9 882 gam9 ATG TTT AAC CGG GCA CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCT GTG AAA AAT ATC CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCG GCT GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA TCA TAT GGC GCC GGA GCC ACT GCA TTC TAT GAA AAG ATT GAG GCT GCT CCC GTC GCC GAT AAA CCC AAG CAT CTG ATC ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCC GTA TGC AGA ATG ATC AAG GCA GAG ATT GCA GCG TCT CCA ACG CCA GAG AAT GTG GCG GTG GTG TGT GTG GGC GAC AAG TCG CGA TTG CAA CTG CAG AGG TTG TTC TCC GCC AAC ATT TTG TTT CAG GTT AAC GAG GTT GGC CGC AAA TCA GCC ACC TTT GAG GAC GCT GCG GCC ATT GCC TCT GCC GTC ATC AAC ACT GGT TAT GAC TTC GGC ACT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTG TCC TAT AAC ACA CTG GCG CTG CCC ATC TTC ACC TCC GAG TCC ATC TCC TCT GCC GAG AAG CTG AGC GTG TAC GAC TCT TTG GAC GCT GAT GTC ATC CAG AGC TTC CTG GAG TAC TCG ATG GCG TCA CTG TTG TTC TAC ACC TTG AAG GAA GGC GCG TGC AGC GAG CAA AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCT GCC GAG ATG ATT GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam36.2 ATG TTT AAC CGG GCC CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAA CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCG GTG AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCA GCA GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA GCA TAT GGT GCG GGA GCC TCA GCA TTC TAT GAA AAG ATT GAG GCT GCT CCT AAC GCC GAG AAA CCC AAG CAA CTG ATC ATC GCC ATG TCC TCT GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCC GTA TGC AGA TTG ATC AAG GCA GAG ATT GCA GCG TCT CCA TCG CCA GAG AAT GTG GCG GTG GTA TGT GTG GGT GAC AAG TCG CGA TTG CAA CTG CAG AGG TTG TTT GCC GCC AAC ATT TTG TTT CAG GTC AAC GAG GTT GGT CGC AAA TCG GCT ACC TTT GAG GAC GCG GCG GCC ATT GCC TCT GAA ATC ATC AAC AGT GGT TAT GAC TTT GGC GCT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTA TCC TAC AAC ACA CTA GCG CTG CCC GTC TTC ACC GCC GAA TCC GTC TCC TCT GCC GAA AAG CTC AGC GTG TAT GAT TCT TTG GAC GCT GAC GTC ATC CAG AGT TTT CTG GAG TAC TCG ATG GCG TCG CTG TTG TAC TAC ACC CTG AAG GAG GGT GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCG GCT GAG ATG ATC GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATT TCC GGC GCC GCT GCC ATC gam42.4 ATG TTC AAC CGG GCC CTA ATT TTT ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCT GTG AAG AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCA GCA GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA TCA TAT GGC GCG GGA GCC TCT GCA TTC TAT GAA AAG ATT GAG GCT GCT CCT GTC GCT GAG AAA CCC AAG CAA CTG ATC ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCT GTG TGC AGA TTG ATC AAA GCT GAG ATT GCA GCG TCG CCA TCG CCA GAG AAT GTG GCG GTG GTA TGT GTG GGT GAC AAG TCC CGA ATG CAA CTT CAG AGG TTG TTT GCC GCC AAC ATT TTG TTT CAG GTT AAC GAG GTT GGC CGC AAA TCG GCC ACC TTT GAG GAC GCG GCG GCC ATT GCC TCT GAA ATC ATC AAC ACT GGC TAT GAC TTC GGC GCT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTG TCC TAC AAC ACA CTA GCG CTG CCC ATC TTC ACC GCC GAT TCC GTC TCC TCT GCC GAA AAG CTC AGC GTG TAC GAT TCT TTG GAC GCT GAC GTC ATC CAG AGC TTC CTG GAG TAC TCG ATG GCG TCA CTG TTG TAC TAC ACC CTG AAG GAG GGT GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCA AGC AAG AAT GCC GCC GAG ATG ATC GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam39.1 ATG TTT AAC CGG GCA CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCT GTG AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCG GCT GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA TCA TAT GGC GCC GGA GCC ACT GCA TTC TAT GAA AAG ATT GAG GCT GTT CCC GTC GCC GAT AAA CCC AAG CAC CTG ATT ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCC GTA TGC AGA ATG ATC AAG GCA GAG ATT GCA GCG TCT CCG ACG CCA GAG AAT GTG GCG GTG GTG TGT GTG GGC GAC AAG TCG CGA CTG CAA CTG CAG AGG TTG TTC TCC GCC AAC ATT TTG TTT CAG GTT AAC GAG GTT GGG CGC AAA TCA GCC ACC TTT GAG GAT GCT GCG GCC ATT GCC TCT GAA GTC ATC AAC ACT GGT TAT GAC TTC GGC ACT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTG TCC TAT AAC ACA CTG GCG CTG CCC ATC TTC ACC TCC GAG TCA GTC TCC GCT GCC GAG AAG CTG AGC GTG TAC GAC TCT TTG GAC GCT GAT GTC ATC CAG AGC TTC CTG GAG TAC TCG ATG GCG TCG CTG TTG TTC TAC ACC CTG AAG GAG GGC GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCT GCC GAG ATG ATT GAC AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACT GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam4.1 ATG TTT AAC CGG GCC CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAA CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGC CTG AAG TCT GTA AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCA GCA GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCA GTC CGA TCA TAT GGC GCG GGA GCC TCT GCA TTC TAT GAA AAG ATT GAG GCT GCT CCT ATC GCC GAG AAA CCC AAG CAA CTG ATC ATC GCC ATG TCC TCT GAC CGT GGC CTC TGC GGT GGT ATC CAC TCA GCC GTA TGC AGA TTG ATC AAG GCA GAG ATT GCA GCG TCT CCA TCG CCA GAG AAT GTG GCG GTG GTA TGT GTG GGT GAC AAG TCA CGA TTG CAA CTG CAG AGG TTG TTT GCC GCC AAC ATT TTG TTT CAG GTC AAC GAG GTT GGC CGC AAA TCG GCT ACC TTT GAG GAC GCG GCG GCC ATT GCC TCT GAA GTC ATC AAC TCT GGT TAT GAC TTT GGC GCT GGC AAG ATC ATC TAC AAC AAA TTC AAG TCT GTG GTG TCC TAC AAC ACA CTA GCG CTG CCC ATC TTC ACC GCC GAA TCA GTC TCC TCG GCC GAA AAG CTC AGC GTG TAC GAT TCT TTG GAC GCT GAC GTC ATC CAG AGC TTC CTG GAG TAC TCT ATG GCG TCG CTG TTG TAC TAC ACC CTG AAG GAG GGT GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCG GCT GAG ATG ATC GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam15.1 ATG TTT AAC CGG GCA CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCT GTG AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCG GCT GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA GCA TAT GGC GCC GGA GCC AAG GCA TTC TAT GAA AAG ATT GAG GCT ACT CCC GTC GCC GAT AAA CCC AAG CAT CTG ATC ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCC GTA TGC AGA ATT ATC AAG GCA GAG ATT GCA GCG TCT GCA ACG CCA GAG AAT GTG GCG GTG GTG TGT GTG GGC GAC AAG TCG CGA TTA CAA CTG CAG AGG TTG TTC TCC GCC AAC ATT TTG TTT CAG GTT AAC GAG GTT GGC CGC AAA TCA GCC ACC TTT GAG GAC GCT GCG GCC ATT GCC TCT GCC GTC ATC AAC ACT GGT TAT GAC TTC GGC ACT GGC AAG ATC ATC TAC AAC CAG TTC AAG TCT GTG GTG TCC TAT AAC ACA CTG GCG CTG CCC ATC TTC ACC CAC GAA TCC GTC TCC AAT GCC GAG AAG CTC AGC GTG TAC GAC TCT TTG GAC GCT GAT GTC ATC CAG AGC TTC CTG GAG TAC TCA ATG GCG TCA CTG TTG TTC TAC ACC TTG AAG GAG GGC GCG ACA AGC GAG CAA AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCT GCC GAG ATG ATT GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam34.2 ATG TTT AAC CGG GCA CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAC CGT GGC ATG GCC ACA CTC AAA CAG GTT TCC ATG CGA CTG AAG TCT GTG AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCG GCT GCA AAG TAT AAT CGT GCT AGC AGG GAA CTG AAG CCG GTC CGA TCA TAT GGC GCC GGA GCC ACT GCA TTC TAT GAA AAG ATT GAG GCT GCT CCC GTC GCC GAT AAA CCC AAG CAT CTG ATC ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCA GCC GTC TGC AGA CTG ATC AAG GCA GAG ATT GCA GCG TCT CCA ACG CCA GAG AAT GTG GCG GTG GTG TGT GTG GGC GAC AAG TCG CGA TTG CAA CTG CAG AGG TTG TTC TCC GCC AAC ATT TTG TTT CAG GTT AAC GAG GTT GGC CGC AAA TCA GCC ACC TTT GAG GAC GCT GCG GCC ATT GCC TCT GAG GTC ATC AAC ACT GGT TAT GAC TTC GGC ACT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTG TCC TAT AAC ACA CTG GCG CTG CCC ATC TTC ACC TCC GAA TCC GTC TCC TCT GCC GAG AAG CTC AGC GTG TAC GAC TCT TTG GAC GCT GAT GTC ATC CAG AGC TTC CTG GAG TAC TCG ATG GCG TCA CTG TTG TTC TAC ACC TTG AAG GAG GGC GCG TGC AGC GAG CAA AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCT GCC GAG ATG ATT GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam23.1 ATG TTC AAC CGG GCG CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAG CAA GAT CGT GGC ATG GCC ACA CTC AAA CAT ATT TCC ATG CGA TTG AAG TCT GTG AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCT GCT GCA AAG TAT GCT CGT GCC GAC AGG GAA TTG AAG CCT GTC CGA CCA TAT GGC GCA GGA GCT GCT GCA TTC TAT GAA AAG ATT GAC GCA GTC CCC GCC GCC GAT AAA CCC AAG CAT CTG ATC ATC GCC ATG TCC TCC GAC CGT GGC CTC TGC GGC GGT ATC CAC TCG GCC GTG TGC AGA GTC ATC AAG GCG GAG ATT GCG GCG TCT CCG TCG CCA GAG AAT ATA GCG GTG GTG TGT GTG GGC GAC AAG TCA CGA TTG CAG CTG CAG AGG TTG TTC TCC GCC AAC ATT TTG TTC CAG GTT AAT GAG GTT GGC CGC AAG GCA GCT ACC TTT GAG GAC GCT GCG GCC ATC GCC TCT GCC GTA ATC AAC ACT GGT TAT GAC TTC GGC ACT GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTA GTG GCC TAC AAC ACA CTG GCG CTG CCC ATC TTC ACC GCC GAC TCC ATC ACC TCA GCT GAG AAG ATC AGC GTC TAC GAC TCT CTA GAC GCT GAC GTC ATC CAG AGC TTC CTG GAG TAC TCC ATG GCG TCG CTC TTG TAC TAC TCC CTG AAG GAG GGC GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAG AAT GCA TCC GAG ATG ATC GAA AAG TTG ACG CTG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAA CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC gam12.1 ATG TTT AAC CGG GCC CTC ATT TTG ATT CCT CGC AAT GCA GGA TGT TGG CAG CAA CAA GAC CGT GGC ATG GCC ACA CTC AAA CAA GTT TCC ATG CGA CTG AAG TCT GTA AAA AAT ATT CAG AAA ATT ACC CAG TCC ATG AAG ATG GTG TCA GCA GCA AAG TAT AAT CGT GCT AGC AGG GAA TTG AAG CCG GTC CGA TCA TAT GGC GCG GGA GCC TCT GCA TTC TAT GAA AAG ATT GAG GCT ACT CCT GTC GCC GAG AAA CCC AAG CAA CTG ATC ATC GCC ATG TCC TCT GAC CGT GGC CTC TGC GGC GGT ATC CAC TCG GCC GTA TGC AGA TTG ATC AAG GCA GAG ATT GCA GCG TCT CCA TCG CCC GAG AAT GTG GCG GTG GTA TGT GTG GGT GAC AAG TCG CGA TTG CAA CTG CAG AGG TTG TTT GCC GCC AAC ATT TTG TTT CAG GTC AAC GAG GTT GGC CGC AAA TCG GCT ACC TTT GAG GAC GCG GCG GCC ATT GCC TCT GAA ATC ATC AAC ACT GGT TAT GAC TTT GGC GCC GGC AAG ATC ATC TAC AAC AAG TTC AAG TCT GTG GTG TCC TAC AAC ACA CTA GCG CTG CCC ATC TTC ACT GCC GAA TCC ATC TCC TCT GCC GAA AAG CTC AGC GTG TAC GAT TCT TTG GAC GCT GAC GTC ATC CAG AGC TTC CTG GAG TAC TCG ATG GCG TCG CTA TTG TAC TAC ACC CTG AAG GAG GGT GCG TGC AGC GAG CAG AGC GCC CGC ATG ACG GCC ATG GAC GGA GCC AGC AAA AAT GCG GCT GAG ATG ATC GAA AAG TTG ACG ATG ACG TTC AAC CGC ACC CGC CAG GCC GTC ATC ACA GGA GAG CTC ATT GAG ATC ATC TCC GGC GCC GCT GCC ATC Printing out site pattern counts 9 483 P gam9 AAA AAA AAA AAC AAC AAG AAG AAG AAG AAT AAT ACA ACA ACC ACC ACC ACG ACG ACT ACT ACT AGA AGC AGC AGC AGG ATC ATC ATC ATC ATC ATC ATG ATG ATG ATT ATT ATT CAA CAA CAA CAC CAG CAG CAG CAT CCA CCA CCC CCC CCG CCT CGA CGA CGC CGG CGT CTC CTC CTG CTG CTG CTG CTG CTG GAA GAA GAA GAC GAC GAC GAC GAG GAG GAG GAG GAG GAT GAT GCA GCA GCA GCA GCC GCC GCC GCC GCC GCC GCC GCC GCG GCT GCT GCT GCT GCT GCT GCT GGA GGC GGC GGC GGC GGC GGT GGT GTA GTC GTC GTC GTG GTG GTG GTG GTG GTG GTG GTT GTT GTT TAC TAC TAT TAT TCA TCA TCA TCA TCC TCC TCC TCC TCC TCC TCC TCG TCG TCG TCT TCT TCT TCT TGC TGC TGG TGT TTC TTC TTC TTC TTC TTG TTG TTG TTG TTG TTG TTT TTT TTT gam36.2 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. .G. G.. T.A ... ... ... ..T ... ... ... ..T ..T G.. G.. ... ... T.. ..C ... ... ... ... ..G ... ..A ... ... ..A ... ... ... ..T ... ... ... ... ... ... ... ... ... ..A ..C ... ... ... ... ... ... ..G ... ... ... ..T ..A ..A ... ... ... ..C ..G ... ... ... ..C .AA ... ... ... ... ..G ..T ..T ... ..A ..G ..G ... ... ... ... ... ... ... ..T ..T ..T ... ... ... AA. A.. ... ..A ..A ... ... ... ... ... ..C ... ... ... ..T ..C ... G.. ... ..G ..G G.. G.. ... ... ... ... ..T ..A ... ... ..G ... ... ... ... ... ... ... .A. ... ..T ..T ..T C.. ... ... ... ... ... ... ... ... gam42.4 ... ... ..G ... ... ..A ... ... ... ... ... ... ... ... ... ... ... T.. ... G.. T.. ... ... ... ... ... ... ... ... ..T ... G.. ... ... T.. ..C ... ... ... ... ..G ... ... ... ... ..A ... ... ... ..T ... ... ... ... ... ... ... ..A ... ..A ..C ... ... ... ..T ... ... ..G ... ... ... ..T ..A ..T ... ... ... ..C ..G ... ... ..T ..C .AA ..A ... ... ..T ..G ... ... ... ..A ..C ..G ... ... ... ... ... ... ... ... ... ..T ..C ... ..G ... A.. ... ..A ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ..G G.. G.. ... ... ... ... ... ..A ..C ... ... ..G ... ... ... ... ... ... .A. ... ... ... ..T C.. A.. ... ... ... ..T ..C ... ... gam39.1 ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..T ... G.. ... ... ... ... ... ... ... ... ..G ... ... ... ... ..C ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ..G ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... .AA ... ... ... ... ... ... ... ... ... ... ... ... ... ... .T. ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ..A ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... C.. C.. ... ... ... ... ... ... ... gam4.1 ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... T.. T.. G.. T.. ... ... ... ... ... ... ... ... ..T ... G.. ... ... T.. ..C ... ... ... ... ..G ... ..A ... ... ..A ... ... ... ..T ..A ... ... ..C ... ... ... ... ... ..A ..C ... ... ... ... ... ... ..G ... ... ... ..T ..A ..A ... ... ... ..C ..G ... ... ... ..C .AA ... ... ... ... ..G ..T ..T ... ..A ..G ..G ... ... ... ... ... ... ..T ... ... ..T ... ... ... A.. ... ... ..A ... ..A ... ... ... ... ..C ... ... ... ... ..C ... ... ... ..G ..G G.. G.. ..A ... ... ... ..T ..A ..A ..T ... ... ..G ... ... ... ... ... .A. ... ... ..T ..T C.. ... ... ... ... ... ... ... ... gam15.1 ... ... ... ... ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... .AG ... ... ... ... ... ... ... ... ..T ... G.. ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ..G ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... G.. ... ... ... CA. ... ... ... ... ... ... ... ... ..A ... ... AA. ... ACA ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... gam34.2 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... G.. ... ... C.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ..G ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... .AG ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ... gam23.1 ... ..G ... ... ..T ... ... ... ... ... GC. ... ... ... ... T.. ... T.. ... ... G.. ... ... GA. ... ... ... ... ... ..T ... ... ... C.. G.C ..C ..C ... ... ..G ..G ... ... ... ..T ... ... ..G ... ... ..T ... ... ... ... ... ... ... ... ... A.C ..C ... T.. ... ... ... ..G ... ..T ... ... ... ..C ..A ..C ... ..C ... ... ..G ..G ..G ... ... ... ..T ... ..A ..T T.. ... ... ..A ... ..A ..C ... .TC ... ... ... ... ... ... ... ... ..G .C. ..A ... ... ... ... A.A ..A ..C ... ... A.. ... ... ... ..C ... C.. ..G ..G G.. G.. ... ... A.. G.. ... ... ..T ..A ..C ... ... ..A ... ... ... ... ... .A. ... ... ... ... C.. ... ... C.A ... ... ..C ..C ... gam12.1 ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ..T ... ... T.. ... G.C T.. ... ... ... ... ... ... ... ... ..T ... ... ... ... T.. ..C ... ... ... ... ..G ... ..A ... ..A ..A ..C ... ... ..T ... ... ... ... ... ... ... ... ... ..A ..C ..A ... ... ... ... ... ..G ... ... ... ..T ..A ..A ... ... ... ..C ..G ... ... ... ..C .AA ... ... ... ... ..G ..T ..T ... ..A ..G ..G ... ... ... A.. ... ... ... ... ... ..T ... ... ... ... A.. ... ..A ... ..A ... ... ... ... ..C ... ... ... ... ..C ... ... ..G ..G ..G G.. G.. ... ... ... ... ..T ..A ... ... ... ... ... ... ... ... ... ... .A. ... ... ..T ..T C.. ... ... ... ... ... ... ... ... 3 1 1 6 1 1 1 1 12 4 1 2 1 3 1 1 3 1 1 1 1 1 4 1 1 2 10 1 1 1 1 1 10 1 1 1 1 7 1 1 1 1 1 7 1 1 1 1 2 1 1 1 2 1 5 1 3 1 3 1 1 1 3 1 1 2 1 1 5 1 1 1 1 1 1 1 8 1 1 3 1 1 1 1 1 10 2 2 1 1 1 6 1 1 1 1 1 2 1 4 5 1 1 1 2 1 1 1 1 1 3 1 1 1 1 1 1 3 1 1 1 3 1 1 4 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 3 1 2 1 2 1 4 1 1 1 1 1 1 1 4 1 1 1 1 CODONML (in paml version 4.8, March 2014) acantho.phy Model: several dN/dS ratios for branches for branches, Codon frequency model: F3x4 Site-class models: PositiveSelection ns = 9 ls = 294 Codon usage in sequences -------------------------------------------------------------------------------------------------------------------------------------- Phe TTT 3 6 4 3 5 3 | Ser TCT 6 6 6 5 9 5 | Tyr TAT 5 5 4 5 4 5 | Cys TGT 2 2 2 2 2 2 TTC 8 4 7 8 5 8 | TCC 10 7 9 9 6 9 | TAC 4 5 6 4 6 4 | TGC 3 3 3 3 3 2 Leu TTA 0 0 0 0 0 1 | TCA 4 3 4 4 5 4 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 TTG 9 9 7 7 9 8 | TCG 3 6 4 4 4 2 | TAG 0 0 0 0 0 0 | Trp TGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- Leu CTT 0 0 1 0 0 0 | Pro CCT 1 2 2 1 2 1 | His CAT 1 0 0 0 0 1 | Arg CGT 3 3 3 3 3 3 CTC 4 5 4 4 5 5 | CCC 3 2 2 3 2 3 | CAC 1 1 1 2 1 2 | CGC 5 5 5 5 6 5 CTA 0 1 2 0 1 0 | CCA 2 2 2 1 3 1 | Gln CAA 3 4 3 2 4 3 | CGA 3 3 3 3 2 3 CTG 8 7 6 10 7 7 | CCG 1 1 1 2 0 1 | CAG 9 9 10 10 9 10 | CGG 1 1 1 1 1 1 -------------------------------------------------------------------------------------------------------------------------------------- Ile ATT 9 10 9 11 9 11 | Thr ACT 3 0 1 4 0 3 | Asn AAT 5 5 5 5 5 6 | Ser AGT 0 2 0 0 0 0 ATC 15 13 15 12 15 13 | ACC 5 5 5 5 5 5 | AAC 7 8 7 7 7 7 | AGC 6 5 6 6 6 6 ATA 0 0 0 0 0 0 | ACA 3 3 3 2 3 4 | Lys AAA 5 5 5 5 6 5 | Arg AGA 1 1 1 1 1 1 Met ATG 12 11 12 12 11 11 | ACG 4 3 3 4 3 4 | AAG 15 15 15 15 14 15 | AGG 2 2 2 2 2 2 -------------------------------------------------------------------------------------------------------------------------------------- Val GTT 3 2 3 4 2 3 | Ala GCT 8 8 9 8 8 7 | Asp GAT 2 1 2 3 1 2 | Gly GGT 2 6 3 2 5 2 GTC 5 6 5 6 6 6 | GCC 19 18 18 18 18 19 | GAC 8 8 8 8 8 8 | GGC 10 6 9 9 7 10 GTA 1 3 1 1 3 1 | GCA 6 7 6 6 6 8 | Glu GAA 4 6 5 3 6 4 | GGA 4 4 4 4 4 4 GTG 9 7 9 9 7 9 | GCG 6 9 8 6 9 6 | GAG 12 12 12 13 12 12 | GGG 0 0 0 1 0 0 -------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Phe TTT 3 1 5 | Ser TCT 6 6 8 | Tyr TAT 5 4 4 | Cys TGT 2 2 2 TTC 8 9 5 | TCC 10 10 7 | TAC 4 6 6 | TGC 3 3 3 Leu TTA 0 0 0 | TCA 4 2 2 | *** TAA 0 0 0 | *** TGA 0 0 0 TTG 8 8 9 | TCG 3 3 6 | TAG 0 0 0 | Trp TGG 1 1 1 -------------------------------------------------------------------------------------- Leu CTT 0 0 0 | Pro CCT 1 2 2 | His CAT 1 2 0 | Arg CGT 3 3 3 CTC 5 5 5 | CCC 3 3 3 | CAC 1 1 1 | CGC 5 5 5 CTA 0 1 2 | CCA 2 2 1 | Gln CAA 3 1 5 | CGA 3 3 3 CTG 9 7 6 | CCG 1 1 1 | CAG 9 10 8 | CGG 1 1 1 -------------------------------------------------------------------------------------- Ile ATT 10 9 9 | Thr ACT 3 2 3 | Asn AAT 5 5 5 | Ser AGT 0 0 0 ATC 13 17 16 | ACC 5 5 4 | AAC 7 6 7 | AGC 6 5 6 ATA 0 1 0 | ACA 3 3 3 | Lys AAA 5 4 6 | Arg AGA 1 1 1 Met ATG 11 10 11 | ACG 4 3 3 | AAG 15 16 14 | AGG 2 2 2 -------------------------------------------------------------------------------------- Val GTT 3 2 2 | Ala GCT 8 9 6 | Asp GAT 2 2 1 | Gly GGT 2 2 4 GTC 7 6 5 | GCC 18 18 19 | GAC 8 11 8 | GGC 10 10 8 GTA 0 2 3 | GCA 6 7 6 | Glu GAA 4 4 6 | GGA 4 4 4 GTG 9 7 7 | GCG 6 9 9 | GAG 13 10 12 | GGG 0 0 0 -------------------------------------------------------------------------------------- Codon position x base (3x4) table for each sequence. #1: gam9 position 1: T:0.19728 C:0.15306 A:0.31293 G:0.33673 position 2: T:0.29252 C:0.28571 A:0.27551 G:0.14626 position 3: T:0.18027 C:0.38435 A:0.12245 G:0.31293 Average T:0.22336 C:0.27438 A:0.23696 G:0.26531 #2: gam36.2 position 1: T:0.19388 C:0.15646 A:0.29932 G:0.35034 position 2: T:0.28571 C:0.27891 A:0.28571 G:0.14966 position 3: T:0.19728 C:0.34354 A:0.14286 G:0.31633 Average T:0.22562 C:0.25964 A:0.24263 G:0.27211 #3: gam42.4 position 1: T:0.19388 C:0.15646 A:0.30272 G:0.34694 position 2: T:0.28912 C:0.28231 A:0.28231 G:0.14626 position 3: T:0.18367 C:0.37415 A:0.13265 G:0.30952 Average T:0.22222 C:0.27098 A:0.23923 G:0.26757 #4: gam39.1 position 1: T:0.18707 C:0.15986 A:0.30952 G:0.34354 position 2: T:0.29592 C:0.27891 A:0.27891 G:0.14626 position 3: T:0.19048 C:0.37075 A:0.10884 G:0.32993 Average T:0.22449 C:0.26984 A:0.23243 G:0.27324 #5: gam4.1 position 1: T:0.20068 C:0.15646 A:0.29592 G:0.34694 position 2: T:0.28912 C:0.28231 A:0.28231 G:0.14626 position 3: T:0.18707 C:0.36054 A:0.14966 G:0.30272 Average T:0.22562 C:0.26644 A:0.24263 G:0.26531 #6: gam15.1 position 1: T:0.18367 C:0.15646 A:0.31633 G:0.34354 position 2: T:0.29252 C:0.27891 A:0.28571 G:0.14286 position 3: T:0.18367 C:0.38095 A:0.13265 G:0.30272 Average T:0.21995 C:0.27211 A:0.24490 G:0.26304 #7: gam34.2 position 1: T:0.19388 C:0.15986 A:0.30612 G:0.34014 position 2: T:0.29252 C:0.28231 A:0.27891 G:0.14626 position 3: T:0.18367 C:0.38435 A:0.11905 G:0.31293 Average T:0.22336 C:0.27551 A:0.23469 G:0.26644 #8: gam23.1 position 1: T:0.18707 C:0.15986 A:0.30272 G:0.35034 position 2: T:0.28912 C:0.28912 A:0.27891 G:0.14286 position 3: T:0.17347 C:0.40816 A:0.11905 G:0.29932 Average T:0.21655 C:0.28571 A:0.23356 G:0.26417 #9: gam12.1 position 1: T:0.19728 C:0.15646 A:0.30612 G:0.34014 position 2: T:0.28912 C:0.28231 A:0.28231 G:0.14626 position 3: T:0.18367 C:0.36735 A:0.14286 G:0.30612 Average T:0.22336 C:0.26871 A:0.24376 G:0.26417 Sums of codon usage counts ------------------------------------------------------------------------------ Phe F TTT 33 | Ser S TCT 57 | Tyr Y TAT 41 | Cys C TGT 18 TTC 62 | TCC 77 | TAC 45 | TGC 26 Leu L TTA 1 | TCA 32 | *** * TAA 0 | *** * TGA 0 TTG 74 | TCG 35 | TAG 0 | Trp W TGG 9 ------------------------------------------------------------------------------ Leu L CTT 1 | Pro P CCT 14 | His H CAT 5 | Arg R CGT 27 CTC 42 | CCC 24 | CAC 11 | CGC 46 CTA 7 | CCA 16 | Gln Q CAA 28 | CGA 26 CTG 67 | CCG 9 | CAG 84 | CGG 9 ------------------------------------------------------------------------------ Ile I ATT 87 | Thr T ACT 19 | Asn N AAT 46 | Ser S AGT 2 ATC 129 | ACC 44 | AAC 63 | AGC 52 ATA 1 | ACA 27 | Lys K AAA 46 | Arg R AGA 9 Met M ATG 101 | ACG 31 | AAG 134 | AGG 18 ------------------------------------------------------------------------------ Val V GTT 24 | Ala A GCT 71 | Asp D GAT 16 | Gly G GGT 28 GTC 52 | GCC 165 | GAC 75 | GGC 79 GTA 15 | GCA 58 | Glu E GAA 42 | GGA 36 GTG 73 | GCG 68 | GAG 108 | GGG 1 ------------------------------------------------------------------------------ Codon position x base (3x4) table, overall position 1: T:0.19274 C:0.15722 A:0.30574 G:0.34429 position 2: T:0.29063 C:0.28231 A:0.28118 G:0.14588 position 3: T:0.18481 C:0.37491 A:0.13001 G:0.31028 Average T:0.22273 C:0.27148 A:0.23898 G:0.26682 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG): 0.01064520 0.02159517 0.00748865 0.01787262 0.01034066 0.02097737 0.00727441 0.01736131 0.01029913 0.02089312 0.00000000 0.00000000 0.00534337 0.01083971 0.00000000 0.00897117 0.00868314 0.01761489 0.00610839 0.01457845 0.00843473 0.01711095 0.00593364 0.01416138 0.00840086 0.01704223 0.00590981 0.01410451 0.00435851 0.00884180 0.00306611 0.00731766 0.01688621 0.03425587 0.01187905 0.02835088 0.01640312 0.03327586 0.01153921 0.02753980 0.01633724 0.03314222 0.01149287 0.02742920 0.00847604 0.01719476 0.00596270 0.01423074 0.01901525 0.03857491 0.01337678 0.03192540 0.01847125 0.03747133 0.01299409 0.03101206 0.01839707 0.03732085 0.01294191 0.03088752 0.00954472 0.01936270 0.00671448 0.01602497 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) gam9 gam36.2 0.1209 (0.0266 0.2201) gam42.4 0.1203 (0.0235 0.1954) 0.0768 (0.0120 0.1567) gam39.1 0.1248 (0.0083 0.0662) 0.1230 (0.0274 0.2227) 0.1155 (0.0243 0.2103) gam4.1 0.0931 (0.0204 0.2196) 0.1004 (0.0090 0.0898) 0.0599 (0.0090 0.1506) 0.0983 (0.0212 0.2159) gam15.1 0.5948 (0.0208 0.0350) 0.1856 (0.0395 0.2126) 0.2112 (0.0410 0.1942) 0.2964 (0.0247 0.0833) 0.1808 (0.0375 0.2075) gam34.2 0.1687 (0.0053 0.0311) 0.0982 (0.0212 0.2161) 0.0947 (0.0182 0.1916) 0.0761 (0.0060 0.0789) 0.0701 (0.0151 0.2156) 0.7466 (0.0224 0.0300) gam23.1 0.1644 (0.0391 0.2381) 0.1439 (0.0502 0.3492) 0.1469 (0.0470 0.3201) 0.1809 (0.0447 0.2472) 0.1509 (0.0471 0.3120) 0.2307 (0.0550 0.2386) 0.1775 (0.0415 0.2340) gam12.1 0.0886 (0.0189 0.2135) 0.1245 (0.0105 0.0846) 0.0498 (0.0075 0.1507) 0.1024 (0.0228 0.2223) 0.1015 (0.0075 0.0740) 0.1699 (0.0355 0.2092) 0.0794 (0.0166 0.2096) 0.1456 (0.0455 0.3122) TREE # 1: ((((7, 6), (4, 1)), (((5, 2), 9), 3)), 8); MP score: 178 This is a rooted tree. Please check! check convergence.. lnL(ntime: 16 np: 21): -2139.199097 +0.000000 10..11 11..12 12..13 13..7 13..6 12..14 14..4 14..1 11..15 15..16 16..17 17..5 17..2 16..9 15..3 10..8 0.098894 0.036477 0.000004 0.014821 0.240959 0.007262 0.055776 0.014441 0.091001 0.027645 0.000500 0.039499 0.052981 0.035140 0.067970 0.157740 2.259006 0.862012 0.114270 0.023203 215.297334 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). tree length = 0.94111 ((((7: 0.014821, 6: 0.240959): 0.000004, (4: 0.055776, 1: 0.014441): 0.007262): 0.036477, (((5: 0.039499, 2: 0.052981): 0.000500, 9: 0.035140): 0.027645, 3: 0.067970): 0.091001): 0.098894, 8: 0.157740); ((((gam34.2: 0.014821, gam15.1: 0.240959): 0.000004, (gam39.1: 0.055776, gam9: 0.014441): 0.007262): 0.036477, (((gam4.1: 0.039499, gam36.2: 0.052981): 0.000500, gam12.1: 0.035140): 0.027645, gam42.4: 0.067970): 0.091001): 0.098894, gam23.1: 0.157740); Detailed output identifying parameters kappa (ts/tv) = 2.25901 dN/dS (w) for site classes (K=4) site class 0 1 2a 2b proportion 0.86201 0.11427 0.02094 0.00278 background w 0.02320 1.00000 0.02320 1.00000 foreground w 0.02320 1.00000 215.29733 215.29733 Naive Empirical Bayes (NEB) analysis (please use the BEB results.) Positive sites for foreground lineages Prob(w>1): 72 T 0.941 120 P 0.897 186 K 0.764 203 S 0.969* 208 S 0.991** 244 C 1.000** Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positive sites for foreground lineages Prob(w>1): 72 T 0.692 120 P 0.865 186 K 0.882 203 S 0.937 208 S 0.914 244 C 0.996** The grid (see ternary graph for p0-p1) w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500 Posterior on the grid w0: 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 w2: 0.001 0.004 0.010 0.020 0.035 0.059 0.097 0.157 0.246 0.371 Posterior for p0-p1 (see the ternary graph) 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.024 0.009 0.082 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.008 0.001 0.114 0.010 0.746 0.004 sum of density on p0-p1 = 1.000000 Time used: 1:22