Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ro2a- ------------------------------------------------------------------------------------------------------------------------------------------------------------------CCHHHHHHHHHHHC----CCCCEEECCCCCCCCCC----------------CHHHHHCCCCCH-------------------HHHHHHHHHHHHCCEEEEECCHHHEEEEEECCHHHHHHHHCHHHHHHHHHHCCEEECCCCCEEEEEECCCCCCCCCCCCEECC---------------------------CCEEEEEECCCCEEECCCCEEEHHHCCCC-------------CCCCCCCCCEEECEECCCCCCCEECCHHHHHHHHHHHHHHHCCEECHHHHHHHHC >P1;d1v33a- -----CCCCCCCHHHHHHHHHHCCCHHHCCHHHHHHHHHCCEEEECCCCC---------CCEEEECCCCHHHHHHHHHH-HCCCEEEEECEEEEECC-----CCEEEEEECEEEEEEHHHCCCCCCCCC----------------------CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECC-CEEEEEECC-HHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHCHHHHHCCCC-HHHHHHHHHH-------HHH-----CCCCHHHHHHCCCCHHHHHHHHHCHH---HHHHHCCCCCCHHHCCC-----CCHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCEEECCCCEECCCCEECCEEECCHHHHH---HCCHHH------------------HCCCHHHHH----HHHHHHHHHHHCC---CC------------ >P1;d1zt2a1 CCCCCCCCCCHHHHHHHHHHHHCC--CCCC----CCHHHCCEEEEECCCC---------CCCCCCCCCCHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCHHHH-CCCCCCEEEECCHHHHHCCEEEEECCCCCCCCCCCEECCCCEECEEEEECCHHHHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCEEEEECCCCHHHHCCHHHHHHHHHHHCCC------CCCCCC-----------------------------------------------------------------------------------------CCCCCCCCHHHHHHCCCCCCCCCHHHHHCCCCEEECCCCCCCCCCCCCCEE-CCCCCCCCCHHHCCCCCEEEEEECCCEEEECCCCEEEECCCCCEEEEHHHHHHHHHCCCE---EEEEEC-------- >P1;d2atza1 -----------------------------CCCCCCCCCCCEEEECCCCCEEEEECCEEEEECEEEECCCCHHHHHHHHCC--CCCEEEECCCC--------------------------------------------------CCEECCEEEEECCC----CHHHHHHHHHHHHHHC-CCCEEEEECCCCCCEEEEECCC----CEEHHHHHHHHHHHCCHHH-------------CCCCCEEEE-CCCCCCHHHC----EEECCC---EEEEEECC------------------------------------------------------------------------------------------------------------------CCCCC------------------------------------------------------- PSA >P1;d1ro2a- ------------------------------------------------------------------------------------------------------------------------------------------------------------------95820510500172----70100004496670129----------------61440077607a-------------------932750181056432000000073000020743930480077a2056007500002104900000020a6006660230033a---------------------------a910040213622020010334048367b-------------9043555954231611751360470702410540283077490411a50581067 >P1;d1v33a- -----810260458306600672062740081037306300000034256---------47336321643860273037-30010010000106605-----617733000000102027020141938----------------------66502030050002002100100240280950100010-100000011-8500717582067113200006148364036206775b2036977-1020001000-------000-----10063640492808691054028228---6024300651519002b-----b0b37000200100081055003480034153000000000040001043025216303---604007------------------500072048----3064226626875---d6------------ >P1;d1zt2a1 aa8898b69420461048105819--0401----a217300000111d3a---------943422214468502610177400200100000066051985a60-42400000030207710919442001520671b8860a83a4703403102380074006104201300461382-9040003004102000315bb2062849504710340205------b05738-----------------------------------------------------------------------------------------c376a1820400123b19002043600142342020030000600020530-661781704270010935040302151512002762706487535150010000210400---303545-------- >P1;d2atza1 -----------------------------97380613561002349291952638c832524275388077922640365--61200010019--------------------------------------------------95301000000409----7175016201510473-9240000315592200000126----6061770183065004049-------------818450510-0187105420----002011---72233349------------------------------------------------------------------------------------------------------------------aa88a------------------------------------------------------- Translating the sequences ------------------------------------------------------------------------------------------------------------------------------------------------------------------**HHHHHHHHHHH*----CC**EEECCCCC*****----------------*HHHH*CC****-------------------********HHH*******************************************************************C****---------------------------**E******CCC***CC************-------------**************************HHHHHHHH********************* -----************************C*********C*EEE**CCC*---------*******CCC*HHHHHHHH*-*****EEEEC*******-----***************************----------------------***CC******HHHHHHHHHHHHHHC*CCCC*EEEECC-C*EEEEECC-*******HHHHHHHHHHHCCC************************-******HHH*-------***-----**************************---*****************-----C*********************************E******CCC***CC**********---******------------------*********----*HHHHHHHH****---**------------ ************************--***C----*****C*EEE**CCC*---------*******CCC*HHHHHHHH*******EEEEC**************-*************************************************CC******HHHHHHHHHHHHHHC*CC-C*EEEECCCCCEEEEECC********HHHHHHHHHHHCCC------******-----------------------------------------------------------------------------------------C*********************************E******CCC***CC**-************************************************HHHHHHHH****---******-------- -----------------------------C*********C*EEE**CCC*****************CCC*HHHHHHHH**--***EEEEC***--------------------------------------------------***********CC*----*HHHHHHHHHHHHHHC-CCC**EEE*CCCCCEEEEECC*----***HHHHHHHHHHHCC***-------------*********-******HHH*----******---********------------------------------------------------------------------------------------------------------------------*****------------------------------------------------------- 56747.tem _________________________________ -----*******************--***C*********C*EEE**CCC*---------*******CCC*HHHHHHHH*******EEEEC*******-----**-************************--------------***********CC******HHHHHHHHHHHHHHC*CCCC*EEEECCCCCEEEEECC********HHHHHHHHHHHCCC****--******---*********-******HHH*----******---****************************---*****************-----C*********************************E******CCC***CC************-******-*******************************HHHHHHHH****---******-------- Structural block scores 0 4 - 4.3 M 75.0 75.0 9.2 75.0 5 23 * 3.5 M 75.0 3.4 4.6 75.0 24 25 - 4.3 M 75.0 4.0 75.0 75.0 26 28 * 3.5 M 75.0 3.7 1.3 75.0 30 38 * 2.8 P 75.0 3.4 35.9 4.3 41 43 E 4.3 M 75.0 0.0 0.0 1.7 44 45 * 2.3 P 75.0 1.5 1.0 6.5 46 48 C 4.3 M 75.0 3.7 5.8 4.0 50 58 - 4.3 M 75.0 75.0 75.0 5.5 59 65 * 2.3 P 75.0 4.0 3.7 4.0 66 68 C 4.3 M 75.0 3.7 3.0 5.3 70 77 H 4.3 M 75.0 3.6 2.9 4.1 78 84 * 2.8 P 75.0 12.3 2.9 24.3 85 88 E 4.3 M 75.0 0.2 0.2 0.2 90 96 * 3.0 P 75.0 2.6 2.4 44.3 97 101 - 4.3 M 75.0 75.0 6.7 75.0 102 103 * 3.5 M 75.0 3.5 3.0 75.0 105 128 * 3.5 M 75.0 2.2 2.5 75.0 129 142 - 4.3 M 75.0 75.0 4.7 75.0 143 153 * 3.2 M 75.0 56.1 4.0 1.6 154 155 C 4.3 M 75.0 1.0 1.0 2.0 156 161 * 3.1 M 75.0 1.3 3.7 52.7 162 175 H 4.9 H 3.2 0.9 1.9 2.9 178 181 C 4.3 M 39.2 5.5 23.5 3.8 183 186 E 4.7 H 0.0 0.2 1.0 1.0 187 191 C 4.7 H 5.8 15.4 1.6 4.6 192 196 E 4.3 M 3.8 0.0 0.4 0.0 197 198 C 4.3 M 75.0 1.0 2.0 1.5 199 206 * 3.1 M 75.0 12.9 5.8 39.8 207 217 H 4.6 H 42.3 3.2 3.4 3.5 218 220 C 4.5 M 4.7 0.0 2.3 1.3 221 224 * 2.9 P 5.9 4.8 75.0 40.8 225 226 - 4.3 M 75.0 4.5 75.0 75.0 227 232 * 3.5 M 75.0 2.5 5.8 75.0 233 235 - 4.3 M 75.0 6.7 75.0 75.0 236 244 * 3.4 M 67.7 5.6 75.0 3.6 246 251 * 2.3 P 3.8 0.5 75.0 2.8 252 254 H 4.3 M 2.0 0.3 75.0 3.7 256 259 - 4.3 M 2.2 75.0 75.0 75.0 260 265 * 2.9 P 0.0 37.5 75.0 0.7 266 268 - 4.3 M 3.3 75.0 75.0 75.0 269 296 * 3.2 M 3.2 8.9 75.0 54.8 297 299 - 4.3 M 0.7 75.0 75.0 75.0 300 316 * 3.5 M 2.3 3.3 75.0 75.0 317 321 - 4.3 M 3.4 75.0 75.0 75.0 323 355 * 3.3 M 62.5 2.3 3.0 75.0 357 362 * 2.3 P 1.2 0.0 0.5 75.0 363 365 C 4.3 M 3.7 1.3 2.0 75.0 366 368 * 2.3 P 1.3 0.3 0.7 75.0 369 370 C 4.3 M 0.0 2.0 2.5 75.0 371 382 * 2.6 P 4.2 14.6 9.8 75.0 384 389 * 3.5 M 75.0 2.8 2.8 75.0 391 421 * 3.1 M 15.4 51.7 3.1 64.4 422 429 H 4.3 M 2.0 3.5 0.5 75.0 430 433 * 2.3 P 3.2 6.5 1.0 75.0 434 436 - 4.3 M 6.0 75.0 75.0 75.0 437 442 * 3.1 M 4.2 53.2 3.3 75.0 443 450 - 4.3 M 4.0 75.0 75.0 75.0 >>>>>>