Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hc1a2 ---------------------------------------------------CHHHHC-CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHCCCCC---CCCCC-CCC------CCCCCCCCCCCCCCC-CCCCCCCC----------------CCCCCCCCCCCCCHHHHHHHHHHHHHHHHH--CEEECCCCCEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCC----------------------------------------------------------------------------------- >P1;d1js8a1 ----------------------------------------------CEEECCHHHCCHHHHHHHHHHHHHHHHC--C------------------CCCCHHHHHCCCCCCC-CEEC---CCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCCCCCCCHHHHCCC--------------CCCCC----CCEECCCC---EECCCCCCHH-HCCHHHHHHHHHHHC-C-------CHH-------------HHHHHHHH------------HHHHHHHHHHCC---CC------CCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC------CHHHCCCCCCCCCCCCCHHHHH--CCCHHHCCCHHHHCEEECCCCCCCCCHHHHHHHHHHHCC >P1;d1llaa2 ---------------------------------------------------CHHHHC-HHHCCCHHHHHHHHHCC------CCC-CCCCHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHCCCC---CCCCCCCCC------CCC-CCCCCCCCCCCCCCCCCCCC----------------CCCCCCCC-CCCCHHHHHHHHHHHHHHHHH--CEEECCCCCEEECCCCCHHHHHHHHHHCCCCCCCHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCHHHCCCCHHHCHHHHHHHHHHHHHHHHHHCCCC---------------------------------------------------------------------------------- >P1;d3awua1 -----------------------------------------------CEECCHHHCCHHHHHHHHHHHHHHHHC--C---------------------HHHHHHHHHHHHHHHCCC---C----CCCCCCCCCCHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCCHHH-CCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCCCCCCCCC-----------CHHHHHHCCCC-------CCCHHHHHHHHC-------------HHHHCC-CHHHCCHHHHHHHHHHHHHHHHHHHCC------CCCCCCCCCCCCCCCCCCCCCCCC-------------CCCHHHHCCHHH-CCEECC-------------------- >P1;d4z0ya- CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEEEECCC-CHHHHHHHHHHHHHHHHCCCC------------------CCCCHHHHHHHHHHHHCCCCEEHHHCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCHHHCCCCCCCC-------CCCCCCCCCCCCHHHHHHCCCCCCCCCCC---CCCCHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCC-----CCCCCCHHHH------------CCCHHHHHHCCCCCCCC------CCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-----------CHHHHCCEEEEECCC-------CCEEEEEC-CCCCHHHHCEEECCC------------------- PSA >P1;d1hc1a2 ---------------------------------------------------533776-31102226118445628888987a2c656bb3125014111558302400510762045153955851950--024015103400460273067291a---50630-308------630730040802149-69500607----------------662705506b14717403412630360075--03032587743605496011200000000510316930620022003000302015486b323000122200000000000020014006305555----------------------------------------------------------------------------------- >P1;d1js8a1 ----------------------------------------------5240220a60688037401400660182--a------------------7540034000000143-3056---b9972310022a30000000000000003004739--0500000010068189018004579--------------b0103----40506519---55041524a6-033402640060022-5-------502-------------60074007------------105201520008---16------200135510000000000000000000000200641a453480a248------840664040035a903194036--20304500306608030362403a251460173057558 >P1;d1llaa2 ---------------------------------------------------602774-40004549317537755------a2b-b5a7636601610354820140350156222914184a882960--1340162033004701721563a18---608206508------640-80140803347385500406----------------87450650-c70516404511530370055--73032787755705885003100100000640216a402200320130004010058769442200323000000100030020015006403643a---------------------------------------------------------------------------------- >P1;d3awua1 -----------------------------------------------240420260897316401700240073--8---------------------501610420271277063---a----560001200000000020003006002622--970100002006224581500-4670003504b83430450100283a604051375a451010602673870058930470053-7400465111507-----------00001000356-------430021015002-------------000342-000000000000000010003038417------92703056c285000275406317-------------803014037036-306039-------------------- >P1;d4z0ya- 6202004015505505570c7396022428020263c3278030d2404002021-8a7325103400530372679------------------0010040001000000000010341a45a320100000000000000000001000401a28700000000024900401202b-------88b1102072009a02864000419163b---27a71472047017300486064283000250201473298-----b395001004------------20500140000392205------0000220000000000000000000012036359407119-----------362047000000128-------32011040-403707502030439------------------- Translating the sequences ---------------------------------------------------CHHH*C-******HHHHHHHHH*************************C*HHHHHHHHHHHHHCCC***CCCC*CCCCC--C**HHHHHHHHHHHHHHHHH*CCCC---CCCCC-CCC------CCC*CCCCCCCCCCC-CCCCCCCC----------------CCCCCCCCCCCCCHHHHHHHHHHHHH*HHH--C***CCCCC***C*******HHHHHH*CCCC*******CCHHHHHHHHHH***CCCC******CHHHCCCC***CCHHHHHHHHHHHHHHHHH*CC----------------------------------------------------------------------------------- ----------------------------------------------**EE*CHHH*CHHHHHHHHHHHHHHHHC--C------------------***CHHHHH*******-***C---CCCC**CCCCCCCCCHHHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCC***CCC****CCC--------------CCC**----CC**CCCC---**CCCCCC**-***HHHHHHHHHHHC-*-------C**-------------HHHHHHH*------------HHHHHHHHHHCC---CC------C***CCCCHHHCCHHHHHHHHHHHHHHHHHH****************------****C*****C***********--*******CCHHH*C*EECC******************** ---------------------------------------------------CHHH*C-HHH***HHHHHHHHHC*------***-*************C*HHHHHHHHHHHHHCCC***CCCC*CCCC*--***HHHHHHHHHHHHHHHHHHCCCC---CCCCCCCCC------CCC-CCCCCCCCCCCCCCCCCCCC----------------CCCCCCCC-CCCCHHHHHHHHHHHHH*HHH--C***CCCCC***C*******HHHHHHHCCCC*******CCHHHHHHHHHHCC*CCCC******CHHHCCCCHHHC*HHHHHHHHHHHHHHHHH*CCC---------------------------------------------------------------------------------- -----------------------------------------------*EE*CHHH*CHHHHHHHHHHHHHHHHC--C---------------------*HHHHHHHHHHHHHHCCC---C----CCCCCCCCCCHHHHHHHHHHHHHHHHHH*C--CCCCCCCCCCCC***CCC***-CCCCCCCCCCCCCCCCCCCC******CC**CCCC**CCCCCCCCCCCCC****HHHHHHHH*C-****C***CCCCC-----------*HHHHHHCCCC-------CC*HHHHHHHH*-------------*HHHCC-CHHHCCHHHHHHHHHHHHHHHHHH*CC------*****************C*****C-------------*******CCHHH-C*EECC-------------------- ************************************************EE*****-CHHHHHHHHHHHHHHHHC**C------------------***CHHHHHHHHHHHH**CC*****C*****CCCCCCCCHHHHHHHHHHHHHHHHHH*CCCCCCCC**CCCCC***CCCCCC*C-------CCCCCCCCCCCC******CC**CCCC**C---CCCC*****HHHHHHHH*****CHHH**C***CCCCC***C-----******HHH*------------***HHHHHH*CC*CCCC------C***C***H**C*HHHHHHHHHHHHHHHHHHCCC******-----------******C*****C**-------********-**CCHHH*C*EECC*------------------- 48056.tem _________________________________ -----------------------------------------------*EE*CHHH*CHHHHHHHHHHHHHHHHC*-C------------------***CHHHHHHHHHHHHHHCCC***CCCC*CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC***CCCCCC*CCCCCCCCCCCCCCCCCCCC**----CC**CCCC--CCCCCCCCCCCCCHHHHHHHHHHHHHCHHH--C***CCCCC***C-----**HHHHHHHCCCC-------CCHHHHHHHHHHCC*CCCC------CHHHCCCCHHHCCHHHHHHHHHHHHHHHHHHCCC-------------------****C*****C-------------****-**CCHHH-C*EECC-------------------- Structural block scores 0 46 - 4.5 M 75.0 73.5 75.0 75.0 3.7 48 49 E 4.2 M 75.0 2.0 75.0 2.0 2.0 52 54 H 4.5 M 4.3 5.5 3.0 2.7 1.0 57 72 H 4.6 H 7.6 3.5 8.4 3.2 3.3 77 94 - 4.0 M 6.1 75.0 25.3 75.0 75.0 95 97 * 2.1 P 2.0 5.3 2.3 75.0 0.3 99 112 H 4.5 M 3.3 6.6 3.1 2.9 0.4 113 115 C 4.5 M 2.0 3.7 2.0 3.0 0.3 116 118 * 3.0 P 3.7 75.0 4.7 75.0 2.3 119 122 C 4.3 M 5.5 9.1 5.9 58.9 5.1 124 133 C 4.3 M 17.6 2.1 18.3 1.4 0.6 134 151 H 5.0 H 2.7 0.8 2.7 1.1 0.3 152 167 C 4.6 H 21.7 10.9 17.7 11.2 1.9 168 170 * 3.0 P 75.0 5.7 75.0 2.7 4.3 171 176 C 4.0 M 39.0 3.0 39.2 3.2 1.2 178 197 C 4.5 M 7.0 54.2 3.5 3.4 28.9 198 199 * 3.0 P 75.0 1.5 75.0 0.0 9.8 200 203 - 3.8 M 75.0 75.0 75.0 5.9 4.0 204 205 C 4.2 M 75.0 2.0 75.0 3.0 2.0 206 207 * 3.0 P 75.0 2.5 75.0 2.0 0.0 208 211 C 4.2 M 75.0 5.2 75.0 4.0 3.8 212 213 - 3.8 M 75.0 75.0 75.0 7.8 4.5 214 226 C 4.4 M 4.7 14.8 10.3 3.3 21.3 227 239 H 4.5 M 3.1 2.3 3.1 3.7 3.5 241 243 H 4.0 M 4.0 51.7 3.3 28.7 4.3 244 245 - 3.8 M 75.0 75.0 75.0 0.0 0.0 247 249 * 2.1 P 2.0 75.0 2.0 4.0 2.3 250 254 C 4.6 H 5.8 31.4 6.2 2.8 2.8 255 257 * 3.0 P 4.3 75.0 5.7 75.0 4.7 259 263 - 3.8 M 4.8 75.0 5.2 75.0 75.0 264 265 * 3.0 P 1.0 75.0 1.5 75.0 7.2 266 272 H 4.5 M 0.3 2.4 0.3 0.1 2.1 273 276 C 4.1 M 1.5 58.0 2.5 3.5 57.2 277 283 - 3.8 M 3.1 75.0 3.4 75.0 75.0 284 285 C 4.2 M 4.0 75.0 2.0 3.5 75.0 286 295 H 4.7 H 0.7 1.6 0.9 1.1 1.2 296 297 C 4.1 M 1.5 4.0 2.0 75.0 1.5 299 302 C 4.3 M 2.5 39.2 3.2 75.0 2.2 303 308 - 3.8 M 5.6 75.0 5.3 75.0 75.0 310 312 H 3.8 M 0.3 0.3 1.0 1.0 0.0 313 316 C 4.5 M 1.5 3.5 1.2 20.2 1.0 317 319 H 4.0 M 0.0 0.0 0.0 0.0 0.0 320 321 C 4.4 M 0.0 0.0 0.5 0.0 0.0 322 339 H 4.9 H 1.4 0.1 1.7 0.8 0.7 340 342 C 4.1 M 28.3 2.0 5.8 4.0 5.7 343 361 - 3.9 M 75.0 27.1 75.0 26.8 45.1 362 365 * 3.0 P 75.0 4.5 75.0 2.2 3.2 367 371 * 3.0 P 75.0 1.6 75.0 2.8 0.0 373 385 - 4.3 M 75.0 15.4 75.0 75.0 41.6 386 389 * 3.0 P 75.0 1.2 75.0 2.8 1.2 391 392 * 3.0 P 75.0 2.5 75.0 2.0 2.0 393 394 C 4.2 M 75.0 1.5 75.0 5.0 5.0 395 397 H 4.2 M 75.0 4.0 75.0 3.0 4.0 401 402 E 4.2 M 75.0 1.5 75.0 3.0 1.5 403 404 C 4.2 M 75.0 4.5 75.0 6.0 3.5 405 424 - 4.5 M 75.0 3.9 75.0 75.0 71.7 >>>>>>