Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2yzsa- --------------CCEEEECCCEEEEEECCEEEEECC----CCEEEECHHHCCEEEECCCEECCHHHHHHHHHHCCCEEEECCCCC----------EEEEECCCCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHH---------CCC---------CHHHHHHHHHCCCCCCC-CHHHHHHHHHHHHHHHHHC-CCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHCHHHHHHHHHCCCCCHHHEECCCCCEECHHHHHHHHHHHHHHHHCEEEEHHHCEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHC >P1;d3goda- CCCHHHHHHHHHHCCCEEEEECCEEEEEECCEEEEEEEECCEEEEEECCHHHEEEEEECCCEEEC-CCCCHHHHCCCEEEEECCCCCCCEEECCEEECEEEECCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCHHHHHHHHCC-------------CCC-----HHHHHHHHHHHHHH----------CCCCCCC-HHHHHHHHHCCC------------- >P1;d3nkea- -------------------------------------------------------------------------------------------------------------------------CHHHHHHHHHHHHHCHHHHHHHHHCCHHHHC----------------CCCCCC----CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCHHHHHHHHHHCCCCHHHHHHHHHHHCCC---------------CHHHHHHHHHHHHHHHH----------CHHHHHHHHHHHHHHCCCCCCC---------- >P1;d4w8ka- --------CCCHHHCCEEEEECCEEEEEECCEEEEEC--CCC-CEEEECHHHEEEEEECCCEEECHHHHHHHHHCCCEEEECCCC---------CCCCCEEECCCCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCC------CCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH------------CCC-----HHHHHHHHHHHHHH----------CCHHH---HHHHHHHHHHHCC------------ PSA >P1;d2yzsa- --------------540210267250333981020429----945551508503000000907278702900273100003057508----------14603109376729704710440275a9312400100030002003200---------628---------08712750881952840-6017501740363048309-1807-----b351202001600330010000000030404041001372-462000200010020000040014005585056910354990002670043007002620565151584a66020220042005301410255770801602716 >P1;d3goda- b44885571581061430200370501259950010274ca724456032960000000680715-930520562100003023c15024269a211105062088393375147204802756752070011004200710361015176076490807683036006305630570561860281175028401600070092b9092396071a44004001002000001000000002051710001597264000100010021000000000005-------------917-----47501620171054----------3700420-600340066149------------- >P1;d3nkea- -------------------------------------------------------------------------------------------------------------------------a57723700450085880233003204211a----------------580359----4608604a3266427830661086271b0a6266c---6640040042007202a10440044030215500345b-783000210021210860022003006582c---------------72353044206611864----------7047703620350042073a42---------- >P1;d4w8ka- --------b48205024020127060205b8500123--b79-63550435400000017a0705b602720473100002090b---------77150505208a79248621620460365795027002400400260055051b------3008175a50560287048306909617401a317501810171018419-2a08155--a3a541040031031000000100011010628220045991712002000000100000000020046------------827-----57502740271048----------35003---2017003600394------------ Translating the sequences --------------CCEEEE*CCEEEEEECCEEEEE**----**EEE*CHHH**EEEECCCEE*C*****HHHH*CC*EEE*CCC**----------**EEECCCCCCCC*HHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHHHH*---------CCC---------*HHHHHHHH*CCC****-*HHHHHHHHHHHHHHHH*C-CCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHH*CCCCCCCCCCCCC-CCCHHHHHHHHHH*****HHHHHHHHH*************CC******HHHHHHHHHHHHH*************HHH***HHHHHHHHH*CCC************ **************CCEEEE*CCEEEEEECCEEEEE********EEE*CHHH**EEEECCCEE*C-****HHHH*CC*EEE*CCC**************EEECCCCCCCC*HHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHHHH**********CCC**********HHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHHH*C*CCCCCCC**CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC*CCCHHHHHHH****CCCHHHHHHHH**-------------CC*-----HHHHHHHHHHHHHH----------*C*****-HHHHHHHHH*CC------------- -------------------------------------------------------------------------------------------------------------------------**HHHHHHHHHHHH*HHHHHHHHH*******----------------******----CCHHHHHHHHHHHHHHHHHHHHHH*C*CCCCCCC*---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CCCHHHHHHHHHH*CCCHHHHHHHHHH****---------------**HHHHHHHHHHHHHH*----------CHHH***HHHHHHHH**CCC**---------- --------******CCEEEE*CCEEEEEECCEEEEE*--***-*EEE*CHHH**EEEECCCEE*C*****HHHH*CC*EEE*CCC---------*****EEECCCCCCCC*HHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHHH****------*CCC**********HHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHHH*C-CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHH*CCCCCCCCCCCC*CCC*HHHHHHHHH*CCCHHHHHHHHHH*------------CC*-----HHHHHHHHHHHHHH----------*CHHH---HHHHHHHHH**CC------------ 310599.tem _________________________________ --------******CCEEEE*CCEEEEEECCEEEEE**-*****EEE*CHHH**EEEECCCEE*C*****HHHH*CC*EEE*CCC**-------*****EEECCCCCCCC*HHHHHHHHHH*CHHHHHHHHHHHHHHHHHHHHHH*******--*CCC**********HHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHHH*C*CCCCCCC*-CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC*CCCHHHHHHHHHH*CCCHHHHHHHHHH****---------CC*---**HHHHHHHHHHHHHH*---------*CHHH***HHHHHHHHH*CCC**---------- Structural block scores 0 7 - 4.3 M 75.0 6.6 75.0 75.0 8 13 * 3.5 M 75.0 3.5 75.0 5.1 14 15 C 4.3 M 4.5 2.5 75.0 1.0 16 19 E 4.3 M 0.8 1.2 75.0 1.5 21 22 C 4.3 M 6.5 5.0 75.0 4.5 23 28 E 4.3 M 2.7 2.2 75.0 2.2 29 30 C 4.3 M 8.5 9.0 75.0 9.8 31 35 E 4.3 M 1.4 1.2 75.0 1.6 36 37 * 2.9 P 5.5 4.5 75.0 39.0 39 43 * 3.3 M 47.6 7.2 75.0 21.7 44 46 E 4.3 M 5.0 5.0 75.0 4.3 49 51 H 4.3 M 4.3 5.7 75.0 4.0 52 53 * 2.3 P 1.5 0.0 75.0 0.0 54 57 E 4.3 M 0.0 0.0 75.0 0.0 58 60 C 4.3 M 3.0 4.7 75.0 6.2 61 62 E 4.3 M 3.5 3.5 75.0 3.5 65 69 * 2.5 P 5.2 18.4 75.0 5.3 70 73 H 4.3 M 2.2 3.2 75.0 3.2 75 76 C 4.3 M 0.5 0.5 75.0 0.5 78 80 E 4.3 M 1.0 1.0 75.0 0.7 82 84 C 4.3 M 5.7 5.8 75.0 6.8 85 86 * 3.5 M 4.0 3.0 75.0 75.0 87 93 - 4.3 M 75.0 4.8 75.0 75.0 94 98 * 3.0 P 46.0 1.0 75.0 4.0 99 101 E 4.3 M 3.0 3.7 75.0 3.3 102 109 C 4.3 M 4.4 4.5 75.0 5.3 111 120 H 4.3 M 2.9 3.3 75.0 3.0 123 144 H 4.9 H 1.8 2.4 3.4 2.6 145 151 * 2.8 P 64.3 2.9 2.9 45.4 152 153 - 4.3 M 75.0 6.5 75.0 75.0 155 157 C 4.3 M 5.3 5.7 75.0 2.7 158 167 * 3.4 M 67.5 3.3 75.0 4.2 168 175 H 4.3 M 4.8 3.5 22.5 4.5 177 179 C 4.8 H 5.0 3.7 28.3 5.0 180 201 H 4.8 H 6.7 3.0 4.4 3.2 205 211 C 4.7 H 34.4 6.2 6.0 4.5 214 217 C 4.7 H 5.1 5.6 40.5 7.2 218 240 H 5.0 H 0.9 0.5 2.3 0.9 241 253 C 4.9 H 2.0 2.4 3.0 3.0 255 257 C 5.0 H 4.0 4.0 6.0 3.0 258 267 H 4.7 H 0.3 0.2 0.8 0.4 269 271 C 4.3 M 0.0 0.3 4.7 0.0 272 281 H 4.8 H 1.4 0.5 1.3 0.6 282 285 * 3.2 M 4.5 75.0 6.9 57.8 286 294 - 4.3 M 4.7 75.0 75.0 75.0 295 296 C 4.3 M 4.5 5.0 75.0 5.0 298 300 - 4.3 M 2.7 75.0 75.0 75.0 301 302 * 3.5 M 3.5 75.0 4.5 75.0 303 316 H 5.0 H 2.5 3.1 3.5 3.7 318 326 - 4.3 M 5.2 75.0 75.0 75.0 329 331 H 4.3 M 1.3 1.3 3.7 1.0 332 334 * 2.7 P 1.3 25.7 3.3 75.0 335 343 H 4.9 H 1.8 2.8 2.4 2.1 345 347 C 4.5 M 4.0 29.3 6.8 5.3 348 349 * 3.5 M 7.0 75.0 3.0 75.0 350 359 - 4.3 M 3.1 75.0 75.0 75.0 >>>>>>