test_pair.mlc

Before deleting alignment gaps
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normal_MH0058|normal_MH0058.peg.10458  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GAA GAG GTT ATC ACT ATT GGA GCC GGG GGA AAA CCG CAG TTA GAT GAA GGG GCT TTT GCA GAA CAC ATT GTA GAG TTT AAC CAC CTC --- --- --- --- --- ATT TGT TAC AAG GGT ATC TTA TAT GAC CGT TTC GGC GGA ACC GTA AGC AGA --- --- GCA GAA TGT GAA CAC GAA ATT TAT AAG ATA CTT CGG GGT CTG GGG ATT ACC TCT AAT ATG TCC AGC CGG ATT AAG AAC TTA TGT GAA GTT GTT CAA ATT CAG GCA TAT GTC GAT AGT ATT TCA ACC CCA CAG AAC CAA ATT GCC GTT CAA AAT GGC ACA GTG --- ACA ATG GAT TTG AAG ACT GGG GAA TGG AGT TTC GAT GAA AAG CCG --- --- --- --- TCC TTT TCC CTA CAC AGG ATG AAT TGC AGC TTC AAT CCC TAT GCC ACA ACT AAG CCC CCT --- --- --- --- GAA CGC TTC CTC GAA TGG GTA GAT AAC CTT ATC CAC GAA TAC GAC AGG --- --- --- GAC GGA TTT CAG GAG TAT TTG GGC TAC CTC CTT CTC CCT ATC ACG AAG TTG CAA AAG GCC ATG GTG CTT CTT GGC AAG GGG CAA GAG GGA AAG AGT CGG TTG GGT TTG ATC TTG CAA TAT CTC TTA GGA AAT TCC TTT GTA AGT TCC TCT GTT --- --- --- --- GAG TAT TTT GAA AAT AAC CAA TTT GCT ATG CCA CGG GCG GAA AAC AAA CTG GTT CTC TTT CAA GAT GAC CTG AAG AAA GAA AAA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 
normal_MH0058|normal_MH0058.peg.10459  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GAG GTT TTT AAG ATG GTT GTG TCA GCA GAG GTA CCT ATG CAG GCC GAA CAG AAG CAC GAA GCC ACT TAC TCC TTT ACC CCC --- --- --- --- TAT GCA AGA TGG --- --- GTG ATT TGC TCT AAC GCT CCT TTC ACG GCT TTA TCT GAT AGC --- --- --- --- GGA CAT GGT TTT --- TTT CGC CGC CTG TAT GTA ATC CGG GTG AAA AAC CGC CCC CCT GAT CGT AAA GAT GAC --- --- CCT TTC TAT TTT GAG CCA ATG AAA --- --- GAA GAA ATG GAC GGG ATC TTC ATT TGG ATG TTG CAA GGG TTA CAG CGG CTC --- ATT CAA AAC GGT TGG CGG CTT AGT GTA AGC GAA GAG TCA AAA GAA CTT --- --- TTG GAA GAT CAA CAG GAA CAG GCG AAT TCC CTC ATT AGT TTT ATG --- --- AAA AGC GAG TTA GCG TTT GGA GCC TAC AGT GTG ACT AAG GAA AGT CTT TAT AAG GCT TAT CTG GCC TAT TGC AAA CAA AAC CAC CTC ATA GCA GAG AAA CGG CCT GCA ATG TGG GCT TTC TTT GAA GAG CAG ATG GAC AAC CTG AAA ATC AAG AAG GAT AAG CAT TTA GGC GAG AAC AGG GGT AAA GAG GGC TAT GTA GGT ATG ACG CTG AAA ACA ACT GCG GCG GTA CTT GAT AGT CTG AAA 
normal_MH0048|normal_MH0048.peg.5129  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG AAA ATG AGC GAA GAA ATG ATA GCT GAG GTA ACT CCC GAA CTG TTC CAA CTG AAA AGT GGT CAG CTC ATC CTA TCC GAA GAG CTT TCG AGA AAG ATG TTC TAC ATT ATG AAC GCT CAC CCG GAA TCC CGG CAG CTC GAC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAC AGC GGG TAT TCA TGG GAT GAA AGC GGC ATG GCA GAA CTC TTC TCG GAG TGT TAC AAG AAC GAC ACC CGG TAC TGC CCG GAA GCG AAG TCG TGG TAC ACC TAC GAC AAC GGT GCA TGG CGT AAG GAT GTC GGC TCT CTG CTT GTG GCT GAG AAA ATC AAA GAG TTC ACT CGT TTG ATG GTC TTA TAC TGC GGA GAA ATT ACC GAT GAG GAA AAG CGC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAA AGC TAT TTT GCG TTC GTA AAT AAG ATG GGG GAT AGG CGT TTC CGT GAC AGA CTA ATG AAG GAT GCT GCT TCC GTC TAC CCC ATC TCA GTA TCT CAG TTC GAT GCA AAC CCT AAC CTC ATC AAC TGT CTC AAT GGT ACA TAC GAC TTG GAG ACA ATG AGC TTC CGA GAA CAC GAT TGG CGT GAC TAT CTC ACA ATG CAG ACC AAT TTT GAG TAT ACC ATG CAG GAT GAC ATT CGC TGT GAG CGT TGG GAA GAG TTC ATC CGT GAA GTT ACG AGT AAC GAC AAA GAG AAA GCT GAC TAC CTA CAA CGG GCG TTA GGC TAC TCC ATG CTC GGT ACT TCC AAA GAG GAG TGT ATG TTC ATC CTT CAC GGC AAA ACG ACC CGT AAT GGT AAG --- --- --- --- --- TCA ACG CTG CTC GGA ACG ATT CAC CAC CTG CTC GGC GAT TAT GCT TCT GTC TCC CCC GTG TCG ATT ATT TGT AAG ACC GAC AGG GCA AAG AAC GCA GAA GCA GCT TCC CCT ACA ATC GCC GCC CTC AAA GGA AAG CGG TTT GTG ACA ATG GCA GAA AGC AAT CAG TAC GGT AAA CTC GAT GAA --- GAA GTT ATC AAG CAG CTC ACA GGC GGC GAG GAA --- ATA ACT GCT CGG AAT CTG TAT GAG AGC ATG ATG ACC TTC CTT CCG --- --- --- --- CAA TTC ACA ATG --- --- TGG CTG TCT TGT AAT GAC --- CTT CCG AGT GTG CAG GAT AAA --- --- --- --- TCC CTG TTC GCT --- TCC GAC CGT GTA AGG GTC ATT GAG TTC AAC AGG CAC TTC ACT GAG GAA GAA CGG GAT --- --- GAG AGT TTG AAG GAT GCT TTC AGA ACG CCC GAA GCG ATG AAG GGT ATC TTC ACT TGG CTC GTG ATA GGG TAC TTC CGT --- --- --- TAT AAG CGT TTC GGA CTG AAA ATG TCC GAG AAG ATG AAG GAA GTC --- --- ATC AAG CAG TAT GAG CGT GAC AAT GAC CTT GTA TTG CAG TTC CTT GAA --- GAG CGT TGC GAG AGA AAT GAG GAT GCA AGC ACG AGG GCA AAG AGC CTA TTC GAT GCC TAT AAG ATT TGG TGT AAG AGT AAT GGG TAT TAT GTC TGC ACA TCG AAA AAG TTC AAT GCC GGA CTT GAA CAA CAC CCG GAA TGG CAC AAC GGT AAG AAG GTA TCA CAT GGG TAC ACT GTT TTT GAT GGT GTT TCC CTG AAA ACT TGT TCA --- --- --- --- --- --- --- --- --- --- --- --- 
normal_MH0027|normal_MH0027.peg.1804  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- CAA AAA GCA GTA GGC TAT AGC CTG ACG GGT TCA ACA TCA GAA CAG TGT GCG TTC TTT CTT TAT GGT --- ACA GGT AGA AAC GGC AAA --- --- --- --- --- TCA ACA TTT ATT GAT GTT ATT CGA GAT GTT TTC GGT GAC TAT GCA GCA AAC --- --- ATT CAG CCG GAA ACA ATT ATG GTG AGA AAT TCT CAA AGC AGT GCT ATA AAT AGC GAT ATT GCA CGA TTA AAA GGT GCA AGA CTT GTA ACA TCA GTT GAA CCG AAT GAG GGA GTA CGC ATA AAC GAA --- GGA CTC CTC AAA CAG CTT ACA GGT GAT GAT ATT --- GTA ACA GCT CGA AAG CTA TAT AGT GAG GAA TTT GAG TTC AAG CCT --- --- --- --- GAG TTT AAG TTG --- --- TGG ATG GCT ACG AAC CAC --- AAA CCG ATT ATC AGA GGT ACG --- --- --- --- GAT ACA GGT ATA --- TGG CGA AGA ATA CAT TTG ATA CCG TTT AAT GTA CAG ATT CCA GAG AAT AAA GTA GAT --- --- AAA AAC CTT ACA CAC AAG CTT AAA --- --- GCA GAA ATG ACA GCA ATA TTC AAA TGG TGT ATT GAC GGT TGT TTA --- --- --- CTT TGG CAA AAG GAG GGC TTG AAT ATG CCC TCT GCT GTC CTT GAG AGT --- --- GTG AGG GAG TAT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 
normal_MH0048|normal_MH0048.peg.6479  ATG AGA TTG ACT ATA TTT AGT GCA AGC TGT GTG GGT AAC GCT GCA AAC ACC ATC TAT CCC AAT AAA GCA GTA ATC ACA AAT AAA GAC GAT ATG ATT TCG GTT ATT GCA AGG GAT CAT GTA TGT GCT GAA TTT AAG AAA GCA CAT CGC AGT ATT GAT GAT TTT CTA TCT TCT GAT GTT GAA GTT ATG GAT TGT GAT AAT GAC CAC AGC GAC AAT CCG AAA GAC TGG ATT ACT CCT GAA AAG TAT GAG GAG CTG TTC CCG GAT GTA TCT TAC ATC GTT GTT CCA AGC CGT AAC GAT GGA AAG GTC AAA GGT AAT AAA TCA GCA AGA CCA AGA CAT CAT ATT TAT TTC CCA CAT GAA CCG ATT ACT GTA GCT GAT GAG GTC GCA GGT ATC AAA ACA AGA CTC CAG GAG ATT GCC CCA TTT TTT GAT GAC AAT GCT TTA GAT GCT GCA AGA TTT ATC TTT GGA CAT ACA CCT GCA GAT ATT GTA TGG CAT GAA GGC AGC AGA ACA ATT GTG GAT TTT TTG GAT GAA CTG GAC TTT GCA GAA TAT GAC AAT AAT TCG CAG AGC ATT GTT GAA GGT TCC CGT AAC AGT ACT ATG AGC CAT ATT GCA GGG AAA CTT ATA AAA AGA TAC GGA AAT ACA GAT AAG GCT CAT GAT ATT TTT CTT GAG AAG GCA GCT CTT TGC AAT CCG CCA CTT GAG GAT AGT GAA CTT TCT CTT ATT TGG AGC AGT GCC ATT AAA TTC GGT AAG AAG GTA CAG TCG CAG GTC GGC TAT GTA TCG CCC GAA GAA TTT AAT ACG GGA TAC AGC TTA AAG CCA GAC GAT TAT TCT GAT ATT GGC CAA GCA AAG GTT CTG GCA AGA GAG TAT GAA GGA GAA CTT GCC TTT ACA --- GAC TCC ACA GAT TAT ATG CGT TAT GAC GGT ACG CAT TGG --- --- TCG GAA TCA AAG CAG TTA GCC GTT GGT GCC TGC GAG GAA TTT TTG GAT GAA CAG TTA AAG GAG GCG ACG GCA GCA GTG GAG AAG GCG AAA AAG TTA CTC CTT GAC GCA GGT GTT GAT AAG GAT GTT GTT ATG GCA GGT GGT AAA GCA CTG GAA AAA GCC ATC GAT GAA AAC AGT GAG AAG GCA TTC AAG GAA TTT GTG ATG GCA TCA AAA TAT TAT GCC TTC GTT ATG AAA CGC AGG GAT ATG AAG TAT GTA ACC TCT GCA CTG CAG GCG GCA AAG CCT ATG TTA CTT AAG AAA ATC ACA GAT TTC GAT AAC CAG GAG TTT TTA CTG AAC ACT CCG ACA GCT ACC TTT GAT TTA CAG AAT GGA AAC AGT AAA GAA CAT TCA GCA GAA GAT TTA ATT ACA AAG ATT ACT ACA GTA TCG --- --- --- CCA AGC GAT GAA GGT ATG GAT TTG TGG CTT TCT GCC CTG GAT AGC TTT TTC TGT GGA GAT GCA GAA CTA ATG GAT TAT GTT CAG CAG ATT GTC GGA CTT TCA GCA ATC GGT AAG GTG TAT GTT GAG GCA CTT GTT ATT GCA TAT GGT --- GAG GGA AGC AAT GGT AAG --- --- --- --- --- AGT ACC TTT TGG AAT ACC ATC GCA AGG GTG CTT GGA ACG TAC AGC GGA ACG --- --- ATC TCA GCC GAT GCT CTG ACA GTT GGT TGC AAG CGT AAT --- --- GTA AAG CCG GAG ATG GCA GAA CTT AAG GGT AAG AGA TTA GTT ATT GCA GCG GAA CTT GAA GAA GGA ATG CGC CTT AAT ACT --- TCC ATT GTA AAA CAG CTT TGT TCT ACC GAT GAA --- GTT ACG GCT GAA AAG AAA TAT AAG GAT CCG TTC AAA TAC GTG CCG --- --- --- --- ACA CAC ACC CTC --- --- GTC TTA TAT ACC AAT CAT --- CTC CCA AGG GTG GGA GCT AAT --- --- --- --- GAT GAT GGT ATC --- TGG CGA AGG CTT ATT GTT ATA CCT TTT AAT GCA AAG ATT ACA GGA AAT AGT GAT AGA --- --- AAA AAT TAT GCT GAT TTC CTT TAT GAA --- AAT GCT GGT GGT GCT GTG CTT TCA TGG ATT ATC GAA GGA GCA GAG AAA GCC --- ATC AAA AAC AAG TAC AAA TTA AAG GTT CCA AAG GTG GTC GAG GCA GCC --- --- ATC AAT AAA TAT CGT GAG AAC AAT GAC TGG TTC TCT GCA TTT GTG GAC --- GAG TGC TGT GAG GTG GAT GTG ACA TTC CAG CAG AAG TCA GGA GAG TTC TAC CAG GAG TAT CGT TCT TAC TGT GCA AGG ACG GGA GAA TAT ACG AGA AGT ACC ACA GAT TTT TAT ACG GCA CTT GAG AAT GCA --- --- --- GGT TTT GAG AGA AAG AAA ACG AAA GCG GGT GTG ATA GTC CGT GGA ATA CGC TTA AAA TCA GAC TTT TTA GAT AAT --- --- --- --- --- --- --- --- --- 
normal_MH0027|normal_MH0027.peg.256  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG GCA CAC ACA CGA TTA GAT ACA ATT AGA CAA GCT ACA AGA GAT TAT CTT GCA TCA ATT AAA GGT ACA ACA CCA GCT CCG GCT GAT GTT GAA GAA GGC ATT CTG GCT CTT ACA AGA AAT TAT TTT GAT TTA TAT AAT GCG GCA GCT GCA AAG GGT GCA AAA TGG AGA ACA CCA ACT GAA TTA ATG CCT ATT CAG --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- GTT GCT GAA ATC ATT GAG AGT TTA TAT CAG GTT GCA TTA GTT GAA CTG GTC GAT AAA GGC GGT CCT GAG CTG AGA ACA CAG TCT GCT GTC CTT GGT ATC TAT CAG GAA TCT GGA GAG TAT GAA GGA TTG TAT GAT TGC ACA GAA GCA ACA TTT GAA AAA CTG GCT GGC GGA TAT TGT TAT GGA ATG TCT GCA AAA GAC AGA ATC GAG ATG ATT AAA CAT CTC AGA CTG ATT GCA CCG CAT GTA AAG CTT TGC AGA AAG CCG AAT CTG ATT GCA GTC AAC AAT GGT ATT TTT GAT TAT AAT ACA AAG GTG TTG ATG CCT TTT ACG CCG GAT TTT GTG TTC ATT ACA AAA TCA AGA GTT GAT TAT AAT CCG AAT GCA AGG AAT GTC GTG ATT CAC AAT CCT GTA GAT AAT ACA GAC TGG GAT GTT GAG AAT TGG GTG TGT TCA TTG TCG GAT GAC CCT GAG ATT GTC AAT ACG CTT TGG GAA GTG ATG GGT GCT ATC ATC AGA CCA AAT GTA CGT TGG AAC AAG TCA GCA TGG TTC TAT GCG GAA TCA GGT AAC AAT GGT AAG GGA ACA CTC TGT GAG CTT ATG AGA AAT CTT TGT GGT GAT GGT ACG GCT GTG TCA TTG CCA TTG GCT GAT ATG AGC AAA GAT --- TTC TTG CTT GAG CCT CTT ATC AAT GCA TCA GCT ATC ATC GTT GAT GAG AAT GAT GTC GGT ACA TAC ATC GAC AAG GCT GCG AAT CTG AAA GCT ATC ATT ACA AAT GAT GTC ATT CAG ATT AAC CGT AAG TTC AAG ACG CCG ATT ACA TAT CAG TTC CAT GGA TTC ATG GTA CAG TGT CTG AAT GAA CTT CCA AGA GTG AAG GAT AAG TCT GAT TCA TTC TTC AGA CGT CAG CTC --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 
normal_MH0048|normal_MH0048.peg.5652  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAA AAG CTG GTT ACA GGT GAT CGG --- GTG AAT GTG GAG CGG AAA GGA CAA GAC CCC TTC GAG TTC AAC AAC --- --- --- --- TAC GCC AAG TTC --- --- TTA TTC AGC GCC AAC AAC --- ATT CCC CGC ATG AAG GAT AAA --- --- --- --- ACC GGA GCC GTT --- CAA AGG CGG CTT GTG ATT GTC CCC TTT GAT GCC AAA TTC ACC CCA AAT GAT CCT GAC TTT CGT CCA TTC ATC AAA GAT GAA CTT TGT GAA CAG GAT TCA ATG GAA TAT CTG ATT CTT TTG GGC CTG AAG GCA TTG CGC CGG --- --- GTT CTG ATG AAT GCC CAA TTC ACC ACT TCC AGC AGA GTT CAG GGA CAG --- --- TTG GAC GAA TAC GAA CAG AAC AAC AAC CCC ATT ATT GGT TTC ATC --- --- AAG GAA GTT GGC CTT GAA GGG ATT GAA AAT GAA CCC ACA AAG ACA GTT TAT CGA AAA TAC AAA GAA TAC TGC ATT TCC AAT AAC TTT CAG GCA CTT TCC AAT ATC GAA TTT TCA CGG CAA ATC ACC AAA CGC TGT GGG TTC ATT ATT GTT GAT AAG TGG ATC AGT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 
normal_MH0058|normal_MH0058.peg.3815  --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ATG GAC CGT CTG TTT ATG GGC TAC GTC AAG CTC AAC GGC AAG AAG TGT GCG CAG AAG CTG AAG GAC GGC CAG TAC CTC ACA CTT GCG CAG GCA CGC AAG CTC GAC GGC TAC GGC GGA GTG CTC GCA CCT GAG ACG ATC TTC GTC GAT GTC GAC GAC ATG GAG CAG AGC GAG AAG CTG ATG GAC ATC GTC GAG GCC GAG CAG GTC GCA TGC AAG GTC GTC GCC ACG ACC CGC GGC AAG CAT TTC TAT TTC GTC GGC TAC CCC AGA GGC ATG AAA TGC AAG ACA CAT GCA CGC CTG GCC GTC GGC ATC GAT GCA GAC ATC AAA GTC GGC TCG AAG GCC ACG TAC GGC AGC CTG AAA GTC GAC GGA CAT GAG CGC GAC GTG ATA TAC GAC ATC GAG CCG GAC GAA GAT TAC GAC GAG CTG CCG GTC TGG CTC AGG CCT GTG CAG TAT ACT CCT GAG TTC GAT GAG ATG GAA GAA GGC GAC GGC CGC AAC CAA GCG TTA TTC AAC TAC ATC TTG ACG CTG CAG TCG GAG GGC TTC ACG AAA GAC GAG GCG CGC GAG ACC CTG GGC ATC ATC AAC AGG TAT ATG TTC GAG AAG CCC ATG GAG CAG CAG GAG CTC GAC GTC GTC TAC CGC GAC GAC GCC TTC GCC GAA GAC GTT TTC TTC CAT AAA GGA ACG TTC CTA TTC GAC AAG TTC GCC GAG TAC CTC AAG AAC GAG CAC CGC ATC ATC AAG ATC GGC CAT CAG CTC CAC GTA TAC CGC AAT GGC GTC TAT GTG TCC GGC AAT CTG CTC ATC GAG --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- AAC GCG ATG ATC CAG CAC TTG CCC ATG TTG TCG AAG GCC AAG CGC ACC GAG GTG CTC AAC TAC CTC GAC GTG CTC ATC CAA GAT GAC GCA CCT GCT GCC GAT GCC GAT TAC ATC GCT TTC GCT AAC GGC GTG TAC GAC CTC AAG ACG GGT GAG CTC ATG CCG TTC TCG CCG GAA TTA GTG ATC ACG AAC CGC ATT CCT TGG GAT TAC --- --- GAC CCG ACG ATC TGG TCG GAG TTC ACC GAC AAG ACG CTG CGC CGC CTC GCC TGC GGT GAC GAC GGA ATC TAT GCA TTG TTG GAG GAG GTC ATC GGC TAC CTG TTC TAT CGG CGC AAT GAG CTC CGT AAG AGT TTC ATC TTG ATT GGC --- GAC AAG GCA AAC GGC AAG --- --- --- --- --- TCG ACG TAT CTC GAC ATG CTC AAG ACA CTG CTC GGC GAC AGC AAT ACG TCG --- --- --- --- --- --- --- --- --- GCC CTC GAC CTG GCC GAG CTC GGC GAG AGG TTC AAG ACA GCT GAG CTG TTC GGA AAG CTG GCC AAC ATC GGC GAC GAC ATC GGC GAC GAG TTC ATC GCA AAC CCC --- GCG ATT TTC AAA AAG CTC GTC AGC GGT GAC CGC --- GTC AAC GCC GAG CGT AAA GGC CAA GAC CCG TTT GAT TTC TCG AGT --- --- --- --- TAC GCC AAG CTC --- --- CTG TTT TCG GCG AAT TCG --- ATG CCT CGT ATC AGG GAC AAG --- --- --- --- ACC GGC GCC GTG --- CTC GAC CGC ATC GTG CTC GTG CCG TTC AAG GCG ACG TTT TCG AAA GAC GAC CCG GAC TTC GAC CCC TAT ATC AAG TAC AAG CTC CAT TCG CCC GAG GTC ATG AGC CAC TTG ATC AAT ATC GGC CTC AAG GGG CTC GAG CGT --- --- GTG TTG GCG AAC CGC TCA TTC ACG ATG CCT GAG GTC GTC GTC AGG GAA --- --- ATT AAG GAT TAC CAC GTG GCC AAC AAC CCT GTC CTC GGT TAT TTC --- --- GAA GAC ACA CCC GTC GAC GAG GTG GTG AAC GAG TCG ACG GCG CTG GTA TAC GAC TAC TAT --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- 



After deleting gaps. 300 sites
      8    300

normal_MH0058|normal_MH0058.peg.10458  ATT GCC GTT CAA AAT GGC ACA GTG ACA ATG GAT TTG AAG ACT GGG GAA TGG AGT TTC GAT GAA AAG CCG TCC TTT TCC CTA ATG AAT TGC AGC TTC AAT TAT GCC ACA ACT AAG CCC CCT GAA CGC TTC CTC TGG GTA GAT AAC CTT ATC CAC GAA TAC GAC AGG GAC GGA TTT CAG GAG GGC TAC CTC CTT CTC CCT ATC ACG CAA AAG GCC ATG GTG CTT CTT GGC AAG GGG CAA GAG GGA AAG AGT ATC TTG CAA TAT CTC TTA GGA AAT TCC TTT GTA AGT TCC TCT GTT GAG TAT 
normal_MH0058|normal_MH0058.peg.10459  AAG ATG GTT GTG TCA GCA GAG GTA ATG CAG GCC GAA CAG AAG CAC GAA GCC ACT TAC TCC TTT ACC CCC TAT GCA AGA TGG GTG ATT TGC TCT AAC GCT TTC ACG GCT TTA TCT GAT AGC GGA CAT GGT TTT TTT CGC CGC CTG TAT GTA ATC CGG GTG AAA AAC GAT CGT AAA GAT GAC CCT TTC TAT TTT GAG CCA ATG AAA GAA GAA ATG GAC GGG ATC TTC ATT TGG ATG TTG CAA GGG TTA CAG CAA AAC GGT TGG CGG CTT AGT GTA AGC GAA GAG TCA AAA GAA CTT GAT CAA 
normal_MH0048|normal_MH0048.peg.5129  AAG CAG CTC ACA GGC GGC GAG GAA ATA ACT GCT CGG AAT CTG TAT GAG AGC ATG ATG ACC TTC CTT CCG CAA TTC ACA ATG TGG CTG TCT TGT AAT GAC CTT CCG AGT GTG CAG GAT AAA TCC CTG TTC GCT TCC GAC CGT GTA AGG GTC ATT GAG TTC AAC AGG GAG GAA GAA CGG GAT GAG AGT TTG AAG GAT GCT TTC AGA GAA GCG ATG AAG GGT ATC TTC ACT TGG CTC GTG ATA GGG TAC TTC TAT AAG CGT TTC GGA CTG AAA ATG TCC GAG AAG ATG AAG GAA GTC CAG TAT 
normal_MH0027|normal_MH0027.peg.1804  AAA CAG CTT ACA GGT GAT GAT ATT GTA ACA GCT CGA AAG CTA TAT AGT GAG GAA TTT GAG TTC AAG CCT GAG TTT AAG TTG TGG ATG GCT ACG AAC CAC AAA CCG ATT ATC AGA GGT ACG GAT ACA GGT ATA TGG CGA AGA ATA CAT TTG ATA CCG TTT AAT GTA GAG AAT AAA GTA GAT AAA AAC CTT ACA CAC AAG CTT AAA GCA GAA ATG ACA GCA ATA TTC AAA TGG TGT ATT GAC GGT TGT TTA TGG CAA AAG GAG GGC TTG AAT ATG CCC TCT GCT GTC CTT GAG AGT GAG TAT 
normal_MH0048|normal_MH0048.peg.6479  AAA CAG CTT TGT TCT ACC GAT GAA GTT ACG GCT GAA AAG AAA TAT AAG GAT CCG TTC AAA TAC GTG CCG ACA CAC ACC CTC GTC TTA TAT ACC AAT CAT CTC CCA AGG GTG GGA GCT AAT GAT GAT GGT ATC TGG CGA AGG CTT ATT GTT ATA CCT TTT AAT GCA GGA AAT AGT GAT AGA AAA AAT TAT GCT GAT TTC CTT TAT AAT GCT GGT GGT GCT GTG CTT TCA TGG ATT ATC GAA GGA GCA GAG AAA AAC AAG TAC AAA TTA AAG GTT CCA AAG GTG GTC GAG GCA GCC AAA TAT 
normal_MH0027|normal_MH0027.peg.256  GAT TTT GTG TTC ATT ACA AAA TCA GTT GAT TAT AAT CCG AAT GCA AGG AAT GTC GTG ATT CAC AAT CCT GAC TGG GAT GTT TGG GTG TGT TCA TTG TCG GAC CCT GAG ATT GTC AAT ACG ATG GGT GCT ATC AGA CCA AAT GTA CGT TGG AAC AAG TCA GCA TGG GAA TCA GGT AAC AAT GGA ACA CTC TGT GAG CTT ATG AGA TGT GGT GAT GGT ACG GCT GTG TCA TTG CCA TTG GCT GAT ATG AGC TTG CTT GAG CCT CTT ATC AAT GCA TCA GCT ATC ATC GTT GAT GAG ACA TAC 
normal_MH0048|normal_MH0048.peg.5652  AAA AAG CTG GTT ACA GGT GAT CGG GTG AAT GTG GAG CGG AAA GGA CAA GAC CCC TTC GAG TTC AAC AAC TAC GCC AAG TTC TTA TTC AGC GCC AAC AAC ATT CCC CGC ATG AAG GAT AAA ACC GGA GCC GTT CAA AGG CGG CTT GTG ATT GTC CCC TTT GAT GCC CCA AAT GAT CCT GAC CCA TTC ATC AAA GAT GAA CTT TGT GAT TCA ATG GAA TAT CTG ATT CTT TTG GGC CTG AAG GCA TTG CGC CTG ATG AAT GCC CAA TTC ACC ACT TCC AGC AGA GTT CAG GGA CAG GAA TAC 
normal_MH0058|normal_MH0058.peg.3815  AAA AAG CTC GTC AGC GGT GAC CGC GTC AAC GCC GAG CGT AAA GGC CAA GAC CCG TTT GAT TTC TCG AGT TAC GCC AAG CTC CTG TTT TCG GCG AAT TCG ATG CCT CGT ATC AGG GAC AAG ACC GGC GCC GTG CTC GAC CGC ATC GTG CTC GTG CCG TTC AAG GCG AAA GAC GAC CCG GAC CCC TAT ATC AAG TAC AAG CTC CAT GAG GTC ATG AGC CAC TTG ATC AAT ATC GGC CTC AAG GGG CTC GAG TTG GCG AAC CGC TCA TTC ACG ATG CCT GAG GTC GTC GTC AGG GAA GAT TAC 



Printing out site pattern counts


         8        300  P

normal_MH0058|normal_MH0058.peg.10458  AAC AAG AAG AAG AAG AAG AAG AAT AAT AAT AAT ACA ACA ACA ACG ACT ACT AGC AGG AGT AGT AGT ATC ATC ATC ATG ATG ATG ATT CAA CAA CAA CAA CAC CAG CCC CCG CCT CCT CGC CTA CTC CTC CTC CTC CTT CTT CTT CTT GAA GAA GAA GAA GAC GAC GAG GAG GAG GAT GAT GAT GCC GCC GCC GGA GGA GGA GGC GGC GGC GGG GGG GTA GTA GTG GTG GTT GTT TAC TAC TAT TAT TAT TCC TCC TCC TCC TCT TGC TGG TGG TTA TTC TTC TTC TTG TTG TTT TTT TTT 
normal_MH0058|normal_MH0058.peg.10459  CTG .CC C.. G.A TCT TG. TTA .T. GC. GTA TCA .TG GAG G.T .AA .AG TTA TCT .AC .C. CAG TCA ..G CAA G.A CA. GAC G.. .AG G.. GGT GTG TTG AT. G.T GAT ..C AGC ..A .AT TGG .GG GAG TAT T.T A.C TA. T.C T.. CGG ... .G. TTT A.A ..T C.A ..C ..T CGC .CC TCC A.G ATG ATG A.T C.T ..G ATT CCT .CA AT. CAC CGC .AG .G. ..A C.. ... GTG .T. C.A .GG .TC AAA AGA AG. .AT GAA ... GCC .TT C.T AA. GGT .A. AAC GAA AAA GAA GCA 
normal_MH0048|normal_MH0048.peg.5129  GTA CTT ..T GC. C.. TG. T.C CTG G.C .TG GGC .T. GAG .GT .GA CTG GTG T.T ... .TG TTC .TG T.. TAT G.. .CT .A. TG. .AG G.. .GT AC. GTG ATT .G. GAT ... AAA G.. .TG A.G GGA GAT T.G GCT A.C AGG T.C AAG ..G ..G TCC TTC A.. ..G ATA ..T C.. CG. .C. ACC C.G ATG CAG AA. .A. ..G ACT .AG ... CTC TAT .AC AAG .GT .AA ..C C.C .T. AGT ... .TC CT. AAG A.A ... CAA GAA .CT A.C .CC C.G AAT ... A.G AA. CG. GAA GAG ..C 
normal_MH0027|normal_MH0027.peg.1804  .TA ... ... G.A .GA TG. TGT .TG C.C .TG GG. GT. GAT .TT .AA CTA .TC .CG GTA GAA TTA GTC C.T TGG T.G .CA .CA TG. .AA GC. A.G AC. ATT ATA GTA GGT ..T A.G AAG ACA T.G GG. .A. ..T A.A A.A .A. T.C ACA CCG AGT ..T TTC A.T ..G ..C ..T ... AGA .C. ..G C.G ATG CAG AAT AAT ..T AAA AAA .AT T.T TAT CG. .CT .CA A.T AG. C.. .TT A.. ... G.G A.A CTT AAG C.. GAG GAG GCT GA. ... ..G AA. GGT ..T CAA CGA AAA .C. ... 
normal_MH0048|normal_MH0048.peg.6479  CTT GT. ... GCT GGA TG. GCA TTA C.. GT. TC. GTT GAT .GG TAT .AA GTG .C. GCA CCG GAG GTC C.T .AA G.T .C. GGT G.C .AA A.T A.G TGT ATC ATA G.T G.T ... AA. TTC GAT ..C AAA GAT TAT A.. G.G A.. ... GC. CCT A.G ..T T.C A.T .GA ..A AGA A.A AGG .C. A.A C.A .GT CAG AAG AAT ... TCA AAA AC. ATT TAT CG. ..G .CT .AA .CC C.. .TT A.T ... ..C CTC GAG A.. C.A A.A G.A .AT GAT ... ... AAT GGT ... AAC GAA AG. AAG CAC 
normal_MH0027|normal_MH0027.peg.256  GTA ..T CC. GGT GTC TT. .T. GTG TCG GCA .T. GTT .A. GAG .GA .A. .T. TCA T.. GTC ..C .TC ..G T.G TGG GAT GGT TG. GA. TGT G.G TTC TTG A.. A.C AAT ..T A.G .T. G.T G.T ..T GAG ... A.. GC. .G. G.G TG. A.G AGG ATG C.C .CA ..A .CT A.T ACA A.. T.. AT. C.T .AT TTT AAT TC. .AT TCA ..A ACA CCA .CA CC. A.C AC. TCA .AG ..G .CA ACA ..C CC. G.C GTT GAT ..A GA. GA. ..T AAT A.A A.C ..G GCT G.G C.T AAT GG. GC. .GG 
normal_MH0048|normal_MH0048.peg.5652  CTT ..C CG. TCA ... TT. TT. TTC ..C .C. .CA GTG GAT CGC TGT .AA .TG GC. GCC CCC C.C GT. C.T C.G ..T .AT GAA T.A .AA G.T A.T GTT .TG GT. .CT GAT AAC AAA GAA G.A T.C .AA GAT A.. G.T ..G G.G A.. AAA CCC C.. ACC TTC ..T CCA A.. ..C ..A CGG .TG ..G C.. ATG AAG ACC AAT .C. CTT CCA ..T ..C ..A AGG AG. TAT CG. CAG C.G .TT .T. ..C GCC AT. CAG AAG ... .A. GGA A.. GAC CAA ..C AA. GC. ... A.. GA. GA. AGC GCC 
normal_MH0058|normal_MH0058.peg.3815  .T. TC. CGT GTC .G. .TC CTC TT. TCG .TG .GC GTC GAC CGT CAT .AA .TC GCG GC. CCG GAG GTC C.. T.G C.. .AC .GC C.. .AA G.G A.C GTC .TC GTG .C. GA. AGT AAG AAG G.. ..C TCA TA. A.. G.G T.G G.G A.C AAG CCG C.. ACC TTC A.G A.A A.. ..C ..T CGC .CC ... C.T ATG AAG ACG .AC ..G AAT CC. ..T ..C ..C .AC ..C CAC CGC .AA C.C .T. ..T ..C CGC ATG GT. AAG C.T .A. AGG .CG GAC CTC ..C AAT GC. ..T GC. GA. GAC GAG GCC 

    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1

CODONML (in paml version 4.9, March 2015)  codon.phy
Model: One dN/dS ratio for branches, 
Codon frequency model: F3x4
ns =   8  ls = 100

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT   3   4   0   3   1   1 | Ser TCT   1   2   1   1   1   0 | Tyr TAT   3   3   3   2   5   1 | Cys TGT   0   0   1   2   1   3
    TTC   3   3   8   2   2   1 |     TCC   4   1   3   0   0   0 |     TAC   2   1   1   0   2   1 |     TGC   1   1   0   0   0   0
Leu TTA   1   2   0   1   2   0 |     TCA   0   2   0   0   1   6 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
    TTG   2   1   1   3   0   4 |     TCG   0   0   0   0   0   1 |     TAG   0   0   0   0   0   0 | Trp TGG   2   3   2   4   2   4
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT   4   2   2   4   4   3 | Pro CCT   2   1   0   1   1   3 | His CAT   0   1   0   1   1   0 | Arg CGT   0   1   2   0   0   1
    CTC   4   0   2   0   2   1 |     CCC   1   1   0   1   0   0 |     CAC   1   1   0   2   1   1 |     CGC   1   2   0   0   0   0
    CTA   1   0   0   1   0   0 |     CCA   0   1   0   0   2   2 | Gln CAA   4   3   1   1   0   0 |     CGA   0   0   0   2   1   0
    CTG   0   1   4   0   0   0 |     CCG   1   0   2   2   2   1 |     CAG   1   3   3   1   1   0 |     CGG   0   2   2   0   0   0
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT   1   2   1   3   2   3 | Thr ACT   2   1   2   0   0   0 | Asn AAT   4   0   2   3   6   8 | Ser AGT   3   1   2   2   1   0
    ATC   3   2   1   1   2   4 |     ACC   0   1   1   0   3   0 |     AAC   1   3   1   2   1   2 |     AGC   1   2   1   0   0   1
    ATA   0   0   2   4   1   0 |     ACA   3   0   2   5   1   3 | Lys AAA   0   4   2   6   7   1 | Arg AGA   0   1   1   2   1   2
Met ATG   3   5   6   3   0   3 |     ACG   1   1   0   2   1   2 |     AAG   6   2   6   5   5   1 |     AGG   1   0   2   0   2   1
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT   2   1   0   0   3   3 | Ala GCT   0   2   3   3   5   4 | Asp GAT   3   4   3   4   6   6 | Gly GGT   0   2   1   4   3   4
    GTC   0   0   2   1   2   2 |     GCC   3   2   0   0   1   0 |     GAC   2   2   2   1   0   2 |     GGC   3   0   2   1   0   0
    GTA   2   3   1   3   0   1 |     GCA   0   2   0   2   3   3 | Glu GAA   4   6   5   2   3   1 |     GGA   3   1   1   0   3   1
    GTG   2   3   2   0   4   4 |     GCG   0   0   1   0   0   0 |     GAG   3   3   6   7   2   4 |     GGG   2   2   1   0   0   0
--------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------
Phe TTT   1   2 | Ser TCT   0   0 | Tyr TAT   1   1 | Cys TGT   1   0
    TTC   6   3 |     TCC   1   0 |     TAC   2   3 |     TGC   0   0
Leu TTA   1   0 |     TCA   1   1 | *** TAA   0   0 | *** TGA   0   0
    TTG   2   2 |     TCG   0   3 |     TAG   0   0 | Trp TGG   0   0
----------------------------------------------------------------------
Leu CTT   3   0 | Pro CCT   1   2 | His CAT   0   1 | Arg CGT   0   2
    CTC   0   7 |     CCC   3   1 |     CAC   0   1 |     CGC   2   3
    CTA   0   0 |     CCA   2   0 | Gln CAA   3   1 |     CGA   0   0
    CTG   4   1 |     CCG   0   3 |     CAG   2   0 |     CGG   3   0
----------------------------------------------------------------------
Ile ATT   3   0 | Thr ACT   1   0 | Asn AAT   3   2 | Ser AGT   0   1
    ATC   1   5 |     ACC   2   1 |     AAC   4   2 |     AGC   2   2
    ATA   0   0 |     ACA   1   0 | Lys AAA   4   3 | Arg AGA   1   0
Met ATG   3   3 |     ACG   0   1 |     AAG   4   7 |     AGG   1   2
----------------------------------------------------------------------
Val GTT   3   0 | Ala GCT   0   0 | Asp GAT   6   2 | Gly GGT   1   1
    GTC   1   6 |     GCC   5   3 |     GAC   2   7 |     GGC   1   3
    GTA   0   0 |     GCA   1   0 | Glu GAA   3   1 |     GGA   3   0
    GTG   3   3 |     GCG   0   3 |     GAG   2   4 |     GGG   0   1
----------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: normal_MH0058|normal_MH0058.peg.10458
position  1:    T:0.22000    C:0.20000    A:0.29000    G:0.29000
position  2:    T:0.31000    C:0.18000    A:0.34000    G:0.17000
position  3:    T:0.28000    C:0.30000    A:0.18000    G:0.24000
Average         T:0.27000    C:0.22667    A:0.27000    G:0.23333

#2: normal_MH0058|normal_MH0058.peg.10459
position  1:    T:0.23000    C:0.19000    A:0.25000    G:0.33000
position  2:    T:0.29000    C:0.17000    A:0.36000    G:0.18000
position  3:    T:0.27000    C:0.22000    A:0.25000    G:0.26000
Average         T:0.26333    C:0.19333    A:0.28667    G:0.25667

#3: normal_MH0048|normal_MH0048.peg.5129
position  1:    T:0.20000    C:0.18000    A:0.32000    G:0.30000
position  2:    T:0.32000    C:0.15000    A:0.35000    G:0.18000
position  3:    T:0.23000    C:0.24000    A:0.15000    G:0.38000
Average         T:0.25000    C:0.19000    A:0.27333    G:0.28667

#4: normal_MH0027|normal_MH0027.peg.1804
position  1:    T:0.18000    C:0.16000    A:0.38000    G:0.28000
position  2:    T:0.29000    C:0.17000    A:0.37000    G:0.17000
position  3:    T:0.33000    C:0.11000    A:0.29000    G:0.27000
Average         T:0.26667    C:0.14667    A:0.34667    G:0.24000

#5: normal_MH0048|normal_MH0048.peg.6479
position  1:    T:0.17000    C:0.15000    A:0.33000    G:0.35000
position  2:    T:0.25000    C:0.21000    A:0.40000    G:0.14000
position  3:    T:0.40000    C:0.16000    A:0.25000    G:0.19000
Average         T:0.27333    C:0.17333    A:0.32667    G:0.22667

#6: normal_MH0027|normal_MH0027.peg.256
position  1:    T:0.22000    C:0.12000    A:0.31000    G:0.35000
position  2:    T:0.30000    C:0.25000    A:0.28000    G:0.17000
position  3:    T:0.40000    C:0.15000    A:0.20000    G:0.25000
Average         T:0.30667    C:0.17333    A:0.26333    G:0.25667

#7: normal_MH0048|normal_MH0048.peg.5652
position  1:    T:0.16000    C:0.23000    A:0.30000    G:0.31000
position  2:    T:0.31000    C:0.18000    A:0.36000    G:0.15000
position  3:    T:0.24000    C:0.32000    A:0.20000    G:0.24000
Average         T:0.23667    C:0.24333    A:0.28667    G:0.23333

#8: normal_MH0058|normal_MH0058.peg.3815
position  1:    T:0.15000    C:0.22000    A:0.29000    G:0.34000
position  2:    T:0.32000    C:0.18000    A:0.35000    G:0.15000
position  3:    T:0.14000    C:0.47000    A:0.06000    G:0.33000
Average         T:0.20333    C:0.29000    A:0.23333    G:0.27333

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      15 | Ser S TCT       6 | Tyr Y TAT      19 | Cys C TGT       8
      TTC      28 |       TCC       9 |       TAC      12 |       TGC       2
Leu L TTA       7 |       TCA      11 | *** * TAA       0 | *** * TGA       0
      TTG      15 |       TCG       4 |       TAG       0 | Trp W TGG      17
------------------------------------------------------------------------------
Leu L CTT      22 | Pro P CCT      11 | His H CAT       4 | Arg R CGT       6
      CTC      16 |       CCC       7 |       CAC       7 |       CGC       8
      CTA       2 |       CCA       7 | Gln Q CAA      13 |       CGA       3
      CTG      10 |       CCG      11 |       CAG      11 |       CGG       7
------------------------------------------------------------------------------
Ile I ATT      15 | Thr T ACT       6 | Asn N AAT      28 | Ser S AGT      10
      ATC      19 |       ACC       8 |       AAC      16 |       AGC       9
      ATA       7 |       ACA      15 | Lys K AAA      27 | Arg R AGA       8
Met M ATG      26 |       ACG       8 |       AAG      36 |       AGG       9
------------------------------------------------------------------------------
Val V GTT      12 | Ala A GCT      17 | Asp D GAT      34 | Gly G GGT      16
      GTC      14 |       GCC      14 |       GAC      18 |       GGC      10
      GTA      10 |       GCA      11 | Glu E GAA      25 |       GGA      12
      GTG      21 |       GCG       4 |       GAG      31 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19125    C:0.18125    A:0.30875    G:0.31875
position  2:    T:0.29875    C:0.18625    A:0.35125    G:0.16375
position  3:    T:0.28625    C:0.24625    A:0.19750    G:0.27000
Average         T:0.25875    C:0.20458    A:0.28583    G:0.25083

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
  0.01699397  0.01461927  0.01172510  0.01602925
  0.01059457  0.00911410  0.00730979  0.00999313
  0.01998036  0.01718834  0.00000000  0.00000000
  0.00931469  0.00801307  0.00000000  0.00878590
  0.01610540  0.01385486  0.01111202  0.01519111
  0.01004060  0.00863755  0.00692758  0.00947061
  0.01893563  0.01628960  0.01306476  0.01786068
  0.00882764  0.00759409  0.00609069  0.00832651
  0.02743471  0.02360104  0.01892875  0.02587728
  0.01710365  0.01471362  0.01180077  0.01613270
  0.03225587  0.02774850  0.02225514  0.03042475
  0.01503743  0.01293613  0.01037517  0.01418378
  0.02832328  0.02436544  0.01954183  0.02671541
  0.01765761  0.01519017  0.01218298  0.01665521
  0.03330059  0.02864724  0.02297596  0.03141017
  0.01552448  0.01335512  0.01071121  0.01464317



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)

normal_MH0058|normal_MH0058.peg.10458
normal_MH0058|normal_MH0058.peg.10459-1.0000 (1.8199 -1.0000)
normal_MH0048|normal_MH0048.peg.5129-1.0000 (1.4584 -1.0000) 0.6603 (0.9634 1.4591)
normal_MH0027|normal_MH0027.peg.1804-1.0000 (1.5622 -1.0000) 0.4846 (1.1586 2.3910)-1.0000 (0.7352 -1.0000)
normal_MH0048|normal_MH0048.peg.6479-1.0000 (1.7510 -1.0000)-1.0000 (0.9638 -1.0000)-1.0000 (0.9504 -1.0000) 0.3610 (0.7283 2.0178)
normal_MH0027|normal_MH0027.peg.256 0.4579 (1.7182 3.7524)-1.0000 (2.0463 -1.0000) 0.9291 (2.2295 2.3997) 1.6787 (1.9301 1.1498) 1.3570 (1.6616 1.2245)
normal_MH0048|normal_MH0048.peg.5652-1.0000 (1.7878 -1.0000)-1.0000 (1.0021 -1.0000)-1.0000 (1.1055 -1.0000)-1.0000 (0.9555 -1.0000) 0.4042 (0.9120 2.2565)-1.0000 (1.6218 -1.0000)
normal_MH0058|normal_MH0058.peg.3815 0.7591 (2.0932 2.7575)-1.0000 (1.0803 -1.0000) 0.6408 (1.0487 1.6365)-1.0000 (0.8865 -1.0000)-1.0000 (0.9753 -1.0000)-1.0000 (2.0199 -1.0000)-1.0000 (0.3615 -1.0000)
NOTE: -1 means that NG86 is inapplicable.

pairwise comparison, codon frequencies: F3x4.


2 (normal_MH0058|normal_MH0058.peg.10459) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -807.631500
 50.00000  0.40000  0.02684
SEs for parameters:
  0.00000  0.37927  0.00000

t= 50.0000  S=    56.0  N=   244.0  dN/dS=  0.0268  dN = 2.1441  dS =79.8982
dN = 2.14410 +- 0.53124   dS = 79.89818 +- 0.00000 (by method 1)
dN = 2.14410 +- 0.00000   dS = 79.89818 +- 0.00000 (by method 2)


3 (normal_MH0048|normal_MH0048.peg.5129) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -797.833518
 16.35765  0.40000  0.06650
SEs for parameters:
 182.48486  1.07170  0.98601

t= 16.3576  S=    52.6  N=   247.4  dN/dS=  0.0665  dN = 1.5752  dS =23.6869
dN = 1.57517 +- 0.35072   dS = 23.68688 +- 347.90814 (by method 1)
dN = 1.57517 +- 0.35072   dS = 23.68688 +- 347.90814 (by method 2)


3 (normal_MH0048|normal_MH0048.peg.5129) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -785.829492
  4.20858  0.65140  0.39007
SEs for parameters:
  0.80381  0.39842  0.18644

t= 4.2086  S=    59.1  N=   240.9  dN/dS=  0.3901  dN = 1.0724  dS = 2.7493
dN = 1.07242 +- 0.15280   dS = 2.74932 +- 1.23695 (by method 1)
dN = 1.07242 +- 0.15280   dS = 2.74932 +- 1.23695 (by method 2)


4 (normal_MH0027|normal_MH0027.peg.1804) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -799.493040
 50.00000  1.99604  0.03003
SEs for parameters:
 77.59324  1.67198  0.04909

t= 50.0000  S=    73.3  N=   226.7  dN/dS=  0.0300  dN = 1.8748  dS =62.4331
dN = 1.87485 +- 0.78700   dS = 62.43311 +- 105.26686 (by method 1)
dN = 1.87485 +- 0.78700   dS = 62.43311 +- 105.26686 (by method 2)


4 (normal_MH0027|normal_MH0027.peg.1804) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -785.081152
  5.77823  0.40000  0.23605
SEs for parameters:
  1.87860  0.35764  0.17551

t= 5.7782  S=    53.0  N=   247.0  dN/dS=  0.2361  dN = 1.2254  dS = 5.1912
dN = 1.22539 +- 0.18640   dS = 5.19124 +- 3.61930 (by method 1)
dN = 1.22539 +- 0.18640   dS = 5.19124 +- 3.61930 (by method 2)


4 (normal_MH0027|normal_MH0027.peg.1804) ... 3 (normal_MH0048|normal_MH0048.peg.5129)
lnL = -750.495188
 50.00000  1.90910  0.01010
SEs for parameters:
 134.86799  0.54524  0.02816

t= 50.0000  S=    69.7  N=   230.3  dN/dS=  0.0101  dN = 0.7006  dS =69.4062
dN = 0.70064 +- 0.11455   dS = 69.40615 +- 193.44910 (by method 1)
dN = 0.70064 +- 0.11455   dS = 69.40615 +- 193.44910 (by method 2)


5 (normal_MH0048|normal_MH0048.peg.6479) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -796.391807
  7.32125  2.34651  0.73819
SEs for parameters:
  1.77812  1.19331  0.41746

t= 7.3213  S=    76.0  N=   224.0  dN/dS=  0.7382  dN = 2.2392  dS = 3.0334
dN = 2.23917 +- 0.61592   dS = 3.03335 +- 1.49160 (by method 1)
dN = 2.23917 +- 0.61592   dS = 3.03335 +- 1.49160 (by method 2)


5 (normal_MH0048|normal_MH0048.peg.6479) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -775.211025
 50.00000  1.18296  0.01295
SEs for parameters:
 106.08416  0.44770  0.02903

t= 50.0000  S=    65.3  N=   234.7  dN/dS=  0.0129  dN = 0.9478  dS =73.1988
dN = 0.94781 +- 0.16097   dS = 73.19883 +- 162.58384 (by method 1)
dN = 0.94781 +- 0.16097   dS = 73.19883 +- 162.58384 (by method 2)


5 (normal_MH0048|normal_MH0048.peg.6479) ... 3 (normal_MH0048|normal_MH0048.peg.5129)
lnL = -772.056817
 50.00000  2.30843  0.01573
SEs for parameters:
 70.68607  0.93194  0.02316

t= 50.0000  S=    73.8  N=   226.2  dN/dS=  0.0157  dN = 1.0162  dS =64.6056
dN = 1.01620 +- 0.21192   dS = 64.60560 +- 95.66103 (by method 1)
dN = 1.01620 +- 0.21192   dS = 64.60560 +- 95.66103 (by method 2)


5 (normal_MH0048|normal_MH0048.peg.6479) ... 4 (normal_MH0027|normal_MH0027.peg.1804)
lnL = -746.216467
  5.24981  1.12743  0.12720
SEs for parameters:
  2.25843  0.39441  0.08876

t= 5.2498  S=    58.6  N=   241.4  dN/dS=  0.1272  dN = 0.7478  dS = 5.8788
dN = 0.74776 +- 0.11244   dS = 5.87885 +- 3.88908 (by method 1)
dN = 0.74776 +- 0.11244   dS = 5.87885 +- 3.88908 (by method 2)


6 (normal_MH0027|normal_MH0027.peg.256) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -803.787124
 50.00000  1.04511  0.02663
SEs for parameters:
  0.00000  0.49930  0.00000

t= 50.0000  S=    67.4  N=   232.6  dN/dS=  0.0266  dN = 1.8086  dS =67.9192
dN = 1.80863 +- 0.38607   dS = 67.91915 +- 0.00000 (by method 1)
dN = 1.80863 +- 0.00000   dS = 67.91915 +- 0.00000 (by method 2)


6 (normal_MH0027|normal_MH0027.peg.256) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -802.437875
 13.67431  2.93893  0.26445
SEs for parameters:
  8.21597  1.85633  0.26478

t= 13.6743  S=    79.5  N=   220.5  dN/dS=  0.2644  dN = 2.6239  dS = 9.9220
dN = 2.62386 +- 1.08954   dS = 9.92196 +- 9.53441 (by method 1)
dN = 2.62386 +- 1.08954   dS = 9.92196 +- 9.53441 (by method 2)


6 (normal_MH0027|normal_MH0027.peg.256) ... 3 (normal_MH0048|normal_MH0048.peg.5129)
lnL = -801.431326
 31.62613  0.40000 14.73969
SEs for parameters:
  0.00000  0.00000  0.00000

t= 31.6261  S=    56.3  N=   243.7  dN/dS= 14.7397  dN =12.7791  dS = 0.8670
dN = 12.77911 +- 0.00000   dS = 0.86699 +- 1.06221 (by method 1)
dN = 12.77911 +- 0.00000   dS = 0.86699 +- 0.00000 (by method 2)


6 (normal_MH0027|normal_MH0027.peg.256) ... 4 (normal_MH0027|normal_MH0027.peg.1804)
lnL = -787.752895
  8.96903  1.50834  0.25137
SEs for parameters:
  6.61494  0.83956  0.34417

t= 8.9690  S=    64.5  N=   235.5  dN/dS=  0.2514  dN = 1.8231  dS = 7.2526
dN = 1.82306 +- 0.37857   dS = 7.25258 +- 10.00084 (by method 1)
dN = 1.82306 +- 0.37857   dS = 7.25258 +- 10.00084 (by method 2)


6 (normal_MH0027|normal_MH0027.peg.256) ... 5 (normal_MH0048|normal_MH0048.peg.6479)
lnL = -785.753114
  5.98059  0.89123  0.74753
SEs for parameters:
  1.01315  0.56867  0.50326

t= 5.9806  S=    60.4  N=   239.6  dN/dS=  0.7475  dN = 1.8666  dS = 2.4971
dN = 1.86664 +- 0.38910   dS = 2.49709 +- 1.42116 (by method 1)
dN = 1.86664 +- 0.38910   dS = 2.49709 +- 1.42116 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -804.293248
 50.00000  0.40000  0.02249
SEs for parameters:
 87.51811  0.48242  0.04516

t= 50.0000  S=    55.3  N=   244.7  dN/dS=  0.0225  dN = 1.8497  dS =82.2661
dN = 1.84971 +- 0.54623   dS = 82.26610 +- 158.78002 (by method 1)
dN = 1.84971 +- 0.54623   dS = 82.26610 +- 158.78002 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -792.520008
  5.19811  0.84850  0.27092
SEs for parameters:
  1.40039  0.38936  0.15387

t= 5.1981  S=    65.2  N=   234.8  dN/dS=  0.2709  dN = 1.0930  dS = 4.0345
dN = 1.09301 +- 0.16407   dS = 4.03450 +- 2.13715 (by method 1)
dN = 1.09301 +- 0.16407   dS = 4.03450 +- 2.13715 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 3 (normal_MH0048|normal_MH0048.peg.5129)
lnL = -791.138123
  6.00883  2.00213  0.33111
SEs for parameters:
  2.33889  0.85683  0.27089

t= 6.0088  S=    73.5  N=   226.5  dN/dS=  0.3311  dN = 1.3400  dS = 4.0470
dN = 1.34000 +- 0.26593   dS = 4.04703 +- 3.14556 (by method 1)
dN = 1.34000 +- 0.26593   dS = 4.04703 +- 3.14556 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 4 (normal_MH0027|normal_MH0027.peg.1804)
lnL = -787.756919
  9.30480  1.04084  0.10230
SEs for parameters:
  8.82963  0.47361  0.13416

t= 9.3048  S=    65.5  N=   234.5  dN/dS=  0.1023  dN = 1.0640  dS =10.4006
dN = 1.06395 +- 0.17751   dS = 10.40060 +- 13.48642 (by method 1)
dN = 1.06395 +- 0.17751   dS = 10.40060 +- 13.48642 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 5 (normal_MH0048|normal_MH0048.peg.6479)
lnL = -777.981435
 50.00000  2.28692  0.01716
SEs for parameters:
 153.95622  0.73955  0.05530

t= 50.0000  S=    77.5  N=   222.5  dN/dS=  0.0172  dN = 1.0548  dS =61.4854
dN = 1.05478 +- 0.20044   dS = 61.48543 +- 198.60631 (by method 1)
dN = 1.05478 +- 0.20044   dS = 61.48543 +- 198.60631 (by method 2)


7 (normal_MH0048|normal_MH0048.peg.5652) ... 6 (normal_MH0027|normal_MH0027.peg.256)
lnL = -803.166362
 50.00000  0.97079  0.02379
SEs for parameters:
 98.04860  0.50918  0.05087

t= 50.0000  S=    68.5  N=   231.5  dN/dS=  0.0238  dN = 1.6067  dS =67.5274
dN = 1.60665 +- 0.32264   dS = 67.52743 +- 143.10539 (by method 1)
dN = 1.60665 +- 0.32264   dS = 67.52743 +- 143.10539 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 1 (normal_MH0058|normal_MH0058.peg.10458)
lnL = -793.338577
 50.00000  0.40000  0.02274
SEs for parameters:
 129.67072  0.43428  0.06656

t= 50.0000  S=    49.6  N=   250.4  dN/dS=  0.0227  dN = 2.0550  dS =90.3963
dN = 2.05501 +- 0.53161   dS = 90.39625 +- 261.54914 (by method 1)
dN = 2.05501 +- 0.53161   dS = 90.39625 +- 261.54914 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 2 (normal_MH0058|normal_MH0058.peg.10459)
lnL = -783.734664
 50.00000  0.64354  0.01225
SEs for parameters:
 100.77261  0.31561  0.02614

t= 50.0000  S=    57.3  N=   242.7  dN/dS=  0.0122  dN = 1.0169  dS =83.0174
dN = 1.01687 +- 0.16145   dS = 83.01739 +- 176.03574 (by method 1)
dN = 1.01687 +- 0.16145   dS = 83.01739 +- 176.03574 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 3 (normal_MH0048|normal_MH0048.peg.5129)
lnL = -771.140390
 39.97495  2.12318  0.01843
SEs for parameters:
 94.96797  0.72022  0.04740

t= 39.9749  S=    63.5  N=   236.5  dN/dS=  0.0184  dN = 1.0851  dS =58.8856
dN = 1.08505 +- 0.21610   dS = 58.88560 +- 149.58457 (by method 1)
dN = 1.08505 +- 0.21610   dS = 58.88560 +- 149.58457 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 4 (normal_MH0027|normal_MH0027.peg.1804)
lnL = -774.971827
 50.00000  1.04020  0.01108
SEs for parameters:
 55.45546  0.36568  0.01293

t= 50.0000  S=    63.4  N=   236.6  dN/dS=  0.0111  dN = 0.8388  dS =75.6987
dN = 0.83884 +- 0.13308   dS = 75.69871 +- 87.42955 (by method 1)
dN = 0.83884 +- 0.13308   dS = 75.69871 +- 87.42955 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 5 (normal_MH0048|normal_MH0048.peg.6479)
lnL = -775.448859
 50.00000  1.69499  0.01474
SEs for parameters:
 72.05287  0.54184  0.02236

t= 50.0000  S=    71.7  N=   228.3  dN/dS=  0.0147  dN = 0.9814  dS =66.5654
dN = 0.98138 +- 0.17304   dS = 66.56542 +- 100.41571 (by method 1)
dN = 0.98138 +- 0.17304   dS = 66.56542 +- 100.41571 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 6 (normal_MH0027|normal_MH0027.peg.256)
lnL = -797.950922
 50.00000  1.61401  0.02867
SEs for parameters:
 71.28440  0.69917  0.04586

t= 50.0000  S=    71.9  N=   228.1  dN/dS=  0.0287  dN = 1.8270  dS =63.7353
dN = 1.82702 +- 0.46204   dS = 63.73535 +- 99.24812 (by method 1)
dN = 1.82702 +- 0.46204   dS = 63.73535 +- 99.24812 (by method 2)


8 (normal_MH0058|normal_MH0058.peg.3815) ... 7 (normal_MH0048|normal_MH0048.peg.5652)
lnL = -690.870969
 50.00000  2.11970  0.00459
SEs for parameters:
 70.48004  0.64420  0.00662

t= 50.0000  S=    67.7  N=   232.3  dN/dS=  0.0046  dN = 0.3341  dS =72.7598
dN = 0.33412 +- 0.05628   dS = 72.75984 +- 104.18015 (by method 1)
dN = 0.33412 +- 0.05628   dS = 72.75984 +- 104.18015 (by method 2)