PAL2NAL output

                                M   T   Q   P   -   K   V   K   L   A   D   G   N   I   M   P   Q   L   G   L
gi|50119308|ref|YP_048475.1|    ATG ACG CAA CCG --- AAA GTT AAG CTG GCG GAC GGC AAT ATC ATG CCC CAG TTG GGC CTT
                                M   A   N   P   T   V   I   K   L   Q   D   G   N   V   M   P   Q   L   G   L
sw|Q46857|DKGA_ECOLI            atg gct aat cca acc gtt att aag cta cag gat ggc aat gtc atg ccc cag ctg gga ctg

                                G   V   W   R   A   S   S   E   D   T   V   I   A   V   N   E   A   L   S   I
gi|50119308|ref|YP_048475.1|    GGG GTC TGG CGA GCA AGC AGT GAA GAC ACG GTG ATC GCC GTG AAT GAA GCC TTG TCC ATC
                                G   V   W   Q   A   S   N   E   E   V   I   T   A   I   Q   K   A   L   E   V
sw|Q46857|DKGA_ECOLI            ggc gtc tgg caa gca agt aat gag gaa gta atc acc gcc att caa aaa gcg tta gaa gtg

                                G   Y   R   A   I   D   T   A   A   I   Y   K   N   E   E   A   V   G   Q   A
gi|50119308|ref|YP_048475.1|    GGT TAT CGG GCG ATC GAT ACC GCC GCG ATT TAT AAG AAT GAG GAA GCG GTC GGT CAG GCG
                                G   Y   R   S   I   D   T   A   A   A   Y   K   N   E   E   G   V   G   K   A
sw|Q46857|DKGA_ECOLI            ggt tat cgc tcg att gat acc gcc gcg gcc tac aag aac gaa gaa ggt gtc ggc aaa gcc

                                L   S   S   A   N   L   P   R   E   E   V   F   I   T   T   K   L   W   N   G
gi|50119308|ref|YP_048475.1|    CTA AGT TCT GCG AAT TTA CCG CGC GAA GAG GTA TTC ATC ACC ACC AAG CTC TGG AAT GGC
                                L   K   N   A   S   V   N   R   E   E   L   F   I   T   T   K   L   W   N   D
sw|Q46857|DKGA_ECOLI            ctg aaa aat gcc tca gtc aac aga gaa gaa ctg ttc atc acc act aag ctg tgg aac gac

                                D   H   T   D   P   Q   K   A   L   E   E   S   L   R   K   L   R   L   D   Y
gi|50119308|ref|YP_048475.1|    GAT CAC ACC GAT CCG CAA AAA GCG CTG GAA GAG AGC CTG CGA AAA CTT CGG TTA GAT TAT
                                D   H   K   R   P   R   E   A   L   L   D   S   L   K   K   L   Q   L   D   Y
sw|Q46857|DKGA_ECOLI            gac cac aag cgc ccc cgc gaa gcc ctg ctc gac agc ctg aaa aaa ctc cag ctt gat tat

                                I   D   L   Y   L   I   H   W   P   L   P   Q   Q   N   T   F   V   D   A   W
gi|50119308|ref|YP_048475.1|    ATC GAT CTC TAT CTG ATT CAC TGG CCG CTT CCG CAG CAG AAT ACC TTT GTG GAT GCC TGG
                                I   D   L   Y   L   M   H   W   P   V   P   A   I   D   H   Y   V   E   A   W
sw|Q46857|DKGA_ECOLI            atc gac ctc tac tta atg cac tgg ccc gtt ccc gct atc gac cat tat gtc gaa gca tgg

                                R   G   L   I   K   L   Q   E   Q   G   L   A   K   S   I   G   V   S   N   F
gi|50119308|ref|YP_048475.1|    CGT GGA CTC ATC AAA CTT CAG GAA CAA GGT CTC GCG AAA AGT ATC GGC GTC AGT AAT TTC
                                K   G   M   I   E   L   Q   K   E   G   L   I   K   S   I   G   V   C   N   F
sw|Q46857|DKGA_ECOLI            aaa ggc atg atc gaa ttg caa aaa gag gga tta atc aaa agc atc ggc gtg tgc aac ttc

                                H   I   H   H   L   Q   R   L   K   E   E   T   G   V   L   P   V   I   D   Q
gi|50119308|ref|YP_048475.1|    CAT ATT CAC CAT TTA CAG CGA TTA AAA GAA GAA ACT GGC GTA TTG CCG GTC ATC GAT CAG
                                Q   I   H   H   L   Q   R   L   I   D   E   T   G   V   T   P   V   I   N   Q
sw|Q46857|DKGA_ECOLI            cag atc cat cac ctg caa cgc ctg att gat gaa act ggc gtg acg cct gtg ata aac cag

                                V   E   L   H   P   L   L   Q   Q   K   Q   L   H   A   W   N   A   T   H   H
gi|50119308|ref|YP_048475.1|    GTC GAA CTG CAC CCG CTT CTC CAG CAA AAG CAG CTC CAT GCC TGG AAT GCC ACA CAC CAT
                                I   E   L   H   P   L   M   Q   Q   R   Q   L   H   A   W   N   A   T   H   K
sw|Q46857|DKGA_ECOLI            atc gaa ctt cat ccg ctg atg caa caa cgc cag cta cac gcc tgg aac gcg aca cac aaa

                                I   Q   T   E   S   W   S   P   L   A   Q   G   G   E   G   V   F   D   H   P
gi|50119308|ref|YP_048475.1|    ATC CAG ACT GAA TCC TGG AGC CCG CTG GCG CAG GGT GGT GAA GGG GTC TTT GAT CAC CCT
                                I   Q   T   E   S   W   S   P   L   A   Q   G   G   K   G   V   F   D   Q   K
sw|Q46857|DKGA_ECOLI            atc cag acc gaa tcc tgg agc cca tta gcg caa gga ggg aaa ggc gtt ttc gat cag aaa

                                I   I   R   K   L   A   M   K   Y   G   K   T   P   A   Q   I   V   I   R   W
gi|50119308|ref|YP_048475.1|    ATT ATC CGT AAA CTG GCG ATG AAA TAC GGA AAA ACA CCG GCA CAG ATT GTG ATC CGC TGG
                                V   I   R   D   L   A   D   K   Y   G   K   T   P   A   Q   I   V   I   R   W
sw|Q46857|DKGA_ECOLI            gtc att cgc gat ctg gca gat aaa tac ggc aaa acc ccg gcg cag att gtt atc cgc tgg

                                H   L   D   S   G   L   V   V   I   P   K   S   V   T   P   A   R   I   K   E
gi|50119308|ref|YP_048475.1|    CAT CTG GAC AGT GGG CTA GTG GTG ATT CCT AAA TCG GTG ACG CCG GCA CGC ATC AAG GAA
                                H   L   D   S   G   L   V   V   I   P   K   S   V   T   P   S   R   I   A   E
sw|Q46857|DKGA_ECOLI            cat ctg gat agc ggc ctg gtg gtg atc ccg aaa tcg gtc aca cct tca cgt att gcc gaa

                                N   F   E   V   F   D   F   R   L   D   K   D   E   L   S   E   I   T   K   L
gi|50119308|ref|YP_048475.1|    AAC TTC GAA GTG TTT GAT TTC CGC CTG GAT AAA GAC GAG CTG AGT GAA ATT ACC AAG CTG
                                N   F   D   V   W   D   F   R   L   D   K   D   E   L   G   E   I   A   K   L
sw|Q46857|DKGA_ECOLI            aac ttt gat gtc tgg gat ttc cgt ctc gac aaa gac gaa ctc ggc gaa att gca aaa ctc

                                D   C   G   K   R   L   G   S   D   P   D   E   P   R   N   D
gi|50119308|ref|YP_048475.1|    GAC TGC GGA AAA CGT CTG GGA TCG GAT CCT GAC GAA CCA AGA AAC GAC
                                D   Q   G   K   R   L   G   P   D   P   D   Q   F   G   G   -
sw|Q46857|DKGA_ECOLI            gat cag ggc aag cgt ctc ggt ccc gat cct gac cag ttc ggc ggc ---