Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3c0na2 CCCCCCEEECCCCHHHHHHHHHCCCCCCHHHHHH--HHHHHCCCCCCCCCCCCCCCCEEEEECCCCEEEEECCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEEECCCCEEEEEEEEE--------EEEEEEECCCCCCCCEEEEEEEEEEEEEEECCCC---------CHHHCCCCCCCEECCCCC-CCCCCCEECCCCCHHHCCEEEEEEEECCEECCCCCCCEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCHHHHHHCCCCHHHCCCCCHHHHHHHHCHHHHHHHHHHHCCCEEEEEEEEEEEEEEEECCCEEC----------CCEECCCEEECCCCHHHHHHCCCEEEEEEEEECC- >P1;d3ziwa1 ----------------------------------------------------------------------------------------------------------CCEEEEEECCCCEECCHHHEEEEEEECCC-----CEEEEEEEEEEECEEEEEEECCCCCCHHHHHHHHHHHHCCCCC-----------------------CEEEEEEEEEEECC--------------CCEEEEEEEEEEEEEEEEEEEC------------------------------------------------------------------------CEEEEEEEEEEEEEEEEEEEEE--CCHHHCCHHHHCCCCCEECCCCCCCCCCCC---------------- >P1;d3zjxa1 -------CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHC--------------CCCCCCC----------------------CCCEEEEEECCCE-------EEEEEEEEEEEE--------CCCEEEECCCCCEEECC-CEEEEEEEEEEEECCC---------CCCCCCC--EEEECCCCCCCCCCEEEEECCCC--------CEEEEEEEEEEEECC-CEEEECCCEEEECCEEEEEEEEEECCEEEEECEEEECCCCC-----CCCCCCEEEE-------HHHCCC------------------------------CCCCCCCEEEECCEEEEEEEEEEEEEEEEC-------CCCCEEEEECCCCC-----------CCCCCCEEECCCC PSA >P1;d3c0na2 0463a22607005254006400237830120003--003100003020061962043050755bb100040158b92b573165000030570605033911638b27547264032--------0714000568852462301061304070606154---------500760308961602617-9050504041a530261609647270834350504251203040201402020402020401020101400367200136317832a271401048566441104200642868a335202021017539584048100501240200020705060210470626----------9368140505071689605a3704a05041563a- >P1;d3ziwa1 ----------------------------------------------------------------------------------------------------------95511000264020103802143540728-----5424046505351404353684b806593027002801a3809-----------------------75341746350506--------------952020000000310102225a------------------------------------------------------------------------7952010000302202115232--85897087850519735304a798846552---------------- >P1;d3zjxa1 -------54285037007603542136105713968812872--------------a261539----------------------5707138260647-------b9073764b348--------17461408398546318-6361614040503049---------2018471--6206025181b370514010056--------644644452206036-03020127020411202111054700303043104333587-----9465420614-------048019------------------------------a24b89003050050203011500040303-------6666455340357a-----------7106427060071 Translating the sequences *********CCC*HHHHHHHHH******HHHH**--*HHHHC**************C*****C**********************C**EEEEEE***E********CCEEEEEEEEE--------EEEEEEECCCCC****EEEEEEEEEEEEEE*CCC---------CHHHCCC***CEECCCCC-CCCC**EE*CCCC*******EEEEEE**EE*CC*CC**EEEE***EEEEEEEEEEEEEEEEEEEEEEE*E***CCCCC*****CCC***EEEE************************************************CC*EEEEEEEEEEEEEEEE***EEC----------CCEEC*C***CCCC********C*****EEE*CC- ----------------------------------------------------------------------------------------------------------CCEEEEEE***********EEEEEEECCC-----CEEEEEEEEEEE*EEE*************HHH******C**CC-----------------------*EEEEEEEEEEECC--------------**EEEEEEEEEEEEEEEEEEEC------------------------------------------------------------------------C*EEEEEEEEEEEEEEEEEEEE--C**********CC**CE*CCCCCCC*****---------------- -------**CCC*HHHHHHHHH******HHHH*****HHHHC--------------C*****C----------------------C**EEEEEE***E-------***EEEEEEEEE--------***EEEECCCCC***C*-*EEEEEEEEEEEECCC---------C***CCC--**EECCCCC*CCCC**EE*CCCC--------*EEEEEEEEE***CC-*EEEE***EEEE**EEEEEEEEEE**EEEEECE***CCCCC-----CCC***EEEE-------******------------------------------*****CCEEEE**EEEEEEEEEEEEEEEEC-------***C*EE*ECCCCC-----------C*****EEE*CC* 56973.tem _________________________________ -------**CCC*HHHHHHHHH******HHHH**--*HHHHC--------------C*****C----------------------C**EEEEEE***E-------*CCEEEEEEEEE--------EEEEEEECCCCC***CEEEEEEEEEEEEEEECCC---------CHHHCCC***CEECCCCC-CCCC**EE*CCCC------*EEEEEEEEEEECC*CC-*EEEE***EEEEEEEEEEEEEEEEEEEEEEECE***CCCCC-----CCC***EEEE-------******------------------------------*****CCEEEEEEEEEEEEEEEEEEEEEEC-------***CCEECECCCCCCCC*****---C*****EEE*CC- Structural block scores 0 6 - 4.0 M 3.9 75.0 75.0 7 8 * 2.7 P 3.0 75.0 4.5 9 11 C 4.0 M 2.3 75.0 5.0 13 21 H 4.0 M 2.3 75.0 3.4 22 27 * 2.7 P 3.8 75.0 2.8 28 31 H 4.0 M 0.8 75.0 3.2 32 33 * 2.7 P 1.5 75.0 6.0 34 35 - 4.0 M 75.0 75.0 7.0 37 40 H 4.0 M 1.0 75.0 4.5 42 55 - 4.0 M 2.4 75.0 75.0 57 61 * 2.7 P 3.4 75.0 3.4 63 84 - 4.0 M 4.7 75.0 75.0 86 87 * 2.7 P 0.0 75.0 3.5 88 93 E 4.0 M 3.5 75.0 4.5 94 96 * 2.7 P 1.7 75.0 3.3 98 104 - 4.0 M 4.4 75.0 75.0 106 107 C 4.0 M 4.5 7.0 4.5 108 116 E 4.7 H 3.7 2.1 5.9 117 124 - 4.0 M 75.0 1.8 75.0 125 131 E 4.6 H 1.7 2.7 3.3 132 136 C 4.6 H 6.4 33.4 6.6 137 139 * 2.7 P 4.0 75.0 4.3 141 155 E 4.7 H 2.5 3.1 8.1 156 158 C 4.0 M 3.3 3.7 4.3 159 167 - 4.0 M 75.0 6.4 75.0 169 171 H 4.0 M 2.3 3.0 3.0 172 174 C 4.0 M 3.0 0.7 4.0 175 177 * 2.1 P 5.7 3.0 52.0 179 180 E 4.0 M 3.5 5.5 3.0 181 185 C 4.4 M 3.2 46.8 3.2 187 190 C 4.0 M 3.5 75.0 5.4 191 192 * 2.7 P 2.5 75.0 3.0 193 194 E 4.0 M 2.0 75.0 2.0 196 199 C 4.0 M 4.9 75.0 2.8 200 205 - 4.0 M 2.5 75.0 75.0 207 217 E 4.5 M 4.5 3.9 10.5 218 219 C 4.0 M 2.5 3.0 3.0 221 222 C 4.0 M 3.0 75.0 4.5 225 228 E 4.0 M 1.2 75.0 1.2 229 231 * 2.7 P 2.0 75.0 3.3 232 254 E 4.7 H 1.1 8.0 1.8 257 259 * 2.7 P 3.0 75.0 2.3 260 264 C 4.0 M 2.0 75.0 5.2 265 269 - 4.0 M 4.0 75.0 75.0 270 272 C 4.0 M 4.3 75.0 6.3 273 275 * 2.7 P 6.5 75.0 3.7 276 279 E 4.0 M 1.5 75.0 2.8 280 286 - 4.0 M 4.7 75.0 75.0 287 292 * 2.7 P 2.0 75.0 3.7 293 322 - 4.0 M 3.9 75.0 75.0 323 327 * 2.7 P 1.2 75.0 7.2 328 329 C 4.5 M 1.5 8.0 4.5 330 351 E 4.6 H 2.2 8.2 1.5 353 359 - 4.0 M 75.0 6.3 75.0 360 362 * 2.7 P 75.0 4.3 6.0 363 364 C 4.5 M 6.0 3.0 5.0 365 366 E 4.0 M 7.0 8.0 5.0 369 376 C 4.1 M 3.0 6.2 31.3 377 381 * 2.7 P 5.6 4.4 75.0 382 384 - 4.0 M 6.8 75.0 75.0 386 390 * 2.7 P 3.9 75.0 2.6 391 393 E 4.0 M 3.3 75.0 4.3 395 396 C 4.0 M 6.8 75.0 3.5 >>>>>>