Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cb8a1 ----------------CHHHHHHHHHHHHHCC---------------CCCCHHHHHHHHHHHCCC---------CCCCCCCCCCC-----------------CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHC-CHHHHHHHCCCCC------CHHHHHCHHHHHHHHHHHHHHH--CCCCCCHHHHHHCCC-------CCCHHH-------CCHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHHC--CCCEECC-CCEEECCCCEECCCCCC--CCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-----CCCCCHHHCCHHHHHHHCH-HHHHHHHHHHHHHCCCCCCCCC--------------------------- >P1;d1egua1 ---------------CCCHHHHHHHHHHHHCCHHHCCCCCHHHH--HHHHHHHHHHHHHHHHCCCCC-----CCCCCCHHHCCCC-----------------CC--HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCCHHHHHCHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHCCCCCEECCCCCCCE--ECCHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHHH--HHCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC--HHHHHHHHCCHHHEECCEECHHHCHHHHHCH-HHCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHHHHHHHHCCCCCCCCC >P1;d1hn0a1 CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCC--CCEECCCCCEECCCEECCCHHHHHCHHHCCHHHHHHHCCCEEH--HHHHHHHHHHHHHHHH--CCCHHHH--HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHH--H--CCCHHHHHHHHHHHHHHHH--HHHCCCCCCCCCCHHHHHHCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-HHCCCCCCCCEECCCCCEEECC-EE--CHH-HHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHHHHHH-HHHHCCC-CCCCHHHCCCCCC------CCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC-----------CCHHHHHHHHC----CCCCCCCC >P1;d1rwaa1 -------------CCHHHHHHHHHHHHHHHHCCCCCCCCCHHHH--HHHHHHHHHHHHHHHCCCCCC-----CCCCCCCCCC-CC-----------------CH--HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCCHHHHHCHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHCCCCCEECCHHHCCE--ECCHHHHHHHHHHHHHHHHHHCC----HHHHHHHHHHHHH--HHCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC-HHHHHHHHHHHHHC-CCCCCC >P1;d1x1ia1 ---------------CCHHHHHHHHHHHHHHCCCCCCCCCHHHH--HHHHHHHHHHHHHHHHCCCCC-----CCCCCCHHHCCCC-----------------CH--HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHCHHHHHHHCC-CCCHH--HCCHHHHHHHHHHHHHHCCCCC-------------CCHHHHHHHHHHHHHHHHHHCC----HHHHHHHHHHCCCCCCCCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-CCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHCC-HHHHHHHHHHHCCCCCCCCCC >P1;d3evha1 --------CCCCCCCCCCCCCCCCCHHHHHHHHHHC--CCC-----HHHHHHCCCCCCHHHCCCC---CCCCCCCCCCC-----CCCCCCCCCCCCCHHHH--H--HHHHHHHHHHHHHHHHHHHH-----CCHHHHHHHHHHHHHHHHCCCCCCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-----CCCCCCHHHHHHHHHHHHHHHHHCC----HHHHHHHHHHHHH--HHC-------CCCCCCCCCCHHHC-HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCHHHHHHHHHHHHHC-----CHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHH--------CCCCCCCCCCCCCEEHHHCEEHHHHCCCCCC------------ PSA >P1;d1cb8a1 ----------------b436500510154225---------------75a70285068107506a---------7200c050a35-----------------468b05024006302200000018709245589017403-0042026220506------2441220200120020000042--0580a0384004204-------206046-------2500100100001000000485----6910630060005--0042177-72000782201057554--010210240040002001003807230588326--2004000310072072060577003714858-----a23415a042062034008-7358504101220267294545--------------------------- >P1;d1egua1 ---------------5472151054021100017406692a304--701841184038018610b1b-----7491007822717-----------------60--6100300420120010020540613638501620370040024500139380-586130000000200010000008--3054920540040023003314402322a833--40300100000000000000124----7900430070013--00823a9-82202780602048947--000110040010001003003609440699317--202300450015207804045800461585a-b2701300030010000004219a73373023100001550a71501610410300310380285aa071884 >P1;d1hn0a1 68509153269336349803710650161016101892917709235828503741860--70865aba2080240004312763609918a944981672140--3900200000001124--1a68833--75046001100400052503563428405502500200000000018005--9--3b11750030021000212--a10207364700403002310000000000036447001000000600250-043606c241000680303258-62--104-20030010000001002802040766016--2025002-1017209-4608583066658------90230670230020002008a211750020001029-----------275b506a209----450722a8 >P1;d1rwaa1 -------------588950570174003210037416bc17207--801651384075028312a7b-----d162006505-09-----------------72--8301400500120020110380715559901720260043018310147370-787130000000300020000029--406a9228401400240043044000855b26--60400300000100000000333----4930740160037--00323a9-52202882502077836--000130040030003014005a25040738537--201700480015206502027910470584a-834135001300100000048169a20650201010026319664028907-0220100150883a-385394 >P1;d1x1ia1 ---------------8541170173032101018906582a304--72085008405722870347b-----a082007715745-----------------60--63013006203201100103409055498015200400310375001693648592431010000200010-00029--407a921630070034004808-------------4500220100000001000334----5a20450270044600033198-52002781602067766--000010220060002001002b17130728626--1004001500452085010457105615839-817313100800200000021059722830340001005209746018405-0000310270274891732a7 >P1;d3evha1 --------3525925075241001518611730673--b04-----a106604194370582a11---9029b606017-----4368b988652672552--1--42054006000200000011-----25340040006000300635101606395-50031001000000000000161780667016401600250054006282a-----b712200000000000000000052----3700230011013--004-------20393000520074-6530002002000000000000130917007254a93102300700050166-----5840472093804540064332100000001133--------828240810662041230001000011518f------------ Translating the sequences ----------------CHHHHHHHHHHHHH*C---------------****HHHHHHHHHH*CCC---------CCCCC**C*CC-----------------C******HHHHHHHHHHHHHH*CCCCCCCCCHHHHHHH*-*HHHHHHHCCCCC------CHHHHHCHHHHHHHHHHHH***--CCC***HHHHHH***-------**C***-------CCHHHHHHHHHHHHHHHHH*CC----HHHHHHHHHHHH*--**C**CC-CCEE*CCCCEE*CCC**--CCCCHHHHHHHHHHHHHHHHCCCCCCCC*HHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-----*****HHH**HHHHH**C*-*HHHHHHHHHHHH***CCCCC*--------------------------- ---------------CC*HHHHHHHHHHHH*C***CCCCC****--HHHHHHHHHHHHHHH*CCCCC-----CCCCCC***C*CC-----------------C*--HHHHHHHHHHHHHHHHH*CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCCHHHHHCHHHHHHHHHHHHC**--CCCHHHHHHHHHHHHHH****C**C*******--*CCHHHHHHHHHHHHHHHHH*CC----HHHHHHHHHHHHH--HHCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCC*****--HHHHHHHHCCHHHEECCEECHHHCHHHHHC*-**C****HHHHHHHHHHHH**CC**HHHHHHHHHHHHH**CCCCC*****C*HHHHHHHH*****C*CCCCCC ***************C*HHHHHHHHHHHHHH****CCCCC********HHHHHHHHH**--*C**CC*****CCC**CC************************H--HHHHHHHHHHHHHHHH--CCC****--HHHHHHHHHHHHHHHH*CCCCCCCC*CCC*HHHH*HHHHHHHHH*HH***--*--***HHHHHHHHHHH*****--***********CCHHHHHH*HHHHHHHHH**CC****HHHHHHHHHHHHH*-HHCCCCC*CCEECCCCCEEECC-EE--C**-HHHHHHHHHHHHHHHHCCCCCCCC*HHHH--HHHHHHH-**HH***-C**CHHHC*****------****HHHHHHHHHHHH**CC****HHHHHHHHHHH*-----------C*HHHHHHHH*----C*CCCCCC -------------****HHHHHHHHHHHHHHC***CCCCC****--HHHHHHHHHHHHHHH*CCCCC-----CCCCCCC**C-CC-----------------CH--HHHHHHHHHHHHHHHHH*CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CCCHHHHHCHHHHHHHHHHHHC**--CCCHHHHHHHHHHHHHH****C**C*******--*CCHHHHHHHHHHHHHHHHH*CC----HHHHHHHHHHHHH--HHCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCC*HHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-**C****HHHHHHHHHHHH**CC**HHHHHHHHHHHHH**CCCCC*****C-HHHHHHHH*****C-CCCCCC ---------------CCHHHHHHHHHHHHHHC***CCCCC****--HHHHHHHHHHHHHHH*CCCCC-----CCCCCC***C*CC-----------------CH--HHHHHHHHHHHHHHHHH*CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC*CCCHHHHHCHHHHHHH**-**C**--*CCHHHHHHHHHHHHHH****C-------------CCHHHHHHHHHHHHHHHHH*CC----HHHHHHHHHH*******CCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCC*HHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-**C****HHHHHHHHHHH***CC**HHHHHHHHHHHHH**CCCCC*****C-HHHHHHHH*****C*CCCCCC --------*******CC********HHHHHH****C--CC*-----HHHHHH******HHH*CCC---****CCCCCCC-----C****************--H--HHHHHHHHHHHHHHHHH***-----CCHHHHHHHHHHHHHHHH*CCCCCCCC*C-*HHHHH*HHHHHHHHHHH*C****CCCHHHHHHHHHHHHHH****C**C**-----***CC*HHHHHHHHHHHHHHHH*CC----HHHHHHHHHHHHH--HHC-------**CCCCC*******-******HHHHHHHHHHHHHHHH*CCCCC**********HHHHHHH**HHH**-----*HH*H****CC***C******HHHHHHHHHH***--------**********CCC*********HHH******------------ 48230.tem _________________________________ -------------**CCHHHHHHHHHHHHHHC***CCCCC****--HHHHHHHHHHHHHHH*CCCCC-----CCCCCCC**C*CC-----------------CH--HHHHHHHHHHHHHHHHH*CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC*CCCHHHHHCHHHHHHHHHHHHC**--CCCHHHHHHHHHHHHHH****C**C*******--*CCHHHHHHHHHHHHHHHHH*CC----HHHHHHHHHHHHH--HHCCCCC-CCEECCCCCEEECCCEE--CCCCHHHHHHHHHHHHHHHHCCCCCCCC*HHHH--HHHHHHHHCCHHHEECCEECHHHCHHHHHCC-**C****HHHHHHHHHHHH**CC**HHHHHHHHHHHHH**CCCCC*****C*HHHHHHHH*****C*CCCCCC Structural block scores 0 12 - 4.3 M 75.0 75.0 4.6 75.0 75.0 48.0 13 14 * 3.4 M 75.0 75.0 4.5 6.5 75.0 3.5 15 16 C 4.2 M 43.2 4.5 6.5 8.5 6.5 3.5 17 30 H 4.6 H 2.7 2.1 2.8 2.5 2.2 3.0 32 34 * 1.9 P 75.0 4.0 0.7 4.7 6.0 4.3 35 39 C 4.4 M 75.0 4.6 5.8 6.4 4.2 32.9 40 43 * 2.5 P 75.0 4.4 5.8 4.0 4.4 57.2 44 45 - 4.5 M 75.0 75.0 2.5 75.0 75.0 75.0 46 60 H 4.5 M 9.4 3.6 13.8 3.9 3.9 4.3 62 66 C 4.5 M 33.3 5.0 5.9 6.4 5.1 32.5 67 71 - 4.2 M 75.0 75.0 6.4 75.0 75.0 19.0 72 78 C 4.6 H 24.5 4.0 1.4 4.1 3.9 4.5 79 80 * 1.9 P 2.5 5.0 2.0 2.5 4.0 75.0 83 84 C 4.3 M 4.0 4.0 4.5 4.5 4.5 39.5 85 101 - 4.1 M 75.0 75.0 5.6 75.0 75.0 9.9 104 105 - 4.5 M 9.8 75.0 75.0 75.0 75.0 75.0 106 122 H 4.9 H 1.4 1.2 5.7 1.6 1.6 1.4 124 132 C 4.4 M 4.6 3.1 21.1 3.8 3.3 42.7 133 149 H 4.9 H 7.2 2.8 2.1 3.2 2.8 1.7 150 157 C 4.8 H 29.8 3.0 3.5 2.9 3.6 2.8 159 161 C 4.4 M 50.7 6.3 3.0 7.3 5.3 28.3 162 166 H 4.9 H 2.6 0.8 2.4 0.8 1.8 0.8 168 179 H 4.7 H 0.6 0.2 0.9 0.4 6.5 0.1 181 182 * 1.0 P 3.0 4.0 2.5 5.5 5.5 3.5 183 184 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.0 185 187 C 4.4 M 4.3 2.7 53.0 3.3 3.7 4.7 188 201 H 4.6 H 13.2 2.4 2.5 3.3 3.2 2.7 202 205 * 1.9 P 75.0 1.8 0.8 1.8 3.0 2.2 207 208 * 2.7 P 1.0 2.0 75.0 2.0 75.0 4.0 210 216 * 2.9 P 44.3 4.5 2.7 5.4 75.0 55.4 217 218 - 4.1 M 75.0 75.0 5.5 75.0 75.0 9.2 220 221 C 5.0 H 3.5 1.5 2.0 2.0 4.5 2.0 222 238 H 4.9 H 0.2 0.1 0.5 0.2 0.4 0.0 240 241 C 5.0 H 6.5 3.0 4.5 3.0 3.5 3.5 242 245 - 4.5 M 75.0 75.0 3.8 75.0 75.0 75.0 246 258 H 4.9 H 2.8 2.6 1.1 3.4 3.3 1.6 259 260 - 4.3 M 75.0 75.0 37.5 75.0 3.0 75.0 261 262 H 4.1 M 0.0 0.0 2.0 0.0 0.0 0.0 263 267 C 4.5 M 4.2 6.5 5.5 5.5 4.8 60.8 269 270 C 4.5 M 4.5 5.0 2.5 3.5 3.5 75.0 271 272 E 4.5 M 0.0 1.0 0.0 1.0 0.0 1.0 273 277 C 4.9 H 3.8 4.6 3.4 5.0 4.8 3.0 278 280 E 4.4 M 0.3 0.7 1.7 0.7 0.7 2.3 281 283 C 4.4 M 5.7 7.0 29.3 7.3 6.7 2.3 284 285 E 4.2 M 4.5 5.5 4.0 4.5 6.0 39.5 286 287 - 4.5 M 75.0 75.0 75.0 75.0 75.0 5.5 288 291 C 4.2 M 0.8 0.2 20.0 0.2 0.0 0.8 292 307 H 5.0 H 0.9 0.6 0.4 1.1 0.9 0.2 308 315 C 4.8 H 3.5 4.0 2.9 4.2 4.1 2.6 317 320 H 4.1 M 4.8 5.0 3.2 5.8 5.5 5.4 321 322 - 4.5 M 75.0 75.0 75.0 75.0 75.0 6.0 323 330 H 4.9 H 1.1 2.0 10.8 2.8 1.4 1.6 331 332 C 4.1 M 0.5 0.0 0.5 0.0 0.0 0.0 333 335 H 4.8 H 3.0 2.7 3.3 2.7 3.7 2.0 336 337 E 4.1 M 3.5 3.5 4.5 3.0 4.0 6.0 338 339 C 4.4 M 1.0 4.0 39.5 2.5 2.5 75.0 340 341 E 4.2 M 3.0 2.0 3.0 1.0 0.5 75.0 343 345 H 4.8 H 4.7 4.3 5.3 5.7 4.3 5.7 347 351 H 4.2 M 4.6 4.8 6.2 4.8 5.0 4.4 352 353 C 4.3 M 6.5 7.8 75.0 7.2 6.0 5.5 355 356 * 2.7 P 75.0 6.8 75.0 5.5 4.5 4.5 358 361 * 1.2 P 22.6 1.0 3.5 2.2 2.0 2.5 362 373 H 4.7 H 3.1 0.3 1.7 0.4 0.8 0.8 374 375 * 1.0 P 2.0 3.0 1.0 6.0 1.5 2.0 376 377 C 4.3 M 4.0 5.0 4.0 3.5 2.5 39.0 378 379 * 2.3 P 41.0 8.8 6.2 9.8 8.0 75.0 380 392 H 4.4 M 2.5 1.8 1.5 1.5 1.8 31.4 393 394 * 1.4 P 6.5 5.0 42.0 4.5 3.5 3.0 395 399 C 4.4 M 4.8 4.7 75.0 5.2 5.2 2.6 400 404 * 2.5 P 61.0 1.6 75.0 3.8 2.6 1.0 407 414 H 4.3 M 75.0 1.2 5.0 0.8 0.8 2.0 415 419 * 3.1 M 75.0 4.6 61.8 4.8 4.0 64.5 422 427 C 4.3 M 75.0 4.7 4.9 5.3 5.1 75.0 >>>>>>