feature
 - lib/bio-alignment.rb
+- lib/bio-alignment/alignment.rb
+- lib/bio-alignment/codonsequence.rb
+- lib/bio-alignment/sequence.rb
 - spec/bio-alignment_spec.rb
 - spec/spec_helper.rb
+- test/data/fasta/codon/aa-alignment.fa
+- test/data/fasta/codon/codon-alignment.fa
+- test/data/fasta/codon/nt.fa
+- test/data/regression/aa-aln.fa
+- test/data/regression/nt-aln.fa
+- test/data/regression/pal2nal.fa
 homepage: http://github.com/pjotrp/bioruby-alignment
 licenses:
 - MIT
@@ -93,17 +137,17 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1744402862562390387
+      hash: 3814717210769440369
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
-  - - ! '>'
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: Multiple sequence alignments (MSA)
+summary: Support for multiple sequence alignments (MSA)
 test_files: []