Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1aora1 CCCHHHHHHHHHHHHHHHHHCHHHHCHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHHHCEEEEECCCCCCCCCEEEEEECCCEEEECCCHHHHHHHCHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC-CHHHHCCCHHHHHHHCCCHHHCCEECCEECCCCCHHHCHHHHHHHHHCCCCCCCHHHCCHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHHHCCCHHHHC--CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHCCCCHHHHHCCCCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHC---------- >P1;d1b25a1 --CHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHH-HEEEEECCCCCCCCCEEEEECCCCCEEEE-CHHHHHHHCHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC-------CCCCCCCHHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHCCHHHCCEECCEECCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCC-CCCCCHHHHHHHHHHHHHCCHHHHHCCCCHHHHHHCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCHHHHHHCCCCCC PSA >P1;d1aora1 44687636814760254069173016402730102103401840000040032030660740003002842136554aa7220125000507727515205010000000000054030001002206629271230020000000014483076940ab10306132360054005201555c-0054014403500561933600000243000000000000000000001500013301000000122465172141647006001410110-10055193613110--30827103311201465b461850243014300450183156--8050a8304016002665045350774304---0650143005307038705025810560902766---------- >P1;d1b25a1 --698447603651364059193-16206500300003001812000030031040460950006302a-21451538892303310005025753030-401100000000001604200000300652926112000000000101458319-------82040441940360032016488b1042014405500771a0760001002300000000000000000000140021200100140095301729-251666104200410110000043175522121008052711162250658663729504410133005400720444909061630100400053004437168440477502600320071060072000348105706067015504811906 Translating the sequences **CHHHHHHHHHHHHHHHHHCHH*H*HHHHH*HHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHH**EEEEECCCCCCCCCEEEEEECCCEEEE**CHHHHHHHCHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC*******CCCCCCC*HHHHHHHHHHHCCC*-*HHHHCCCHHHHHHH*CCHHHCCEECCEECCCCCHHHCHHHHHHHHHCCCCCCCHHHCCHHHH*CCCCCCCC*CCCCHHHHHHHHHHHHHH-HHHHHHCCCHHHH*--CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCHHHH*CCCHHHHHCCCCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHH*---------- --CHHHHHHHHHHHHHHHHHC**-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHH-HEEEEECCCCCCCCCEEEEE*CCC*EEEE-CHHHHHHHCHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC-------CCCCCCCHHHHHHHHHHHHCCCH*HHHHHCCCHHHHHHHHCCHHHCCEECCEECCCCC***CHHHHHHHHHCCCCCCC***CCHHHHHCCCCCCCC-CCCC*HHHHHHHHHHHHH**HHHHHCCC*HHHH**CCC**HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH**CCC*HHHHCCC*HHHHCCCCCCCCCCCCCC***HHHHHHHHHHHHCCCCCCCCCHHHHHH*CC**HH********** 48310.tem _________________________________ --CHHHHHHHHHHHHHHHHHCHH-HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHH-HEEEEECCCCCCCCCEEEEEECCCEEEEE-CHHHHHHHCHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC-------CCCCCCCHHHHHHHHHHHHCCCH-HHHHHCCCHHHHHHHHCCHHHCCEECCEECCCCCHHHCHHHHHHHHHCCCCCCCHHHCCHHHHHCCCCCCCC-CCCCHHHHHHHHHHHHHH-HHHHHHCCCHHHHH--CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHCCCHHHHHCCCCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHH---------- Structural block scores 0 1 - 3.0 P 4.0 75.0 3 19 H 5.0 H 4.8 4.7 21 22 H 3.0 P 5.0 6.0 24 41 H 4.8 H 2.4 1.9 42 57 C 5.0 H 1.8 1.5 58 61 H 5.0 H 2.8 3.5 63 68 H 5.0 H 2.2 3.6 71 75 E 5.0 H 4.0 3.2 76 84 C 5.0 H 4.3 4.3 85 90 E 4.7 H 1.7 1.0 91 93 C 5.0 H 5.3 4.7 94 98 E 4.2 M 4.0 2.2 101 107 H 5.0 H 0.1 0.3 109 111 H 5.0 H 0.0 0.0 112 115 C 5.0 H 2.2 1.8 116 129 H 5.0 H 1.6 1.6 130 132 C 5.0 H 6.0 5.7 133 148 H 5.0 H 0.8 0.6 149 153 C 5.0 H 4.4 5.2 154 160 - 3.0 P 6.0 75.0 161 167 C 5.0 H 2.1 3.1 168 179 H 4.8 H 2.2 2.4 180 182 C 5.0 H 5.0 6.0 185 189 H 4.6 H 1.8 1.4 190 192 C 5.0 H 3.0 3.0 193 200 H 4.8 H 2.5 3.1 201 202 C 5.0 H 6.0 5.2 203 205 H 5.0 H 3.0 4.3 206 207 C 5.0 H 0.0 0.0 208 209 E 5.0 H 0.0 0.5 210 211 C 5.0 H 3.0 1.0 212 213 E 5.0 H 1.5 1.5 214 218 C 5.0 H 0.0 0.0 219 221 H 3.0 P 0.0 0.0 223 231 H 5.0 H 0.0 0.0 232 238 C 5.0 H 1.0 1.1 239 241 H 3.0 P 2.0 0.7 242 243 C 5.0 H 0.5 0.5 244 248 H 4.6 H 0.0 1.0 249 256 C 5.0 H 3.5 4.5 258 261 C 5.0 H 3.0 3.5 262 275 H 4.9 H 1.8 1.9 277 282 H 4.7 H 2.0 1.3 283 285 C 5.0 H 6.0 5.7 286 290 H 4.2 M 1.2 1.6 291 292 - 3.0 P 75.0 0.0 293 295 C 5.0 H 3.7 4.3 296 307 H 4.7 H 2.1 3.2 308 312 C 5.0 H 6.5 6.0 313 334 H 5.0 H 2.9 2.6 335 336 - 3.0 P 75.0 6.5 337 339 C 5.0 H 4.3 3.0 340 344 H 4.2 M 4.3 3.2 345 347 C 5.0 H 1.7 0.3 348 352 H 4.6 H 2.8 1.8 353 366 C 5.0 H 3.8 3.4 367 369 - 3.0 P 75.0 6.3 370 381 H 5.0 H 2.2 1.8 382 390 C 5.0 H 3.6 2.0 391 397 H 4.7 H 3.6 3.6 398 399 C 5.0 H 4.5 3.0 400 403 H 3.5 M 5.2 3.5 404 413 - 3.0 P 75.0 3.9 >>>>>>