AeruginosaPAML: Difference between revisions

Latest revision as of 17:41, 28 June 2013

seed used = 1194797141

Before deleting alignment gaps
11 840

Paeruginosa_PAO1_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_C3719_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_2192_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
strain=39016_ ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTT CTC GGT CCC GGC GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCC ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGA ATC GGC GAT TCA GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGT ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_LESB58_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_M18_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_NCGM2.S1_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTT CTC GGT CCC GGC GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCC ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGA ATC GGC GAT TCA GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGT ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_UCBPP-PA14_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGA ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_PA7_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGT CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGG CTT ACG CCC AAG CGC ACC CTC GCC GAC GTG ATC GAA GGA CGC TGC GAG CTG CGC GAC GTC CTC CTG CTC GGT CCC GGC GGC GTG CGT ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAT CTC TCG CCC ATG CAG CAC GCC GGC CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAC GTG CTG GTG GTG GAC ACC GCC GCC GGG ATC GGC GAT TCG GTG GTC AGC TTC GTC CGC GCG GCG CAG GAG GTG CTG CTG GTG GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCG AAC ATG GCC CAC AGT CCG CAG GAA GGG CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACG GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCC TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGC TCG GCC GTA
Paeruginosa_PACS2_fleN ATG AAG CAG ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_DK2_fleN --- --- --- ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGT GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA

After deleting gaps. 831 sites
11 831

Paeruginosa_PAO1_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_C3719_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_2192_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
strain=39016_ ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTT CTC GGT CCC GGC GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCC ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGA ATC GGC GAT TCA GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGT ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_LESB58_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_M18_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_NCGM2.S1_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTT CTC GGT CCC GGC GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCC ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGA ATC GGC GAT TCA GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGT ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_UCBPP-PA14_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGA ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_PA7_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGT CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGG CTT ACG CCC AAG CGC ACC CTC GCC GAC GTG ATC GAA GGA CGC TGC GAG CTG CGC GAC GTC CTC CTG CTC GGT CCC GGC GGC GTG CGT ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAT CTC TCG CCC ATG CAG CAC GCC GGC CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAC GTG CTG GTG GTG GAC ACC GCC GCC GGG ATC GGC GAT TCG GTG GTC AGC TTC GTC CGC GCG GCG CAG GAG GTG CTG CTG GTG GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAG CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCG AAC ATG GCC CAC AGT CCG CAG GAA GGG CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACG GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCC TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAC AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGC TCG GCC GTA
Paeruginosa_PACS2_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACC GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGC GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA
Paeruginosa_DK2_fleN ATG GGT AGC ATG CAT CCC GTA CAG GTG ATC GCA GTA ACT GGC GGC AAG GGC GGC GTC GGC AAG ACC AAT GTG TCG GTG AAC CTG GCA CTG GCT CTG GCC GAT CTC GGC CGT CGC GTC ATG CTG CTG GAT GCC GAC CTC GGC CTG GCC AAC GTC GAC GTC CTG CTG GGA CTC ACG CCC AAG CGC ACC CTG GCC GAC GTG ATC GAG GGA CGC TGC GAA CTG CGC GAT GTC CTC CTC CTC GGT CCC GGT GGC GTG CGC ATC GTT CCC GCG GCC TCC GGC ACG CAG AGC ATG GTG CAC CTC TCG CCG ATG CAG CAT GCG GGG CTG ATC CAG GCG TTC AGC GAT ATC AGC GAC AAC CTC GAT GTC CTG GTC GTC GAC ACT GCC GCC GGG ATC GGC GAT TCG GTG GTC AGT TTC GTC CGC GCC GCG CAG GAG GTG CTG CTG GTC GTC TGC GAC GAG CCG ACC TCG ATC ACC GAT GCC TAC GCC CTG ATC AAA CTG CTC AAC CGT GAC CAC GGC ATG ACC CGC TTC CGG GTC CTG GCC AAC ATG GCC CAC AGC CCG CAG GAA GGA CGC AAC CTG TTC GCC AAA CTG ACC AAG GTC ACT GAC CGT TTC CTC GAC GTC GCA CTA CAG TAT GTA GGT GTC ATC CCT TAC GAC GAG TCG GTA CGC AAG GCC GTG CAG AAA CAG CGA GCC GTA TAC GAG GCA TTC CCC CGC TCG AAG GCG TCC CTG GCC TTC AAG GCG GTC GCG CAG AAG GTC GAT AGC TGG CCG CTG CCG GCC AAC CCG CGC GGG CAC CTG GAG TTC TTC GTC GAA CGA CTG GTC CAA CAC CCC GCG ACA GGT TCG GCC GTA

Printing out site pattern counts

11 228 P

Paeruginosa_PAO1_fleN AAA AAA AAC AAG AAT ACA ACC ACG ACT ACT ACT AGC AGC AGT ATC ATG CAA CAC CAC CAG CAT CAT CCC CCG CCG CCT CGA CGC CGC CGC CGG CGT CTA CTC CTC CTC CTG CTG GAA GAA GAC GAG GAG GAT GAT GAT GCA GCC GCC GCG GCG GCT GGA GGA GGC GGC GGC GGG GGG GGG GGT GGT GGT GTA GTC GTC GTG GTT TAC TAT TCC TCG TCG TGC TGG TTC
Paeruginosa_C3719_fleN ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Paeruginosa_2192_fleN ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
strain=39016_ ... ..G ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ..T ..A ... ... ..C ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ...
Paeruginosa_LESB58_fleN ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Paeruginosa_M18_fleN ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Paeruginosa_NCGM2.S1_fleN ... ..G ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ..T ..A ... ... ..C ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ...
Paeruginosa_UCBPP-PA14_fleN ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Paeruginosa_PA7_fleN ... ..G ... ... ... ... ... ... ..C ..G ... ... ..T ..C ... ... ... ... ..T ... ..C ... ... ..C ... ..C ... ... ... ..T ... ... ... ... ..T ..G ..C ... ... ..G ... ..A ... ..C ..C ... ... ... ..G ..C ... ... ... ..G ... ..T ... ... ..C ... ..C ..C ... ... ... ..G ... ... ... ... ... ... ... ... ... ...
Paeruginosa_PACS2_fleN ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Paeruginosa_DK2_fleN ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...

2 1 7 8 1 1 6 2 1 1 1 5 1 1 9
7 1 4 1 10 1 1 6 1 5 1 2 10 1 1
1 2 1 8 1 1 1 22 2 1 10 1 5 1 2
5 4 16 2 1 7 1 1 2 9 1 1 1 1 1
1 1 3 6 16 4 9 1 3 1 2 1 6 2 1
9

CODONML (in paml version 4.4c, August 2010) flen.paml
Model: One dN/dS ratio for branchesdGamma (ncatG=11)
Codon frequency model: Fcodon
Warning: Gamma model for codons. See documentation.Site-class models:
ns = 11 ls = 277

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 0 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 1 1 1 1 1 1 | Cys TGT 0 0 0 0 0 0
TTC 9 9 9 9 9 9 | TCC 2 2 2 2 2 2 | TAC 3 3 3 3 3 3 | TGC 2 2 2 2 2 2
Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 1 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 0 0 0 0 0 0 | TCG 7 7 7 6 7 7 | TAG 0 0 0 0 0 0 | Trp TGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
Leu CTT 0 0 0 1 0 0 | Pro CCT 1 1 1 1 1 1 | His CAT 2 2 2 2 2 2 | Arg CGT 2 2 2 2 2 2
CTC 10 10 10 9 10 10 | CCC 6 6 6 7 6 6 | CAC 5 5 5 5 5 5 | CGC 12 12 12 12 12 12
CTA 1 1 1 1 1 1 | CCA 0 0 0 0 0 0 | Gln CAA 1 1 1 1 1 1 | CGA 2 2 2 2 2 2
CTG 23 23 23 23 23 23 | CCG 6 6 6 5 6 6 | CAG 10 10 10 10 10 10 | CGG 1 1 1 1 1 1
--------------------------------------------------------------------------------------------------------------
Ile ATT 0 0 0 0 0 0 | Thr ACT 3 3 3 2 3 3 | Asn AAT 1 1 1 1 1 1 | Ser AGT 1 1 1 1 1 1
ATC 9 9 9 9 9 9 | ACC 6 6 6 7 6 6 | AAC 7 7 7 7 7 7 | AGC 6 6 6 6 6 6
ATA 0 0 0 0 0 0 | ACA 1 1 1 1 1 1 | Lys AAA 3 3 3 2 3 3 | Arg AGA 0 0 0 0 0 0
Met ATG 7 7 7 7 7 7 | ACG 2 2 2 2 2 2 | AAG 8 8 8 9 8 8 | AGG 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------------
Val GTT 1 1 1 1 1 1 | Ala GCT 1 1 1 1 1 1 | Asp GAT 8 8 8 7 8 8 | Gly GGT 5 5 5 5 5 5
GTC 20 20 20 20 20 20 | GCC 18 18 18 18 18 18 | GAC 10 10 10 11 10 10 | GGC 11 11 11 11 11 11
GTA 6 6 6 6 6 6 | GCA 4 4 4 4 4 4 | Glu GAA 3 3 3 3 3 3 | GGA 3 3 3 4 3 3
GTG 9 9 9 9 9 9 | GCG 8 8 8 8 8 8 | GAG 6 6 6 6 6 6 | GGG 3 3 3 2 3 3
--------------------------------------------------------------------------------------------------------------

--------------------------------------------------------------------------------------------------
Phe TTT 0 0 0 0 0 | Ser TCT 0 0 0 0 0 | Tyr TAT 1 1 1 1 1 | Cys TGT 0 0 0 0 0
TTC 9 9 9 9 9 | TCC 2 2 2 2 2 | TAC 3 3 3 3 3 | TGC 2 2 2 2 2
Leu TTA 0 0 0 0 0 | TCA 1 0 0 0 0 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
TTG 0 0 0 0 0 | TCG 6 7 7 7 7 | TAG 0 0 0 0 0 | Trp TGG 1 1 1 1 1
--------------------------------------------------------------------------------------------------
Leu CTT 1 0 1 0 0 | Pro CCT 1 1 0 1 1 | His CAT 2 2 2 2 2 | Arg CGT 2 2 3 2 3
CTC 9 10 9 10 10 | CCC 7 6 8 6 6 | CAC 5 5 5 5 5 | CGC 12 12 11 12 11
CTA 1 1 1 1 1 | CCA 0 0 0 0 0 | Gln CAA 1 1 1 1 1 | CGA 2 2 2 2 2
CTG 23 23 23 23 23 | CCG 5 6 5 6 6 | CAG 10 10 10 10 10 | CGG 1 1 1 1 1
--------------------------------------------------------------------------------------------------
Ile ATT 0 0 0 0 0 | Thr ACT 2 3 1 2 3 | Asn AAT 1 1 1 1 1 | Ser AGT 1 1 1 1 1
ATC 9 9 9 9 9 | ACC 7 6 7 7 6 | AAC 7 7 7 7 7 | AGC 6 6 6 6 6
ATA 0 0 0 0 0 | ACA 1 1 1 1 1 | Lys AAA 2 2 2 3 3 | Arg AGA 0 0 0 0 0
Met ATG 7 7 7 7 7 | ACG 2 2 3 2 2 | AAG 9 9 9 8 8 | AGG 0 0 0 0 0
--------------------------------------------------------------------------------------------------
Val GTT 1 1 1 1 1 | Ala GCT 1 1 1 1 1 | Asp GAT 7 7 5 8 8 | Gly GGT 5 5 4 5 5
GTC 20 20 16 20 20 | GCC 18 18 17 18 18 | GAC 11 11 13 10 10 | GGC 11 11 13 11 11
GTA 6 6 6 6 6 | GCA 4 4 4 4 4 | Glu GAA 3 3 3 3 3 | GGA 4 4 1 3 3
GTG 9 9 13 9 9 | GCG 8 8 9 8 8 | GAG 6 6 6 6 6 | GGG 2 2 4 3 3
--------------------------------------------------------------------------------------------------

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

#1: Paeruginosa_PAO1_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09386 C:0.49097 A:0.08664 G:0.32852
Average T:0.17569 C:0.34055 A:0.17569 G:0.30806

#2: Paeruginosa_C3719_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09386 C:0.49097 A:0.08664 G:0.32852
Average T:0.17569 C:0.34055 A:0.17569 G:0.30806

#3: Paeruginosa_2192_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09386 C:0.49097 A:0.08664 G:0.32852
Average T:0.17569 C:0.34055 A:0.17569 G:0.30806

#4: strain=39016_
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09025 C:0.49819 A:0.09025 G:0.32130
Average T:0.17449 C:0.34296 A:0.17690 G:0.30566

#5: Paeruginosa_LESB58_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09386 C:0.49097 A:0.08664 G:0.32852
Average T:0.17569 C:0.34055 A:0.17569 G:0.30806

#6: Paeruginosa_M18_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09386 C:0.49097 A:0.08664 G:0.32852
Average T:0.17569 C:0.34055 A:0.17569 G:0.30806

#7: Paeruginosa_NCGM2.S1_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09025 C:0.49819 A:0.09025 G:0.32130
Average T:0.17449 C:0.34296 A:0.17690 G:0.30566

#8: Paeruginosa_UCBPP-PA14_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09025 C:0.49458 A:0.08664 G:0.32852
Average T:0.17449 C:0.34176 A:0.17569 G:0.30806

#9: Paeruginosa_PA7_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.07581 C:0.49458 A:0.07581 G:0.35379
Average T:0.16968 C:0.34176 A:0.17208 G:0.31649

#10: Paeruginosa_PACS2_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09025 C:0.49458 A:0.08664 G:0.32852
Average T:0.17449 C:0.34176 A:0.17569 G:0.30806

#11: Paeruginosa_DK2_fleN
position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09747 C:0.48736 A:0.08664 G:0.32852
Average T:0.17690 C:0.33935 A:0.17569 G:0.30806

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 0 | Ser S TCT 0 | Tyr Y TAT 11 | Cys C TGT 0
TTC 99 | TCC 22 | TAC 33 | TGC 22
Leu L TTA 0 | TCA 2 | *** * TAA 0 | *** * TGA 0
TTG 0 | TCG 75 | TAG 0 | Trp W TGG 11
------------------------------------------------------------------------------
Leu L CTT 3 | Pro P CCT 10 | His H CAT 22 | Arg R CGT 24
CTC 107 | CCC 70 | CAC 55 | CGC 130
CTA 11 | CCA 0 | Gln Q CAA 11 | CGA 22
CTG 253 | CCG 63 | CAG 110 | CGG 11
------------------------------------------------------------------------------
Ile I ATT 0 | Thr T ACT 28 | Asn N AAT 11 | Ser S AGT 11
ATC 99 | ACC 70 | AAC 77 | AGC 66
ATA 0 | ACA 11 | Lys K AAA 29 | Arg R AGA 0
Met M ATG 77 | ACG 23 | AAG 92 | AGG 0
------------------------------------------------------------------------------
Val V GTT 11 | Ala A GCT 11 | Asp D GAT 82 | Gly G GGT 54
GTC 216 | GCC 197 | GAC 116 | GGC 123
GTA 66 | GCA 44 | Glu E GAA 33 | GGA 34
GTG 103 | GCG 89 | GAG 66 | GGG 31
------------------------------------------------------------------------------

Codon position x base (3x4) table, overall

position 1: T:0.09025 C:0.29603 A:0.19495 G:0.41877
position 2: T:0.34296 C:0.23466 A:0.24549 G:0.17690
position 3: T:0.09124 C:0.49294 A:0.08631 G:0.32950
Average T:0.17482 C:0.34121 A:0.17558 G:0.30839

Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
0.00000000 0.03249097 0.00000000 0.00000000
0.00000000 0.00722022 0.00065638 0.02461437
0.00361011 0.01083032 0.00000000 0.00000000
0.00000000 0.00722022 0.00000000 0.00361011
0.00098457 0.03511651 0.00361011 0.08303249
0.00328192 0.02297342 0.00000000 0.02067607
0.00722022 0.01805054 0.00361011 0.03610108
0.00787660 0.04266492 0.00722022 0.00361011
0.00000000 0.03249097 0.00000000 0.02527076
0.00918937 0.02297342 0.00361011 0.00754841
0.00361011 0.02527076 0.00951756 0.03019363
0.00361011 0.02166065 0.00000000 0.00000000
0.00361011 0.07088940 0.02166065 0.03380374
0.00361011 0.06465376 0.01444043 0.02920906
0.02691172 0.03807023 0.01083032 0.02166065
0.01772235 0.04036757 0.01115852 0.01017394

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

Paeruginosa_PAO1_fleN
Paeruginosa_C3719_fleN-1.0000 (0.0000 0.0000)
Paeruginosa_2192_fleN-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000)
strain=39016_ 0.0000 (0.0000 0.0415) 0.0000 (0.0000 0.0415) 0.0000 (0.0000 0.0415)
Paeruginosa_LESB58_fleN-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0415)
Paeruginosa_M18_fleN-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000)-1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0415)-1.0000 (0.0000 0.0000)
Paeruginosa_NCGM2.S1_fleN 0.0000 (0.0000 0.0415) 0.0000 (0.0000 0.0415) 0.0000 (0.0000 0.0415)-1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0415) 0.0000 (0.0000 0.0415)
Paeruginosa_UCBPP-PA14_fleN 0.0000 (0.0000 0.0136) 0.0000 (0.0000 0.0136) 0.0000 (0.0000 0.0136) 0.0000 (0.0000 0.0274) 0.0000 (0.0000 0.0136) 0.0000 (0.0000 0.0136) 0.0000 (0.0000 0.0274)
Paeruginosa_PA7_fleN 0.0000 (0.0000 0.1541) 0.0000 (0.0000 0.1541) 0.0000 (0.0000 0.1541) 0.0000 (0.0000 0.1431) 0.0000 (0.0000 0.1541) 0.0000 (0.0000 0.1541) 0.0000 (0.0000 0.1431) 0.0000 (0.0000 0.1486)
Paeruginosa_PACS2_fleN 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0368) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0368) 0.0000 (0.0000 0.0182) 0.0000 (0.0000 0.1486)
Paeruginosa_DK2_fleN 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0463) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0045) 0.0000 (0.0000 0.0463) 0.0000 (0.0000 0.0182) 0.0000 (0.0000 0.1597) 0.0000 (0.0000 0.0090)

Model 0: one-ratio

AeruginosaPAML: Difference between revisions

Latest revision as of 17:41, 28 June 2013

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