Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b3qa2 ------------CCEEEEEEEEEECCEEEEEEHHHEEEEECCCCCCCEEECC-----EEEEEECCEEEEEEEHHHHCCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEEE---ECCC--HHHHCCCCCEEEEEECCCCCEEEEECHHHCC---------------- >P1;d2ho9a- CHHHHCCCCCCCCCCEEEEEEEEECCEEEEEEHHHEEEEEECC--CEECCCCCCCCCCEEEEECCEEEEEEEHHHHHCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEEECCCCCCCCCCCCCCCHHHCCEEEEE-CCEEEEECCHHHHHHHHHHHHHHHHCCCCC >P1;d2qdla1 --------------CCEEEEEEEECCEEEEEEHHHCCEEEECC--CCCCCCCCCCCEEEEEEECCEEEEEEEHHHHHCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEECHHHCCCCCC-CCCCCHHHEEEEEEE-CCEEEEEECCCCCCCCCCCCCC-------- >P1;d4jpbw- -------------CCEEEEEEEECCCCEEEEEHHHEEEEEECC--CCCCCCCCCCCEEEEEEECCEEEEEEEHHHHHCC-CCCHHHCCEEEEEEECCEEEEEEECEEEEEEEEECCCEECCCCCCCC--HHHEEEEEEE-CCEEEEEECHHHHHHHHCC----------- PSA >P1;d1b3qa2 ------------c5663300102018720001494047225026850756a8-----51105399560201101620a39567458703000054bb82100002524863704---2383--ca71784841500030a87540300307405---------------- >P1;d2ho9a- 3b66915575487394650000400842000229113232609--328409b0473020105157950100003200416b075a20430000509b25000003322641500400150104691505a701031003-ba4300004054006223770580027856 >P1;d2qdla1 --------------a6250000100742000259404322718--908838a02a102010817977000010031081456766a7030000405764000100125541517796168159-a14073510500062-8b55000041540035b92320-------- >P1;d4jpbw- -------------685340000203930000139203522838--907758a358123020819947030000030061-91579606100004199410000006437426035840367877961--a813321053-a95502001053006404c----------- Translating the sequences ------------*C*EEEEEEEEECCEEEEEEHHHEEEEE*CC**CC***CC-----EEEEEECCEEEEEEEHHHH*CCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEEE---*CCC--****CC***EEEEEE**CC*EEEEECHHH**---------------- *************CCEEEEEEEEECCEEEEEEHHHEEEEEECC--C**CCCCCCCC**EEEEECCEEEEEEEHHHHHCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEEE****CCCCC*CCCCCHHH**EEEEE-CCEEEEE*CHHH****************** --------------C*EEEEEEEECCEEEEEEHHH**EEEECC--CC*CCCCCCCC*EEEEEECCEEEEEEEHHHHHCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEE*****CCCCC-CCCCCHHHEEEEEEE-CCEEEEEEC*************-------- -------------CCEEEEEEEE*CC*EEEEEHHHEEEEEECC--CC*CCCCCCCC*EEEEEECCEEEEEEEHHHHHCC-CCC***CCEEEEEEECCEEEEEEECEEEEEEEEE*****CCCC*CCC--HHHEEEEEEE-CCEEEEEECHHH*******----------- 50341.tem _________________________________ ------------*CCEEEEEEEEECCEEEEEEHHHEEEEEECC--CC*CCCCCCCC*EEEEEECCEEEEEEEHHHHHCCCCCCCCCCCEEEEEEECCEEEEEEECEEEEEEEEE****CCCCC*CCCCCHHHEEEEEEE-CCEEEEEECHHH**********-------- Structural block scores 0 11 - 4.3 M 75.0 5.9 75.0 75.0 13 14 C 4.3 M 5.5 6.0 42.8 7.0 15 23 E 4.8 H 1.7 2.1 1.6 1.6 24 25 C 5.0 H 4.5 4.0 3.5 6.0 26 31 E 4.9 H 1.7 1.3 1.3 0.7 32 34 H 5.0 H 5.7 4.0 6.0 4.7 35 40 E 4.7 H 3.3 2.8 3.0 3.3 41 42 C 5.0 H 1.0 4.5 4.5 5.5 43 44 - 4.3 M 7.0 75.0 75.0 75.0 45 46 C 4.7 H 2.5 2.5 4.5 4.5 48 55 C 4.5 M 41.2 4.8 5.4 5.9 57 62 E 4.9 H 2.5 1.5 2.0 2.3 63 64 C 5.0 H 9.0 6.0 8.0 9.0 65 71 E 5.0 H 2.1 2.1 2.1 2.0 72 76 H 4.9 H 1.8 1.0 0.8 0.6 77 87 C 4.7 H 5.9 4.6 5.5 11.4 88 94 E 5.0 H 1.7 1.1 1.0 0.9 95 96 C 5.0 H 11.5 10.2 6.0 9.0 97 103 E 5.0 H 1.6 1.0 1.6 0.7 105 113 E 4.9 H 4.3 2.6 3.4 3.9 114 117 * 2.0 P 56.8 1.2 5.8 4.2 118 122 C 4.6 H 32.8 2.0 5.8 6.2 124 128 C 4.3 M 6.7 4.0 4.5 33.2 129 131 H 4.3 M 5.3 5.8 3.0 6.5 132 138 E 4.7 H 1.3 1.1 1.9 2.4 140 141 C 5.0 H 7.5 11.0 9.8 9.8 142 147 E 4.8 H 2.0 1.2 1.7 2.0 149 151 H 4.3 M 3.7 3.0 3.3 2.7 152 161 * 2.4 P 60.5 3.2 3.5 25.1 162 169 - 4.3 M 75.0 4.5 75.0 75.0 >>>>>>