Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vrma1 --------------------CCEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHCCHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHCCHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCEEEEEECCCCCCEEEEECCCCCCCCEEEEEC----CCEEEEEECCCCEEECCEEECCCCCCCCCCCCCCEEEEEEEE-CHHHHHHHHHHHHCCCC--CHHHHHHHCCC-----CCEEEEEECCCCEEEC-HHHHCCC >P1;d2o34a1 CCEECCCCCCCCCCCCCCCCCCEEEEEEECCEEEEEEECC------CCCCCCHHHHHHHHHHH----HCCCCCCCCCCCCCCCCCC------------------------------------------CCCHHHHCCHHHHH------HC-----CCHHHHHHHHHHC-CHHHHHHHCC--CEEEEECCEEEEECC---CCEEEEEEEECCCCEEEEEECCCCCCEEEEECCC---CCCC------------CCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCEEEEEEEE-CCEEEEEE--CCEEC PSA >P1;d1vrma1 --------------------9123264811c360300020b637175006201613402420216297010250055496408062028004401710771a230000103013200116ba824307b406037205181051278300465020209401102001303620283089010102048001002275763241112036b731250405----940002000433154aa5210400008505005502000000-40220001020000016--62761185208-----9020000169373330-8403831 >P1;d2o34a1 05047491823519638846c1332705288060400004------914a4481046127418----70773890582a821906a------------------------------------------b0360043070052------06-----1002203300000-103512a604--000011700000105---0000020041695870001040550200000146---941a------------70233744000000640000100040018078392087027404714a3704000000-98534434--66345 Translating the sequences --------------------CCEEEEEEECCEEEEEEEEC******HHHHHHHH**HHHHH*******CHHHHHHCCCCCCCCCCC******************************************CCC*HHHHC*HHH********C*****CC****HHHHHHH*HHHHHHHHCC**EEEEEECCEEEEEEC***CCEEEEE***CCCC*EEEEEC----C*EEEEEEC***EEEC************CCCCCCEEEEEEEE-CHHHHHHHHHHHHCCCC--*HHHHHHH***-----**EEEEEE*CC*EEE*-**HH**C ********************CCEEEEEEECCEEEEEEE*C------******HHHHHHHHHHH----HC******CCCCCCCCCCC------------------------------------------CCCHHHH*CHHHHH------HC-----CCHHHHHHHHHH*-*HHHHHHHCC--*EEEEECCEEEEE*C---CCEEEEEEEECCCCEEEEEEC****CEEEEE**C---***C------------CCCCCC**EEEEEE*CHHHHHHHHHHHHCCCC**HHHHHHHHHHH*****EEEEEEEE-CCEEEEE*--**EEC 143631.tem _________________________________ --------------------CCEEEEEEECCEEEEEEEEC------HHHHHHHHHHHHHHHHH----HCHHHHHHCCCCCCCCCCC------------------------------------------CCCHHHHHCHHHHH------HC-----CCHHHHHHHHHHH-HHHHHHHHCC--EEEEEECCEEEEEEC---CCEEEEEEEECCCCEEEEEEC----CEEEEEEEC---EEEC------------CCCCCCEEEEEEEE-CHHHHHHHHHHHHCCCC--HHHHHHHHHHH-----EEEEEEEE-CCEEEEE---HHEEC Structural block scores 0 19 - 3.0 P 75.0 4.7 20 21 C 5.0 H 5.0 6.8 22 28 E 5.0 H 3.7 3.1 29 30 C 5.0 H 6.8 8.0 31 38 E 4.8 H 1.8 1.2 40 45 - 3.0 P 5.9 75.0 46 62 H 3.8 M 2.2 4.4 63 66 - 3.0 P 4.5 75.0 69 74 H 3.0 P 1.3 5.7 75 85 C 5.0 H 4.5 5.6 86 127 - 3.0 P 2.9 75.0 128 130 C 5.0 H 5.2 4.8 131 135 H 4.2 M 3.6 2.6 137 141 H 4.2 M 3.0 2.8 142 147 - 3.0 P 4.3 75.0 150 154 - 3.0 P 3.4 75.0 155 156 C 5.0 H 1.0 0.5 157 167 H 4.1 M 1.6 0.9 169 176 H 4.8 H 3.0 3.6 177 178 C 5.0 H 4.0 2.0 179 180 - 3.0 P 4.5 75.0 181 186 E 4.7 H 0.7 0.3 187 188 C 5.0 H 6.0 3.5 189 194 E 4.7 H 0.5 0.2 196 198 - 3.0 P 6.3 75.0 199 200 C 5.0 H 4.5 0.0 201 208 E 4.2 M 1.8 0.9 209 212 C 5.0 H 6.9 7.0 213 218 E 4.7 H 2.0 1.3 220 223 - 3.0 P 75.0 2.5 225 231 E 4.1 M 0.9 0.7 233 235 - 3.0 P 3.3 75.0 236 238 E 3.0 P 3.3 4.7 240 251 - 3.0 P 3.0 75.0 252 257 C 5.0 H 2.5 3.7 258 265 E 4.5 M 0.2 1.0 268 279 H 5.0 H 0.6 0.5 280 283 C 5.0 H 1.8 5.8 284 285 - 3.0 P 75.0 6.0 286 296 H 4.3 M 4.2 3.7 297 301 - 3.0 P 75.0 5.1 302 309 E 4.5 M 1.5 0.5 311 312 C 5.0 H 6.0 8.5 313 317 E 4.2 M 3.2 3.8 318 320 - 3.0 P 29.0 51.3 321 322 H 3.0 P 1.5 6.0 323 324 E 3.0 P 5.5 3.5 >>>>>>