Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a12a- CCCCCCCCCCCCCCCEEEEEEE-CCCCCCCCCCCCCEEEEEEEECCCCCEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCHHHCCEECCCCCCEEEEEECCCEEEEEECCCCEEEEECEEECCEEEECCCCCCCEEEEEEECCCCCEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCHHHCCCCCHHHHHHHHHCCEECCCCCCCCCCCCCEEEEEEECCEEEEEECCCCEEEEECCCCCCCCCCCCCCEEEEEECHHHCCCCCCEEEEEECCCEEEEEECCCCEEEEECCHHHCCCCCCCCCCEEEEEECCCCCCEEEEEECCCEEEEEECCCCEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCEEEEEEEECCCC >P1;d3qhyb- -------------CCEEEEECCCCCCCCCCCCHHHCC-----------CCCEEEECCCEEEEEE-CCEEEEEECCCCCCCCCC----HHHHC--------CCCEEEECCCEEEEEE-CCEEEEEECC--CCCCCCCCHHHC---C--------CEEEEEEECCEEEEEE-CCEEEEEECCCCCCCCCCHHHHC----------------------------CEEEEEECCCEEEEEE-CCEEEEEECCCCCCCC-----------CCHHHHC---CEEEEEECCCEEEEEE-CCEEEEEECCCCCCCCCC-----------HHHHCCCCEEEECCCCEEEEE-CCEEEEECC---------------CCCCC--HHHCC-CEEEEEECCCCEEEEEC----- PSA >P1;d1a12a- 9877281630485314000001-0540000136b2434550130a06360010200230000005604000003081000019089a03305043081a2502000003000000021010100000418863000263864248044050924010010021000000360101000003300000037008b491463175006131061715e38a2130410100030000006754000001042200019a4a1135041072055a82704201003200000046040000020650000108b19333703407603504501003000000067140100020711000317482123052073820791102401015400000027468e >P1;d3qhyb- -------------185020142936350070497055-----------9074000021000003-b24010003453501813----86068--------a064010114000002-9240100034--a46008037505---7--------9074010002000003-a2400010147460080397047----------------------------8072030003000001-a320101025725007-----------1395068---9074000011000002-a14000100555701603-----------950489074010013000002-a23000003---------------b2803--96048-b0650200120000028----- Translating the sequences *************CCEEEEEEE-CCCCCCCCC***CE***********CEEEEEECCCEEEEEE*CC*EEEEECCCCCCCCCC*****HHHC********CEEEEEECCCEEEEEE*CC*EEEEECE**CCEEEECC***C***E********CEEEEEE*CCEEEEEE*CC*EEEEECCCCCCCCCCHHH*C****************************CEEEEEEECCEEEEEE*CC*EEEEECCCCCCCC***********ECHHH*C***CEEEEEECCCEEEEEE*CC*EEEEECCHHHCCCCC***************CCEEEEEECCCEEEEEE*CC*EEEEEC***************EEEEC*****CC*EEEEEEECCCEEEEEEE***** -------------CCEEEEE***CCCCCCCCCHHHC*-----------C**EEEECCCEEEEEE-CCEEEEEECCCCCCCCCC----HHHHC--------C**EEEECCCEEEEEE-CCEEEEEEC*--CC****CCHHHC---*--------CEEEEEEECCEEEEEE-CCEEEEEECCCCCCCCCCHHHHC----------------------------CEEEEEE*CCEEEEEE-CCEEEEEECCCCCCCC-----------*CHHHHC---CEEEEEECCCEEEEEE-CCEEEEEECC***CCCCC-----------HHHHCC**EEEECCC*EEEEE-CCEEEEE*C---------------****C--HHHCC-*EEEEEECCC*EEEEE*----- 50985.tem _________________________________ -------------CCEEEEEEE-CCCCCCCCCHHHCE-----------CEEEEEECCCEEEEEE-CCEEEEEECCCCCCCCCC----HHHHC--------CEEEEEECCCEEEEEE-CCEEEEEECE--CCEEEECCHHHC---E--------CEEEEEEECCEEEEEE-CCEEEEEECCCCCCCCCCHHHHC----------------------------CEEEEEEECCEEEEEE-CCEEEEEECCCCCCCC-----------ECHHHHC---CEEEEEECCCEEEEEE-CCEEEEEECCHHHCCCCC-----------HHHHCCEEEEEECCCEEEEEE-CCEEEEEEC---------------EEEEC--HHHCC-EEEEEEECCCEEEEEEE----- Structural block scores 0 12 - 3.0 P 5.2 75.0 13 14 C 5.0 H 2.0 4.5 15 21 E 4.4 M 0.7 2.0 23 31 C 5.0 H 1.4 3.1 32 34 H 3.0 P 6.5 5.3 37 47 - 3.0 P 3.4 75.0 49 54 E 4.3 M 0.5 1.8 55 57 C 5.0 H 1.7 1.0 58 63 E 5.0 H 0.0 0.5 65 66 C 5.0 H 3.0 6.8 67 72 E 4.7 H 0.7 0.8 73 82 C 5.0 H 2.2 3.3 83 86 - 3.0 P 6.9 75.0 87 90 H 4.5 M 1.5 5.0 92 99 - 3.0 P 3.6 75.0 101 106 E 4.3 M 0.3 1.8 107 109 C 5.0 H 1.0 2.0 110 115 E 5.0 H 0.0 0.3 117 118 C 5.0 H 0.5 5.5 119 124 E 4.7 H 0.3 0.8 127 128 - 3.0 P 2.5 75.0 129 130 C 5.0 H 8.0 7.2 131 134 E 3.0 P 2.2 3.5 135 136 C 5.0 H 1.0 1.5 137 139 H 3.0 P 5.7 4.0 141 143 - 3.0 P 3.3 75.0 145 152 - 3.0 P 3.0 75.0 154 160 E 4.7 H 0.3 1.7 161 162 C 5.0 H 1.5 1.0 163 168 E 5.0 H 0.0 0.5 170 171 C 5.0 H 3.0 6.2 172 177 E 4.7 H 0.3 0.8 178 187 C 5.0 H 0.6 3.3 188 191 H 4.5 M 2.5 5.0 193 220 - 3.0 P 4.3 75.0 222 228 E 4.7 H 0.9 1.7 229 230 C 5.0 H 1.5 1.5 231 236 E 5.0 H 0.0 0.2 238 239 C 5.0 H 6.0 6.8 240 245 E 4.7 H 0.7 0.7 246 253 C 5.0 H 1.1 3.5 254 264 - 3.0 P 4.5 75.0 267 270 H 4.5 M 3.5 5.0 272 274 - 3.0 P 6.8 75.0 276 281 E 5.0 H 1.2 1.8 282 284 C 5.0 H 1.7 0.7 285 290 E 5.0 H 0.0 0.3 292 293 C 5.0 H 3.0 5.8 294 299 E 4.7 H 0.7 0.8 300 301 C 5.0 H 1.0 2.5 302 304 H 3.0 P 3.7 5.7 305 309 C 5.0 H 0.2 2.0 310 320 - 3.0 P 4.8 75.0 321 324 H 3.0 P 3.2 4.5 325 326 C 5.0 H 4.0 8.5 327 332 E 4.3 M 1.7 2.0 333 335 C 5.0 H 1.0 1.3 336 341 E 4.7 H 0.0 0.3 343 344 C 5.0 H 4.0 6.2 345 350 E 4.3 M 0.8 0.5 352 366 - 3.0 P 2.5 75.0 367 370 E 3.0 P 2.5 5.4 372 373 - 3.0 P 5.0 75.0 374 376 H 3.0 P 3.3 5.0 377 378 C 5.0 H 8.0 6.0 380 386 E 4.7 H 1.1 3.5 387 389 C 5.0 H 3.3 1.0 390 396 E 4.4 M 0.3 1.4 397 401 - 3.0 P 7.9 75.0 >>>>>>