Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1zjca1 CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHCCCCCEEEEECCCHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECCCCCCCCCEEEHHHCCCEEECCCCCCCEEECEEEEEEEEEEECCCCEEECCEEEEEEEEEEECCEEEEEEEEECHHHHHHHHCCCHHHHCEEEEEECCCCCCCHHHCCCCCCHHHHCCCCCEEEEECCCHHHCCCHHHCCHHHHHHHCCCCCCCEEEEECCCCCCEEEEECCCCCEEEEEECCEECCCC >P1;d2ayia1 CCHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCC--CCCHHHHHHHHHHHHCCCEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCHHHHCCCCCHHHHHHHHHHHHHHHCC------HHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCCCCEECCCCCCC-CCCCCCCCCCCCEEECCCCCCEEEEEECCCCEEECCEEECCCEEEEECCEEEEEECCCCHHHHHHHCCCCCHHHCEEEEECCCCCCHHHHHCCCCCCHHHHHCCCCEEEEECCCHHHCCCC-----CCHHHHCCCCCCCEEEEECCCCCCEEEEECCCCCEEEEEECCEECC-- PSA >P1;d1zjca1 849520420030005200304691100030035056006202600572707505153821773364047474720356114a7728212500947000010304203108b0636104112333153118124110204001030000056004300682747702750171004002047860742066027814730730372604002040a5040400007704021021416a85250012000000100021630664030220001112001604020670306727085356005100514600310000000137140162a2401230000000000000001010089028264861482100202111100002860203013598744300490410a90 >P1;d2ayia1 a39951450020006100406971301050144239007302510572506505132a125763740582859606--81358216700730587001000306217047b15892264188157822730660058230010200100400072028aa559602460151018006------79806621751582173038440400106266060400007603031002709b-9380003001110100001640643050212011d453034020505703043040873393037406346001100000001140300726230228000200000000040484005bd-----a826830006082200000048604010138888434004806158-- Translating the sequences CHHHHHHHHHHHHHHCCCCCCCCC*EEEEEECCCHHHHHHHHHHHHHCCCC*EEEEEECHHHHHHHHHHCCHHHHH**CCCHHHHHHHHHHHHCCCEEEEEECCC***CCCCCHHHHHHHHHHHHHH*HHHHHHHHCCCCCEEEEECCCHHHHHHHCCCCCHHHHHHHHHHHHHHHCC******HHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECCCCCC**CEEEHHH*CCEEECCCCCCCEEECEEEEEEEEEEECCCCEEECCEEEEEEEEEEECCEEEEEEEEECHHHHHHHHCCCHHHHCEEEEEECCCCC**HHHCCCCCCHHHH*CCCCEEEEECCCHHHCCCH*****HHHHHHCCCCCCCEEEEECCCCCCEEEEECCCCCEEEEEECCEECC** C*HHHHHHHHHHHHHCCCCCCCCCEEEEEE*CCCHHHHHHHHHHHHHCCCCEEEEEE*CHHHHHHHHHHCC*****--CCCHHHHHHHHHHHHCCCEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC***EECCC***HHHHCCCCCHHHHHHHHHHHHHHHCC------HHHHHHHHHHHHHHHHHHHH*CCCEEEEEECCEEEEEE*CCCCCCEEC******-CC***CCCCCCCEEEC*****EEEEEECCCCEEECCEEE***EEEEECCEEEEEE***CHHHHHHH*CCC*HHHCEEEEE*CCCCCHHHHHCCCCCCHHHHHCCCCEEEEECCCHHHCCC*-----**HHHHCCCCCCCEEEEECCCCCCEEEEECCCCCEEEEEECCEECC-- 144052.tem _________________________________ CHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHHHHCCHHHHH--CCCHHHHHHHHHHHHCCCEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHCCCCCHHHHHHHHHHHHHHHCC------HHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEECCCCCCEECEEEHHH-CCEEECCCCCCCEEECEEEEEEEEEEECCCCEEECCEEEEEEEEEEECCEEEEEEEEECHHHHHHHHCCCHHHHCEEEEEECCCCCHHHHHCCCCCCHHHHHCCCCEEEEECCCHHHCCCH-----HHHHHHCCCCCCCEEEEECCCCCCEEEEECCCCCEEEEEECCEECC-- Structural block scores 1 14 H 4.9 H 2.4 3.1 15 23 C 5.0 H 2.8 3.1 24 30 E 4.4 M 0.6 1.4 31 33 C 5.0 H 2.7 3.3 34 46 H 5.0 H 3.0 3.2 47 50 C 5.0 H 4.0 3.2 51 57 E 4.4 M 3.9 3.8 59 68 H 5.0 H 4.2 4.7 69 70 C 5.0 H 5.5 5.0 71 75 H 3.0 P 3.2 5.2 76 77 - 3.0 P 5.5 75.0 78 80 C 5.0 H 2.0 4.0 81 92 H 5.0 H 4.5 3.7 93 95 C 5.0 H 3.7 5.0 96 101 E 5.0 H 0.7 0.7 102 104 C 5.0 H 2.0 2.7 105 107 H 3.0 P 1.3 2.7 108 112 C 5.0 H 5.1 5.7 113 135 H 4.9 H 2.4 4.3 136 140 C 5.0 H 1.2 2.6 141 145 E 3.8 M 0.8 0.6 146 148 C 5.0 H 0.0 0.3 149 155 H 4.1 M 2.6 1.9 156 160 C 5.0 H 4.6 7.2 161 175 H 5.0 H 3.0 3.2 176 177 C 5.0 H 1.0 3.0 178 183 - 3.0 P 4.2 75.0 184 204 H 4.9 H 3.8 4.4 205 207 C 5.0 H 3.3 2.7 208 213 E 5.0 H 1.0 1.5 214 215 C 5.0 H 7.8 6.0 216 222 E 4.7 H 1.1 1.4 223 228 C 5.0 H 3.0 2.7 229 230 E 3.0 P 1.5 2.0 232 234 E 3.0 P 2.3 3.0 235 237 H 3.0 P 5.8 6.8 239 240 C 5.0 H 3.5 6.0 241 243 E 3.0 P 1.7 2.7 244 250 C 5.0 H 0.4 0.9 251 253 E 5.0 H 0.3 0.3 255 265 E 4.1 M 2.8 2.6 266 269 C 5.0 H 1.0 1.2 270 272 E 5.0 H 0.3 0.7 273 274 C 5.0 H 1.0 8.8 275 285 E 4.5 M 1.9 2.5 286 287 C 5.0 H 3.5 3.5 288 296 E 4.3 M 4.2 3.2 298 305 H 4.8 H 2.1 3.6 306 308 C 5.0 H 3.3 4.3 309 312 H 4.5 M 2.2 1.8 314 319 E 4.7 H 0.0 0.0 320 324 C 5.0 H 2.4 1.2 325 329 H 4.2 M 2.6 2.4 330 335 C 5.0 H 3.2 2.5 336 340 H 4.6 H 0.6 2.0 341 344 C 5.0 H 0.0 0.0 345 349 E 5.0 H 0.0 0.0 350 352 C 5.0 H 0.3 2.7 353 355 H 5.0 H 0.3 4.0 356 358 C 5.0 H 5.7 5.5 360 364 - 3.0 P 4.4 75.0 365 370 H 4.3 M 4.8 6.2 371 377 C 5.0 H 0.9 2.3 378 382 E 5.0 H 0.6 0.4 383 388 C 5.0 H 2.7 3.0 389 393 E 5.0 H 1.2 1.2 394 398 C 5.0 H 6.4 7.0 399 404 E 5.0 H 2.5 2.5 405 406 C 5.0 H 4.5 4.0 407 408 E 5.0 H 2.5 3.5 409 410 C 5.0 H 5.2 6.5 411 412 - 3.0 P 4.5 75.0 >>>>>>