Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fo8a- ---------------------------------------------------------------------------------------------------------------------CCCCCEEEEECCC--CCHHHHHHHHHHHCCCCCCCCEEEEECCC---------CHHHHHHHH-----HHHHHCEEEECCCCCCCCCCC----CCHHH-----------HHHHHHHHHHHH-HHHHHHCCCCCCEEEEEECCE-EECCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHCCC----------CCCC-CEEEE----CCCCCCCEEEEHHHHHHHHHH----CCCCC-HHHHHCCHHHHCCCEEEEECCCCEEECC-------------------------------------------------------------------------CCC-----CCCCCCCCCHHHCCC-HHHCHHHHHH-----HHHHHHHHCCCCCHHHHHCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCEECCEECCCCCCCEEEEECCEEEEEECCCCCCCCCCCCC------------------------------------- >P1;d1jvga- --CHHHHHHHHHHCCCHHHHCCHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCCCCCCCC-CCEEECCCC-CCHHHHHHHHHHHHH-CCCEEEEEECCCCC--CCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCCEE---EEECCCC-HHHHHHHHHHCHHHHCCHHHEEEEECCEEECEECCC-CCC----EEECCEECEEECCHHHHHHHHHHCCHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHC-----CCCEEEEEEECCC--CCCCCCEEEEE--C---CEEEEECHHHCC----------HHHHHCCCCC----------------------CCCCCCEEEEEEEEEEHHHHH-HHHHCCHH--HCCCEEEEECCCEECCCCCEECCCCCCEEEEE---CCHHHHHHHCC-------CEEEEECCHHHHCCCCCCCCC-----CCCCCCHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCCCEEECC------------CCCCCCCCCHHHHCCCEECCCEEEECCEEEEC----------------------------------------------- >P1;d1s4na- -------------------------------------------CCHHHHHHHHCC-------CCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCC----------------------HHHHHHHHHHCC-------CCEEEEECCHHHCCCCCCCCHHHHHHHHHHHCC----------------------------------CCCCCCC--HHHHHHHHHHHHCHHHCHHHCCCCEEEECCCCCEECCCCCCCHHHHHHHC-----CCCEEECCEEECC--------------------------HHHCCCH--------HHHHHHHHHHCHHHCCCCCCHHHHCC---CCCCCCCCEEECCCCEEEEHHHHCCHHHHHHHHHHHHH------------------CHHHH--CCCCHHHHHHHHHHHHCCHHHEEECCCCCEEEC---CEEECCCCHHHHHHCCCCCCHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHHC--------------------------------------------------------------------------------------------------------- >P1;d1xhba2 -------------------------------------------------------------------------------------------------CCCCCCCCCHHHHCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHCCC-HHHEEEEEEEECCCCC---HHHCHHHHHHHH-----------CCCCCEEEEECC----------------------------CCCCHHH-HHHHHHHHCCCCEEEEEECCE-EECCCCHHHHHHHHHH---CCC-EEEEEEEEEECCC---CCCEE-----CCCCC-EEEEECC----CCCEEEEECCHHHHHHCC---------------CCCCC----CEECCCCCCCCEEEEHHHHHHCC------------------------CCCCCCCCC-------CCCCCHHHHHHHHC-CCEEEE-EEEEEE-----EEECC---------HHHHHHHHHHHHHHCHHHHHHHHHCCC------------CHHHCCCCCC----HHHHHHHHHC-----------------------------------CCCCHHHHHHHCCCCC----------------------------- >P1;d2bo4a1 ------------------------------------------------------------------------------------------------------------------------CEEEEECCCCCHHHHHHHHHHHHH----CCCCCEEEEEEC--CC---CHHHHHHHHHHH-----HHHHHHCCCEEEEECCCCCC----------------------CCCCHHHHHHH-HHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHHC----CC-CEEEEECCCCCCCCHHHHHCH---HHHHHHH-CCCCCHHHCCCCCCCCEEEEHHHHHHHHHCHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCC---------------------------------CCCHHHH-------HHHHHHHHHHHHHHCCCCCCC-CCCEEE-----CCCCCCCHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHCC----HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH------HCCC-------------------CCHHHHHHHHHHHHHHHHHHHHHCHHHCHHHHHHHHHHHHHHHHHHHHHC >P1;d2icya2 CCCHHHHHHHHHHCC---------------------CCCHHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCEEEHHHCCCCCCC-CHHHHHHHC---CEEEEEECCCCCHHHCCCCCHHHCEEE--CCEEHHHHHHHHHHHHHHHH-------CCCCCEE---EEECCCC-HHHHHHHHHCCCCCCCC---EEEEECCCEECEECCCCEEHHHHCCCCHH--HEECCCHHHHHHHHHHCCHHHHHHHCCCCEEEEEECCCCCCCC-CHHHHHHHHHH-----CCCEEEEEEECCC--CCCCCEEEEEE--C---CEEEEEEHHHCC----------HHHHHHHHCC------------------------CCCCEEEEEEEEEEHHHHH-HHHHC--CCCCCCCCCCCEEEC------------CEEEECCC---CCHHHHHHHCC-------CCEEEECCH-HHCCCCCC----------------------HHHHHHHHCC---------------------CEEEE--------------CCEEEEC------------------------------------------------------------------------ >P1;d2yqca- CCCHHHHHHHHHHCCCHHHHCCHHHCCHHHHC-CHHHHHCCCCC-CC-CHHHHHC---CCCCEECCC-CCEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEEEECCCHHHCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEE---EEECHHH-HHHHHHHHC-CHHHHCCHHHEEEEECCEEECCCCCCCCCC----EEECCEECEEECCHHHHHHHHHHCCHHHHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHH-----CCCEEEEEECCC-------CCEEEEECCC---CEEEEEC----------------CCC--CCCC----------------------CCCCCCCEEEEEEEEEHHHHH-HHHHHHCCCCCCCCEEEEECCCEECCCCCEE-CCCCCEEEEE---CCHHHHHHHCCHH-----HEEEEECCHHHHCCCC-CCC------CCCCCCHHHHHHHHHHHHHHHHHHCCCEECC-------------CCCCCCCC------------CCCCCCCCCHH-HCCCEE-CCCCC------------------------------------------------------- PSA >P1;d1fo8a- ---------------------------------------------------------------------------------------------------------------------8450000000346--37055005301720435920200000036---------486017106-----71ab4051160565782b078----82883-----------2a5035020052-001200663925000004140-1001000200100051048182000000000004590025----------9403-30000----000012000013800730264----01703-144000558005710000000000211b-------------------------------------------------------------------------577-----030067504048390-6405482037-----61076019145082640451556729201020674a3036208409043503100010003000001157010000046a297156628------------------------------------- >P1;d1jvga- --839716760371a06200402b5089733770263068070a30361165037a--449706402-a11102663-a53860152004100-56400000000a70--0b2a4010113050027110020000002101520386385-8030000---0000430-195047205748109067810200409210102461-501----04532400142025000040048480054049290500000210000010000300000243-----a020000002077--27251000022--8---741302157506----------69105644b6----------------------850203100030000005003-40066206--60702155551430389175481984300302---01002003108-------400002054840011053346-----756830044024300710061029080300399575266a1a8750400000------------11001168079304973051201025862435----------------------------------------------- >P1;d1s4na- -------------------------------------------680153056107-------b607000000032832a103500720051005335020000015806----------------------880373068305-------17121250498215119307684047318804a----------------------------------5175013--44201200000000030720770200000106040102064100330154-----5200000000106--------------------------6500430--------1710160187267132a810270008---3b087022000102000000100203004500640054------------------00002--100101000000000002481020063000224---621000177932762806092a700003650013201501a5a13a627612a--------------------------------------------------------------------------------------------------------- >P1;d1xhba2 -------------------------------------------------------------------------------------------------648174113970483a259a023000000031273700020011004303-5900300000002075---a30585038409-----------916040503318----------------------------9321203-002400730705000001020-0003200200002037---344-0000001040269---63607-----24603-4000036----503244470283017409---------------75415----10300001030000015006503------------------------310560236-------06410000000000-702000-000000-----01159---------846320010001000473375018338------------80681a2781----7a14311782-----------------------------------9045053017400342----------------------------- >P1;d2bo4a1 ------------------------------------------------------------------------------------------------------------------------000001059172740150052006----084051000006--65---5a0042057316-----603752a0503044154107----------------------34321000000-003001650a3810000404074046700320061048----71-100000002010210000000---0000001-018010050010020000033710420072a2035000300000000000155120200003502343a---------------------------------7300352-------25200100000130193a0b9-447063-----39459228701727002395037103471394037106405----6602620210376212a1061920140042007------3064-------------------92820200000000000000135007691a40341047005401740267 >P1;d2icya2 576385058405919---------------------907962177014104221b39271a40880768501139608717a9-672047004---200000000821661a1b002023702--78210000002102410771-------8080000---0000120-483067218518b1608---02204003001003860100033826784--00010340000300152920640185b1400000100000030-11100220265-----8020000005048--60675000030--7---b61100127204----------a823a50454------------------------a308100000000207004-61266--740301014554517------------72701002---00000003106-------701002043-70001025----------------------891185043a---------------------41407--------------9140675------------------------------------------------------------------------ >P1;d2yqca- b5757600530481806300620a80889517-01930371b18-10-3048319---7b4602304-b132115828a52760333016000-652000000083408809395020124060216200020002002100430184295b3130000---0000560-3b6037306-6a108074a002004094200035803300----045332002140140000600554501830584a0610000302000010000100000324-----802000000016-------4410000555---620100b----------------655--917a----------------------8b2304200030000209004-7005401764404040375505004780754-1a84100304---1302200310729-----4000030447201020-355------b49740042025401500030066260505a-------------a1300010------------82001157086-079660-75540------------------------------------------------------- Translating the sequences ---------------------------------------------------------------------------------------------------------------------**C*******CC*--**HHHHHHHHHH******C*C***EE***---------*HHHHHHHH-----*********E******C**C*----*****-----------**HHHHHHHHHH-*HHHHH**CCCCEEEEEECC*-**CCC*HHHHHHHHH******C**EEE****CCC******----------***C-*EEE*----C**********HHHHHHH***----*****-************CC****E*****EE**-------------------------------------------------------------------------***-----CCCCCCC*******C-****HHHHH*-----HHHHHHH*CC*******************************************************************************------------------------------------- --******************************************************--*********-*********-***************-***********C**--*********C*******CC**HHHHHHHHHHHHH******C-C****EE---*******-HHHHHHHHH**************E******C**C**-***----*************HHHHHHHHHH**HHHHHHHCCCCEEEEEECCC**CCCCCHHHHHHHHH*-----C*CEEEEEE*CCC--***********--*---C**EEE*****C----------HHHHH*****----------------------CCC*C*EE****EEEEHHHH*-********--********************************---**HHHHHHH*C-------****EE******CCCCCCC**-----C*****HHHHH*****HHHHHHHH*CC******************C******------------********************************----------------------------------------------- -------------------------------------------************-------*******************************************C***----------------------HHHHHHHHHH**-------C*****E*************HHHHHHHHH****----------------------------------*******--*HHHHHHHHHH**HHH*HHHCCCCEEEE**CCC**CCCCC**HHHHHHH*-----C*CEEE**E**CC--------------------------****C**--------HHHHHHH*******************---***CCC*C*EE****EEEEHHHH***************------------------*****--*********HHHHHHH*C***********EE**---****CCCC*******C*****HH*********HHHHHHH*CC***********--------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------********C*************C*******CC**HHHHHHHHHHHHH***-********EEE*****---****HHHHHHHH-----------**********C*----------------------------****HHH-*HHHHHHHCCCCEEEEEECC*-**CCCCHHHHHHHHH*---**C-*EEEEEE***C**---*****-----****C-*EEE***----**********HHHHHH**---------------*****----C**C*******EEEEHHHH****------------------------*********-------*****HHHHHHH*C-******-***EE*-----***CC---------******HHHHH*****HHHHHHHH*CC------------******C***----**********-----------------------------------****************----------------------------- ------------------------------------------------------------------------------------------------------------------------*******CC**HHHHHHHHHHHHH----**C*C***EEE*--**---***HHHHHHHHH-----*********E******C**C----------------------****HHHHHHH-*HHHHHHHCCCCEEEE**CCC**CC***HHHHHHHHH*----*C-CEEEEE**CCC**********---*******-*********C**********HHHHHHH*************************CCC***EE*********---------------------------------*******-------*****HHHHHHH*********-***EE*-----CCCCCCC*******C*****HHHHH*****HHHHHHHH*CC----**************C******************------****-------------------************************************************** ***************---------------------***********************************************-*********---*********C*************C***--******HHHHHHHHHHHHH*-------C****EE---*******-HHHHHHHHH********---***E******C**C***************--******HHHHHHHHHH**HHHHHHHCCCCEEEEEECCC**CCC-CHHHHHHHHH*-----C*CEEEEEE*CCC--***********--*---C**EEE*****C----------HHHHHHH***------------------------C*C*EE****EEEEHHHH*-*****--***************------------********---**HHHHHHH*C-------****EE***-**CCCCCC----------------------**HHHHHH**---------------------C****--------------*******------------------------------------------------------------------------ ********************************-***********-**-*******---*********-*************************-***********C*************C*******CC**HHHHHHHHHHHHH******C*C***EEE---*******-HHHHHHHH*-*************E******C**C******----*************HHHHHHHHHH**HHHHHHH*CCCEEEEEECCC**CCCCCHHHHHHHHH*-----C*CEEEEEE*CC-------**********---C**EEE*----------------***--****----------------------CCC*C**E****EEEEHHHH*-*******************************-**********---**HHHHHHH*C**-----****EE******CCCC-CC*------C*****HHHHH*****HHHHHHHH*CC****-------------*C******------------***********-******-*****------------------------------------------------------- 53448-1.tem _________________________________ --*************---------------------*******************---*********-*************************-***********C*************C*******CC**HHHHHHHHHHHHH******C*C***EEE**-********HHHHHHHHH**************E******C**C**-***----*************HHHHHHHHHH**HHHHHHHCCCCEEEEEECCC**CCCCCHHHHHHHHH*----*C*CEEEEEE*CCC*************--****C**EEE*****C**********HHHHHHH***----*****-************CCC*C*EE****EEEEHHHH*-**********************----*********************HHHHHHH*C***********EE***-**CCCCCCC*******C*****HHHHH*****HHHHHHHH*CC******************C******-**********-***********-******-*****-----***--********------------------------------------- Structural block scores 0 1 - 4.2 M 75.0 75.0 75.0 75.0 75.0 6.0 8.2 2 14 * 3.7 M 75.0 5.3 75.0 75.0 75.0 4.8 4.2 15 35 - 4.2 M 75.0 3.9 75.0 75.0 75.0 75.0 7.5 36 54 * 3.4 M 75.0 3.7 29.8 75.0 75.0 3.9 11.2 55 57 - 4.5 M 75.0 53.5 75.0 75.0 75.0 4.7 75.0 58 66 * 3.4 M 75.0 4.0 36.1 75.0 75.0 5.1 4.2 68 92 * 3.1 M 75.0 6.0 2.1 75.0 75.0 7.2 3.6 94 104 * 2.8 P 75.0 1.4 1.3 23.4 75.0 13.8 1.9 106 118 * 3.0 P 64.4 14.4 58.8 5.4 75.0 3.3 3.8 120 126 * 2.0 P 0.0 2.4 75.0 0.0 0.1 24.9 2.7 127 128 C 4.3 M 3.5 1.0 75.0 2.0 7.0 1.5 1.0 129 130 * 2.1 P 40.5 0.0 75.0 4.5 4.0 0.0 0.0 131 143 H 4.8 H 8.5 1.0 9.7 1.4 2.5 1.8 1.1 144 149 * 2.9 P 3.8 4.7 75.0 15.8 51.3 62.7 4.0 153 155 * 1.0 P 0.0 1.0 1.7 0.0 0.3 2.7 1.3 156 158 E 4.3 M 0.0 0.0 3.0 0.0 0.0 0.0 0.0 159 160 * 3.4 M 4.5 75.0 8.5 1.0 40.5 75.0 75.0 162 169 * 2.5 P 75.0 10.2 3.4 31.3 31.4 9.8 10.8 170 178 H 4.9 H 3.7 3.7 4.6 4.7 3.1 4.3 4.4 179 192 * 2.8 P 29.7 3.8 55.2 60.1 29.5 19.2 8.9 194 199 * 1.8 P 5.2 2.7 75.0 2.5 2.8 1.2 3.2 201 202 * 2.1 P 5.8 1.0 75.0 41.5 0.5 0.0 1.5 204 205 * 3.4 M 41.5 3.5 75.0 75.0 75.0 7.0 4.0 207 209 * 3.5 M 52.7 2.0 75.0 75.0 75.0 0.3 1.0 210 213 - 4.2 M 5.2 75.0 75.0 75.0 75.0 3.5 75.0 214 226 * 3.3 M 64.4 2.1 30.8 75.0 69.5 13.9 1.9 227 236 H 4.6 H 2.2 2.1 0.9 24.5 1.0 1.3 2.0 237 238 * 2.0 P 37.5 6.0 0.0 37.5 37.5 5.5 4.5 239 245 H 4.8 H 2.1 3.1 1.7 2.3 2.1 3.0 3.6 246 249 C 4.9 H 4.8 4.0 4.0 3.0 5.4 5.4 5.1 250 255 E 4.7 H 0.7 0.3 0.2 0.2 0.8 0.2 0.7 256 258 C 4.7 H 1.7 0.3 2.0 0.7 1.3 0.0 0.7 259 260 * 1.8 P 38.0 0.0 2.0 37.5 5.5 0.0 0.0 261 265 C 4.5 M 0.2 0.2 1.8 1.0 3.4 15.8 0.2 266 274 H 4.9 H 0.9 1.0 1.9 0.8 1.8 1.6 0.7 276 279 - 4.5 M 3.2 75.0 75.0 57.0 75.0 75.0 75.0 284 289 E 4.6 H 0.0 0.0 0.0 0.2 0.0 0.0 0.0 291 293 C 4.5 M 1.3 4.7 2.3 2.0 1.0 4.0 27.3 294 306 * 3.1 M 42.0 13.2 75.0 37.5 17.5 13.6 35.3 307 308 - 4.2 M 75.0 75.0 75.0 75.0 0.0 75.0 5.0 309 312 * 3.4 M 22.0 58.2 75.0 3.0 0.0 58.0 57.5 314 315 * 2.8 P 39.0 2.5 75.0 39.5 37.5 3.5 1.0 316 318 E 4.3 M 0.0 1.7 75.0 0.0 3.0 0.3 0.3 319 323 * 2.6 P 60.0 3.6 17.2 31.8 1.2 2.4 62.3 325 334 * 3.6 M 0.4 75.0 60.3 10.4 0.6 75.0 75.0 335 341 H 4.5 M 3.0 4.4 2.3 3.6 2.4 5.6 35.7 342 344 * 1.3 P 4.0 7.2 5.3 28.0 3.0 4.3 6.2 345 348 - 4.2 M 75.0 75.0 4.0 75.0 3.9 75.0 75.0 349 353 * 3.7 M 2.2 75.0 4.9 75.0 1.6 75.0 75.0 355 366 * 3.6 M 2.7 75.0 21.4 45.6 0.5 75.0 75.0 367 369 C 4.4 M 2.7 4.3 5.0 25.3 2.7 53.5 7.2 373 374 E 4.2 M 0.0 0.5 0.0 0.0 0.0 0.5 1.0 375 378 * 1.0 P 0.0 0.8 0.8 1.0 2.0 0.0 0.8 379 382 E 4.4 M 3.9 0.0 0.0 0.0 3.0 0.5 0.5 383 386 H 4.4 M 75.0 1.2 0.2 1.5 58.9 1.8 2.2 389 410 * 3.4 M 75.0 9.8 32.1 68.3 75.0 9.9 3.2 411 414 - 4.2 M 75.0 3.5 75.0 75.0 75.0 75.0 2.8 415 435 * 3.1 M 75.0 13.8 25.2 26.8 33.5 40.2 17.1 436 442 H 4.6 H 75.0 0.9 0.0 0.0 0.3 0.6 1.1 445 455 * 3.1 M 75.0 48.1 2.2 14.5 12.2 48.5 35.5 456 457 E 4.6 H 6.0 1.0 1.0 0.0 3.0 1.0 1.5 458 460 * 2.6 P 52.3 3.0 27.0 50.0 51.0 2.3 2.7 462 463 * 3.4 M 75.0 2.0 40.5 75.0 75.0 3.5 1.0 464 470 C 4.5 M 3.0 1.9 1.6 23.7 4.9 11.9 12.3 471 477 * 3.4 M 4.0 55.0 5.1 75.0 4.6 75.0 65.0 479 483 * 1.9 P 18.0 4.4 3.4 3.0 3.8 75.0 4.8 484 488 H 4.4 M 3.4 2.0 3.5 0.2 2.2 75.0 1.6 489 493 * 2.1 P 61.4 2.8 2.8 1.0 3.6 48.4 3.0 494 501 H 4.8 H 12.0 2.4 1.5 4.2 3.8 4.1 1.9 503 504 C 4.6 H 2.5 4.0 7.8 5.5 2.5 75.0 3.0 505 522 * 3.1 M 3.9 5.4 32.5 51.9 19.1 75.0 55.9 524 529 * 2.4 P 3.2 0.7 75.0 40.2 3.4 27.0 0.7 531 540 * 3.7 M 3.5 75.0 75.0 4.5 1.3 75.0 75.0 542 552 * 3.1 M 1.5 3.1 75.0 75.0 48.9 30.2 3.5 554 559 * 3.7 M 0.5 3.8 75.0 75.0 75.0 75.0 4.7 561 565 * 3.7 M 2.8 0.8 75.0 75.0 75.0 75.0 4.2 566 570 - 4.2 M 0.2 4.6 75.0 75.0 75.0 75.0 75.0 571 573 * 3.7 M 3.3 4.0 75.0 75.0 6.3 75.0 75.0 574 575 - 4.2 M 6.2 75.0 75.0 75.0 1.0 75.0 75.0 576 583 * 3.7 M 5.5 75.0 75.0 3.2 0.2 75.0 75.0 584 620 - 4.5 M 75.0 75.0 75.0 59.4 2.7 75.0 75.0 >>>>>>