Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iq8a1 CCEEEEEEEEECCEEEEEEEECCEEEEECEEEECCCCCCC-CCCHHHHHHCCCCEEEEEHHHHHHCHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC------CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEECCCHHHHHCCCHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHCCCCEEEECHHHHHHHCCEEEECCEEEEHHHCC--------CCCCCCCCCCCCCHHHHCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHCHHHHHHHC >P1;d3blda- CCCEEEEEEEECCEEEEEEEECCEEEEECEECCEECCCCCCCCCHHHHHHCCCCCEEECHHHHHHC-CCHHHHCCCCHHHHHCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEEECCCC-CCCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHH-CCCCCEEEECCCCC---CCCHHHHHHHHHHHHHHCCCCCCEEECCCC-CHHHHHHHCCCCCEEC-----------CCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCC-CCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCHHHHHC--------------------- PSA >P1;d1iq8a1 9406073424100000030206834140010003040572-10504402716040000100301439814750475402500508100001000420147970707055003002609010000001104060759404720540063054029108------100000000013460034006301708010000000230185340640030000005104761000023001000000000000000004201720383400025203606407--------905191500563305603818---6a3114000100030025006402710555502500450050476043005304628a106725 >P1;d3blda- 53050607354c500014040544504000100305606083072820370500000110240139-230670268200731908300001001a394805a3602053003004208000000014-0827196a-0282052005005201610473039700000000001368005600740-42601000003037---a0b3a2015005200410278300002805-0330000032000001-----------00300615270558705929630075080600-7311240060144a69304400210310010100440040056650-8116049405--------------------- Translating the sequences CCEEEEEEEEECCEEEEEEEECCEEEEECEEEE**CCCCC-CCCHHHHHHCCCCEEEEEHHHHHHC*HHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHCCCCCCCHHHHHHHHHH*CCC***CCCC*CCCCCCHH*HHHHHHHHHHHHHHHHHH**------C******CCCCCHHHHHHHHHHH*HCCCC*EEECCCHH***CCCHHHHHHHHHHHHHHCCCCCCEEECCCC*HHHHHHHHHCCCCEEE***********EEEECCEEEEHHH**--------CCCCCCCCC*CCCHHHH****---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH*HHHHHHH**C********************* CC*EEEEEEEECCEEEEEEEECCEEEEECEE**EECCCCC*CCCHHHHHHCCCC*EEE*HHHHHHC-**HHHH****HHHHHCCCC*EEE*CCCC****CCCCCCCHHHHHHHHHHHCCCEEECCCC-CCCCCC**-*HHHHHHHHHHHHHHHHHHH******CEEEEEECCCCCHHHHHHHHHHH-*CCCCEEEECCC**---CCCHHHHHHHHHHHHHHCCCCCCEEECCCC-*HHHHHHH*CCCCEE*-----------****CC*******HH********CCCCCCCCC-CCCHHHHHHHH****HHHHHHHHHHHHHHHHHHHHHHHHHHH*CC*-****HHHHHC--------------------- 51713.tem _________________________________ CCEEEEEEEEECCEEEEEEEECCEEEEECEEEEEECCCCC-CCCHHHHHHCCCCEEEEEHHHHHHC-HHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHCCCCCCCHHHHHHHHHHHCCCEEECCCC-CCCCCCHH-HHHHHHHHHHHHHHHHHHHH------CEEEEEECCCCCHHHHHHHHHHH-HCCCCEEEECCCHH---CCCHHHHHHHHHHHHHHCCCCCCEEECCCC-HHHHHHHHHCCCCEEE-----------EEEECCEEEEHHHHH--------CCCCCCCCC-CCCHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHC--------------------- Structural block scores 0 1 C 5.0 H 6.5 4.0 2 10 E 4.8 H 3.0 3.3 11 12 C 5.0 H 0.0 8.8 13 20 E 5.0 H 0.6 1.1 21 22 C 5.0 H 7.0 4.5 23 27 E 5.0 H 2.4 2.6 29 34 E 3.7 M 0.7 0.7 35 39 C 5.0 H 3.6 3.4 41 43 C 5.0 H 2.0 3.3 44 49 H 5.0 H 2.8 3.7 50 53 C 5.0 H 2.8 1.2 54 58 E 4.2 M 0.2 0.4 59 64 H 5.0 H 1.3 1.7 67 81 H 4.2 M 3.5 3.1 82 85 C 5.0 H 3.5 5.0 86 90 E 4.2 M 0.2 0.2 91 94 C 5.0 H 1.0 2.9 95 98 H 3.0 P 1.8 6.0 99 105 C 5.0 H 5.3 3.8 106 116 H 4.8 H 1.9 1.5 117 119 C 5.0 H 3.3 2.7 120 122 E 3.0 P 0.0 0.0 123 126 C 5.0 H 0.2 1.2 128 133 C 5.0 H 2.8 4.5 134 135 H 3.0 P 7.0 8.2 137 156 H 4.7 H 3.0 2.1 157 162 - 3.0 P 75.0 4.8 164 169 E 3.0 P 0.0 0.0 170 174 C 5.0 H 0.8 0.8 175 185 H 5.0 H 2.4 3.3 188 191 C 5.0 H 2.2 2.2 192 195 E 4.5 M 0.0 0.0 196 198 C 5.0 H 0.0 1.0 199 200 H 3.0 P 2.5 5.0 201 203 - 3.0 P 3.0 75.0 204 206 C 5.0 H 4.0 7.3 207 220 H 5.0 H 1.4 2.4 221 226 C 5.0 H 3.0 3.3 227 229 E 5.0 H 0.0 0.0 230 233 C 5.0 H 1.2 3.8 235 243 H 4.6 H 0.0 1.0 244 247 C 5.0 H 0.0 0.5 248 250 E 4.3 M 0.0 0.3 251 261 - 3.0 P 2.7 75.0 262 265 E 3.0 P 1.0 0.8 266 267 C 5.0 H 3.5 3.0 268 271 E 3.0 P 2.8 3.8 272 276 H 3.0 P 3.4 5.0 277 284 - 3.0 P 75.0 4.2 285 293 C 5.0 H 3.3 2.9 295 297 C 5.0 H 4.0 3.7 298 305 H 4.0 M 3.9 1.8 306 308 - 3.0 P 75.0 6.2 309 337 H 4.9 H 2.3 2.0 338 339 C 5.0 H 5.0 5.5 342 350 H 3.7 M 2.1 3.7 352 372 - 3.0 P 3.8 75.0 >>>>>>