Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ew4a- -----------------CCHHHHHHHHHHHHHHHHHHHHCC-CCCCC---CEEEEE----------------CCEEEEE-CCCC-CEEEEEEEC---CCCEEEEECCC--CEEEEEEE-CCEEEECCCCCCHHHHHHHHHHHHHCCCCCCC--------- >P1;d3iam7- --------------------CCHHHHHHHHHHHHHHHHHHHHHHCCCC--EEEEEECHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEECCCCCCCCCEEEEECCCCEEEEEEEECCCEEEEC-CEECCHHHHHHHHHHHHHHHCCC---------- >P1;d3oeqa- CCCCCCCCCCCCCCCCCCCC---CCHHHHHHHHHHHHHCCCCCCCCCCC--EEEEC----------------CCEEEEE-CCCC-CCEEEECCC---CC-CCEEEECCC-EEEEEEEC-CCCEEECCCCCCHHHHHHHHHHHHHHC-------------- >P1;d3t3la- -----------------CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEE----------------CCEEEEECCCCC-CEEEEEEEC---CCCEEEEECCCC-CCEEEEEC-CCCEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC PSA >P1;d1ew4a- -----------------297950572077005203630981-a4a19---061658----------------d740203-0678-250403235---76200305086--75230518-aa602048566302610161047009370416--------- >P1;d3iam7- --------------------9846730051036006104600764916--135342052457379480a14431220000086652003040141738a12010501449552505257c75010a-96605493027203802781256---------- >P1;d3oeqa- aa7b5bb87576575959a9---85604510691376048418a45304--50816----------------a050504-0541-850402337---6b-203040144-55220537-aa3020467464046206700670577-------------- >P1;d3t3la- -----------------a66a504710540052006105804b4830595070719----------------a050405004a2-740403143---754003040274-95140424-871021785740004102510473083917027153014b5 Translating the sequences -----------------CC***HHHHHHHHHHHHHHHHH**-CCCCC---*EEEEE----------------CCEEEEE-CCCC-CEEEEEE*C---CCC*EEEE*CC--*EEEEEE*-CC*EEECCCCCCHHHHHHHHHHHHH*C*CCC*--------- --------------------**HHHHHHHHHHHHHHHHH*****CCCC--*EEEEE****************C*EEEEE*CCCC**EEEEEE*C***CCC*EEEE*CCC**EEEEEE**CC*EEEC-C**C*HHHHHHHHHHHH***CCC---------- *****************CC*---**HHHHHHHHHHHHH****CCCCCC*--EEEE*----------------CCEEEEE-CCCC-C*EEEE**C---CC-**EEE*CCC-*EEEEEE*-CC*EEECCCCCCHHHHHHHHHHHHH*C-------------- -----------------CC***HHHHHHHHHHHHHHHHH***CCCCCC***EEEEE----------------CCEEEEE*CCCC-CEEEEEE*C---CCC*EEEE*CCC-**EEEEE*-CC*EEECCCCCCHHHHHHHHHHHHH*C*CCC********** 55387.tem _________________________________ -----------------CC***HHHHHHHHHHHHHHHHH***CCCCCC*-*EEEEE----------------CCEEEEE*CCCC-CEEEEEE*C---CCC*EEEE*CCC-*EEEEEE*-CC*EEECCCCCCHHHHHHHHHHHHH*C*CCC*--------- Structural block scores 0 16 - 4.3 M 75.0 75.0 7.7 75.0 17 18 C 4.3 M 5.5 75.0 9.8 8.2 19 21 * 2.3 P 7.0 30.7 53.0 7.2 22 38 H 4.8 H 3.3 2.7 8.2 2.4 39 41 * 1.4 P 28.0 2.0 4.3 4.0 42 47 C 4.7 H 18.3 5.5 5.1 5.2 51 55 E 4.9 H 5.2 3.4 4.0 4.8 56 71 - 4.3 M 75.0 4.6 75.0 75.0 72 73 C 4.7 H 10.2 2.0 5.2 5.2 74 78 E 5.0 H 1.8 0.8 2.8 2.8 80 83 C 5.0 H 5.2 5.0 2.5 4.1 86 91 E 4.8 H 2.3 1.2 2.3 2.0 94 96 - 4.3 M 75.0 3.7 75.0 75.0 97 99 C 4.8 H 5.0 6.5 30.8 5.3 101 104 E 4.8 H 2.0 1.5 1.8 1.8 106 108 C 4.8 H 29.7 3.0 3.0 4.3 111 116 E 4.9 H 2.7 3.2 2.8 2.7 119 120 C 5.0 H 10.5 9.8 10.5 7.5 122 124 E 5.0 H 0.7 0.3 0.7 1.0 125 130 C 4.7 H 5.3 17.8 5.2 5.2 131 143 H 4.9 H 2.2 3.5 3.3 2.1 147 149 C 4.3 M 1.7 4.3 75.0 2.7 151 159 - 4.3 M 75.0 75.0 75.0 4.2 >>>>>>