Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1nd6a- ----------------------------------------------CEEEEEEEEEECCCCCCC-----CCCCCCCC-------------------CHHHCCCCCCCCC----HHHHHHHHHHHHHHHHHCC--CCCC--CCCCHHHEEEEEECCHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEE-CHH-HCCCCCCCCC----CCHHHHHHHHHHHHC---HHHHHHHHHHHHHHHHHHHHHCCC--------------------------------CCCHHHHHHHCHHHHHHHHHCCCC----CCCCC---CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHCC----------------CCCCEEEEEECHHHHHHHHHHCCCCCC---------------------CCCCCCCEEEEEEEEEC--C----EEEEEEEEECCC-------------CCCC--EECCCCCCC-------CEEEHHHHHHHHHHHCCCCHHHHCCC------------------------------------ >P1;d1qfxa- CCCCCCC-------CHHHCHHHCCCCCCCCCCCC-CCCCCCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH--HCCCC-----CCEEEEEECCHHHHHHHHHHHHHHHHHHHHH-------HEEE-EEECCCHHHCCCCCCCCCCC-------------CCCCCC--CCCCCHHH---HHHHHHHHHCC----------------------------CCCCC----HHHHHH-HHHHHHHHCCCC----CC-CCCHHHCCHHHHHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHH---------CHHH---------HCCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCC---CCCCCHHHCCCCCCEEEEEEEEECCCCCCCCEEEEEEEECCEEECCC---------------------CC-CCCHHH--CEEHHHHHHHHHH-HCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC >P1;d1qwoa- ------CEECCCEECCCHHHHCCCHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEC-CCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC----CCCCCC----HHHHHHHHHHHHHHHHHCHH--HHC-C-----CCCEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCHHHH--------CCCHHHHHHHHHHHHHHH---HHHHHHHHHCC----------------------------CCCCC----HHHHHH-HHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHCCCCC--CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCHHHHCCCCCEEEEEEEEEC---CC-CCCEEEEEECCEECCCC---------------------CC-CCCCCC--CEEHHHHHHHCHHHHHCCCHHHHC------------------------------------- >P1;d2wnha1 ---------------------------------------------CEEEEEEEEEEECCCCCCCHHHHHHHHHHHCC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCCCEEEEECCCHHHHHHHHHHHHHHCC------------CCCCCCCCCCC--CCCCCCCHHHCHHHCCC---HHHHHHHHHHHHC-CHHHHHHHCHHHHHHHHHHHCCC-------CCCCHHHH-CCCCEEECCCC-CEEEC-CHHHHHH-HHHHHHHHHHCCCCHHHHCCCCCC--CHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHCC------------------CCCCCCCEEEEEECHHHHHHHHHHHCC-CC--CCC------------CCCCCCCCCCCEEEEEEEEECCCC----CEEEEEEEEECC-HHHHHHCCCCCCCCCCEEEECCCCCC-EEEC-CEEEEEHHHHHHHHCCCCCHHHCCCCCCCCC--------------------------------- >P1;d3ntla1 -------------------------------------------CCCEEEEEEEEEEECCCCCCCHHHHHHHHHCCCC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCC------------CCCCCEECCCCCCCCCHHHCCCCC---CCCHHHHHHHHHHHHHHHH-----CCC-CHHHHHHHHHHCCHHHCHHHHCCCCCCCCC-CCCEEECC-CCCCCEEECHHHHHHH-HHHHHHHHHHHCCCHHHCHHHCCC--CHHHHHHHHHHHHHHHHHHHCC---HHHHHHHCHHHHHHHHHHHCC------------------CHHHCCCEEEEEECHHHHHHHHHHCCCCCC--CCC------------CCCC-CCCCCCEEEEEEEEECCCC----EEEEEEEEEECC-HHHHHCCCCCCCCCCCEEEEECCCCC-CCCC-CC-CEEHHHHHHHHHHHC---------------------------------------------- >P1;d4arua- ------------------------------------------CCCCCEEEEEEEEEECCCCCCC-CCCHHHHHCCCC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHEEEEECCCHHHHHHHHHHHHHHCC------------CCCCCCEECCCCCCCCCCCCCCCCCCCCCC---HHHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHCHHHCHHHHH--CCCHHHHCCCEEEECCCCCCEEEECHHHHHHH-HHHHHHHHHHCCCC--CCHHHCCC--CHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHCCCCCCCCCC----------CCCCCCCEEEEEECHHHHHHHHHHHCC-CC--CCC------------CCCC-CCCCCCEEEEEEEECC-CC----CEEEEEEEEECC-HHHHHCCCCCCCCCCCEEEECCCCCCCCCCC-CC-CEEHHHHHHHHHHHCCHHHCCC--------------------------------------- PSA >P1;d1nd6a- ----------------------------------------------581300000000000004-----40054071-------------------55a4066311201----8404730540051036206--a107--521475204010041610240052003000205bb42637966416050524-53a-7090040105----804208403540671---86036407523b207800840527--------------------------------958062013400100400422a3b----12b10---7a8114304400110021100024263002000020033004105501867----------------922300000001100000000040053---------------------61040100000001449--7----712000200145-------------9680--551504805-------55041a40372065010862863077------------------------------------ >P1;d1qfxa- 7887989-------7ab65121200010021706-569191721a30702000000000010033930640560073046-2b7067505104a091004774501200673430025204810560392026--10859-----63110000010000100030030007b5057-------1000-1013165730010000308b-------------a32880--83306307---60182038307----------------------------90a06----271012-000000000003----49-0601800547002000000103000200103--93130000000610040043---------11a7---------08200000011510000000060030ba602496127---b2404001000000000001040862b71a77200000002000106---------------------a1-280036--0021960283078-60370283090599244803002839572830647783752128254 >P1;d1qwoa- ------117276004445810210010000000365315408419507030000000-0012038941930691075027608615a605205819070----834700----50036001100110052049--203-6-----1301000012a2024006201600271088185086375080304052589-34000223108702--------837318703790155003---a0273038303----------------------------70807----362020-00000000000338604620200600758104302001004100220410--7001000000000010003548090701039920767820138240000001120000000002007409604577336067060000010000000000000308---83-a4300000000000403---------------------80-935930--00319301820740370040b605------------------------------------- >P1;d2wnha1 ---------------------------------------------72301000000000000038a21940280071-------------------80270b2821300----b1034002100321064028280069-b506a70010000034103100600050005------------c0d180441aa--b2030020464960406---5970371069409-7098238814711650460003a-------a5805109-35061616a81-70402-0022003-001000000016154850025606--7175044003001121103110---410022200000410071052------------------a09190400000011400000010080-40--606------------602500000100000010313856----640000000003-06201732203a84612442152980-571a-2200031a60163028313970059190518--------------------------------- >P1;d3ntla1 -------------------------------------------3a11504000000000000137b18a20740032-------------------a11a062711400----72005004200400130006280069c6408aa2030100015101100640071005------------c0b060424883942071020104---4858712660471046228-----61a-079006101700507501206777642019-49170506-5574050760042010-001000002012159850014307--4972161004012011300020---650060005300720041015------------------738903400000012100100020060471--905------------7030-3000000000020307769----530010000000-26102734701297402114030470-516a-71-004095037105a22---------------------------------------------- >P1;d4arua- ------------------------------------------23b4170430000000001005-704850420023-------------------9039052740400----620350022006001410173700468b407661000000132102300510062005------------a0b180332a62971010030051811505---39604820592093507600741590072017003058031086--62700921606020597026050520001005-00000000201109--71015307--6982161005002121300020---610030200000100052030c2b14816----------821981400000011400000000070-70--907------------9010-4000000000010119-87----531000100002-17203733704398404225080470a6049-52-0000920272057202770308--------------------------------------- Translating the sequences ----------------------------------------------*EEEEEEEEEECCCCCCC-----******CC-------------------C***CCCCCCCCC----HHHHHHHHHHHHHHHHH**--CCCC--CCCC***EEEEE*CCHHHHHHHHHHHHHHCC************CCCCC*EE*-C**-*CCCCCCCCC----CC***HHHHHHHHH*---**HHHHHH**HHHHHHHHHH*C**--------------------------------***HHHHHH**HHHHHHHHHCCCC----*CCCC---CHHHHHHHHHHHHHHHHHH*CC***HHHHHH**HHHHHHHHHHH*******----------------CCCCEEEEEECHHHHHHHHHH*CCCCC---------------------*CCCCCCEEEEEEEEEC--C----*EEEEEEEE*CC-------------CCCC--EE*CCCCC*-------**EEHHHHHHHHHHHCC**H****C*------------------------------------ *******-------********************-********CCCEEEEEEEEEEECCCCCCCHHHHHHHHH*******-***************CCCCC***CCCCC******HHHHHHHHHHHHHHHHHH--*CCCC-----CCEEEEE*CCHHHHHHHHHHHHHH*******-------****-*EECCC***CCCCCCCCCC*-------------******--*****HHH---HHHHHHHHH*C----------------------------CCC**----HHHHHH-HHHHHHHH**CC----*C-CCC****CHHHHHHHHHHHHHHHHHHCCC**--**HHHHHHHHHHHHHHHH**---------****---------*CCEEEEEECHHHHHHHHHH*CCCCC**CCC******---***CC***CCCCCCEEEEEEEEEC*CC*****EEEEEEE********---------------------CC-CCC***--CEEHHHHHHHHHH-*C**H****C************************************* ------*************************************CCCEEEEEEEEEE*-CCCCCCHHHHHHHHH***********************CCC----CCCCCC----HHHHHHHHHHHHHHHHH*HH--**C-C-----CC*EEEE*CCHHHHHHHHHHHHHH**************CCC***EECCC**-CCCCCCCCCC****--------***HHHHHH***HHHHHH---HHHHHHHHH*C----------------------------CCC**----HHHHHH-HHHHHHHHHH**CC***C*CCC****CHHHHHHHHHHHHHHHHHHCCC**--***HHHHHHHHHHHHHHH*C******************C**CCCCEEEEE*CHHHHHHHHHH*CCCCC**CCC************CC****CCCCCEEEEEEEEEC---**-***EEEEEE********---------------------CC-CCCC*C--CEEHHHHHHH*HHH*********C------------------------------------- ---------------------------------------------CEEEEEEEEEEECCCCCCCHHHHHHHHH**CC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHH*CCCCC-CCCC*CCEEEEE*CCHHHHHHHHHHHHHHCC------------CCCCC***CCC--*CCCCCC***C****CC---HHHHHHHHHHHH*-*HHHHHH**HHHHHHHHHH*C**-------********-**********C-C****-*HHHHHH-HHHHHHHHHHCCCC*****CCCC*--CHHHHHHHHHHHHHHHH**CCC---HHHHHHHHHHHHHHHHHHH*C------------------C**CCCCEEEEEECHHHHHHHHHH*CC-CC--CCC------------CC***CCCCCCEEEEEEEEEC*CC----*EEEEEEEE*CC-************CCCC**EE*CCCCC-***C-C***EEHHHHHHHH***CC**H****C****--------------------------------- -------------------------------------------CCCEEEEEEEEEEECCCCCCCHHHHHHHHH**CC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHH*CCCCCCCCCC*CCEEEEE*CCHHHHHHHHHHHHHHCC------------CCCCC*E*CCC***CC***CCCCC---*CC***HHHHHHHHHHHH*-----***-*HHHHHHHHHH*C*****************-********-*CCC******HHHHHH-HHHHHHHHHH*CCC***C***CC*--CHHHHHHHHHHHHHHHHHH*CC---HHHHHHH*HHHHHHHHHHH*C------------------C***CCCEEEEEECHHHHHHHHHH*CCCCC--CCC------------CC**-CCCCCCEEEEEEEEEC*CC----*EEEEEEEE*CC-************CCCC**EE*CCCCC-CCCC-C*-CEEHHHHHHHHHHHC---------------------------------------------- ------------------------------------------*CCC*EEEEEEEEEECCCCCCC-***HHHHH**CC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHH*CCCCCCCCCC***EEEEE*CCHHHHHHHHHHHHHHCC------------CCCCC*EECCC***CCCCCCCCCC****CC---HHHHHHHHHHHH***HHHHHH**HHHHHHHHHH*C*********--*****************CCC******HHHHHH-HHHHHHHHHHCCCC--*C***CC*--CHHHHHHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHH*C********----------C**CCCCEEEEEECHHHHHHHHHH*CC-CC--CCC------------CC**-CCCCCCEEEEEEEE*C-CC----*EEEEEEEE*CC-************CCCC**EE*CCCCC*CCCC-C*-CEEHHHHHHHHHHHCC**H***--------------------------------------- 53254-2.tem _________________________________ ------------------------------------------*CCCEEEEEEEEEEECCCCCCCHHHHHHHHH**CC-------------------CCCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHH*CCCCCCCCCC*CCEEEEE*CCHHHHHHHHHHHHHHCC*****-------CCCCC*EECCC***CCCCCCCCCC****CC---HHHHHHHHHHHH***HHHHHH**HHHHHHHHHH*C**---------******-********-*CCC******HHHHHH-HHHHHHHHHHCCCC***C*CCCC*--CHHHHHHHHHHHHHHHHHHCCC**-HHHHHHHHHHHHHHHHHHH*C*****-------------C**CCCCEEEEEECHHHHHHHHHH*CCCCC--CCC------------CC***CCCCCCEEEEEEEEEC*CC----*EEEEEEEE*CC-************CCCC**EE*CCCCC-CCCC-C*-CEEHHHHHHHHHHHCC**H****C*------------------------------------ Structural block scores 0 41 - 4.2 M 75.0 18.0 12.8 75.0 75.0 75.0 43 45 C 4.4 M 75.0 4.8 5.0 52.3 4.8 6.2 46 56 E 4.9 H 1.5 0.8 0.9 0.5 0.9 1.4 57 63 C 4.9 H 0.6 0.6 11.6 0.4 0.6 0.9 64 72 H 4.4 M 42.7 4.0 5.4 4.9 5.7 11.7 73 74 * 1.0 P 2.0 0.0 0.5 0.0 0.0 0.0 75 76 C 4.1 M 4.0 5.0 6.0 4.0 2.5 2.5 77 95 - 4.1 M 75.0 8.1 4.3 75.0 75.0 75.0 96 108 C 4.7 H 3.4 2.4 25.3 3.4 3.4 3.3 109 112 - 4.5 M 75.0 5.0 75.0 75.0 75.0 75.0 113 132 H 4.9 H 6.7 2.9 1.9 2.4 1.7 2.0 134 143 C 4.4 M 18.1 39.8 46.1 12.1 5.3 4.8 145 146 C 4.1 M 3.5 4.5 2.0 3.5 6.2 3.5 147 151 E 4.9 H 1.0 0.4 0.2 0.2 0.8 0.0 153 154 C 5.0 H 2.5 0.5 1.5 1.5 0.5 2.0 155 168 H 5.0 H 1.6 0.5 2.4 1.4 1.9 1.6 169 170 C 4.1 M 1.0 3.5 4.5 2.5 2.5 2.5 171 175 * 3.4 M 6.4 5.7 3.6 75.0 75.0 75.0 176 182 - 4.1 M 5.6 75.0 5.3 75.0 75.0 75.0 183 187 C 4.4 M 3.2 15.2 3.2 7.0 6.0 6.2 189 190 E 4.3 M 3.5 0.5 2.0 4.0 3.0 3.0 191 193 C 4.7 H 28.0 3.3 4.0 7.3 6.7 6.2 194 196 * 2.2 P 29.5 5.0 30.7 53.8 5.3 6.0 197 206 C 4.7 H 2.6 1.2 1.5 2.1 1.7 1.1 207 210 * 3.0 P 75.0 59.1 4.2 4.8 57.2 3.8 211 212 C 4.3 M 4.0 75.0 75.0 3.0 6.5 2.5 213 215 - 4.1 M 2.0 75.0 75.0 75.0 5.3 75.0 216 227 H 4.3 M 15.7 40.1 22.1 4.2 3.3 4.0 228 230 * 2.4 P 29.7 28.7 5.3 30.3 52.7 5.7 231 236 H 4.4 M 3.3 3.2 2.3 5.0 40.4 3.3 237 238 * 3.0 P 3.5 75.0 75.0 4.5 37.5 2.5 239 248 H 4.9 H 4.3 10.6 11.2 3.4 3.1 3.1 251 252 * 2.7 P 4.5 75.0 75.0 6.8 3.5 2.5 253 261 - 4.1 M 75.0 75.0 75.0 60.1 3.9 19.6 262 267 * 3.4 M 75.0 75.0 75.0 3.8 3.7 4.0 269 276 * 3.4 M 75.0 75.0 75.0 3.5 4.0 2.5 279 281 C 4.4 M 75.0 6.5 5.0 27.7 5.3 2.7 282 287 * 2.7 P 41.2 51.0 51.2 13.5 3.0 2.0 288 293 H 5.0 H 2.0 2.2 2.2 1.2 1.2 1.0 295 304 H 4.8 H 1.1 0.0 0.0 0.1 0.3 0.2 305 308 C 4.4 M 6.8 38.2 3.5 3.2 2.2 2.8 309 311 * 2.9 P 75.0 51.3 3.3 5.7 7.3 52.3 314 317 C 4.3 M 3.6 1.8 0.5 3.2 2.0 2.2 319 320 - 4.1 M 75.0 0.0 0.0 75.0 75.0 75.0 322 339 H 4.9 H 2.3 1.1 1.7 1.8 2.1 2.3 340 342 C 4.7 H 0.0 0.3 2.0 0.7 0.7 0.7 343 344 * 3.4 M 3.0 1.5 0.5 75.0 75.0 75.0 346 364 H 4.8 H 1.3 5.4 4.4 1.3 2.1 1.1 367 371 * 3.4 M 4.4 75.0 4.2 75.0 75.0 6.2 372 384 - 4.3 M 75.0 53.4 4.5 75.0 75.0 58.8 386 387 * 2.7 P 75.0 75.0 0.5 4.5 5.5 1.5 388 391 C 4.7 H 4.0 21.2 4.2 3.5 4.0 5.5 392 397 E 4.9 H 0.0 0.0 0.0 0.0 0.0 0.0 399 408 H 5.0 H 0.2 0.7 0.3 0.6 0.6 0.5 410 414 C 4.9 H 2.4 1.8 2.6 17.4 3.6 17.8 415 416 - 4.1 M 75.0 11.0 4.5 75.0 75.0 75.0 417 419 C 4.5 M 75.0 2.7 3.3 4.0 4.7 5.3 420 431 - 4.2 M 75.0 22.6 4.2 75.0 75.0 75.0 432 433 C 4.5 M 75.0 2.0 0.0 3.0 3.5 4.5 434 436 * 2.2 P 52.0 0.3 0.3 2.3 26.0 25.3 437 442 C 4.9 H 1.0 0.0 0.0 0.2 0.5 0.7 443 451 E 4.9 H 1.0 0.6 0.3 0.6 0.6 0.3 454 455 C 4.4 M 41.0 6.8 75.0 5.5 7.5 7.5 456 459 - 4.2 M 75.0 6.4 24.1 75.0 75.0 75.0 461 468 E 4.8 H 0.6 0.2 0.4 0.5 0.5 0.6 470 471 C 4.1 M 4.5 0.0 0.0 1.5 0.0 1.0 473 484 * 3.0 P 75.0 56.8 56.8 3.0 2.9 3.3 485 488 C 4.3 M 5.8 75.0 75.0 4.8 5.0 5.2 489 490 * 3.4 M 75.0 75.0 75.0 3.0 1.5 3.0 491 492 E 4.3 M 5.0 75.0 75.0 3.0 2.5 3.5 494 498 C 4.6 H 3.4 47.3 46.6 4.8 2.8 3.8 500 503 C 4.2 M 75.0 2.5 6.5 5.9 5.6 4.8 509 510 E 5.0 H 2.0 1.0 1.5 1.5 2.0 0.0 511 521 H 4.8 H 3.5 10.8 3.2 3.7 3.9 3.3 522 523 C 4.2 M 0.5 3.0 5.0 2.0 38.5 1.0 524 525 * 1.9 P 7.0 5.0 0.0 8.0 75.0 7.0 527 530 * 2.1 P 4.2 3.2 4.4 3.8 75.0 21.5 533 568 - 4.5 M 75.0 4.5 75.0 69.1 75.0 75.0 >>>>>>