Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iega- CCCCCEEEEEEEEECCCCCCCHHHCCCHHHHHHCC----CCEEEECCEEEEEEEEEEEEEEECCEEEEEEEECCHHHHHHHHHHHCCCHHHHHCCCCCCCC-CHHHHHHHHHCCEEEEE--------------CCCEEEEECCCCCCCCCCEEECCHHHHHCCCCCCCHHHHHHHHHHHC--------CCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCC >P1;d2pbka- C---CCEEEEEEEECCCCCCCHHHCCCHHHHHHHCCCCCCCEEEECCCCCCCCEEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCC-CCCC-CHHHHHHHHHCCEEEEEECCHHHHCCCCCCCCEEEEEEECCCCCCCCCCEEECCHHHHHHCCCCCCHHHHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCCCCC >P1;d4v08a- ---CCEEEEEECCCCCCCC--HHHCCCHHHHHHHCCCCCCCEEEECCCC-CEEEEEEEEEEECCEEEEEEEECCHHHHHHHHHHCCC-CCCCCC---CCCHHHHHHHHHHHHCCEEEEEEC-------CCCCCCEEEEEEECCCCCCCCCCEEECCHHHHHCCCC-CCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCC--------- PSA >P1;d1iega- 73245020000000182918598041549305762----6240004357501004010031072000000003075004203750582a406720586296-24000200130000103--------------92600000100612000000026132004105207982166037416--------d340714687189366727858525540560192070237501010 >P1;d2pbka- b---40200000003718196a51503394058205248412010141850200100000209200000000206603710554079396055719-8175-34200000310000202024182067a0878007200000005130000000372720021041069922870192087272861870706065840673477099496188307702a30405-6400023 >P1;d4v08a- ---b30100000000940b--c924075930640181586030003439-0400000300408200000000204204500367289-a51ab6---915876211510343000020326-------9454720120001110612000020374264007306-03a50477018079181485307274830560073056826838735840761492021--------- Translating the sequences C**CCEEEEEEEEECCCCCCCHHHCCCHHHHHH*C----CCEEEECC****EEEEEEEEEEECCEEEEEEEECCHHHHHHHHHHHCCC*****CCC*CCCC-CHHHHHHHHHCCEEEEE--------------C**EEEEECCCCCCCCCCEEECCHHHHHCCCCCCCHHHHHHHHHHHC--------CCCCCCCHHHHHHHHHHH*CCCCHHHHHHHHHHHHCCC*CCCCCCC C---C*EEEEEEEECCCCCCCHHHCCCHHHHHHHCCCCCCCEEEECCCC*C**EEEEEEEEECCEEEEEEEECCHHHHHHHHHHH**CCCCCCCCC-CCCC-CHHHHHHHHHCCEEEEEEC*******CCCCCCEEEEEEECCCCCCCCCCEEECCHHHHH*CCCCCCHHHHHHHHHHH**CC***CCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHH*CCC-CCCCCCC ---CCEEEEEE***CCCCC--HHHCCCHHHHHHHCCCCCCCEEEECCCC-CEEEEEEEEEEECCEEEEEEEECCHHHHHHHHHH*CC-CCCCCC---CCC***HHHHHHHHHCCEEEEEEC-------CCCCCCEEEEEEECCCCCCCCCCEEECCHHHHHCCCC-CCHHHHHHHH***C*CC***CCCCC****HHHHHHHHHHHCCCCCHHHHHHHHHHHHCC--------- 50789.tem _________________________________ C--CCEEEEEEEEECCCCCCCHHHCCCHHHHHHHCCCCCCCEEEECCCC*CEEEEEEEEEEECCEEEEEEEECCHHHHHHHHHHHCCCCCCCCCCC-CCCC-CHHHHHHHHHCCEEEEEEC-------CCCCCCEEEEEEECCCCCCCCCCEEECCHHHHHCCCCCCCHHHHHHHHHHHC*CC***CCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC-CCCCCCC Structural block scores 1 2 - 4.0 M 2.5 75.0 75.0 3 4 C 4.5 M 4.5 39.5 7.2 5 13 E 4.6 H 0.2 0.2 0.1 14 20 C 4.7 H 4.9 5.0 24.9 21 23 H 5.0 H 5.7 5.5 7.8 24 26 C 5.0 H 3.3 2.7 3.7 27 33 H 4.9 H 4.9 4.4 3.9 34 40 C 4.4 M 44.3 3.4 4.1 41 44 E 5.0 H 1.0 0.8 0.8 45 48 C 4.5 M 4.8 3.5 4.8 51 61 E 4.8 H 0.9 0.5 1.0 62 63 C 5.0 H 4.5 5.5 5.0 64 71 E 5.0 H 0.0 0.0 0.0 72 73 C 5.0 H 1.5 1.0 1.0 74 84 H 4.9 H 3.0 3.4 3.0 85 95 C 4.1 M 4.5 5.5 26.0 97 100 C 4.8 H 5.8 5.2 5.8 103 111 H 5.0 H 1.1 1.1 2.2 112 113 C 5.0 H 0.0 0.0 0.0 114 119 E 4.8 H 13.2 0.7 1.2 121 127 - 4.0 M 75.0 4.0 75.0 128 133 C 4.2 M 64.0 5.6 5.2 134 140 E 4.7 H 1.1 1.3 0.6 141 150 C 5.0 H 1.0 0.9 1.1 151 153 E 5.0 H 0.0 0.0 1.7 154 155 C 5.0 H 4.0 5.0 5.5 156 160 H 5.0 H 1.2 2.2 2.4 161 167 C 4.7 H 2.7 2.0 13.4 168 178 H 4.7 H 4.3 4.5 4.5 181 182 C 4.0 M 75.0 4.5 4.5 183 185 * 2.7 P 75.0 5.3 5.7 186 194 C 4.3 M 20.3 3.9 3.8 195 205 H 5.0 H 5.7 4.6 3.8 206 210 C 4.8 H 6.6 7.4 6.4 211 222 H 4.9 H 3.2 4.1 4.1 223 225 C 4.7 H 3.0 3.0 26.0 227 233 C 4.0 M 2.0 2.1 75.0 >>>>>>