Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c4za- ---------------------CCCCCEEECCCCHHHHHHHHHHHHHHCCHHHHHCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCHHHCCEEECC--CCCCEEECCCCC--CCHHHHHHHHHHHHHHHHCC-------CCCCCCCCHHHHHHHCCCCCCHHHHHHHCHHHHH-HHHHHHHCCCCHHHH-CCCCCEEEECCCCCCCEEEECC---CCCC-----CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCEEECCCCC--CCHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCHHHH-------CCEEEEEEECCCCCCEEEHHHCEEEEEECCCHHHHHHHHHHHHHHC >P1;d3h1da1 CHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHCCCC---CCHHHCEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCHHHCCEEECC-CCCCEEEECCC----CHHHHHHHHHHHHHHHHHHC-------CCCCCEECHHHHHHHHCCCCCHHHHHHHCHHHHH-HHHHHHHC--CHHHCCCCEEEECC---------CCCEEECCHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHCCC-CHHHHHHHHHCCCCCCHHHHHHCEEEE-CCCC--CCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCCEEEHHHCEEEEECCCCHHHHHHHHHHHHHC- >P1;d6jx5a- CHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHHCCCCC---CHHHHCEEEEEECCCCC-CCHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHCCCCCCCHHHHHCHHHHHHHHHHHHHC--CCCCC--CCCCEEEEECCCCEEEEEECCC---CHHH-----CCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHHHC-CHHHHHHHHHCCCCCCHHHHHHHCEEE-CCCHHHHHCHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCHHHHCC------CCEEEEEEEEC-CCCEEEHHHCEEEEEECCCHHHHHHHHHHHCC-- PSA >P1;d1c4za- ---------------------a730405044a500720272076219974630135010406b4ba709712012004301750046935006339--837210023409--71653000000000001315-------210505003000200034705292037022a226-70370264a860374-4542021344589884854304---9906-----932023931840083103100041057106104600520047721872960520354010554150840396070879089--73900620060038087831130041003132008710261-------8030134683386206062151102004075392055103500588 >P1;d3h1da1 807734750352074318c294751305044940040015302735---4740117060306a39c7a8922173005100620148615005405-24820210128----b5442030000000000016-------3505010020001100247072510431126315-90371174--41871c54100238---------646186068814793a5334043930761052006330353066107102600230025700430-420000000012290708304810514-6088--9351061006004405711300000100300421a930520513a753301024175628540504314010100107618303610250047- >P1;d6jx5a- 7067317602730453059272652408014930182037106907---5620022010407a55a-74361164004300530053945003123b6711000012a03a80618101000200000000102899550204110000000100848042600210026112830340274--60794--a34001555698845732304b---7029-----36066a31470033002120153076006302600320033b10530-6152000000435b0649406740625-a28840435007201600650852200200030000021069506305------60302019553-55070510402010030663620362036006-- Translating the sequences ---------------------CC***EEEC***HHHHHHHHH********HHHHC***EEECCCCCCCCCHHHHHHHHHHHHHHCCHHHCCEEECC--CCCCEEECCCCC--CCHHHHHHHHHHHHHHHH*C-------CCCCCCCCHHHHHHH*CCCCCHHHHHHHCHHHHH-HHHHHHHC**CHHH*-CCCCCEEEE*CCCC**EEEECC---*C**-----*CCCCCCCHHHHHHHHHHHHHC***HHHHHHHHHHHHHH*C****CCC*C*HHHHHHHHCCCCCC******CCEEE*CCCC--CCHHHHHHHHHHH*CCHHHHHHHHHHH*CCCCCCCCCHHH*-------CCEEEEEEECCCCCCEEEHHHCEEEEEECCCHHHHHHHHHHHHH** CHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHCCCC---C*HHHCEEEEEECCCCCCCCC*HHHHHHHHHHHH*CCHHHCCEEECC-CCCC*EEECCC----C*HHHHHHHHHHHHHHHHHC-------CCCCC**CHHHHHHHHCCCCCHHHHHHHCHHHHH-HHHHHHHC--CHHHC*CC***E**---------**********HH********CCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHCCC-CHHHHHHHHHCCCCCCHHHHHHC*EEE-CCCC--CCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCHHHCC******C*EEEEE**CCCCCCEEEHHHCEEEEE*CCCHHHHHHHHHHHHH*- CHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHH*CCCC---CHHHHCEEEEEECCCCC-CC*HHHHHHHHHHHHHH*C***CCEEECC*CCCCCEEECCCCC**CC*HHHHHHHHHHHHHHHH********CCCCCCCCHHHHHHHHCCCCC**HHHHHCHHHHH*HHHHHHHC--C***C--CCCCEEEE*CCCC**EEEECC*---CHH*-----CCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHH**C-CHHHHHHHHHCCCCCCHHHHHH*CEEE-CCC******HHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCC*HHHCC------CCEEEEEEE*C-CCCEEEHHHCEEEEEECCCHHHHHHHHHHH**-- 56204.tem _________________________________ CHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHHHHHHHHCCCC---CHHHHCEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCHHHCCEEECC-CCCCCEEECCCCC--CCHHHHHHHHHHHHHHHHHC-------CCCCCCCCHHHHHHHHCCCCCHHHHHHHCHHHHH-HHHHHHHC--CHHHC-CCCCCEEEE*CCCC**EEEECC*--*CHH*----*CCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCHHHHCCC-CHHHHHHHHHCCCCCCHHHHHHCCEEE-CCCC--CCHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCCCHHHCC------CCEEEEEEECCCCCCEEEHHHCEEEEEECCCHHHHHHHHHHHHH*- Structural block scores 1 15 H 4.0 M 75.0 3.8 3.6 16 22 C 4.3 M 56.1 6.2 4.4 23 28 E 4.5 M 2.0 2.3 3.2 30 41 H 4.7 H 3.3 2.5 3.2 42 45 C 4.0 M 4.0 4.2 5.5 46 48 - 4.0 M 8.3 75.0 75.0 50 53 H 4.8 H 2.5 3.0 2.0 55 60 E 4.5 M 1.7 2.7 1.2 61 69 C 4.8 H 7.4 8.4 14.1 70 83 H 4.9 H 1.9 2.1 2.4 84 85 C 4.5 M 2.0 2.5 2.5 86 88 H 4.0 M 6.0 5.0 5.3 89 90 C 5.0 H 2.5 2.5 2.5 91 93 E 5.0 H 3.0 3.0 1.3 94 95 C 5.0 H 6.0 2.5 2.5 97 101 C 4.6 H 19.0 3.2 3.0 102 104 E 5.0 H 0.3 1.0 0.0 105 109 C 4.6 H 3.6 32.2 3.3 110 111 - 4.0 M 75.0 75.0 9.2 112 113 C 4.5 M 4.0 8.2 3.0 114 130 H 4.9 H 1.1 0.8 0.8 132 138 - 4.0 M 75.0 75.0 5.4 139 146 C 4.8 H 1.6 1.8 1.0 147 154 H 4.9 H 0.6 0.5 0.1 155 159 C 5.0 H 3.8 4.0 4.8 160 166 H 4.7 H 3.3 2.3 1.6 168 172 H 5.0 H 4.5 3.4 2.4 174 180 H 5.0 H 3.6 4.0 2.7 182 183 - 4.0 M 9.2 75.0 75.0 185 187 H 4.0 M 3.3 5.3 5.3 190 194 C 4.2 M 3.0 2.0 18.5 195 198 E 4.2 M 2.5 22.0 2.8 200 203 C 4.0 M 7.5 75.0 7.8 204 205 * 2.7 P 6.0 75.0 4.5 206 209 E 4.0 M 5.0 22.8 3.8 210 211 C 4.0 M 2.0 4.5 2.0 213 214 - 4.0 M 75.0 3.0 75.0 217 218 H 4.0 M 3.0 2.5 1.0 220 223 - 4.0 M 75.0 6.9 75.0 225 231 C 4.7 H 3.1 3.7 4.9 232 244 H 5.0 H 2.2 2.5 1.8 246 262 H 4.8 H 2.5 2.5 2.5 263 264 C 4.5 M 2.0 1.0 1.5 265 268 H 4.0 M 4.2 3.0 3.9 269 271 C 4.3 M 5.7 2.3 2.7 274 282 H 4.9 H 2.2 0.2 0.9 283 288 C 5.0 H 3.3 3.5 4.9 289 294 H 4.0 M 4.0 3.8 5.0 295 296 C 4.0 M 3.0 0.5 2.0 297 299 E 5.0 H 5.0 3.3 4.3 301 304 C 4.8 H 6.5 5.5 7.1 305 306 - 4.0 M 75.0 75.0 2.0 307 308 C 4.0 M 5.0 6.0 3.5 309 320 H 4.8 H 2.8 2.2 2.7 321 322 C 5.0 H 4.0 2.5 4.0 323 334 H 4.9 H 2.3 1.1 1.2 335 343 C 4.9 H 2.8 3.6 2.6 344 346 H 5.0 H 2.7 2.3 3.0 347 348 C 4.0 M 38.0 2.5 2.5 349 354 - 4.0 M 75.0 4.9 75.0 355 356 C 4.5 M 4.0 1.5 3.0 357 363 E 4.7 H 3.6 2.9 2.9 364 369 C 4.7 H 3.7 4.2 15.5 370 372 E 5.0 H 4.0 3.0 4.0 373 375 H 5.0 H 2.7 2.7 1.7 377 382 E 4.8 H 1.2 0.5 1.0 383 385 C 5.0 H 4.0 4.3 4.0 386 398 H 4.8 H 2.9 2.5 2.8 >>>>>>