Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hfoa- ----CEEEEEECCC-HHH-CCCCHHHHHHHHHHHHHC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEEC--------- >P1;d1otga- ----CEEEEEEEHHHHHHHCHHHHHHHHHHHHHCC------CCCCHHHCEEEEEEEC--CCCCCCCC---------CCEEEEEEEEEECCC-CCHHHHHHHHHHHHHHHHHHCHHHHCCCEEEEEEEEEECCCCCCCCC------CHHHHHCC >P1;d2aala1 ----CEEEEEEECCCCHH-HHHHHHHHHHHHHHHHHC------CCCCCCCEEEEEECCCCCCCC-----CCCCCCCCCCCCEEEEEEECCC--CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCCCCCCCCHHHHCCCC-- >P1;d2os5a- ----CEEEEEECCC-HHH-CCCCHHHHHHHHHHHHHC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEEHHHH----CC >P1;d2xcza- ----CEEEEEECCC-CCC-CHHHHHHHHHHHHHHHHC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEEECCCC-CCCHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEECC-------- >P1;d3b64a- -----CEEEEECCCCCHH-HHHHHHHHHHHHHHHCCC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEECCCCC-CCCHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEECCC--CCEE-CCEEC--------- >P1;d3gada- ----CEEEEEECCCCCHH-HHHHHHHHHHHHHHHHHC------CCHHHCEEEEEECC--CCCCC-----------CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEECC-------- >P1;d3kana- ----CEEEEEECCC-HHH-CCCCHHHHHHHHHHHHHC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEEECHHHCEE-CCEEHHHC------ >P1;d4dh4a- ----CEEEEEECCCCCHH-HHHHHHHHHHHHHHHHHC------CCHHHCEEEEEECC--CCCCC-----------CCCCCCEEEEEEEECCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEEECHHHCEE-CCEEC--------- >P1;d4grpa- CCCCEEEEEEECCC-HHH-CCCCHHHHHHHHHHHHHC------CCHHHEEEEEECCC--CCCCC-----------CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEECC-------- >P1;d4jj9a1 ----CEEEEEEEHHHHHCCC-CHHHHHHHHCC-CCCCCCCCCCCCHHHCEEEEEEEC--CCCCCCCCHHHHHCCCCCCCEEEEEEEE-CCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCC------CCCHHHC- >P1;d4lhpa- ----CEEEEEEECCCC---CHHHHHHHHHHHHC-CCC------CCCCCCCEEEEEECHHHCCCC-----CCCCCCCCCCCCEEEEEEEECC--CCCCHHHHHHHHHHHHCCC--CCCHHH---EEEEEEEECHHHCCCCCCCCHHHHCCCCCC >P1;d4lkba1 ----CEEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHC------CCCCCCEEEEEEECHHHCCCC-----C-----CCCCCCEEEEEECCCC--CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEECCCCHHHCEE-CCEECCC------- >P1;d6cuqa1 ---CCEEEEEECCCCCHH-HHHHHHHHHHHHHHHHHC-------CCC-CEEEEEE-C--CCCCC-----------C-CCCCEEEEEEE-CCC---CCHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCCC-CCCC---------- >P1;d6lr3a- ----CEEEEEECCC-HHH-CCCCHHHHHHHHHHHHHC------CCHHHCEEEEECCC--CCCCC-----------CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHCEE-CCEEC--C----CC PSA >P1;d1hfoa- ----0502030016-676-13b606830372019008------36794070614154--b162b-----------a4885005020303820-58843a70384016104720-8045a1---080713629297265-8c754--------- >P1;d1otga- ----0202040033049606075028402530182------9304501050417238--92636647---------68102040103061a-2778327711740372048006a14872604060514325697397a------2a458759 >P1;d2aala1 ----020403015b18b9-617402400180027009------168b23405162278a40828-----2aa6a4b179400204030251--79942640474026105751-805440---02070733756514188a631156855a-- >P1;d2os5a- ----0403000114-885-03b60474015201700b------26595070704064--8134d-----------94685002030303820-7a922740583016101600-805791---040415627466167-ab643266----6c >P1;d2xcza- ----0103050118-82b-73a70185015500a209------26473080507063--91637-----------a6773004030302620-9c734940492017004820-904491---070615505376265-9c8433-------- >P1;d3b64a- -----1400400270697-245301630340056109------56383081514363--92739-----------94775002030313b31-5a623950574028105700-8066a1---060415339--8436-9b876--------- >P1;d3gada- ----020302002616a9-618601640271028109------35685050604457--92638-----------84584001030202931-69923740474027102830-906671---060316627498448-8b8637-------- >P1;d3kana- ----0404020105-7a6-13b70694027201910a------26586060514254--a1408-----------a4783002010103a30568752761386027202720-908991---050615527474164-8c433474------ >P1;d4dh4a- ----04030302270789-43750273027201600a------2669508030452c--a153a-----------84675004050102871-7aa22960384013004620-9046a1---070704536585246-ca755--------- >P1;d4grpa- 43310302040106-7a5-13b806830362017209------04583080603164--a142b-----------a4774005020200430-78852770493028003530-705491---070714538258165-8b8419-------- >P1;d4jj9a1 ----2502061020058228-75127303813-705189682016425140626357--93a17590671576a4806104030204-b6b-37a70484035304721983066058917052416264193a86599------ab58784- >P1;d4lhpa- ----030503005609---33750041008103-109------068912405251362970818-----2aa7a4a05720030303015b--2991286046303840662--707640---0504153433651527ab331065864a44 >P1;d4lkba1 ----12020200374055-23a501720050036118------256963405142386a70915-----b-----8273300302023595--57802660382036204640-906490---050515333566284-9c54146------- >P1;d6cuqa1 ---5120503000b1877-217402620340025217-------95a-0507065-3--9422c-----------c-84400503040-890---d55a80363027006610-6085b1---070614438487287-8a65---------- >P1;d6lr3a- ----0301020114-895-02a604830172038308------17782070505063--9243b-----------85664004010301a40-69a33880266016103720-905380---060602726278465-9c853--a----6c Translating the sequences ----CEEEEEE*CC-*HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC***--------- ----CEEEEEE*****HH*****HHHHHHHHHH**------**CCHHHCEEEEE**C--CCCCC***---------CC***EEEEEEECCC-*CHHHHHHHHHHHHHHHHHH***********EEEEEEECC***C***------******** ----CEEEEEE*CC**HH-****HHHHHHHHHHHHHC------CC***C*EEEE**C**CCCCC-----******CCCCCCEEEEEEECCC--CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC***CC**********-- ----CEEEEEE*CC-*HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC******----** ----CEEEEEE*CC-***-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-C**HHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC****-------- -----*EEEEE*CC**HH-****HHHHHHHHHHH**C------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEE*CCC*-C**HHHHHHHHHHHHHHHHH-CCCHHH---EEEEEE*CC--*C**-CC***--------- ----CEEEEEE*CC**HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC****-------- ----CEEEEEE*CC-*HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEE*CC**CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEE*CHHHC**-CC******------ ----CEEEEEE*CC**HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEE*CC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEE*CHHHC**-CC***--------- *****EEEEEE*CC-*HH-****HHHHHHHHHHHHHC------CCHHH*EEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC****-------- ----CEEEEEE*****H***-**HHHHHHH**-***C******CCHHHCEEEEE**C--CCCCC***********CCCC**EEEEEE-CCC-*CHHHHHHHHHHHHHHHHHHH****HH****EEEEE**CC***C***------*******- ----CEEEEEE*CC**---****HHHHHHHHH*-**C------CC***C*EEEE**C***CCCC-----******CCCCCCEEEEEEE*CC--C***HHHHHHHHHHHH***--CCCHHH---EEEEEEE*CHHHC***CC************ ----CEEEEEE*****HH-****HHHHHHHHHHHHHC------CC***CEEEEE**C***CCCC-----*-----CCCCCCEEEEEE*CCC--CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEE**CCHHHC**-CC*****------- ---*CEEEEEE*CC**HH-****HHHHHHHHHHHHHC-------C**-CEEEEE*-C--CCCCC-----------C-CCCCEEEEEEE-CC*---**HHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC**---------- ----CEEEEEE*CC-*HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC***--*----** 55331-1.tem _________________________________ ----CEEEEEE*CC**HH-****HHHHHHHHHHHHHC------CCHHHCEEEEE**C--CCCCC-----------CCCCCCEEEEEEECCC*-CHHHHHHHHHHHHHHHHHHH-CCCHHH---EEEEEEECCHHHC**-CC******----*- Structural block scores 0 3 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 2.8 75.0 75.0 75.0 57.5 75.0 5 10 E 5.0 H 1.7 1.3 1.5 1.2 1.5 1.5 1.2 1.7 1.7 1.5 2.3 1.8 1.0 1.7 1.0 12 13 C 4.5 M 3.5 3.0 8.2 2.5 4.5 4.5 4.0 2.5 4.5 3.0 1.0 5.5 5.0 5.8 2.5 14 15 * 2.0 P 40.5 2.0 4.5 41.5 41.5 3.0 3.5 41.0 3.5 41.0 2.5 4.5 2.0 4.5 41.5 16 17 H 4.6 H 6.5 7.5 10.2 6.5 6.8 8.0 9.8 8.2 8.5 7.8 5.0 75.0 5.0 7.0 7.0 19 22 * 1.1 P 5.4 4.5 4.5 5.1 6.9 3.5 5.2 5.6 4.8 5.9 23.8 4.5 5.1 3.5 4.6 23 35 H 4.8 H 3.0 8.5 1.8 2.4 2.9 2.2 2.5 3.2 2.3 2.9 8.8 7.2 2.0 2.1 3.0 37 42 - 4.7 H 75.0 52.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.5 75.0 75.0 75.0 75.0 43 44 C 4.9 H 4.5 2.0 3.5 4.0 4.0 5.5 4.0 4.0 4.0 2.0 3.5 3.0 3.5 42.0 4.0 45 47 H 4.2 M 6.7 2.0 7.2 6.3 4.7 4.7 6.3 6.3 6.7 5.3 3.7 6.0 7.0 30.2 5.7 49 53 E 4.9 H 3.6 3.4 3.2 3.6 4.0 3.8 3.0 3.2 3.0 3.4 3.6 3.2 2.8 3.6 3.4 54 55 * 1.2 P 3.0 2.5 2.0 3.0 3.0 4.5 4.5 3.5 3.5 3.5 4.0 2.0 2.5 40.0 3.0 57 58 - 4.5 M 75.0 75.0 9.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.5 8.2 75.0 75.0 59 63 C 4.9 H 6.4 5.2 4.4 5.9 5.2 6.0 5.6 4.7 6.0 5.8 6.1 4.8 4.4 5.9 5.9 64 74 - 4.6 H 75.0 56.1 38.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5.5 38.1 69.2 75.0 75.0 75 80 C 4.8 H 5.9 15.3 5.4 5.3 5.6 5.3 4.8 5.4 5.0 5.4 3.2 4.1 3.8 17.2 4.8 81 87 E 4.9 H 1.4 1.1 1.3 1.1 1.4 1.3 0.9 0.6 1.4 1.3 12.0 1.3 1.4 1.7 1.1 88 90 C 4.8 H 4.3 5.8 2.7 4.3 3.3 5.8 4.7 5.5 5.7 2.3 9.7 5.8 6.3 30.7 5.2 94 112 H 4.9 H 4.0 3.7 4.0 3.4 4.0 3.9 3.8 3.9 3.7 3.9 4.1 8.0 3.5 7.9 4.0 114 116 C 4.6 H 4.0 5.2 4.3 4.3 4.3 4.7 5.0 5.7 4.3 4.0 3.7 4.7 5.0 4.7 4.7 117 119 H 4.7 H 5.5 5.7 2.7 5.7 4.7 5.8 4.7 6.3 5.8 4.7 6.0 3.3 4.3 5.8 3.7 120 122 - 4.6 H 75.0 3.3 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 4.0 75.0 75.0 75.0 75.0 123 129 E 4.9 H 3.6 2.7 2.7 2.9 3.4 2.7 3.1 3.1 3.3 3.4 3.6 2.6 2.7 3.1 3.0 130 131 C 4.8 H 5.5 3.5 5.0 4.5 2.5 6.0 4.5 4.5 4.5 5.5 5.0 3.5 3.0 5.5 4.0 132 134 H 4.5 M 6.0 7.3 5.3 5.3 5.3 52.7 7.0 5.0 6.0 5.0 7.2 4.7 5.7 6.3 5.7 136 137 * 1.0 P 5.5 8.0 2.5 6.5 5.5 4.5 6.0 5.0 5.0 5.5 7.0 3.5 6.0 7.5 5.5 139 140 C 4.7 H 10.2 75.0 9.2 11.0 10.8 10.2 9.8 10.2 11.5 9.8 75.0 11.0 10.8 9.2 10.8 141 146 * 2.6 P 40.2 52.1 3.7 4.5 28.0 41.0 29.0 4.2 40.3 28.7 53.7 3.0 15.8 51.8 29.4 147 150 - 4.2 M 75.0 6.0 7.1 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.0 7.1 75.0 75.0 75.0 >>>>>>