Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fr3a- -------------------------------------------------------------CCCCCCEEEEEEEEEEEECCCEEEEEEEEC-C-EEEEEEEEHHHHHH--HCCCCCCEEEEEECHHHCCCCC--------------- >P1;d1guta- -------------------------------------------------------------C-CCCCCEEEEEEEEEEECCCEEEEEEEECCC-CEEEEEEEHHHHHH--HCCCCCCEEEEECCHHHCCCCC--------------- >P1;d1h9ra1 -------------------------------------------------------------CCCCCCEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEEEHHHHHH--HCCCCCCEEEEEECHHHCCCCCCHHHHHHC------- >P1;d1h9ra2 ------------------------------------------------------------------CEEEEEEEEEEECCCCEEEEEEECCCC-CEEEEEEECHHHC----CCCCCCEEEEEECHHHCCCCCC-------------- >P1;d1oxxk1 --CCEEEEEEEE---CCEEEEC-----CEEECCCCCCC------EEEEEECHHHEEEECCCCCCCCEEEEEEEEEEEEEECCEEEEEEEECC--CCCEEEEEC-------CCCCCC-CCEEEECHHHCEEEEC-------------- >P1;d1v43a1 ----------------------------------------------------------------CCCEEEEEEEEC---------CEEEECC----EEEECCC--CCCCH--HHCCCEEEEEECHHHCCC------------CCC-- >P1;d1v43a2 -------------------------------------------------------------CC-CCEEEEEEEEEEEEECCCEEEEEEEEC--CEEEEEEEECCC------CCCCCCEEEEEEEHHHCCCCCC--CCCCCCC----- >P1;d2d62a3 -------------------------------------------------------------CCCCCCCEEEEEEEEEEECCCEEEEEEEEC--CEEEEEEEECCC------CCCCCCEEEEECC-CCCCEECC--CCCCEEE----- >P1;d3d31a1 --CCEEEEEEEEEEECCEEEEEEC---CEEEEEECC---CCCCCEEEEEECHHHEEEECCCCCCCCCEEEEEEEEEEEECCCEEEEEEEC-CC--EEEEEEECCHHHH--CCCCCCCEEEEEECHHHCEEEC--------------- >P1;d3rlfa2 CCCCEEEEEEEEEECCCCEEEECCCCCCCEEEECCCCCCCCCCCEEEEEECCCCCEE---HH--HCCCEEEEEEEEEEECCCEEEEEEECCCCCCCEEEEEE----CC--CCCCCCCEEEEECCHHHCEEECCCCCCCCCCCCCCCC >P1;d6yira2 --------------------------------------------------------------CCCCCEEEEEEECC---------CEEEECC----EEEECCHHHHHHHHHCCCCCCEEEEEECHHHCCC------------CCCCC >P1;d6yira3 -------------------------------------------------------------CCCC-CCEEEEECCEEEEECCEEEEEEEEC--CEEEEEEEECCC------CCCCCCEEEEECCHHHCCCCCC--CCCCCCC----- PSA >P1;d1fr3a- -------------------------------------------------------------aa59163339030470769a8504010428-9-75244635394089--690658382424455875999b--------------- >P1;d1guta- -------------------------------------------------------------b-6b483349250341858a950302041bc4-96344635284068--770865383313487875889f--------------- >P1;d1h9ra1 -------------------------------------------------------------593a183345030440676a950305031767857363227282076--570678462413355684b83a69875999------- >P1;d1h9ra2 ------------------------------------------------------------------63646260460748a95040205185c-7425462439707----a3675493428477955998ab-------------- >P1;d1oxxk1 --6207030613---b610405-----3050326293b------4040004071040259626b6034056060562866d74330001053--a34010248-------942765-3020003695031665-------------- >P1;d1v43a1 ----------------------------------------------------------------9a355550402a---------430508a----453707b--72a38--a54a84262134276588------------bb7-- >P1;d1v43a2 -------------------------------------------------------------92-97135452604603256820202051d--b85463638855------419496526133334846654a--9688466----- >P1;d2d62a3 -------------------------------------------------------------7657a732480204614759a31103045c--c87243616572------a085958361254-8866556a--7588467----- >P1;d3d31a1 --1803081504309a8404041a---92300068a---19552805040706406047739b4a250116470560636b940305060-70--8010117584167--4657552502000617307065--------------- >P1;d3rlfa2 928104060603425a74020202078744040302177076818040004042035---39--60a03061503415449910002050660a9301023a----75--28196648220000343020206787507233938b9 >P1;d6yira2 --------------------------------------------------------------89863464716036---------54041db----6468169b70663487943766253134285558------------9975b >P1;d6yira3 -------------------------------------------------------------8738-c2437070560565ca30104035a--b8925363a26a------90858561513436a876755a--9687467----- Translating the sequences -------------------------------------------------------------***CCC*EEEEEEEEEE**CCEEEEEEEEC-*-**EEEEEE******--*CCCCCCEEEEE*CHHHCC**C--------------- -------------------------------------------------------------*-*CCC*EEEEEEEEEE**CCEEEEEEEEC**-**EEEEEE******--*CCCCCCEEEEE*CHHHCC**C--------------- -------------------------------------------------------------***CCC*EEEEEEEEE***CCEEEEEEEEC*****EEEEEE******--*CCCCCCEEEEE*CHHHCC**C********------- ------------------------------------------------------------------C*EEEEEEEEEE**CCEEEEEEE*C**-**EEEEEE*****----CCCCCCEEEEE*CHHHCC**C*-------------- --**********---*******-----***********------********************CC**EEEEEEEEEE**CCEEEEEEEEC*--***EEEEE*-------*CCCCC-**EEE*CHHHC*****-------------- ----------------------------------------------------------------CCC*EEEEEEE*---------*EEEEC*----EEEE***--*****--**CCCEEEEE*CHHHCC*------------***-- -------------------------------------------------------------**-CC**EEEEEEEEEE**CCEEEEEEEEC--***EEEEEE***------CCCCCCEEEEE**HHHCC**C*--*******----- -------------------------------------------------------------***CCC*EEEEEEEEEE**CCEEEEEEEEC--***EEEEEE***------CCCCCCEEEEE*C-**CC**C*--*******----- --**********************---*********---*************************CCC*EEEEEEEEEE**CCEEEEEEE*-**--*EEEEEE******--*CCCCCCEEEEE*CHHHC***C--------------- *********************************************************---**--*CC*EEEEEEEEEE**CCEEEEEEE*C*****EEEEEE----**--*CCCCCCEEEEE*CHHHC***C*************** --------------------------------------------------------------**CCC*EEEEEE**---------*EEEEC*----EEEE***********CCCCCCEEEEE*CHHHCC*------------***** -------------------------------------------------------------***C-C*EEEEE**EEE**CCEEEEEEEEC--***EEEEEE***------CCCCCCEEEEE*CHHHCC**C*--*******----- 50331.tem _________________________________ -------------------------------------------------------------***CCC*EEEEEEEEEE**CCEEEEEEEEC*****EEEEEE******--*CCCCCCEEEEE*CHHHCC**C*--*******----- Structural block scores 0 60 - 4.4 M 75.0 75.0 75.0 75.0 22.1 75.0 75.0 75.0 13.2 6.7 75.0 75.0 61 63 * 2.6 P 8.7 30.8 5.7 75.0 6.5 75.0 28.7 6.0 8.2 53.0 30.7 6.0 64 66 C 4.6 H 5.3 7.8 6.5 52.0 3.0 7.5 5.7 8.2 5.8 5.5 5.7 31.8 68 77 E 4.8 H 3.6 3.9 2.9 4.1 3.8 18.1 3.5 3.1 3.6 2.8 18.3 3.7 78 79 * 1.9 P 7.5 6.5 6.5 6.0 6.0 75.0 3.5 6.0 4.5 4.0 75.0 5.5 80 81 C 4.6 H 9.2 9.8 9.8 9.8 10.2 75.0 7.0 9.8 10.2 9.0 75.0 11.5 82 89 E 4.7 H 2.0 1.9 2.1 2.1 1.4 29.6 1.5 2.1 2.2 1.0 29.9 2.0 91 95 * 2.8 P 34.2 21.3 6.6 20.7 33.3 62.1 34.9 35.5 33.0 5.7 62.3 35.7 96 101 E 4.8 H 4.0 4.2 3.8 3.8 1.8 4.3 5.0 3.7 1.7 2.8 5.2 4.9 102 107 * 2.5 P 5.5 4.7 4.2 16.8 63.8 30.2 40.5 39.8 5.2 52.0 6.6 40.6 108 109 - 4.6 H 75.0 75.0 75.0 75.0 75.0 5.5 75.0 75.0 75.0 75.0 3.5 75.0 111 116 C 4.9 H 5.2 4.8 5.3 5.9 16.5 18.8 5.5 6.2 5.0 5.7 6.0 5.8 117 121 E 4.9 H 4.0 3.6 3.2 5.2 1.0 3.0 3.4 4.0 1.4 2.4 3.4 3.2 124 126 H 4.8 H 6.7 7.3 6.3 7.0 6.7 5.0 5.0 30.3 3.7 3.3 5.0 8.2 127 128 C 4.7 H 7.0 6.5 7.8 7.0 1.5 6.5 5.0 6.0 3.5 1.0 5.0 6.5 129 130 * 1.4 P 9.0 8.5 5.5 8.5 3.5 41.5 5.5 5.0 3.0 1.0 41.5 6.0 133 134 - 4.6 H 75.0 75.0 8.5 75.0 75.0 75.0 75.0 75.0 75.0 7.5 75.0 75.0 135 141 * 3.8 M 75.0 75.0 27.0 75.0 75.0 75.0 6.7 6.4 75.0 3.9 75.0 6.7 142 146 - 4.4 M 75.0 75.0 75.0 75.0 75.0 36.0 75.0 75.0 75.0 8.1 8.3 75.0 >>>>>>