Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1yu0a1 CCCCEECHHHHHCCCCCCCCEEEECCCCEEEECCCCCCCCEECC-------CHHHHC-----CCEECCCCCCCCEEEEECCEEEECCCEEEEECCEEEEECCCEECCCCCCCCCEEEEEEEECC-------CCEEEECCCC----CCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCEECHHHCEEC-- >P1;d1zrua3 ------------------------------------CEEECCCCHHHHHHHHHHHHCCCCCCCEEEEEE----CCEECC-CEEEEE-EEEEEECCEEEEEE-EEEEECC---CCCEEEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEECC-------------CCEE---EEEECC PSA >P1;d1yu0a1 9a581255980694308592403055481404043755305356-------648856-----74051767942005256557010347030004666040886480613a07443600000015-------5402015749----20ab17774014000031161243a9a9927a621035830503-- >P1;d1zrua3 ------------------------------------8061511a369503540873a071620316256----915467-230202-40003000030202-8240807---2835020001032869a800603027645130340068a74020000203058-------------a305---83762b Translating the sequences ************************************C***EECC-------*HHHHC-----C*EE*******CEEEEE*CEEEE***EEEEECCEEEEE***EE**CC***CCEEEEEEEE*C-------**EEEECCCC----CCCCCCCC*EEEEEEEEEEC*************CEE*****EE*-- ------------------------------------CEEE**CC*******HHHHHC*****CEEEEEE----C*EE**-CEEEEE-EEEEEECCEEEEEE-EEEEECC---CC*EEEEEEEEC*******EEEEEECCCC****CCCCCCCCEEEEEEEEEE*C-------------C*EE---EEEE** 141658.tem _________________________________ ------------------------------------CEEEEECC-------HHHHHC-----CEEEEEE----CEEEEE-CEEEEE-EEEEEECCEEEEEE-EEEEECC---CCEEEEEEEEEC-------EEEEEECCCC----CCCCCCCCEEEEEEEEEEEC-------------CEEE---EEEE-- Structural block scores 0 35 - 3.0 P 4.5 75.0 37 41 E 3.0 P 3.2 2.6 42 43 C 5.0 H 5.5 5.8 44 50 - 3.0 P 75.0 4.4 51 55 H 4.6 H 6.2 4.4 57 61 - 3.0 P 75.0 3.2 63 68 E 3.7 M 3.8 3.8 69 72 - 3.0 P 5.5 75.0 74 78 E 3.8 M 3.6 4.6 81 85 E 4.6 H 2.2 1.4 87 92 E 4.7 H 1.7 1.2 93 94 C 5.0 H 5.0 0.0 95 100 E 4.7 H 4.0 1.2 102 106 E 3.8 M 4.8 4.4 107 108 C 5.0 H 2.0 3.5 109 111 - 3.0 P 5.8 75.0 112 113 C 5.0 H 4.0 5.0 114 122 E 4.6 H 1.1 1.2 124 130 - 3.0 P 75.0 6.2 131 136 E 4.3 M 2.0 1.8 137 140 C 5.0 H 6.2 5.5 141 144 - 3.0 P 75.0 1.8 145 152 C 5.0 H 5.8 4.9 153 163 E 4.6 H 1.3 1.1 165 177 - 3.0 P 6.4 75.0 179 181 E 3.7 M 1.3 2.7 182 184 - 3.0 P 5.3 75.0 185 188 E 4.0 M 2.0 6.0 189 190 - 3.0 P 75.0 6.8 >>>>>>