Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2fffb1 CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCHHHHHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHCHHHHHHCC-CCCCCCEEECCCCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC-------CCCCCCC------CCCCCEEE-----HHHHHHHCCCHHHHHHHHHHHHC-----------CCCHHHHHHHCCCCCCCCCCCCHHHCC-CCCCCHHHHHHHHHHHHCCCEECCCCCEEEEECCCCCEEEECCCCCEECCCHHHHHHHHHHHHHHHHH-CCCCCHHHHHHHHCHHHHCCCCEEEEEECCCCCEEEEEEECC-----CEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEECCCCEEEECCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCC >P1;d2y5oa- ---------------------------------------------------------CHHHHHHHHHHHCCC--HHHC----CCEEEEEEEECCCCCEEEEECCC------------CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCEECCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCCCCHHHCCCHHHCCCCCCCCEECCCCEECEEEEEEE-CCCCCCCCEEECHHHCCCCEEEECCEEECCCCCCCCEEECCC-CCCEEEEECEEECCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCEECCCEEECCCCCCCCCCEEEEEEECCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC---------------------------------CCCHHHHHHCCCCCCCCCHHHHHHHCCC--CCCCCCCCCCEEEEEEEC--CEEEEEEEECCCC-CCEEEEEEEECCCC-----CCCHHHHHHHHHHHHHHHCCCCCC------------------------------------------------------------------------------- >P1;d3a3da1 ---------------------------------------------------------------CCHHHHHC---CCCC----CCEEEEEEEECCCCEEEEEECCC------------CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCEECCEECCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCCCCHHHCCCHHHCCCCCCCC----HH--HEEEEEEECCCCCCCCCEEECCCCC-CCEEECCCEEECCCCHHHCCEEEEEECCCEEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCEECCCEECCC---CCCCCEEEEEEECCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH---------------------------------CHHHHCCHHHCCCCCC-----CHHHCCCHHHCCCCCCCCCEEEEEEEC--CEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHC---------------------------------------------------------------------------------- PSA >P1;d2fffb1 50376123520372026300654791696395981467075204611785a0814210498006203700664072031b39600000000305401010000004387366100173512001000000000000131-3000300000152628--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------88-------730335a------47064103-----05500141120000100410466-----------a08054104606090871433300106-70601001000000000150210720003202167a84125386844400540000000410360033-432030152058226a0091100000042b821000000001-----50000000004767503670053100400010023026226b201b580832970360600650014346071aa962706a8234030018800570746001006a71078008814bb >P1;d2y5oa- ---------------------------------------------------------639604740472084--8509----b0510000223777650024509------------5402001000000000002104383206030006850a96120830000040000036920470055028390810423030016404751208506572204250000000000488433000040305-0476866080605405a1083427050246a59570704037-b42202055300262943422100430020001102510472a0404391736223b90aa24300636055038003000011110000000000015457-4030a20181047104a180808305030000103603000500140043048---------------------------------0801930270002003764340040191--047300231020010429--4000000003066-24000000018097-----90049002400210041043934c------------------------------------------------------------------------------- >P1;d3a3da1 ---------------------------------------------------------------08057117---501b----b0600000103548630053306------------54010010000000000021063a23040001072724a3204550002020002052a4037002405739063044200011220568350620496311635000000000----46--0105030405384965061513a61-007042704006ab516907161534a70302056015337963215000150240003003400870906083824327---75190640132406303500640006121000000000003423864010610270033005745070ca05020000003604000510050031008---------------------------------13a7050170003004-----414048050036730272020000427--300000000504472400000002907186896a27582025005400250266---------------------------------------------------------------------------------- Translating the sequences *********************************************************C*HHHHHHHHHHH****HHHC****CCEEEEEEEECCCCCEEEEECCC************CCCCCHHHHHHHH*HHHHHHCC-CCCC**EEE*CCCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC-------*CCCCCC------*****E**-----HHHHHHHCC*HHHHHHHHHHHH*-----------***HHHHHHHCCCCCCCCCCCC***CC-CCCCCHHHHHHHHHHHHC**********************************HHHHHHHHH*******-***C*HH***HHHC****CCCCEEEEEE*C**CEEEEEEE*C-----CEEEEEEEECCCCCCCCCCCCC*HHHHHHHHHHHHHHH*CCC******************************************************************************* ---------------------------------------------------------C*HHHHHHHHHH*C*--HHHC----CCEEEEEEEECCCCCEEEEECCC------------CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC*E*CCEEEE*CCCCCCCHHHHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCCCCHHHCCCHHHCCCCCCCC*********EEEEEEE-CCCCCCCCEEEC***C*CCEEE*CCEEECCCC***C*EE***-CCCEEEEE*EEECCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCEECCCEE*CCCCCCCCCCEEEEEEECCCHHHHHHHHHH*CCHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHH*CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC---------------------------------C**HHHHHH*CCCCCC******HHHCCC--*CCCCCCCCCEEEEEEEC--CEEEEEEEECCCC-CCEEEEEEEECCCC-----CCC*HHHHHHHHHHHHHH**CCCC------------------------------------------------------------------------------- ---------------------------------------------------------------**HHHHHC---***C----CCEEEEEEEECCCC*EEEEECCC------------CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCC**CC*E*CCEEEE*CCCCCCCHHHHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCCCCHHHCCCHHHCCCCCCCC----**--*EEEEEEE*CCCCCCCCEEEC***C-CCEEE*CCEEECCCC***C*EE****CCCEEEEE*EEECCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCEECCCEECCC---CCCCCEEEEEEECCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHC*CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH*---------------------------------CHHHH**HHHCCCCCC-----CHHHCCCHHHCCCCCCCCCEEEEEEEC--CEEEEEEEE*CCC*C*EEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHC---------------------------------------------------------------------------------- 56601-3.tem _________________________________ ---------------------------------------------------------C*HHHHHHHHHHHC*--HHHC----CCEEEEEEEECCCCCEEEEECCC------------CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC*E*CCEEEE*CCCCCCCHHHHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCCCCHHHCCCHHHCCCCCCCC----**--*EEEEEEE-CCCCCCCCEEEC***C-CCEEE*CCEEECCCC***C*EE***-CCCEEEEE*EEECCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCEECCCEECCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC---------------------------------CHHHHHHHHHCCCCCC*-***CHHHCCCHHHCCCCCCCCCEEEEEEEC--CEEEEEEEECCCC-CCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC------------------------------------------------------------------------------- Structural block scores 0 56 - 4.0 M 4.1 75.0 75.0 59 69 H 4.4 M 3.2 3.9 29.3 72 73 - 4.0 M 2.0 75.0 75.0 74 76 H 4.0 M 3.0 4.3 2.0 78 81 - 4.0 M 6.1 75.0 75.0 82 83 C 5.0 H 3.0 5.8 5.8 84 91 E 5.0 H 0.4 1.2 0.9 92 96 C 4.8 H 2.0 6.0 5.2 97 101 E 5.0 H 0.2 2.2 2.2 102 104 C 5.0 H 0.0 4.7 3.0 105 116 - 4.0 M 3.8 75.0 75.0 117 121 C 5.0 H 2.2 2.2 2.0 122 136 H 4.9 H 0.1 0.3 0.3 137 143 C 4.9 H 11.7 2.9 3.5 144 149 E 4.5 M 0.5 1.5 0.8 150 156 C 4.6 H 14.1 6.4 5.1 160 161 C 4.0 M 75.0 5.5 5.0 162 165 E 4.0 M 75.0 0.0 0.5 167 173 C 4.0 M 75.0 1.0 1.3 174 186 H 4.0 M 75.0 3.7 3.4 187 190 C 4.0 M 75.0 5.0 4.5 191 192 E 4.0 M 75.0 0.5 1.5 193 195 C 4.0 M 75.0 3.0 3.3 196 199 E 4.0 M 75.0 0.8 0.2 200 213 C 4.0 M 75.0 3.5 3.1 214 216 H 4.0 M 75.0 4.7 6.0 217 219 C 4.0 M 75.0 2.0 2.7 220 222 H 4.0 M 75.0 2.3 2.7 223 230 C 4.0 M 75.0 0.0 0.0 231 234 - 4.0 M 75.0 5.0 75.0 235 236 * 2.7 P 75.0 3.5 5.0 237 238 - 4.0 M 75.0 1.5 75.0 240 246 E 4.0 M 75.0 1.7 1.9 248 255 C 4.0 M 75.0 4.6 5.0 256 258 E 4.0 M 75.0 4.7 4.0 260 262 * 2.7 P 75.0 3.0 6.5 265 266 C 4.0 M 75.0 0.5 0.0 267 269 E 4.0 M 75.0 5.0 3.7 271 272 C 4.0 M 75.0 3.5 3.5 273 275 E 4.0 M 75.0 2.3 1.3 276 279 C 4.0 M 75.0 6.4 8.2 280 282 * 2.7 P 75.0 7.0 5.3 285 286 E 4.0 M 75.0 2.0 3.5 287 289 * 2.7 P 75.0 3.3 3.0 291 293 C 4.0 M 75.0 5.8 5.8 294 298 E 4.0 M 75.0 1.8 2.0 300 302 E 4.0 M 75.0 1.0 2.0 303 307 C 4.0 M 75.0 4.6 5.6 308 313 E 4.0 M 75.0 2.0 1.8 314 316 C 4.0 M 75.0 2.3 2.0 317 331 H 4.0 M 75.0 1.5 2.1 332 334 C 4.7 H 30.3 4.2 3.0 335 336 E 4.0 M 75.0 2.0 3.0 337 339 C 4.0 M 75.0 5.3 6.3 340 341 E 4.0 M 41.0 4.0 3.0 342 352 C 4.2 M 36.3 5.4 23.5 353 359 E 4.1 M 13.9 3.1 2.9 360 362 C 4.0 M 26.0 3.3 3.0 363 373 H 4.5 M 28.6 1.4 2.2 374 375 C 5.0 H 1.0 1.0 1.5 376 391 H 4.8 H 10.9 1.0 0.8 394 396 C 4.0 M 75.0 2.3 1.7 397 410 H 4.5 M 24.2 3.5 2.4 411 433 C 4.8 H 6.1 2.1 2.6 434 445 H 5.0 H 0.1 1.8 1.2 447 479 - 4.0 M 3.3 75.0 75.0 481 489 H 4.4 M 0.6 3.3 3.7 490 495 C 4.0 M 2.0 0.8 1.2 498 500 * 2.7 P 3.0 3.7 75.0 502 504 H 4.7 H 1.3 1.3 1.7 505 507 C 4.0 M 2.3 3.7 4.0 508 510 H 4.0 M 5.0 50.0 1.7 511 519 C 4.6 H 3.3 2.2 3.3 520 526 E 4.9 H 0.9 1.3 1.1 528 529 - 4.0 M 5.0 75.0 75.0 531 538 E 4.9 H 0.0 0.0 0.0 539 542 C 4.0 M 56.5 3.8 3.2 544 545 C 4.0 M 40.0 3.0 3.0 546 553 E 5.0 H 0.0 0.1 0.2 554 566 C 4.5 M 3.8 31.7 6.0 567 582 H 4.8 H 1.4 1.9 2.6 583 586 C 4.0 M 5.4 7.1 57.8 587 665 - 4.0 M 4.1 75.0 75.0 >>>>>>