Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gxma1 ---------------------CCCCCCCCCCHHHHHHHHHCCCCC--------------------------------------HHHHHHHHHCCCCCCCCCCCCCCCCCCCC-----CCC-----------CC-CEECHHHCCHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCHHHHCEECHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEECCEECCCCCEECCCCCCCCCCCCCCCCCEECCCHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCEEEEEECHHHCCCCCEEEEEEEEEEECEECCCCCCCCEECCCCCEECCHHHCCHHHHHHCCCEECCHHHHHHHHHHCC-CC >P1;d1r76a- CCCEECCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCCCCCCHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHCCHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCEECHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHCCEECCEECCCCCEECCCCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH--HCCCCC--------------CCC-CCCEECEECCCCCCCCEECCCCEEECCHHHCCHHHHCCCCCEECCCHHHHHHHHHHHHCC PSA >P1;d1gxma1 ---------------------bd5415386010062059028518--------------------------------------79205002210073000237270764b62-----b37-----------88-00001640001000000210379---7664026003500500150029200000235357c412200024300000000000004523003280079a21840760073015001500270887200001000075270260460003000010010000000005-06a60270042007003265003554204785079401277aa230012001177060000158353136046066600461500372057017007509-03 >P1;d1r76a- 663850980530578306734b961650570075075128605840483069c481172079990572023a47692044a704400400330002000002501068-951570000051a7799a5a041720000144000100200020043148940550260026004000401024000000000247210000024100030040043005085207--2048913650670064016001500254ab830000000101538010056000300000000300400082a908960160043007005--813188--------------819-7400010013aa2530001575111443750677127b28022360480174289148a2 Translating the sequences ---------------------CCCC******HHHHHHHHH*****--------------------------------------HHHHHHHHH*CCCCCCCCCCCCCCC*CCC-----CCC-----------CC-CEECHHHCCHHHHHHHHHHHHHH---*CHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCHHHHCEECHHHHHHHHHHHHHHHH*CCCCCC**CCCHHHHHHHHHHHHHHHHHHHHHCCEECCEECCCCCEECCCCCCCCCCCCCCCCCEE***HHHHHHHHCCCC-CCHHHHHHHHHHHHHH****CCEEE**************EEE*EEEEECEECCCCCCCCEECCCC*EECCHHHCCHHHHHHCCCEECCHHHHHHHHHH**-CC *********************CCCCHHHHHHHHHHHHHHHHHHHH**************************************HHHHHHHHHHCCCCCCCCCCCCCCC-CCC*****CCC***********CC*C**CHHHCCHHHHHHHHHHHHH****HCHHHHHHHHHHHHHHHHHCCCCCCCCC**CCCCHHHHCEECHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHCCEECCEECCCCCEECCCCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCC*CCHHHHHHHHHHHHHHH--HCC***--------------***-***EECEECCCCCCCCEECCCCEEECCHHHCCHHHH**CCCEECC*HHHHHHHHHHH*CC 81853.tem _________________________________ ---------------------CCCCHHHHHHHHHHHHHHHHHHHH--------------------------------------HHHHHHHHHHCCCCCCCCCCCCCCC-CCC-----CCC-----------CC-CEECHHHCCHHHHHHHHHHHHHH---HCHHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCHHHHCEECHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHCCEECCEECCCCCEECCCCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHH--HCCEEE--------------EEE-EEEEECEECCCCCCCCEECCCCEEECCHHHCCHHHHHHCCCEECCHHHHHHHHHHHH-CC Structural block scores 0 20 - 3.0 P 75.0 4.6 21 24 C 5.0 H 8.5 6.9 25 44 H 3.9 M 3.5 4.0 45 82 - 3.0 P 75.0 4.8 83 92 H 4.8 H 2.8 1.8 93 107 C 5.0 H 2.9 1.6 109 111 C 5.0 H 6.5 5.0 112 116 - 3.0 P 75.0 2.4 117 119 C 5.0 H 7.2 1.7 120 130 - 3.0 P 75.0 6.7 131 132 C 5.0 H 8.0 4.0 135 136 E 3.0 P 0.0 0.0 138 140 H 5.0 H 3.7 3.0 141 142 C 5.0 H 0.0 0.0 143 156 H 4.9 H 1.6 0.9 157 159 - 3.0 P 75.0 7.0 162 178 H 5.0 H 2.2 2.0 179 187 C 5.0 H 1.4 0.8 188 189 E 3.0 P 2.5 0.0 190 193 C 5.0 H 5.0 1.5 194 197 H 5.0 H 4.9 2.5 199 200 E 5.0 H 0.0 0.0 202 218 H 4.9 H 0.8 1.5 219 224 C 5.0 H 2.2 3.7 225 226 - 3.0 P 5.0 75.0 227 229 C 5.0 H 2.3 2.0 230 250 H 5.0 H 3.3 3.2 251 252 C 5.0 H 1.0 1.0 253 254 E 5.0 H 3.5 4.5 255 256 C 5.0 H 8.0 11.0 257 258 E 5.0 H 4.5 5.5 259 263 C 5.0 H 0.2 0.0 264 265 E 5.0 H 0.0 0.0 266 282 C 5.0 H 2.5 1.9 283 284 E 5.0 H 0.0 0.0 285 295 H 4.5 M 0.2 0.6 296 299 C 5.0 H 1.2 5.1 301 302 C 5.0 H 3.0 4.0 303 317 H 4.9 H 2.8 2.7 318 319 - 3.0 P 4.0 75.0 321 322 C 5.0 H 0.0 2.0 323 325 E 3.0 P 4.3 5.7 326 339 - 3.0 P 3.8 75.0 340 342 E 3.0 P 8.2 6.0 344 348 E 3.8 M 1.2 2.2 350 351 E 5.0 H 0.0 0.0 352 359 C 5.0 H 2.8 4.4 360 361 E 5.0 H 0.0 0.0 362 365 C 5.0 H 4.2 4.5 366 368 E 4.3 M 3.0 1.0 369 370 C 5.0 H 4.5 4.0 371 373 H 5.0 H 3.3 5.0 374 375 C 5.0 H 3.0 3.0 376 381 H 4.3 M 3.7 5.9 382 384 C 5.0 H 2.0 3.3 385 386 E 5.0 H 1.5 2.0 387 388 C 5.0 H 4.5 4.5 389 400 H 4.5 M 3.4 4.0 402 403 C 5.0 H 1.5 6.2 >>>>>>