Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1pt7a- ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCCCCCHHHCCC-CCCC--CCCCHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHHCCEEEECCCCCHHHHCCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCHH-HHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCEEEEECC-HHHHHHHHHHHCCHHHCCCCCCC-----CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCEEECCCHHHHHHCHHHHHCCCEEEEEECCCEEEEEECCCCCCCCCCC--CCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHCCCC---- >P1;d1xk7a2 CCCCCCCCCCCCCEEEEECCCCHHHHHHC-CCCCCCEEEEEECCCCCCHHHHCC-----------CHHHHHCCCCEEEEECCCCHHHHHHHHHC-CCCCEEEEECCCCHHHHCCCCHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHCCCHHHCCCCC--CCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCCEEEEEC-CCCCC--CCCCC--CCC----------------C-CCCCCCC-CCCCCCCCCCCEEECC------EEEE-CCCCHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCEECCCHHHCCCCHHHHHHCCEEEEECC-CCEEEEECC-CCCCCCCCC-CCCCC-CCC-CHHHHHHHCCCCHHHHHHHHHCCCEECCC >P1;d2yima- ------CCCCCCCEEEEECCCCHHHHHHHHHHHCCCEEEEEECCC-CCC-------------------CHHHCCCEEEECCCCCHHHHHHHHHHHCCCCEEEECCCCCHHHHHCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHCCCCHHHCCCCCCCCCCCCCIIIIIIIIHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHCHHHHHHHHC----------------CCCCCCCCCCCCCCCCCCEEEEECCCC-----CEEEEECCCHHHHHHHHHHHCCCHHH----------CCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCEEECCCHHHHHHCHHHHHCCCEEECC------CEEECCCCCCCCCCCC-CCCCCCCCC-CHHHHHHHHCC------------------ >P1;d4ed9a- ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECC--CCHHHHCCCCEEEECCEEEHHHHCCCCCCEEEECCCCC-CCHHHHHHHHHCCCEEEECC-CCCCHHHCCCHHHHHHHCCCCEEEEEECCCCCC--CCCC-CCCHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHH-CCEEEEEEHHHHHHHCCHHHHHHHHHHC-----------------CCCCCCCCCCCCCCCEEEEEECC------EEEEEECCCHHHHHHHHHHCCCHHHCC--CCC-----CHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCC-CCCCEEC---HHH--CCEECCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHC-------------------- >P1;d4hl6a- ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCCCCCHHHHCC-CEEC---CEEHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHCCEEEECCCCCHHHHCCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHHCHHHHCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHCCCCHHHHHHHHHC-----------------CCCCCCCCCCCCCCCEEEECCCC------CCEEEECCCHHHHHHHHHHHCCHHHCCCCCCC-----CHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEECCCHHHHCCCHHHHHCCCEEEE---CC--EEEECCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHCC------------------ >P1;d5yx6a- -----CCCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCC-CCHHHCCC-EEECCEEEECCCCHHHCCCCEEEECCCCCCC-CCHHHHHHHCCCEEEECCCCCCCC-CCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHCCCCCCCCCCC-CCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHCC-CCCC--------------------------------CCCCCEEEEECCC------CEEEEECC--CCHHHHHHHCCCHHHCC--CCC-----C--CCCC--CHHHHHHHHHHCCCCHHHHHHHHHHCCCEEEECCCC-CHHHCHHHHHCCCEEEEC-----CEEEECCCCCCCCCCCCC--CCCCCCCCCHHHHC----------------------- PSA >P1;d1pt7a- ------83407b14000003520000000000003040000061a601500548-3548--9110330041001020010316494046003400530100001475410571605284028015500000020059a1--76494909264006207016142438475543b8210141-0031008403601750774950432420024005551752640372078584073001338790ab60212042146a320120307737957302030102-58006500500925711948613-----74920133048007202720362505702840682804061332884346387339663024070470660307004553b9191--80620032052164005509078a61860796800---- >P1;d1xk7a2 77085910211b14000126512003000-002200200000617820602957-----------84123100000000030157303700040-360400002260220456804282037315600000002001967a84144447064205306327337459--834295622236-1064008302811761654470521300-35158--33936--869----------------b-7a15258-8132240005307036------4505-6054472033005209057016283059526403169163063017405710583509505830871a08162537a74359488377583225060a-954143530-7439a7505-01401-610-204500721927aa418504847002379 >P1;d2yima- ------70226a13000003840102001100002040000384a-84a-------------------6331000310316185b81361024002402000012505205715012a405741750000001001297--941668170550044180163335497927428562012400053008404701951a93760641410027103742762652587----------------a60677104042111000414060325-----55040303577207300840a26798----------0061645940750373068104655085027305a5804072418ac32473683685832165e------7435207753b84707-606718634-80660096093------------------ >P1;d4ed9a- ------91228b13000004301002000000000030000075--10700840875381784103300700020100102175-a1371035004502000022-467067140228304831650000002001198--8427-709176005306215044649794552a6240114-0054007303701852975-5041131003700482289346656768-----------------87250547234830041202045------7605020575b2045007208038035--505-----639302733a40384017306626177016308729050434389934484881-85a2416---068--0545016454ba270329-5100224320a505860-------------------- >P1;d4hl6a- ------80417b21000002410003000101103030000054a900601645-7549---b402400300020200105087a813600310056010000026072067270328304811550000001001197--9546360916400450712623474a484632b5220130-0064005403820a908a656062122002700455182157157777-----------------74311224232730021108065------43020302669205300710917803a28404-----539302823740363026206644094028408819050524279655475871575231030---79--1505015425bc2644572710092352097029504d------------------ >P1;d5yx6a- -----892406c22000004910001000100002030000074b-00911963-6938c58522350121000030020518699-042016004602000012628405-37001a403841780000101001196--89254528165013507029b391ac-8643266520163-00440082037007417759504316000371048427-b379--------------------------------8864027406048------a5040204--85055006209257024--406-----3--6065--96057202710684407601930575a060537388-746929818858232607-----52516116754a900429--6510820524b611----------------------- Translating the sequences ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCC*CCHHH*CC-****--*****HHH**CCCCEEEECCCCCHHHHHHHHHHHH*CCEEEECCCCCHHHHCCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHCC*HHHCCCCCCCCCCCCCC***HH-HHHHHHHHHHHHHHHHHHHCCC*EEEEEHHHHHHH*C*HHHHHHH********************CCCCCCCCCCCCCCCEEEEECCC******CEEEEECC-HHHHHHHHHHHCCHHHCC**CCC-----C****HH*HHHHHHHHHHHHCCCCHHHHHHHHHH*CCCEEECCCHHHHHHCHHHHHCCCEEEE*******EEEECCCCCCCCCCC--C*CCCCCCCCCHHHHHHH*CC**************---- ******CCCCCCCEEEE*CCCCHHHHHH*-***CCCEEEEEECCC*CCHHH*CC-----------*HHHHHCCCCEEEE*CCCCHHHHHHHHH*-*CCCEEEE*CCCCHHHHCCCCHHHHHHHCCCCEEEEE*CCCCCC**CCCCCCCCHHHHHHHCCCHHHCCCCC--CCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCC*EEEE*-*****--C****--***----------------*-*CCCCCC-CCCCCCCC***EE*CC------*EEE-*CCCHHHHHHHHHHHCCHHHCC**CCC*****C*******HHHHHHHHHHHH*CCCHHHHHHHHHHCCCC*EECCCHHH***CHHHHH*CCEEEE***-***EEEECC-CCCCCCCCC-C*CCC-CCC-CHHHHHHH*CC****************** ------CCCCCCCEEEE*CCCCHHHHHHHHHHHCCCEEEEEECCC-CC*-------------------*HH*CCCEEEECCCCCHHHHHHHHHHH*CCCEEEECCCCCHHHH*CCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHH*CCCHHHCCCCCCCCCCCCC********HHHHHHHHHHHHHHHHHHCCC*EEEEEHHHHHHH*C*HHHHHHH*----------------***CCCCCCCCCCCCCCCEEEEECCC*-----CEEEEECCCHHHHHHHHHHHCC*HH*----------*C****HH*HHHHHHHHHHHH*CCCHHHHHHH***CCCCEEECCCHHHHHHCHHHHHCCCEEE**------*EEECCCCCCCCCCCC-C*CCCCCCC-CHHHHHHH*CC------------------ ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECC--CCHHH*CC************HHH**CCCCEEEECCCCC-**HHHHHHHHHCCCEEEECC-CC**HH*CCCHHHHHHHCCCCEEEEEECCCCCC--CCCC-CCCHHHHHHH*CC***CCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHH-CC*EEEEEHHHHHHH*C*HHHHHHH***-----------------CCCCCCCCCCCCCCCEEEEE*CC------*EEEEECCCHHHHHHHHHH*CCHHHCC--CCC-----C****HH*HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEECCCHHHHHHC***-*CCCEE*---***--**EECCCCCCCCCCCC*C-CCCCCCCCCHHHHHHH*-------------------- ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCC*CCHHH*CC-****---****HHHHH*CCCEEEECCCCCHHHHHHHHHHHH*CCEEEECCCCCHHHHCCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHH*C*HHHCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCC*EEEEEHHHHHH**C*HHHHHHH***-----------------CCCCCCCCCCCCCCCEEEE*CCC------C*EEEECCCHHHHHHHHHHHCCHHHCC**CCC-----C****HH*HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEECCCHHHH**CHHHHHCCCEEEE---**--EEEECCCCCCCCCCCC***CCCCCCCCCHHHHHHH*CC------------------ -----*CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCC-CCHHH*CC-*************HHHCCCCEEEECCCCC**-**HHHHHHHCCCEEEECCCCC***-CCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHCCC***CCCCC-CCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCC*EEEEEHHHHHHH*C*-****--------------------------------CCCCCEEEEECCC------CEEEEECC--**HHHHHHH*CCHHHCC--CCC-----C--****--*HHHHHHHHHHCCCCHHHHHHHHHHCCC*EEECCC*-*HHHCHHHHHCCCEEEE*-----*EEEECCCCCCCCCCCC*--CCCCCCCCCHHHH*----------------------- 89796.tem _________________________________ ------CCCCCCCEEEECCCCCHHHHHHHHHHHCCCEEEEEECCC*CCHHH*CC-****--*****HHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCEEEECCCCCHHHHCCCCHHHHHHHCCCCEEEEEECCCCCC--CCCCCCCCHHHHHHHCCCHHHCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHCCC*EEEEEHHHHHHH*C*HHHHHHH***--------------*-*CCCCCCCCCCCCCCCEEEEECCC------CEEEEECCCHHHHHHHHHHHCCHHHCC**CCC-----C****HH*HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCEEECCCHHHHHHCHHHHHCCCEEEE*-***-*EEEECCCCCCCCCCCC*C*CCCCCCCCCHHHHHHH*CC------------------ Structural block scores 0 5 - 4.4 M 75.0 6.0 75.0 75.0 75.0 63.8 6 12 C 5.0 H 4.9 2.5 4.1 4.9 4.8 5.1 13 16 E 5.0 H 1.0 1.0 0.8 0.8 0.2 0.5 17 21 C 4.8 H 2.0 3.0 3.0 1.4 1.4 2.8 22 32 H 4.8 H 0.0 7.5 0.5 0.3 0.5 0.2 33 35 C 5.0 H 1.0 0.7 0.7 0.0 1.0 0.7 36 41 E 5.0 H 0.7 0.3 1.2 0.5 0.5 0.5 42 44 C 4.8 H 5.8 4.7 7.5 29.0 6.5 7.5 46 47 C 5.0 H 0.5 1.0 6.0 0.5 0.0 0.0 48 50 H 4.5 M 1.7 2.7 53.5 2.3 2.3 3.7 52 53 C 4.5 M 6.0 6.0 75.0 2.0 4.5 4.5 55 58 * 2.7 P 5.0 75.0 75.0 5.8 6.2 6.5 59 60 - 4.1 M 75.0 75.0 75.0 4.0 75.0 8.8 61 65 * 2.7 P 2.8 61.6 75.0 3.2 18.5 4.0 66 70 H 4.2 M 1.6 2.2 32.4 2.0 1.4 1.8 71 74 C 4.8 H 0.2 0.0 0.2 0.5 0.5 0.0 75 78 E 5.0 H 0.8 0.0 1.8 0.5 0.8 1.2 79 83 C 4.9 H 2.8 1.8 4.2 3.0 4.0 4.0 84 95 H 4.5 M 2.9 8.5 3.2 9.1 3.1 9.2 96 98 C 4.7 H 1.3 3.3 2.0 2.3 2.3 2.7 99 102 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 103 107 C 4.8 H 4.2 2.4 2.6 17.8 3.0 3.8 108 111 H 4.3 M 3.2 2.8 3.5 5.0 3.8 21.0 112 115 C 4.8 H 3.0 4.5 1.8 1.8 3.0 2.5 116 122 H 5.0 H 3.4 3.6 4.6 4.0 3.7 4.4 123 126 C 5.0 H 2.8 3.0 3.2 3.0 2.8 4.0 127 132 E 4.9 H 0.3 0.0 0.2 0.3 0.2 0.3 133 138 C 5.0 H 4.2 3.0 3.2 3.2 3.0 2.8 139 140 - 4.5 M 75.0 8.8 75.0 75.0 75.0 75.0 141 148 C 4.9 H 6.0 4.5 5.2 14.0 5.2 5.4 149 155 H 4.9 H 2.9 2.9 2.6 3.1 2.9 3.0 156 158 C 4.4 M 2.3 3.0 3.0 2.7 2.7 2.3 159 161 H 4.1 M 2.7 4.0 3.3 2.0 3.3 7.5 162 175 C 4.9 H 5.0 15.4 5.3 5.5 5.3 10.8 176 180 H 4.3 M 1.4 3.0 1.8 2.0 1.2 2.4 182 200 H 5.0 H 2.9 3.3 3.7 3.5 4.0 3.1 201 203 C 4.8 H 4.7 3.7 4.3 26.7 3.7 4.7 205 209 E 4.9 H 2.2 1.2 2.0 1.2 1.4 2.0 210 216 H 4.5 M 2.3 24.6 2.9 3.1 2.6 3.3 220 226 H 4.2 M 3.9 26.0 4.9 5.6 4.0 36.5 227 229 * 2.9 P 3.0 53.0 52.3 7.0 7.0 75.0 230 243 - 4.5 M 4.1 75.0 75.0 75.0 75.0 75.0 247 261 C 4.7 H 3.7 8.4 2.3 3.9 2.7 51.7 262 266 E 4.6 H 1.2 3.0 3.0 1.8 2.4 3.8 267 269 C 4.7 H 4.7 3.0 1.7 3.0 3.7 4.0 270 275 - 4.4 M 5.7 75.0 63.3 75.0 75.0 75.0 277 281 E 4.7 H 1.2 18.2 2.4 2.6 1.6 2.2 282 284 C 4.8 H 25.7 3.0 2.7 4.0 2.7 26.3 285 295 H 4.8 H 2.6 2.4 3.5 3.3 3.0 9.6 296 297 C 5.0 H 5.5 4.5 6.2 4.0 5.0 5.5 298 300 H 4.8 H 4.3 4.0 7.3 3.7 5.0 4.0 301 302 C 4.5 M 5.0 3.5 41.5 4.0 6.8 3.0 303 304 * 3.4 M 6.0 5.0 75.0 75.0 5.0 75.0 305 307 C 4.5 M 3.3 2.7 75.0 3.3 2.7 3.3 308 312 - 4.4 M 75.0 5.2 60.0 75.0 75.0 75.0 314 317 * 1.4 P 3.8 4.8 4.2 3.8 3.8 39.0 318 319 H 4.1 M 2.0 3.5 7.0 4.5 5.0 5.5 321 332 H 4.9 H 2.7 2.8 3.3 3.6 3.0 9.5 333 336 C 4.8 H 4.0 5.2 5.0 5.0 5.0 5.5 337 346 H 4.8 H 4.0 4.5 4.0 4.0 4.3 3.8 347 350 C 4.8 H 3.5 4.9 4.2 4.0 3.8 5.4 351 353 E 4.8 H 2.3 3.0 3.0 2.3 2.3 2.7 354 356 C 5.0 H 2.7 5.0 4.3 5.0 4.3 6.0 357 362 H 4.4 M 5.5 6.4 6.5 6.2 6.0 18.2 364 368 H 4.5 M 6.0 6.6 6.2 20.0 5.6 6.8 369 371 C 4.8 H 5.0 5.3 5.3 5.8 3.3 5.0 372 375 E 4.7 H 1.5 2.2 3.5 21.5 1.0 2.8 378 380 * 3.2 M 3.7 31.5 75.0 4.7 30.3 75.0 383 386 E 4.7 H 2.5 3.2 4.8 3.5 2.8 3.5 387 398 C 4.9 H 10.3 10.7 5.1 4.5 4.8 4.1 402 410 C 4.9 H 2.2 18.2 13.1 2.1 3.2 3.2 411 417 H 4.8 H 3.0 2.6 3.9 4.9 4.6 24.8 419 420 C 4.3 M 4.5 5.5 6.0 75.0 8.8 75.0 421 438 - 4.2 M 20.9 5.0 75.0 75.0 75.0 75.0 >>>>>>