Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2dg1a2 CCCCCCCCCHHHHCCCCCCCHH--------HCCEEECEEEEEEE-C---CCCCEEEEEECC-CCCEEEEECC-------CCEEEEECCCCCCEEEEEECC----C---CCEEEEEECCC---CCEEEEECCCCCCCCEEEEECCCC-----CCCEEEECCCC---CCCCEEEEEECCCCCEEEEECCCC---------C--CCCCEEEEEECCCCCCEEEEEE--EEC-------CEEEEEECC----CCCEEEEEEHHHCEEEEEEECCCCCCEEEEEEEEEEECCC---CCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC-CC-CEEEEEECCCHHHCCCCCCCEEEECCC---CCEEEEEEECHHHC------------CCEEEEEEE-CCCCCCCCHHHC------ >P1;d2ghsa1 -------------------------------CEEECCCCEEEE--C---CCCCEEEEEEECCCCEEEEEEHHH-------CEEEEEECCCC-CEE-EECC---------CCCEEEEEE---CCEEEEEEC------CEEEEEECCCC-----CEEEEECCCCCCC-CCCCCCEE-CCCCCEEEEE-CCCCC-----------CCCEEEEEEE-CC-EEEEEEE--EEC-------CEEEEEECC----CCCEEEEEEC-CCEE-CEECCCCCCCCCC-CCCCCEECC--CCCCC-CCEEECC-CCCEEEECC-CC------------CEEEEECC--CCCEEEEEECC-------CCEEEEEEECC--CCCEEEEEECCCCCC----HHHHHHCCCCCCEEECCC-CCCCCCCCCCCC----- >P1;d2p4oa1 -------------CCCCCCCCC--------CCCCCCCCEEEEEEEC---CCCCEEEEEECC-CCCEEEEECC-------CCEEEEEC----CCCCCEECC--------CEEEEEEEC-----CCEEEEEECC-CCCEEEEEECCCC-----C-EEEEEECC----CCCCEEEEEECCCCEEEEEECC-----------------CCEEEEEECCCCEEEEEEECCCCCCCCCCCCCEEEEEEEC------CEEEEEECCC-CEEEEECCCCC-CCC--CCEEEEC------CCCCCCEEECC-CCCEEEEC-HHH------------CCEEEECC-CC--CEEEEECH---HHCCCCEEEEEECCCCCCCCEEEEEECCCCCCCCC-------CCCCEEEEEEE-CCCCCCCCC--------- >P1;d3o4pa- ------------------------------CCCEECCCCEEEEC-----CCCCCEEEEECC-CCCEEEEECCCEECCEECCEEEEECCCCCCEEEEECCEECCEE---CCEEEEEECCC-C-CEEEEEECC-----CEEEEEECCC-----C-EEECCCCCCCCCCCCCCCEEEECCCCCEEEEECCCCCCCCCCCCCC--CCCCEEEEEECCCC-CEEEEEE--EEC-------CEEEEEEEECCCCCEEEEEEEECCCCEEEEEEEEE-CCEEE--EEEEEEECCCC-CCCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC-CCCCCCEEEECCC------CCEEEEEECCC---CCEEEEEEC--CC---------------CEEEEEE-CCCCCCCCHHHCCCCCCC >P1;d3srea- ----------------CCCHHHHHCCCCCCCCCCCCCCEEECCCC------CCCCEEEECC-CCEEEEEECC-------CCEEEEEECCCCCEEECCEE-CCCCCHHHCCEEEEEEEECCCCEEEEEEECCC--CCCEEEEEEEC-----CCEEECCCC-----CCCCCEEEEEEC-CCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECC--CCCEEEE---EEC-------CEEEEEECC----CCCEEEEEECCCCEEEEEEECCCC-CEEE----CCEEC-----CCEEEEEEECCCCCCEEEEEECCHHHHHCCCCCCCCEEEEEECCCC-CCCEEEEEECCC---CCCCEEEEECCC------CCEEEECC------------------CCEEEECC------------------ >P1;d5gtqa- -----------------------------------CCEEEEC---HHHCCCCCEEEEEEECCCCEEEEEECCC-------CEEEEEEHHHCEEEE-EECC--------CCCCCEEECCC-CCCEEEEEEC------CEEEEEECCCCCCCCCEEEEEEECCCCCC-CEEEEEEEECCCCCEEEEEEECCCCCCC-------CCCCEEEEEECHHH-CEEEEEE--EEC-------CEEEEEECC----CCCEEEEEEHHHCEEEEEEEECCCCEE-E-EEEEEEEHHHHCCCCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECCCCCCCEEEEEECC------CCCEEEEEEECC--CCCEEEEEECCCCCCCCCCC--HHHCC--CCCEEEECCCCCCCCCCCCCC----- PSA >P1;d2dg1a2 7b2220747c5075650a1729--------60221505511303-9---610100000015-9420000005-------501011040973725411404----2---71000010145---820000000658430000003470-----79354005178---551000002005710000002116---------6--9435000010237187244015--900-------000000012----723100000033230030104a6336247a2252117078---84000001004-520000001-10------------00000015-50-400000303428754122000010118---3400000000244a------------500200000-002603650014------ >P1;d2ghsa1 -------------------------------175472816101--8---634020301023565000001035-------63002051977-254-2906---------000002205---872000002------50012032863-----7174117011a58-b1201001-0310000000-04946-----------9330001003-61-8154024--802-------400000013----7052001011-6140-4030539504167-833511514--b7722-0000005-711000002-51------------20002026--80733020402-------01000000019--801400000022828----994288464100001033-507033335075----- >P1;d2p4oa1 -------------3bc168106--------a364741707401408---4a0100000007-8220100105-------50200307----822510509--------330000022-----a200001338-9530101104781-----7-16501416----806100000005b430000002-----------------2000010106625062015370416892973000001229------9300000113-10020306a83-517--8055016------80100000004-60100000-121------------10002035-84--70100033---822000000010043bb053000000000634079-------74350000304-07340274f--------- >P1;d3o4pa- ------------------------------2353371a063005-----904000000003-9640000006256c8821010020629618273004062b941---01000000115-5-220100000-----0000104370-----8-1801176036757010010000016000000000250074a37403--a8540000010676-5021035--602-------0000000004c756042000000121301004055-50707--8363005017b-2a1000001004-621000003-11------------20000024-a086051105040------53000000328---451000001--47---------------5001307-05230252002395929c >P1;d3srea- ----------------b8974581011817096480671831906------9000003006-6000000121-------a0400103056191850814-4b708785040100003348a2110000022c--55000010304-----620304227-----440100000001-133000000153556852660145333501000115--b413402---902-------100002203----747200000002140101414b94-3057----44170-----8000000102695200000000004102547772000000304804-733631001808---502000001117------70000023------------------13002063------------------ >P1;d5gtqa- -----------------------------------a281540---9409502100101002973001000045-------310010118665315-0609--------4200000002c-3973000003------13000030616646077454033004959-6000110300340200000103707179-------34440100002895-5145125--901-------100000019----727100000013320010406296260-8-83440010762a041100001104-751000001-10------------220010009762323630705------000000010006--81420000000444a81829--79504--0100104a0c04044443061----- Translating the sequences **********************--------*CC***C*EEEEE*-*---CCCCEEEEEECC-CC*EEEEECC-------CCEEEEE*CCCCCEEE*EECC----*---CCEEEEEEC*C---C*EEEEECC*****CEEEEE*CCC-----C**EEEECCCC---CCCCEEEEEECCCCCEEEEECCCC---------*--CCCCEEEEEECCCC*CEEEEEE--EEC-------CEEEEEECC----CCCEEEEEE***CEEEEEEECCCCCCE*****EEEEEC**---CCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC-CC-C*EEEEECC******CCC**EEEECCC---CCEEEEEE*C***C------------****EEEEE-CCCCCCCC***C------ -------------------------------C***CCC*EEEE--*---CCCCEEEEEE*C*CC*EEEEE***-------CEEEEE*CCCC-*EE-EECC---------C**EEEE**---*CEEEEEEC------CEEEEEECCC*-----*EEEEECCCC**C-CCC***EE-CCCCCEEEEE-CCCCC-----------CCCEEEEEE*-CC-*EEEEEE--EEC-------CEEEEEECC----CCCEEEEEEC-CCEE-*EE*CCCCCC***-*****EEC*--**CC*-**EEECC-CCCEEEE**-CC------------CEEEEECC--CCC*EEEEECC-------CCEEEEEE*CC--*CCEEEEEECC*CCC----**********C*EEE***-CCCCCCC***C*----- -------------*********--------*CC**CCCEEEEE***---CCCCEEEEEECC-CC*EEEEECC-------CCEEEEE*----C****EECC--------C*EEEEEEC-----C*EEEEE*C*-****EEEEE*CCC-----C-EEEEE*CC----CCCCEEEEEECCCC*EEEEECC-----------------C*EEEEE*CCC**EEEEEE****C*******CEEEEEE*C------CEEEEEEC*C-*EEEEE*CCCC-C**--**EEEE*------CC****EEECC-CCCEEEE*-***------------C*EEEECC-CC--*EEEEEC*---***CCCEEEEEECCC***CCEEEEEECC*CCC***-------******EEEEE-CCCCCCCC*--------- ------------------------------*CC**CCC*EEEE*-----CCCC*EEEEECC-CC*EEEEECC*******CCEEEEE*CCCCCEEE*E*C******---CCEEEEEEC*C-*-CEEEEEECC-----CEEEEEECCC-----C-EEE**CCCC**CCCCC**EEEECCCCCEEEEECCCCCC********--CCCCEEEEEECCCC-CEEEEEE--EEC-------CEEEEEE******C**EEEEEEC*CCEEEEEEE**-CC*E*--**EEEEEC***-*CCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC-CCCC**EEEECC*------CCEEEEEECCC---CCEEEEEEC--CC---------------C*EEEEE-CCCCCCCC***C****** ----------------***************CC**CCCEEE****------CC**EEEECC-CC*EEEEECC-------CCEEEEE*CCCCCEEE**E*-********CCEEEEEE**C****EEEEEECC*--**CEEEEEE*C-----*C*EE***C-----CCCCCEEEEEEC-CCCEEEEECCCCCC**********CCCCEEEEEECC--*C*EEEE---EEC-------CEEEEEECC----CCCEEEEEEC*CCEEEEEEECCCC-CE**----**EEC-----CCEEEEEEECC*CCCEEEEEE*C**************EEEEECC*C-CC*EEEEE*C**---*CCCEEEEE*CC------**EEEECC------------------C*EEEE**------------------ -----------------------------------CC*EEE*---****CCCCEEEEEE*C*CC*EEEEECC*-------CEEEEE****C*EEE-EECC--------CC***EEEC*C-**CEEEEEEC------CEEEEEECCC*****C*EEEEE*CCC**C-C**EEEEEECCCCCEEEEE**CCCC***-------CCCCEEEEEEC***-CEEEEEE--EEC-------CEEEEEECC----CCCEEEEEE***CEEEEEEE*CCCC*E-*-**EEEEE******CCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC*CCCC*EEEEECC------CCCEEEEEE*CC--*CCEEEEEECC*CCC*****--*****--C**EEEE*CCCCCCCC***C*----- 63829.tem _________________________________ ----------------******--------*CC**CCCEEEEE*-*---CCCCEEEEEECC-CC*EEEEECC*------CCEEEEE*CCCCCEEE*EECC----*---CCEEEEEEC*C-**CEEEEEECC*--**CEEEEEECCC-----C*EEEEECCCC**CCCCCEEEEEECCCCCEEEEECCCCCC***----*--CCCCEEEEEECCCC*CEEEEEE--EEC-------CEEEEEECC----CCCEEEEEEC*CCEEEEEEECCCCCCE**-**EEEEEC**--*CCEEEEEEECC-CCCEEEEEE-CC------------CEEEEECC-CCCC*EEEEECC*----*CCCEEEEEECCC--*CCEEEEEECC*CCC----------****C*EEEEE*CCCCCCCC***C*----- Structural block scores 0 15 - 4.4 M 5.2 75.0 62.6 75.0 75.0 75.0 16 21 * 3.4 M 4.9 75.0 3.7 75.0 7.4 75.0 22 29 - 4.5 M 75.0 75.0 75.0 75.0 3.4 75.0 31 32 C 4.3 M 1.0 4.0 4.5 4.0 7.5 75.0 33 34 * 1.9 P 1.5 4.5 5.5 3.0 6.0 75.0 35 37 C 4.5 M 3.3 5.7 4.0 6.2 4.3 6.8 38 42 E 4.5 M 2.0 1.8 2.4 1.8 4.4 17.0 46 48 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.3 49 52 C 4.8 H 2.0 3.2 3.9 3.2 39.8 2.0 53 58 E 4.8 H 0.0 1.0 0.0 0.0 0.5 0.3 59 60 C 4.5 M 3.0 2.5 3.5 1.5 3.0 1.0 62 63 C 5.0 H 6.5 5.5 5.0 7.5 3.0 5.0 65 69 E 5.0 H 0.0 0.2 0.4 0.0 0.2 0.2 70 71 C 4.5 M 2.5 1.5 2.5 3.0 1.5 2.0 73 78 - 4.5 M 75.0 75.0 75.0 6.9 75.0 75.0 79 80 C 4.7 H 2.5 40.5 2.5 0.5 5.2 39.0 81 85 E 5.0 H 0.6 1.0 1.0 0.6 1.0 0.4 87 91 C 4.3 M 5.2 19.8 61.6 5.2 4.2 5.2 92 94 E 4.4 M 3.7 3.7 3.0 4.0 4.7 3.0 96 97 E 4.5 M 2.5 5.5 2.5 2.0 4.5 3.0 98 99 C 4.3 M 2.0 3.0 4.5 3.0 39.5 4.5 100 103 - 4.1 M 75.0 75.0 75.0 6.6 5.6 75.0 105 107 - 4.5 M 75.0 75.0 75.0 75.0 6.7 75.0 108 109 C 4.5 M 4.0 37.5 3.0 0.5 2.0 3.0 110 115 E 4.6 H 0.2 0.7 0.3 0.0 0.2 0.0 120 121 * 3.4 M 75.0 41.5 75.0 40.0 6.2 6.0 123 128 E 4.9 H 0.3 0.3 0.5 0.5 0.2 0.5 129 130 C 4.4 M 0.0 38.5 3.0 0.0 2.0 39.0 132 133 - 4.3 M 6.5 75.0 42.0 75.0 75.0 75.0 134 135 * 3.4 M 3.5 75.0 4.0 75.0 5.0 75.0 137 142 E 4.9 H 0.5 1.0 1.2 0.8 0.7 1.0 143 145 C 4.7 H 3.7 5.3 5.3 3.3 26.3 2.3 146 150 - 4.3 M 75.0 60.6 75.0 75.0 61.2 4.4 153 157 E 4.4 M 2.4 2.8 2.6 2.2 2.2 3.2 158 161 C 4.3 M 5.2 2.2 21.5 4.0 58.0 1.8 162 163 * 3.4 M 75.0 7.8 75.0 6.5 75.0 7.0 164 168 C 4.5 M 17.2 19.5 18.0 2.6 1.8 18.0 169 174 E 4.5 M 0.3 12.8 0.0 0.2 0.0 0.8 175 179 C 4.8 H 2.6 0.8 4.7 1.4 16.6 1.8 180 184 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 185 190 C 4.4 M 26.7 16.3 50.3 1.2 3.2 3.0 191 193 * 3.4 M 75.0 75.0 75.0 7.2 6.3 5.7 194 197 - 4.1 M 75.0 75.0 75.0 3.5 3.5 75.0 199 200 - 4.5 M 75.0 75.0 75.0 75.0 4.5 75.0 201 204 C 4.6 H 5.2 22.5 56.8 6.9 3.5 3.8 205 210 E 4.9 H 0.2 0.2 0.2 0.2 0.3 0.2 211 214 C 4.2 M 3.2 21.2 3.2 4.8 39.0 6.0 217 222 E 4.8 H 2.7 2.7 2.3 1.8 14.2 3.0 223 224 - 4.5 M 75.0 75.0 5.0 75.0 75.0 75.0 225 226 E 4.5 M 4.5 4.0 2.0 3.0 4.5 4.5 228 234 - 4.5 M 75.0 75.0 6.3 75.0 75.0 75.0 236 241 E 5.0 H 0.0 0.0 0.5 0.0 0.7 0.0 242 243 C 4.3 M 1.5 2.0 5.5 0.0 1.5 5.0 244 247 - 4.5 M 75.0 75.0 75.0 7.1 75.0 75.0 248 250 C 4.4 M 4.0 4.0 53.0 3.3 6.0 5.3 251 256 E 5.0 H 0.2 0.7 0.5 0.3 0.3 0.2 259 260 C 4.3 M 2.5 3.5 39.0 1.5 1.5 3.0 261 267 E 4.7 H 1.0 12.3 0.9 1.1 1.6 1.0 268 273 C 4.4 M 5.4 4.3 17.9 16.2 17.8 5.2 275 276 * 2.3 P 5.5 6.5 41.0 41.0 6.0 41.5 278 279 * 1.9 P 2.0 5.5 4.0 5.5 75.0 5.5 280 284 E 4.4 M 3.2 3.0 3.4 2.8 18.2 1.8 286 287 * 3.0 P 7.5 39.5 75.0 4.0 75.0 6.5 288 289 - 4.1 M 75.0 43.2 75.0 43.2 75.0 6.2 291 292 C 5.0 H 6.0 4.5 4.0 5.8 4.0 2.5 293 299 E 4.5 M 0.1 11.0 0.1 0.1 0.1 0.4 300 301 C 5.0 H 2.0 2.5 2.0 2.0 4.0 2.0 303 305 C 5.0 H 2.3 3.0 2.3 3.0 2.3 4.3 306 311 E 4.7 H 0.2 0.3 12.5 0.5 0.0 0.2 313 314 C 4.3 M 0.5 3.0 1.5 1.0 0.0 0.5 315 326 - 4.5 M 75.0 75.0 75.0 75.0 3.2 75.0 328 332 E 4.9 H 0.0 0.4 0.4 0.0 0.6 0.6 333 334 C 5.0 H 3.0 4.0 4.0 3.0 6.0 0.0 336 339 C 4.5 M 21.0 22.5 40.5 6.1 22.2 4.5 341 345 E 4.9 H 0.6 1.8 0.2 2.4 2.0 3.8 346 347 C 4.5 M 1.5 1.0 3.0 2.0 4.5 2.5 349 352 - 4.2 M 5.5 75.0 40.0 75.0 58.2 75.0 354 356 C 4.8 H 1.7 25.3 0.0 27.7 0.7 0.0 357 362 E 4.8 H 0.2 0.0 0.2 0.0 0.3 0.2 363 365 C 4.5 M 3.3 3.3 2.3 4.3 27.7 2.0 366 367 - 4.5 M 75.0 75.0 11.5 75.0 75.0 75.0 369 370 C 4.5 M 3.5 0.5 4.0 4.5 75.0 2.5 371 376 E 4.8 H 0.0 0.7 0.0 0.2 1.2 0.3 377 378 C 4.5 M 0.0 1.0 0.0 38.0 2.5 0.0 380 382 C 4.2 M 6.2 6.0 4.3 28.7 75.0 6.2 383 392 - 4.2 M 75.0 34.0 54.1 75.0 75.0 19.9 393 396 * 3.4 M 38.8 3.8 4.8 75.0 75.0 38.5 399 403 E 4.6 H 0.0 0.8 1.4 2.2 1.6 1.0 405 412 C 4.5 M 2.8 12.0 3.4 2.4 75.0 3.6 413 415 * 2.4 P 0.3 2.7 57.5 0.7 75.0 2.3 418 422 - 4.5 M 75.0 75.0 75.0 7.5 75.0 75.0 >>>>>>