Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4xfma- -CEEEEEECCHHHHHHHHHHHHHCCCCEEECCCH--HHCCHHHC-CCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCC----CCHHHHHHHHHHHHCCCCEEEECCCHHHCEEEECCEEEECCEEHHHCHHHCCCCCCCCCCCHHHHHHCCCCCCEEEECHHHHCC--CCHHHHHHHHHHHCCCEEEECCCCHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHH-----CCCCCCC---CCEEEEECCCCHHHHHHHHHHHCCCCEEEEEEEHHHHHCCCHHHHHHHHHHHHHHHHHC--CCEEEEEEEC--------------HHHHHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCCEEEEEEEECCCEEEEEEECCCCCCCEEEEECCCCCCCCHHHHHHHHHHC- >P1;d5dmha- CCCEEEEECCHHHHHHHHHHHHHCC-CEEEEECCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCC-EEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEECCCHHHCEEEECCEEEECCEEHHHCC-CCCCCCC-CCCCHHHHHHHCCCCCCCEECHHHHCCCHHHHHHHHHHHHHCCCC-CEECCCCHHHHHHHHHHCCC---CCEEEECCHHHCCHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHH-CCCCEEECCHHHHHC------CCCHHHHHHHHHHCCCCCCEEECCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEECHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEC-CC-CCCEEEEECCCCCCCCHHHHHHHHHCCC PSA >P1;d4xfma- -a30000003770045007404723071420953--a8056930-22000020701627564049404300630473908001000001002----0000100210082092400000000086411049020209865037182086781507202025006531a25322042a3046--a802820350075813000000363900430070046062600000041004000610-----90a4529---6000000015492046003005939004104062b2064872a9417601550160047--130000004b--------------967750190003002201740201000001870092028308077166475129103201049040a71200205566296600240063037- >P1;d5dmha- 7010000000001000000003532-6010004309c5306928801000000100226395026404600810443105-00000000001066900001001100730a050000000015160304504032ab4314611-2541104-710103610440096602103250066719104630750396903-0000054590051004004a---030000000001000310165a40683a0560636000000112730380063047-592103405030005------957118600730593c51000000054a51771096185750331108001600440385-90200000101000100630907004006101300000002-7a-8200000012400775003500630069 Translating the sequences -CEEEEEECCHHHHHHHHHHHHHCC*CEEE**CH--HHCCHHHC-CCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCC*EEEEECCCCCC----CCHHHHHHHHHHHHCCCCEEEECCCHHHCEEEECCEEEECCEEHHHCH*HCCCCCC*CCCCHHHHHH*CCCCCEEEECHHHHCC--**HHHHHHHHHHHCCC*EEECCCCHHHHHHHHHHHCC***CCEEEECHHHHHHHHHHH-----CCCCCCC---CCEEEEECCCCHHHHHHHHHHH**CCEEEEEEEHHHHHC******HHHHHHHHHHHHHC--CCEEEEEEEC--------------HHHHHHHHHHHHHHHHHHHH*CCCEEEEECHHHHHHHHHH*CCCEEEEEEEE*CCEEEEEEE*CC*CCCEEEEECCCCCCCCHHHHHHHHHHC- *C*EEEEECCHHHHHHHHHHHHHCC-CEEEEEC*****CC***C*CCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCC-EEEEECCCCCC****CCHHHHHHHHHHHHCCCC**EECCCHHHCEEEECCEEEECCEEHHHC*-*CCCCCC-CCCCHHHHHHHCCCCC**EECHHHHCC**HHHHHHHHHHHH*CCC-*EECCCCHHHHHHHHHH*CC---CCEEEEC*HHH**HHHHH*****CCCCCCC***CCEEEEECCCCHHHHHHHHHHHH-CC**EEE**HHHHHC------***HHHHHHHHHHC**CC*EEE***C**************HHHHHHHHHHHHHHHHHHH*-CCCEEEEECHHHHHHHHHHHCCCEEEEEEEEECCEEEEEE*-CC-CCCEEEEECCCCCCCCHHHHHHHHH*C* 142764.tem _________________________________ -CEEEEEECCHHHHHHHHHHHHHCC-CEEEEECH--HHCCHHHC-CCEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCC-EEEEECCCCCC----CCHHHHHHHHHHHHCCCCEEEECCCHHHCEEEECCEEEECCEEHHHCH-HCCCCCC-CCCCHHHHHHHCCCCCEEEECHHHHCC--HHHHHHHHHHHHHCCC-EEECCCCHHHHHHHHHHHCC---CCEEEECHHHHHHHHHHH-----CCCCCCC---CCEEEEECCCCHHHHHHHHHHHH-CCEEEEEEEHHHHHC------HHHHHHHHHHHHHC--CCEEEEEEEC--------------HHHHHHHHHHHHHHHHHHHH-CCCEEEEECHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEE-CC-CCCEEEEECCCCCCCCHHHHHHHHHHC- Structural block scores 2 7 E 4.7 H 0.5 0.2 8 9 C 5.0 H 1.5 0.0 10 22 H 5.0 H 3.5 0.7 23 24 C 5.0 H 2.5 2.5 27 31 E 4.2 M 3.2 0.2 34 35 - 3.0 P 75.0 4.5 36 37 H 3.0 P 9.2 8.8 38 39 C 5.0 H 2.5 1.5 40 42 H 3.0 P 6.0 5.7 45 46 C 5.0 H 2.0 0.5 47 51 E 5.0 H 0.4 0.0 52 58 C 5.0 H 3.3 1.6 59 75 H 5.0 H 3.5 3.3 76 79 C 5.0 H 5.0 2.2 81 85 E 5.0 H 0.2 0.0 86 91 C 5.0 H 0.5 0.2 92 95 - 3.0 P 75.0 5.2 96 97 C 5.0 H 0.0 0.0 98 109 H 5.0 H 1.2 1.1 110 113 C 5.0 H 3.8 3.9 114 117 E 4.0 M 0.0 0.0 118 120 C 5.0 H 0.0 0.0 121 123 H 5.0 H 4.7 2.3 125 128 E 5.0 H 1.5 1.8 129 130 C 5.0 H 4.5 2.5 131 134 E 5.0 H 1.0 2.2 135 136 C 5.0 H 8.5 11.0 137 138 E 5.0 H 5.5 3.5 139 141 H 5.0 H 3.3 3.7 146 151 C 5.0 H 5.8 2.5 153 156 C 5.0 H 2.8 2.2 157 163 H 4.7 H 2.6 2.6 164 168 C 5.0 H 4.3 4.2 169 172 E 4.0 M 1.8 0.8 174 177 H 5.0 H 3.9 1.8 178 179 C 5.0 H 5.0 6.0 180 181 - 3.0 P 75.0 4.0 182 194 H 4.5 M 3.9 4.1 195 197 C 5.0 H 4.0 4.0 199 201 E 4.3 M 0.0 0.0 202 205 C 5.0 H 2.2 2.2 206 216 H 4.8 H 2.4 2.2 217 218 C 5.0 H 5.0 7.2 219 221 - 3.0 P 2.7 75.0 222 223 C 5.0 H 3.0 1.5 224 227 E 5.0 H 0.0 0.0 229 239 H 4.5 M 1.5 0.5 240 244 - 3.0 P 75.0 5.3 245 251 C 5.0 H 5.6 4.6 252 254 - 3.0 P 75.0 4.0 255 256 C 5.0 H 3.0 4.5 257 261 E 5.0 H 0.0 0.0 262 265 C 5.0 H 2.5 1.0 266 277 H 4.8 H 3.2 3.4 279 280 C 5.0 H 4.5 7.0 281 287 E 3.9 M 2.1 2.1 288 292 H 5.0 H 4.3 0.6 294 299 - 3.0 P 6.8 75.0 300 312 H 4.5 M 2.8 4.0 314 315 - 3.0 P 75.0 7.8 316 317 C 5.0 H 2.0 3.0 318 324 E 3.9 M 0.6 0.0 326 339 - 3.0 P 75.0 5.1 340 359 H 4.9 H 3.1 2.6 361 363 C 5.0 H 1.0 3.7 364 368 E 5.0 H 0.0 0.0 370 380 H 4.8 H 3.5 1.0 381 383 C 5.0 H 5.0 5.3 384 392 E 4.8 H 4.3 1.3 393 394 C 5.0 H 5.0 1.5 395 401 E 4.7 H 1.4 0.3 403 404 C 5.0 H 2.0 8.8 406 408 C 5.0 H 6.2 3.3 409 413 E 5.0 H 0.8 0.0 414 421 C 5.0 H 5.6 3.2 422 431 H 4.8 H 1.8 1.7 >>>>>>