PAL2NAL output

#------------------------------------------------------------------------#
#  WARNING: P07650|TYPH_ECOLI pepAlnPos 34: M does not correspond to ttg
#  WARNING: A5F5S5|A5F5S5_VIBC3 pepAlnPos 1: M does not correspond to ttg
#------------------------------------------------------------------------#

                       -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
P07650|TYPH_ECOLI      --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ---
                       M   C   L   R   A   A   R   G   F   A   L   L   N   L   F   T   L   R   S   F
A5F5S5|A5F5S5_VIBC3    ttg tgt ctg aga gca gcg cga ggc ttc gcg ctg ctt aac ctc ttt aca cta cgc agt ttc

                       -   -   -   -   -   -   -   -   -   -   -   -   -   M   F   L   A   Q   E   I
P07650|TYPH_ECOLI      --- --- --- --- --- --- --- --- --- --- --- --- --- ttg ttt ctc gca caa gaa att
                       F   G   N   W   E   A   A   M   S   L   S   Q   A   K   Y   L   P   Q   E   I
A5F5S5|A5F5S5_VIBC3    ttt ggg aac tgg gag gca gct atg tct tta tct caa gca aag tat tta cct caa gaa att

                       I   R   K   K   R   D   G   H   A   L   S   D   E   E   I   R   F   F   I   N
P07650|TYPH_ECOLI      att cgt aaa aaa cgt gat ggt cat gcg ctg agc gat gaa gaa att cgt ttc ttt atc aac
                       I   R   R   K   R   D   G   E   V   L   T   N   D   E   I   N   F   F   I   Q
A5F5S5|A5F5S5_VIBC3    atc cgc aga aag cgt gat ggt gaa gtt ctc acc aac gat gaa atc aac ttc ttc att caa

                       G   I   R   D   N   T   I   S   E   G   Q   I   A   A   L   A   M   T   I   F
P07650|TYPH_ECOLI      ggt att cgc gac aac act atc tcc gaa ggg cag att gcc gcc ctc gcg atg acc att ttc
                       G   V   A   N   N   T   V   S   E   G   Q   I   A   A   F   A   M   A   I   F
A5F5S5|A5F5S5_VIBC3    ggt gtg gcg aat aac acc gtc tct gaa ggg caa att gcc gcg ttt gcg atg gcg att ttt

                       F   H   D   M   T   M   P   E   R   V   S   L   T   M   A   M   R   D   S   G
P07650|TYPH_ECOLI      ttc cac gat atg aca atg cct gag cgt gtc tcg ctg acc atg gcg atg cga gat tca gga
                       F   R   E   M   T   M   P   E   R   I   A   L   T   C   A   M   R   D   S   G
A5F5S5|A5F5S5_VIBC3    ttc cgt gaa atg act atg cct gag cgt att gca ctg acg tgc gcg atg cgc gat tcc ggt

                       T   V   L   D   W   K   S   L   H   L   N   G   P   I   V   D   K   H   S   T
P07650|TYPH_ECOLI      acc gtt ctc gac tgg aaa agc ctg cat ctg aat ggc ccg att gtt gat aaa cac tcc acc
                       M   V   I   D   W   S   H   M   N   F   D   G   P   I   V   D   K   H   S   T
A5F5S5|A5F5S5_VIBC3    atg gtg att gat tgg agc cac atg aat ttt gat ggt ccg att gtg gat aaa cac tcc acg

                       G   G   V   G   D   V   T   S   L   M   L   G   P   M   V   A   A   C   G   G
P07650|TYPH_ECOLI      ggt ggc gtc ggc gat gtg act tcg ctg atg ttg ggg ccg atg gtc gca gcc tgc ggc ggc
                       G   G   V   G   D   V   T   S   L   M   L   G   P   M   V   A   A   C   G   G
A5F5S5|A5F5S5_VIBC3    ggc ggc gtg ggc gat gtg acc tca ctg atg ctt ggc cct atg gtg gca gcc tgt ggc ggt

                       Y   I   P   M   I   S   G   R   G   L   G   H   T   G   G   T   L   D   K   L
P07650|TYPH_ECOLI      tat att ccg atg atc tct ggt cgc ggc ctc ggt cat act ggc ggt acg ctc gac aaa ctg
                       Y   V   P   M   I   S   G   R   G   L   G   H   T   G   G   T   L   D   K   L
A5F5S5|A5F5S5_VIBC3    tat gtg ccg atg att tct ggc cgc ggc ctt ggt cac act ggg ggg acg ctc gac aaa ctt

                       E   S   I   P   G   F   D   I   F   P   D   D   N   R   F   R   E   I   I   K
P07650|TYPH_ECOLI      gaa tcc atc cct ggc ttc gac att ttc ccg gat gac aac cgt ttc cgc gaa att att aaa
                       E   A   I   P   G   Y   N   I   T   P   T   N   D   V   F   G   K   V   T   K
A5F5S5|A5F5S5_VIBC3    gaa gcc atc ccc ggc tat aac att acc cca acc aat gac gtg ttt ggc aaa gtg acc aaa

                       D   V   G   V   A   I   I   G   Q   T   S   S   L   A   P   A   D   K   R   F
P07650|TYPH_ECOLI      gac gtc ggc gtg gcg att atc ggt cag acc agt tca ctg gct ccg gct gat aaa cgt ttc
                       Q   A   G   V   A   I   I   G   Q   T   G   D   L   A   P   A   D   K   R   V
A5F5S5|A5F5S5_VIBC3    caa gcc ggc gtg gcg atc atc ggc caa act ggc gat ctg gct ccg gcg gat aag cgt gtg

                       Y   A   T   R   D   I   T   A   T   V   D   S   I   P   L   I   T   A   S   I
P07650|TYPH_ECOLI      tac gcg acc cgt gat att acc gca acc gtg gac tcc atc ccg ctg atc acc gcc tct att
                       Y   A   T   R   D   I   T   A   T   V   D   N   I   S   L   I   T   A   S   I
A5F5S5|A5F5S5_VIBC3    tac gca acg cgt gat att acc gcg aca gtg gat aac atc tcg ctg atc acc gct tca att

                       L   A   K   K   L   A   E   G   L   D   A   L   V   M   D   V   K   V   G   S
P07650|TYPH_ECOLI      ctg gcg aag aaa ctt gcg gaa ggt ctg gac gcg ctg gtg atg gac gtg aaa gtg ggt agc
                       L   S   K   K   L   A   A   G   L   E   S   L   V   M   D   V   K   V   G   S
A5F5S5|A5F5S5_VIBC3    ctt tct aag aaa ctg gcg gct ggc ctt gaa tcg ctc gtg atg gat gtg aaa gtt ggc tct

                       G   A   F   M   P   T   Y   E   L   S   E   A   L   A   E   A   I   V   G   V
P07650|TYPH_ECOLI      ggc gcg ttt atg ccg acc tac gaa ctc tct gaa gcc ctt gcc gaa gcg att gtt ggc gtg
                       G   A   F   M   P   T   Y   E   A   S   E   E   L   A   K   S   I   V   A   V
A5F5S5|A5F5S5_VIBC3    ggt gct ttc atg cca act tac gaa gcg tct gaa gag ctc gcc aaa tcg atc gtg gca gtg

                       A   N   G   A   G   V   R   T   T   A   L   L   T   D   M   N   Q   V   L   A
P07650|TYPH_ECOLI      gct aac ggc gct ggc gtg cgc acc acc gcg ctg ctc acc gac atg aat cag gta ctg gcc
                       A   N   G   A   G   T   N   T   T   A   I   L   T   D   M   N   Q   V   L   A
A5F5S5|A5F5S5_VIBC3    gcc aac ggt gca ggc acc aat acc acg gcg atc tta act gat atg aac caa gtg ctg gcg

                       S   S   A   G   N   A   V   E   V   R   E   A   V   Q   F   L   T   G   E   Y
P07650|TYPH_ECOLI      tcc agt gca ggt aac gcg gtt gaa gtt cgt gaa gcg gtg cag ttc ctg acg ggt gaa tat
                       S   S   A   G   N   A   V   E   V   R   E   A   V   R   F   L   T   G   E   Y
A5F5S5|A5F5S5_VIBC3    tct tca gcg ggt aac gcg gtg gaa gtg cgt gaa gca gta cgc ttc ctc acc ggc gaa tac

                       R   N   P   R   L   F   D   V   T   M   A   L   C   V   E   M   L   I   S   G
P07650|TYPH_ECOLI      cgt aac ccg cgt ctg ttt gat gtc acg atg gcg ctg tgc gtg gag atg ctg atc tcc ggc
                       R   N   P   R   L   L   E   V   T   M   A   S   C   A   E   M   L   V   L   G
A5F5S5|A5F5S5_VIBC3    cgt aat ccg cgt ctg ctg gaa gtc act atg gcg tcg tgt gcg gaa atg ctg gta ctt ggc

                       K   L   A   K   D   D   A   E   A   R   A   K   L   Q   A   V   L   D   N   G
P07650|TYPH_ECOLI      aaa ctg gcg aaa gat gac gcc gaa gcg cgc gcg aaa ttg cag gcg gtg ctg gac aac ggt
                       K   L   A   K   D   T   A   Q   A   R   E   K   L   Q   A   V   L   D   N   G
A5F5S5|A5F5S5_VIBC3    aag tta gcc aaa gat acc gcg caa gcg cgt gag aaa ctg caa gca gtg ctg gat aac ggc

                       K   A   A   E   V   F   G   R   M   V   A   A   Q   K   G   P   T   D   F   V
P07650|TYPH_ECOLI      aaa gcg gca gaa gtc ttt ggt cgt atg gta gcg gca caa aaa ggc ccg acc gac ttc gtt
                       Q   A   A   E   R   F   G   K   M   V   A   G   L   G   G   P   S   D   F   V
A5F5S5|A5F5S5_VIBC3    caa gcc gcc gag cgt ttt ggc aaa atg gtc gca ggc ctc ggt ggc cca agc gat ttt gtt

                       E   N   Y   A   K   Y   L   P   T   A   M   L   T   K   A   V   Y   A   D   T
P07650|TYPH_ECOLI      gag aac tac gcg aag tat ctg ccg aca gcg atg ctg acg aaa gca gtc tat gct gat acc
                       E   N   Y   D   K   Y   L   A   K   A   E   I   V   R   P   V   Y   A   Q   Q
A5F5S5|A5F5S5_VIBC3    gaa aac tac gac aag tat ctt gcg aaa gct gag att gtt cgc cca gtt tac gct cag caa

                       E   G   F   V   S   E   M   D   T   R   A   L   G   M   A   V   V   A   M   G
P07650|TYPH_ECOLI      gaa ggt ttt gtc agt gaa atg gat acc cgc gcg ctg ggg atg gca gtg gtt gca atg ggc
                       S   G   V   I   S   A   M   D   T   R   A   I   G   M   A   V   V   G   M   G
A5F5S5|A5F5S5_VIBC3    tct ggc gtt att tct gcg atg gat acc cgt gcc atc ggc atg gcg gtg gtc ggc atg ggc

                       G   G   R   R   Q   A   S   D   T   I   D   Y   S   V   G   F   T   D   M   A
P07650|TYPH_ECOLI      ggc gga cgc cgt cag gca tct gac acc atc gat tac agc gtc ggc ttt act gat atg gcg
                       G   G   R   R   V   A   T   D   R   I   D   Y   A   V   G   F   D   Q   F   I
A5F5S5|A5F5S5_VIBC3    ggt ggc cgc cgc gtg gcg acc gat cgt atc gat tac gct gtc ggt ttt gat cag ttt atc

                       R   L   G   D   Q   V   D   G   Q   R   P   L   A   V   I   H   A   K   D   E
P07650|TYPH_ECOLI      cgt ctg ggc gac cag gta gac ggt cag cgt ccg ctg gcg gtt atc cac gcg aaa gac gaa
                       R   L   G   E   I   A   D   S   N   K   P   L   A   M   I   H   A   R   N   E
A5F5S5|A5F5S5_VIBC3    cgt ctg ggt gaa atc gcc gac agc aac aaa cct tta gca atg att cat gcc cgt aat gaa

                       N   N   W   Q   E   A   A   K   A   V   K   A   A   I   K   L   A   D   K   A
P07650|TYPH_ECOLI      aac aac tgg cag gaa gcg gcg aaa gcg gtg aaa gcg gca att aaa ctt gcc gat aaa gca
                       E   Q   W   Q   Q   A   A   N   A   L   Q   S   A   I   K   V   G   G   D   Y
A5F5S5|A5F5S5_VIBC3    gag cag tgg caa caa gct gcc aat gca cta caa agt gcg att aaa gtg ggc ggt gat tac

                       P   E   S   T   P   T   V   Y   R   R   I   S   E   -   -   -
P07650|TYPH_ECOLI      ccg gaa agc aca cca act gtc tat cgc cgt atc agc gaa --- --- ---
                       L   P   -   T   P   D   V   Y   R   Q   I   R   A   Q   D   V
A5F5S5|A5F5S5_VIBC3    cta cca --- aca ccg gat gtt tac cgt caa att cga gca caa gac gtg