Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1olza2 CCCCCCEEECCCCC----CCEEECCC-CCCCCCEEEECCCCCEEEEECCCEEEEEECCEEEEEEEEEECCCC---------------HHHHHHHHHCCCCCCCCCCCCEEEEEECC-CCEEEEEECCCCCCEEEEEEC----CC--CEEC-CCCEECCCCCCCCCCCCEEEEEECCEEEEEEECC---CCCCCEEEEEECC------CC-CCCCCC-CCCCCCCCEEEEEEEECCCC-CCCCEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEEEEECCEEH-HHC--EECCEEEEEEEECCCCC--------CCCEEEEEEECCCC--CCCEEEEEEEEHHHHHHHHHHCCCEEEECCCCCCCEEEECCCCCCCCCCCCCCCHHHHCCCCCCHHHCCHHHHHHHHHCCEEEEEECCHHHCCCEEEEC--CCEEEEEEEEEECCCCCEEEEEEEEECCCEEEEEEECCCCEEEEEEEECCCCCCCCCEEEECCCCCCCEEEEECCCCEEEEECC----- >P1;d1q47a- CCCCCCCCCCHHHHHCCCCCEEECCCCCCCCCCEEEEECCCCEEEEEECCEEEEEECCCCCCE-EEEECCCC---------------HHHHHHHHHCCCCCCCCCCCCEEEEEECC-CCEEEEEECCCCCCEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCEEEEECCEEEEEEECC---CCCCCEEEEEEEC------CCCCEECCCCCCCCCCCCEEEEEEEECCCCCHHHCEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEEEECCCEECCCCCCCEECCEEEEEEEECCCCC--------CCCEEEEEEECCCC--CCCCEEEEEECHHHHHHHHC-CCCEECCCC---CCCCEECCCCCCCCCCCCCCCCC--CCCCCCHHHCCHHHHHHHHCCCCCCCCCCCHHHCCCEEECCCCCCEEEEEEEEEECCC-CEEEEEEEEECCCCEEEEEC-----CCCEEECCCCCCCCCCEEEEECC--CCEEEEECCCCEEEEECCCCCCC >P1;d6wvzm1 -----------------CCCCEEC----CCCEEEEEEC---CCEEEEECCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-----------------CCCCEEEEEEECCCCEEEEEECC--CCCEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCC-CEEEEECCCCEEEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCC--CCCEEEEEEEEC-------CEEEEEEEECCCC-----CCCEEEEEEEECCC-----------EEEEEEEECCC--------CCCCEEEEEEEECCHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCEEEEEECC-HHHHHHHCCCCEECCCCCCCCCCCC------------------------------CCCCCCCCCCCEECCCCCCC---CCCCCCCCCCCCEEEEEEECC-------CEEEEEEEC-CEEEEEEECCCCCCCCEEEECCC-CCCCCCCEEEC--CCCCEEEEECCCEEEEEC------ PSA >P1;d1olza2 30590745351842----90140517-905201202117745100000110000020640463463131607---------------77414502859263862010000002527-861000000100500002031----85--0715-8573703110011082430010066300000032---280752001061b------a2-303023-56300160601202104654-95212000000010204a68761300000000280400672067100000000030137-a3a--160110410200509a6--------9412000000022b--2a12000000505403710571500323579a8937044176930912004013791386a26304503570051035100014204036760200059--1502200012464b855431100000460100101449a8130312120066534041031054a9941000003300000417----- >P1;d1q47a- a5570517151850573b00210702b903103202113914100000200000030750672-54050418---------------a8236604839255982000101002626-92100000000040100203036749663070379725607000002091700020275000000003---4716100010014------826401015625400250300202203259383311000002021365899b851201000002302008870532000000020000252aaa83630120210301a2a57--------2402000000254b--89500000203064028107-430121657---968263287a3171200400078--a1b154047049700810441020452050388502130581a1201100013574a8-95421000003400000024-----b0302030064635030030058--35200000530000010447736 >P1;d6wvzm1 -----------------7b15537----0460220214---9300000115010020637223432528705264827741a29c6a-----------------66150100102657410000111--5000221416c7707261014549a98a310100034-60202134410100011658227540200002378710513750403047397--040702201416-------b100000004525-----85210000002000-----------32030000029--------6802002002120063007219076b250000000319573246300000003-402630685c3400002123b451d------------------------------99453558150100883083---40004250184101000003d-------601000003-03000030149587153416039-66034302045--c6a110000052002060------ Translating the sequences CCCCCC***C****----CCEEECCC-CCCCCCEEEECCCCCEEEEE*CCEEEEEECC****E*EEEECCCC---------------HHHHHHHHHCCCCCCCCCCCCEEEEEECC-CCEEEEEECCCCCCEEEEEEC----CC--CEEC-CCCEECCCCCCCCCCCCEEEEEECCEEEEEEECC---CCCCCEEEEEECC------CC-CCCCCC-CCCCCCCCEEEEEEEECCCC-***CEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEEEEECCEE*-**C--EECCEEEEEEEECCCCC--------CCCEEEEEEECCCC--CCC*EEEEEE*HHHHHHHHH*CCCEE**CCCCCCC**EECCCCCCCCCCCCCCC****CCCCCCHHHCCHHHHHHHH*CCE*****CCHHHCCCEEE*C--CCEEEEEEEEEECCC*CEEEEEEEEECCCEEEEEEECCCC****EEEECCCCCCCCCEEEE*CC*CCCEEEEECCCCEEEEECC----- CCCCCC***C*******CCCEEECCC*CCCCCCEEEE*CCCCEEEEEECCEEEEEECCCCCCE-EEEECCCC---------------HHHHHHHHHCCCCCCCCCCCCEEEEEECC-CCEEEEEECCCCCCEEEEEECCCCCCCC*CEE*****EECCCCCCCCCCCC*EEEEECCEEEEEEECC---CCCCCEEEEEE*C------CCCC**CCCCCCCCCCCCEEEEEEEECCCC****CEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEEEE*CCEE****C**EECCEEEEEEEECCCCC--------CCCEEEEEEECCCC--CCCCEEEEEECHHHHHHHH*-CCCEECCCC---CCCCEECCCCCCCCCCCCCCC**--CCCCCCHHHCCHHHHHHHHCCC*CCCCCCCHHHCCCEEECCCCCCEEEEEEEEEECCC-CEEEEEEEEECCC*EEEEE*-----CCCEEE*CCCCCCCCCEEEEECC--CCEEEEECCCCEEEEECC***** -----------------CCC*EEC----CCC**EEEEC---C*EEEEECCEEEEE*CCCCCC******CCCC***************-----------------CCCCEEEEEE*C*CCEEEEEECC--CC*EEEEECCCCCCCC**E*C*CCC**CCCCCCCCCC-CEEEEE*CC*EEEEE*CC***CCCCC***EE*CC******CCCCCCCCCCCCC--CCCEEEEEEEEC-------CEEEEEEEE*CCC-----CC*EEEEEEEECCC-----------***EEEEECC*--------**CCEEEEEEEECC***********CCCEEEEEEECCCC**CCCCEEEEEEC*-HHHHHHH*CCCEECCCCCCCCCCC*------------------------------C********CC*ECCCCCCC---CCC***CCCCCCEEEEEEE**-------*EEEEEEEC-CEEEEEEECCCC*CCCEEEECCC-CCCCC**EEEC--CCC*EEEE*CCCEEEEEC------ 101912.tem _________________________________ CCCCCC***C****---CCCEEECCC-CCCCCCEEEECCCCCEEEEEECCEEEEEECCCCCCE*EEEECCCC---------------HHHHHHHHHCCCCCCCCCCCCEEEEEECC-CCEEEEEECCCCCCEEEEEECCCCCCCC*CEEC*CCCEECCCCCCCCCCCCEEEEEECCEEEEEEECC---CCCCCEEEEEECC------CCCCCCCCCCCCCCCCCCEEEEEEEECCCC-***CEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEEEEECCEE*-**C--EECCEEEEEEEECCCCC--------CCCEEEEEEECCCC--CCCCEEEEEECHHHHHHHHH*CCCEECCCCCCCCCCCEECCCCCCCCCCCCCCC**--CCCCCCHHHCCHHHHHHHHCCCECCCCCCCHHHCCCEEECCCCCCEEEEEEEEEECCC-CEEEEEEEEECCCEEEEEEECCCC*CCCEEEECCCCCCCCCEEEEECC-CCCEEEEECCCCEEEEECC----- Structural block scores 0 5 C 4.0 M 4.0 5.4 75.0 6 8 * 2.7 P 4.0 3.0 75.0 10 13 * 2.7 P 3.8 3.5 75.0 14 16 - 4.0 M 75.0 5.0 75.0 17 19 C 4.7 H 28.0 3.8 6.5 20 22 E 4.7 H 1.7 1.0 4.3 23 25 C 4.3 M 4.3 3.0 52.3 27 32 C 4.5 M 2.8 2.7 14.5 33 36 E 5.0 H 1.2 1.2 1.2 37 41 C 4.2 M 4.8 3.6 47.6 42 47 E 4.7 H 0.2 0.2 0.5 48 49 C 5.0 H 1.0 1.0 1.0 50 55 E 4.8 H 0.3 0.5 1.3 56 61 C 4.3 M 3.3 4.2 3.3 64 67 E 4.0 M 3.2 3.5 3.0 68 71 C 5.0 H 3.5 3.2 5.0 72 86 - 4.0 M 75.0 75.0 6.1 87 95 H 4.0 M 4.2 5.3 75.0 96 107 C 4.3 M 3.5 3.7 51.5 108 113 E 5.0 H 1.2 1.5 0.3 114 115 C 4.5 M 4.5 4.0 4.0 117 118 C 5.0 H 7.0 5.5 5.5 119 124 E 5.0 H 0.2 0.2 0.3 125 130 C 4.7 H 1.0 0.7 26.2 131 136 E 4.8 H 0.8 1.0 1.5 137 144 C 4.4 M 48.6 5.1 5.3 147 148 E 4.5 M 4.0 3.5 0.5 151 153 C 4.0 M 6.7 6.0 7.8 154 155 E 4.0 M 5.0 5.5 8.5 156 167 C 4.9 H 1.8 2.2 8.6 168 173 E 4.7 H 0.7 0.7 1.3 174 175 C 5.0 H 6.0 6.0 4.0 176 182 E 4.7 H 0.4 0.0 0.4 183 184 C 5.0 H 2.5 1.5 3.5 185 187 - 4.0 M 75.0 75.0 5.0 188 192 C 5.0 H 4.4 3.8 3.6 193 198 E 4.3 M 1.5 0.2 0.7 199 200 C 4.5 M 6.2 2.5 5.0 201 206 - 4.0 M 75.0 75.0 3.7 207 224 C 4.7 H 10.8 2.8 11.4 225 232 E 5.0 H 1.5 1.1 2.1 233 236 C 4.2 M 4.8 4.8 57.8 238 240 * 2.7 P 5.3 4.7 75.0 242 250 E 4.9 H 0.3 0.6 0.6 251 260 C 4.5 M 4.5 6.5 40.0 261 269 E 4.9 H 0.3 0.4 0.6 270 286 C 4.2 M 2.5 2.4 48.8 287 291 E 4.8 H 0.0 0.4 0.6 292 293 C 5.0 H 1.5 0.0 1.0 294 295 E 4.0 M 2.0 1.0 42.0 298 299 * 2.7 P 6.8 10.5 75.0 301 302 - 4.0 M 75.0 5.5 75.0 303 304 E 4.0 M 3.5 4.5 7.0 305 306 C 5.0 H 0.5 0.5 1.0 307 314 E 5.0 H 1.0 1.1 0.9 315 319 C 4.4 M 6.1 7.0 1.8 320 327 - 4.0 M 75.0 75.0 4.0 328 330 C 5.0 H 4.7 2.0 6.2 331 337 E 5.0 H 0.3 0.3 0.0 338 341 C 5.0 H 3.9 5.6 4.5 342 343 - 4.0 M 75.0 75.0 5.0 344 347 C 4.8 H 3.9 5.5 3.8 348 353 E 5.0 H 0.0 0.3 0.0 355 363 H 4.7 H 2.8 3.1 11.0 365 367 C 5.0 H 2.0 2.3 6.8 368 369 E 5.0 H 1.5 1.5 2.0 370 380 C 4.4 M 5.8 24.5 2.7 381 382 E 4.0 M 4.0 4.5 44.2 383 397 C 4.0 M 3.1 3.0 75.0 398 399 * 2.7 P 8.0 7.5 75.0 400 401 - 4.0 M 2.0 75.0 75.0 402 407 C 4.0 M 5.9 5.5 75.0 408 410 H 4.0 M 3.0 3.7 75.0 411 412 C 4.5 M 1.5 2.0 42.0 413 420 H 4.0 M 2.6 3.6 5.0 421 423 C 4.3 M 2.0 1.7 2.0 425 431 C 4.3 M 1.6 2.3 4.3 432 434 H 4.0 M 5.3 6.3 75.0 435 437 C 5.0 H 2.7 2.3 1.3 438 440 E 4.0 M 0.0 1.3 2.0 441 446 C 4.5 M 28.3 4.6 3.2 447 456 E 4.7 H 1.7 1.8 9.2 457 459 C 4.0 M 7.8 7.5 75.0 462 470 E 4.8 H 1.0 1.3 9.1 471 473 C 4.7 H 3.3 2.3 26.0 474 480 E 4.7 H 1.0 0.9 0.9 481 484 C 4.0 M 7.9 75.0 4.8 486 488 C 4.0 M 2.0 4.8 4.3 489 492 E 4.8 H 1.5 1.2 3.5 493 501 C 4.9 H 3.1 3.0 11.8 502 506 E 4.4 M 1.0 0.6 1.8 507 508 C 4.5 M 4.5 6.5 40.0 510 512 C 4.7 H 7.3 27.7 9.7 513 517 E 4.8 H 0.2 0.4 0.4 518 521 C 4.8 H 1.5 2.0 1.8 522 526 E 5.0 H 0.8 0.2 1.6 527 528 C 4.5 M 4.0 2.0 37.5 529 533 - 4.0 M 75.0 5.4 75.0 >>>>>>