AeruginosaPAML

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Revision as of 17:41, 28 June 2013 by imported>Rayrah (Created page with "<pre> 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 GC...")
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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