Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gtta1 -----------------------------------CCCCEEEEECCC--------HHHHHHHCCHHHC----------------CCCCCCCC---CCEEEEECHHHEECCCCCEEECC-------------------C-CCEECCEEEEEEECCCCC---CCCHHHHHHHEEEEEEEECCCCCCC--CCC---CCCHHHHCCCCCEECC-CCCC---CC----------------------CCCCCEEEEEEC--C----EEEEEEEHHH----CCCCHHHHHHHHHC-CCCCCCCCEEECCCCCC---CCEECC------------------------CCEEEEEEC--------CCCCEEEEEEEHHHCCC-CC >P1;d1gtta2 ----------------------------CCCCCCCCCCCEEEECCCC--------CCCC------------------------------------CCCEEEECHHHEECCCEEEEECC-------------------CCCCEECCEEEEEEECCCCC---CCCCCCHHHHEEEEEEEECCEEHHH--CCCC-CCCCHHHHCCCCCEECCCCCEEHHHCC----------------------CCCCCEEEEEEC--C----EEEEEEEHHH----CCCCHHHHHHHHHC-CCCCCCCCEEECCCC-C---CCCCCC------------------------CCEEEEEEC--------CCEEEEEEEEEHHHHC---- >P1;d1hyoa2 ----------------------------------CCCCCEEEEC-CC--------HHHHHHHHHHHHC----------------HHHCCCCCCCCCCCEEECCCCCEEECCCCEECCEEEECCCCCCCCEE-----EECCCEECCEEEEEEECCCCCCCCCCCHHHHHHHEEEEEEEECCEEHHHHHHHCC-CCCCCHHHH--CCEEECCCCEEHHHHHHHEECCCCCCCCCCHHHCCCCCCEECCEEEEEEECCCCCCCEEEEEEECCC----CCCCHHHHHHHHHCCCCCCCCCCEEECCCCCCCCHHHCCCHHHHCCCCCCCEECCCCCEECCCCCCCEEEEEEEEECCCCEEEEEEEEEEEECCC------- >P1;d1nkqa- -----------------------------CCHHHHHCCCEEEECCCC--------CCCHHHHC---------------------------------CCEEEECHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCC-CEEECEEEEEEECCCCCCCCC-CHHHCHHHEEEEEEEECCCC-CHHHHHHHHCCCCHHHHHCCCC-CCC-CCEEHHHHHHHC-------------CCCCCC----EEEEEEEC--C----EEEEEEECCC-----CCCHHHHHHHHHC-C-CCCCCCEEECCCCC---------------------------CCEEECCCCCEEEEEECC------EEEECCCCEEECCCCCCCCC >P1;d2eb4a- -------------------CCCHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHCCCCCCCCCEEEEEEHHHEEC--------CCEEECHHHCC------------CCEEEEEEEEEECCCCC-CCCCCHHHHHHHEEEEEEEEEEECCCCCCCC----CHHHHHHHCHHHEEEEEECCC---------------CCCCCCCCHH-----HCEEEEEECC------EEEEEEEHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCEEECCCCCC----CEECCCCCEEEEECH--------------HHCEEEEEEC--------------------------- >P1;d2wqta- -------------------CCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHCCCCCCCEEEEEEHHHEEE--------CCEEECHHHCC------------CCEEEEEEEEEECCCCC-CCCCCHHHHHCCEEEEEEEEEEECCCCHHHC----CCHHHHHHCHHHCCEEEECCC---------------CCCCCCCCCC-----CCEEEEEECC------EEEEEEEHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCC----CEECCCCCEEEEEEC--------------CCEEEEEEECC-------------------------- >P1;d3s52a- -----------------CCCCC-----CCCCCCCCCCCEEEEEECCC--------HHHHHCCCCCCC----------------------------CCEEEEEEHHHEEECCC-------------------CCCCCCCCCCEECCEEEEEEECCCCCCC---C-CCHHHHEEEEEEEECCEEHHHHHHHHHHCCCCHHHHCCCCCEEEC-CCEEHHHHC-----------------CHHH-----CEEEEEEC--C----EEEEEEECCC-----CCCHHHHHHC-CC-CCCCCCCCEEECCCCC---------------------------CCCC-CCC--CCEECC--------C-CCEECCC----------- >P1;d5d2ka- -----------------CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHCCCCCEEEEEEHHHEEC--------CCEEEEHHHCC------------CCEEEEEEEEEECCCCC-CCCCCHHHHHHHEEEEEEEEEEECCCCHHHC----CCHHHHHHCHHHEEEEEECCC---------------CCCHHHCCCC-----CCEEEEEECC------EEEEEEEHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCEEECCCCCC----CEECCCCCEEEEEEC--------------CCCEEEEEEE--------------------------- >P1;d6foha- C------------------CCC-----HHH--HHHHCCEEEEECCCC--------CCCHHH---------------------------------CCCCEEEEEHHHEEE--CC---------------C-CEEC-CCCCCCEEECEEEEEEECCCCCCC---CHHHHHHHEEEEEEEECCEEHHHHHHHHHHCCCCHHHHCCCCCEEEC-CCEEHHHCC-----------------CCCC-----CEEEEEEC--C----EEEEEEEHHH----CCCCHHHHHHHHHH-HCCCCCCCEEECCCCC---------------------------CCEEECCCCEEEEEEC--------CCEEEEEEEECCCC------ >P1;d6j5ya1 CCCCCCCCCCEEECCCCCCEEE--------------CCCEEEEECCC--------HHHHHHCCCCCC--------------------------CCCCEEEEECHHHEEECCCC---------------CEEEEECCCCCCCEEECEEEEEEECCCCCCC---CHHHHHHHEEEEEEEECCEEHHHHHHHHHHCCCCHHHHCCCCCEEEC-CCEEHHHHC-----------------CCCC-----CEEEEEEC--C----EEEEEEEHHH----CCCCHHHHHHHHHH-HCCCCCCCEEECCCCC---------------------------CCEECCCCCEEEEEEC--------CCCEEEEEEE---------- PSA >P1;d1gtta1 -----------------------------------4a3401001000--------55027418a4067----------------74186429---80412503a50106785301006-------------------b-350101000000035606---7076750862050000000001218--614---7747910135000002-7328---39----------------------506812050215--7----8822703056----03260340013006-63307460000000049---024062------------------------b1603020a--------80430401032467299-85 >P1;d1gtta2 ----------------------------8787580253400004700--------5485------------------------------------806115057a0027475303106-------------------b0820001000000036504---7075960362040000000000531--2699-b41266000394000017722538608----------------------603702040306--9----7420533042----02130140022007-533012400000010-8---333053------------------------b14000306--------9055010401349738---- >P1;d1hyoa2 ----------------------------------5a06700003-00--------4300201030128----------------9961159702630113916272036183504113360266a867267-----4408300000000000372189754051960461060000000000020153237-794186012--100010482150a4035123823918480784061b4500040503020307c08932300601043----00000000002104904405620000000000977700000000033277518085b45040064003020502052bc6624096010503517------- >P1;d1nkqa- -----------------------------617106707200002800--------05899449---------------------------------332150434000024a036972027615a50022210100640-605020000000357158399-62460060050000000000-211621486a672760001200-001-311537604835-------------850261----03010107--b----9530300053-----3410260026004-6-50331000000107---------------------------7343062a1030101078------84014716056142944177 >P1;d2eb4a- -------------------5288820240063018024647115100232690546000000410162046492634000022055034b92a294000000044011a--------47260418401------------60401000003046404-07a0538402900440100000004005884----651203000002000002224---------------5060953604-----705040315a------7433534028018100400120033006495205490100000007----20505570505030a--------------9073030504--------------------------- >P1;d2wqta- -------------------9a7583146003302505866812620286086955a0014005221642486a372101002102694088092950000000360318--------4667043a302------------31301000002045406-5590548604800430100000000106915----130000000200010002046---------------3261ab1705-----5040603369------8510424034028100400010043005494407571100001007----316074603020608--------------b0430003059-------------------------- >P1;d3s52a- -----------------16033-----183652a2616200003200--------862083b6955a----------------------------61311304560034047-------------------70a1269664000000000001650670---9-6505700200000000004731590585a5827800119400000-00065970b-----------------6145-----06050207--9----7620730056-----4250430021-06-5330630000000005---------------------------5016-968--105004--------b-4406170----------- >P1;d5d2ka- -----------------a4407893146105500501362541920189368034200120021025204649280300003000930253091752000000440507--------46230409601------------30200000001055406-0890848606a00440000000000005806----042200000000001002027---------------4251960605-----506030125a------75236440440292003000400320172a4305471100000003----016065a16020508--------------c093040606--------------------------- >P1;d6foha- b------------------974-----375--015107500003600--------68a278---------------------------------860611604480002--4b---------------4-3011-1a4084010100000001650750---65a303720200000000002420660586a5726700116000000-700449708-----------------4037-----14020305--6----7430436064----01140130002005-5320360000000108---------------------------7326074705030007--------a2160405036298------ >P1;d6j5ya1 c79895797230504a3b8416--------------04400002200--------4300632a2619--------------------------8660311404250012065c---------------52150821890a4010000000002506680---559501600400000000010400461285a682750010b600000-001009428-----------------2268-----04010306--7----8530623036----03240230002006-6450441000000004---------------------------5025087926040407--------b065010405---------- Translating the sequences -----------------------------------*CC*EEEE*CCC--------HHHHHH*******----------------********---CC*EEEE*HHHEE**********-------------------*-*CEE*CEEEEEEECCCCC---C*CHHHHHHHEEEEEEEECC*****--***---CCCHHHH*C*CCEE*C-CC**---**----------------------****CEEEEEEC--C----EEEEEEEHHH----*CCCHHHHHHHHH*-CCCCCCCCEEECCCCC*---******------------------------CC*EEEEE*--------*****************-** ----------------------------********CC*EEEECCCC--------****------------------------------------CC*EEEE*HHHEE**********-------------------***CEE*CEEEEEEECCCCC---C*C***HHHHEEEEEEEECCE****--****-*CCCHHHH*C*CCEE*C*CC*******----------------------****CEEEEEEC--C----EEEEEEEHHH----*CCCHHHHHHHHH*-CCCCCCCCEEECCCC-*---******------------------------CC*EEEEE*--------****************---- ----------------------------------**CC*EEEEC-CC--------HHHHHH*******----------------***********CC*EEE*****EE***********************-----****CEE*CEEEEEEECCCCC*C*C*CHHHHHHHEEEEEEEECCE****HHH***-*CCC*HHH*--CCEEEC*CC************************C********CEEEEEE***C****EEEEEEE***----*CCCHHHHHHHHH**CCCCCCCCEEECCCCC**********************************CC*EEEEE**********************------- -----------------------------*******CC*EEEECCCC--------***HHH**---------------------------------C*EEEE*HHH*********************************-CEE*CEEEEEEECCCCC*C*C-CHHH*HHHEEEEEEEECC**-**HHH*****CCCHHHH*C*CC-**C-CC**********-------------*C****----*EEEEEEC--C----EEEEEEE***-----CCCHHHHHHHHH*-C-CCCCCCEEECCCCC---------------------------*******CC*EEEEE***------******************** -------------------************************CC**********HHHHHH**********************************CC*EEEE*HHHEE*--------***********------------C*E**EEEEEEECCCCC-C*C*CHHHHHHHEEEEEEEE**E********----C**HHHH*C***EEE***C**---------------*******C**-----*CEEEEEEC*------EEEEEEEHHH*****C**HHHHHHHHH**CCCCCCCCEEECCCCC*----***************--------------***EEEEE**--------------------------- -------------------************************CCC*********HHHHHH**********************************CC*EEEE*HHHEE*--------***********------------C*E**EEEEEEECCCCC-C*C*CHHHHH**EEEEEEEE**E****HHH*----CC*HHHH*C*****E***C**---------------*******C**-----*CEEEEEEC*------EEEEEEEHHH********HHHHHHHHH**CCCCCCCCEEE***CC*----***************--------------CC*EEEEE***-------------------------- -----------------*****-----*********CC*EEEE*CCC--------HHHHH*******----------------------------CC*EEEE*HHHEE****-------------------*********CEE*CEEEEEEECCCCC*C---C-**HHHHEEEEEEEECCE****HHH*****CCCHHHH*C*CCEEEC-CC*******-----------------C***-----CEEEEEEC--C----EEEEEEE***-----CCCHHHHHH*-**-CCCCCCCCEEECCCCC---------------------------****-**C--**EE**--------*-*******----------- -----------------**************************CC**********HHHHHH**********************************CC*EEEE*HHHEE*--------***********------------C*E**EEEEEEECCCCC-C*C*CHHHHHHHEEEEEEEE**E****HHH*----CC*HHHH*C***EEE***C**---------------*******C**-----*CEEEEEEC*------EEEEEEEHHH********HHHHHHHHH**CCCCCCCCEEECCCCC*----***************--------------CC*EEEEE**--------------------------- *------------------***-----***--****CC*EEEECCCC--------***HHH---------------------------------*CC*EEEE*HHHEE*--**---------------*-****-*****CEE*CEEEEEEECCCCC*C---CHHHHHHHEEEEEEEECCE****HHH*****CCCHHHH*C*CCEEEC-CC*******-----------------C***-----CEEEEEEC--C----EEEEEEEHHH----*CCCHHHHHHHHH*-*CCCCCCCEEECCCCC---------------------------*******CC*EEEEE*--------**************------ **********************--------------CC*EEEE*CCC--------HHHHHH******--------------------------**CC*EEEE*HHHEE*****---------------************CEE*CEEEEEEECCCCC*C---CHHHHHHHEEEEEEEECCE****HHH*****CCCHHHH*C*CCEEEC-CC*******-----------------C***-----CEEEEEEC--C----EEEEEEEHHH----*CCCHHHHHHHHH*-*CCCCCCCEEECCCCC---------------------------*******CC*EEEEE*--------**********---------- 56529.tem _________________________________ -------------------***-----*********CC*EEEECCCC--------HHHHHH*******----------------***********CC*EEEE*HHHEE*********************-****-*****CEE*CEEEEEEECCCCC*C*C*CHHHHHHHEEEEEEEECCE****HHH*****CCCHHHH*C*CCEEEC*CC*******----------*******C***----*CEEEEEEC*-C----EEEEEEEHHH----*CCCHHHHHHHHH**CCCCCCCCEEECCCCC*----***************-------*******CC*EEEEE**-------**************------ Structural block scores 0 18 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 67.5 67.9 71.7 6.3 19 21 * 3.0 P 75.0 75.0 75.0 75.0 5.0 8.8 2.0 3.7 6.7 3.7 22 26 - 4.1 M 75.0 75.0 75.0 75.0 4.0 4.2 75.0 5.0 75.0 75.0 27 35 * 2.6 P 67.1 13.3 60.1 19.8 2.4 2.1 4.8 2.4 19.1 75.0 36 37 C 4.1 M 6.8 4.0 3.0 3.5 3.0 6.5 3.5 2.0 3.5 2.0 39 42 E 4.1 M 0.2 0.0 0.0 0.0 3.2 4.2 0.0 3.0 0.0 0.0 43 46 C 4.3 M 0.2 2.8 19.5 2.5 1.5 2.5 1.2 3.0 2.2 1.0 47 54 - 4.1 M 75.0 75.0 75.0 75.0 3.9 5.9 75.0 5.1 75.0 75.0 55 60 H 4.4 M 3.8 28.7 1.5 5.8 1.0 2.6 4.5 0.8 6.9 2.7 61 67 * 2.5 P 5.2 75.0 2.1 55.4 2.0 2.9 17.4 1.7 75.0 15.1 68 83 - 4.1 M 75.0 75.0 75.0 75.0 2.6 3.0 75.0 2.4 75.0 75.0 84 94 * 3.4 M 24.2 75.0 5.0 75.0 5.5 5.2 75.0 3.5 68.9 62.6 95 96 C 4.8 H 4.0 4.0 1.5 39.0 2.0 2.5 3.5 3.5 3.0 3.0 98 101 E 4.9 H 2.0 1.8 3.5 2.0 0.0 0.0 1.2 0.0 2.0 1.5 103 105 H 4.7 H 5.2 5.8 3.7 2.3 2.7 3.0 3.7 2.7 4.0 2.3 106 107 E 4.7 H 0.5 1.0 1.5 0.0 1.0 2.0 1.5 2.5 0.0 0.5 108 128 * 3.2 M 41.0 41.0 4.2 3.9 34.4 34.7 61.4 34.1 61.7 55.0 130 133 * 3.8 M 75.0 75.0 58.0 1.0 75.0 75.0 23.1 75.0 1.2 3.5 135 139 * 3.1 M 47.9 33.9 18.2 17.0 75.0 75.0 5.8 75.0 4.7 5.7 141 142 E 4.5 M 0.5 0.0 0.0 2.5 2.0 2.0 0.0 1.0 0.5 0.5 145 151 E 5.0 H 0.0 0.0 0.0 0.0 0.4 0.3 0.0 0.1 0.0 0.0 152 156 C 5.0 H 4.0 3.6 4.2 4.2 3.6 3.8 3.6 4.0 3.8 3.8 163 169 H 4.7 H 4.9 4.4 3.9 2.6 3.7 4.3 14.0 4.9 4.4 3.7 170 177 E 5.0 H 0.6 0.5 0.8 0.6 1.1 1.0 0.2 1.0 0.2 0.5 178 179 C 4.1 M 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 181 184 * 1.1 P 3.0 2.2 0.5 19.5 1.0 0.2 3.5 0.0 2.0 1.2 185 187 H 4.3 M 52.0 50.7 3.0 3.0 7.0 5.3 5.0 4.3 4.0 3.3 188 192 * 2.7 P 46.0 22.1 18.8 5.9 60.8 61.0 5.7 61.2 5.9 5.3 193 195 C 4.6 H 6.0 2.3 4.7 5.0 4.0 1.3 5.0 2.0 4.7 5.3 196 199 H 4.9 H 4.2 3.0 3.8 3.2 1.2 0.0 3.8 0.5 3.2 3.0 203 204 C 4.1 M 0.0 2.0 0.5 0.0 1.0 0.0 2.0 0.0 0.0 3.0 205 207 E 4.4 M 0.0 0.0 0.3 25.0 0.0 0.3 0.0 0.3 0.0 0.0 210 211 C 4.5 M 5.0 4.5 5.0 2.0 2.0 1.0 0.0 1.0 3.5 0.0 212 218 * 2.3 P 35.3 4.6 3.4 3.7 54.4 55.0 5.5 54.9 4.6 3.4 219 228 - 4.6 H 75.0 75.0 4.2 54.1 75.0 75.0 75.0 75.0 75.0 75.0 229 235 * 3.7 M 75.0 75.0 4.4 65.4 4.0 5.0 75.0 3.9 75.0 75.0 237 239 * 2.5 P 75.0 75.0 5.5 2.7 26.3 26.7 3.3 26.7 3.3 5.3 240 243 - 4.2 M 21.5 21.0 1.2 56.5 75.0 75.0 75.0 75.0 75.0 75.0 246 251 E 5.0 H 1.7 1.5 1.7 0.8 2.2 2.7 2.2 2.0 1.5 1.3 256 259 - 4.7 H 75.0 75.0 5.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 260 266 E 5.0 H 4.3 3.4 1.7 2.9 4.1 3.4 3.6 4.4 3.9 3.9 267 269 H 4.1 M 3.7 2.0 2.3 2.7 3.3 2.3 3.7 2.7 3.3 3.0 270 273 - 4.1 M 75.0 75.0 75.0 75.0 2.5 2.8 75.0 3.2 75.0 75.0 275 277 C 4.2 M 3.7 2.0 0.0 2.7 1.3 1.3 3.7 1.0 2.0 3.0 278 286 H 4.9 H 1.2 1.0 0.3 1.8 1.0 0.9 9.4 1.1 0.7 0.8 287 288 * 2.4 P 40.5 41.0 6.5 39.5 5.0 4.5 40.5 4.5 40.0 40.5 289 296 C 4.9 H 3.6 2.2 2.6 11.6 4.2 4.6 2.5 4.3 2.4 3.0 297 299 E 5.0 H 0.0 0.0 0.0 0.0 0.3 0.3 0.0 0.3 0.0 0.0 300 304 C 4.8 H 0.8 15.2 0.0 1.6 0.0 0.2 1.0 0.0 1.8 0.8 306 309 - 4.6 H 56.2 57.0 7.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 310 324 * 3.5 M 50.9 50.9 1.8 75.0 3.2 3.1 75.0 3.4 75.0 75.0 325 331 - 4.7 H 75.0 75.0 5.4 75.0 75.0 75.0 75.0 75.0 75.0 75.0 332 338 * 3.5 M 75.0 75.0 2.7 3.6 75.0 75.0 14.6 75.0 4.1 3.9 339 340 C 4.6 H 6.2 6.2 0.0 5.8 4.5 5.8 41.5 6.2 3.5 5.5 342 346 E 4.8 H 1.0 0.6 1.4 1.0 2.2 1.2 1.2 2.6 0.6 1.6 347 348 * 2.2 P 42.8 40.5 1.0 3.5 2.0 2.5 39.5 3.0 41.0 41.0 349 355 - 4.6 H 75.0 75.0 6.4 65.4 75.0 65.6 75.0 75.0 75.0 75.0 356 369 * 2.9 P 3.0 3.4 8.3 3.5 75.0 75.0 34.5 75.0 4.0 23.8 370 375 - 4.4 M 18.0 51.8 75.0 5.3 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>