Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2bvca1 C--CHHHHHHHHHHCCCCEEEEEEECCCCCEEEEEEEHHHCCHHHHHCCEEEECCCCCCCCCHHHCEEEEEECHHH---CEECCCCC--CCEEEEEEEEECCCCCCCC >P1;d4lnoa1 CCCCHHHHHHHHHHCCEEEEEEEEECCCCCEEEEEEEHHHH-HHHHCCCCEEEHHHHHHHHCCCCCEEEEEEE---EEEEEECCCCCCCCEEEEEEEEEECC-CCCCC >P1;d5zlia1 CHHHHHHHHHHHHHCCCCEEEEEEECCCCCEEEEEEEHHHCCCHHHHHCEEEECCCCCCCCCHHHCEEEEEECCCC---CEECCCCC--CCEEEEEEEEEECCCCEEC PSA >P1;d2bvca1 5--74850274186390640003050746742532153a5067601780371501716602698728010202163---0620693b--4400204071142976763 >P1;d4lnoa1 75274940462096560430302050557772223063941-7500546041200314086489666020305---34305127834985210104071234-86563 >P1;d5zlia1 65940680064067390540001051688542643261b708493038006160071a801898638010405048---24215949--7310004070403477682 Translating the sequences C--CHHHHHHHHHHCCCCEEEEEEECCCCCEEEEEEEHHHCCHHHHHCCEEEECCCCCCCCCHHHCEEEEEEC***---CEECCCCC--CCEEEEEEEEECCCCCCCC C**CHHHHHHHHHHCC**EEEEEEECCCCCEEEEEEEHHH*-HHHH*CC*EEE********C***CEEEEEE*---****EECCCCC**C*EEEEEEEEECC-CCCCC C***HHHHHHHHHHCCCCEEEEEEECCCCCEEEEEEEHHHCC*HHHH*CEEEECCCCCCCCCHHHCEEEEEEC***---CEECCCCC--CCEEEEEEEEE*CCCC**C 54368.tem _________________________________ C**CHHHHHHHHHHCCCCEEEEEEECCCCCEEEEEEEHHHCCHHHHHCCEEEECCCCCCCCCHHHCEEEEEEC***---CEECCCCC--CCEEEEEEEEECCCCCCCC Structural block scores 1 2 * 2.7 P 75.0 3.5 7.0 4 13 H 5.0 H 4.5 4.4 3.7 14 17 C 4.5 M 4.5 3.8 4.2 18 24 E 5.0 H 1.7 1.9 1.4 25 29 C 5.0 H 4.8 4.8 5.6 30 36 E 5.0 H 3.1 3.1 3.9 37 39 H 5.0 H 6.2 5.3 6.5 40 41 C 4.0 M 3.0 38.0 4.0 42 46 H 4.6 H 4.2 3.4 3.8 47 48 C 4.5 M 4.0 5.0 4.0 49 52 E 4.8 H 4.0 1.8 3.2 53 61 C 4.1 M 3.2 2.9 3.9 62 64 H 4.0 M 8.0 7.7 7.7 66 71 E 5.0 H 1.8 1.8 2.2 73 75 * 2.7 P 3.3 75.0 4.0 76 78 - 4.0 M 75.0 3.3 75.0 80 81 E 5.0 H 4.0 3.0 3.0 82 86 C 5.0 H 5.9 4.8 5.6 87 88 - 4.0 M 75.0 8.5 75.0 89 90 C 4.5 M 4.0 3.5 5.0 91 99 E 5.0 H 1.7 1.8 1.8 100 107 C 4.5 M 5.5 13.8 4.6 >>>>>>