Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1boub- CEEEEEEEECCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCEEECCCEECCCCCCCCCCCCCCEECCHHHHHHHHHHHHHCCCCCEEECC-CCCCHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCC-----CCCCCCCCHHHHHHHHHHHHH--CHH--HHCCCCHHHHHHHHCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCEEEEEEEEEECCCCCCCCCCCEEEECCCC >P1;d2pw6a1 ---CCEEEEECC------------CC-------CCCCCCCCCC-----CCCC-CEEEEE---EEE----CCEEEECCC-----------CCCCCCCCCHHHHHHHHHHHC--CCCEEEECCCCCCCHHHHHHHHCCC----CCCCC-CEEEEECC----CCHHHHHC-CCCHHHHHHH------CCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHCCCCCHHHCCCHHHHCCCCCCCHHHHHHHHCCCCCCCEECCCCCCC--CCCCCCEEEC-------------------- PSA >P1;d1boub- 15020000000153006015795295b5134019105302500669b22050000000027101789831500000182060053aa561512305013800420063058690a04225a-050010000000000272b803050000001055480060840250060025004707691200000000000057-----794373125900360073027--517--60071526502750023001000000000004960310000001404600000000114a50992296453231b80 >P1;d2pw6a1 ---410100006------------77-------7210611916-----6280-010003---025----870200293-----------a08052541790073036116--9290854aa7271060034013226----80413-00000035----37122004-0540260065------600200000010483027a7874282055005202720636672770200405818107500274200000000000152917052124406--0020000100-------------------- Translating the sequences ***EEEEEE*CC************CC*******HHHHHHHHHH*****CCCE*EEEE************CC*EEECCC***********CCCCCEECCHHHHHHHHHHHH**CCC*EEECC-CCCCHHHHHHHHHHH****CCCCE*EEEE**CC****CCHHHHHH*HHHHHHHHH*******EEEEEE*CCCCCCC-----CCCCC***HHHHHHHHHHHHH--CHH--HHCC**HHHHHHHHCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEE**CEEEEEEEEE******************** ---**EEEEECC------------CC-------**********-----CCC*-*EEEEE---EEE----CCEEEECCC-----------CCCCC**CCHHHHHHHHHHH*--CCCEEEECC*CCCCHHHHHHHH***----CCCC*-*EEEEECC----CCHHHHH*-***HHHHHHH------***EEEECCCCCCC*****CCCCCHHHHHHHHHHH*******CHH****CCHHH***HHHHC******HHHHHHHHCCCCC**EE*******--C*****EEE*-------------------- 53213.tem _________________________________ ---EEEEEEECC------------CC-------HHHHHHHHHH-----CCCE-EEEEEE---EEE----CCEEEECCC-----------CCCCCEECCHHHHHHHHHHHH--CCCEEEECC-CCCCHHHHHHHHHHH----CCCCE-EEEEEECC----CCHHHHHH-HHHHHHHHHH------EEEEEEECCCCCCC-----CCCCCHHHHHHHHHHHHHHHH--CHH--HHCCHHHHHHHHHHCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEE--CEEEEEEEEE-------------------- Structural block scores 0 2 - 3.0 P 2.0 75.0 3 9 E 4.1 M 0.3 0.9 10 11 C 5.0 H 0.5 3.0 12 23 - 3.0 P 3.6 75.0 24 25 C 5.0 H 7.0 7.0 26 32 - 3.0 P 3.6 75.0 33 42 H 3.0 P 2.5 3.4 43 47 - 3.0 P 6.9 75.0 48 50 C 5.0 H 2.3 5.3 53 58 E 4.0 M 0.0 0.7 59 61 - 3.0 P 3.3 75.0 62 64 E 3.0 P 2.7 2.3 65 68 - 3.0 P 7.0 75.0 69 70 C 5.0 H 3.0 7.5 71 74 E 4.5 M 0.0 0.5 75 77 C 5.0 H 3.0 4.7 78 88 - 3.0 P 4.4 75.0 89 93 C 5.0 H 2.4 4.7 94 95 E 3.0 P 2.5 3.5 96 97 C 5.0 H 0.5 2.5 98 109 H 4.8 H 2.6 3.6 110 111 - 3.0 P 7.0 75.0 112 114 C 5.0 H 6.5 6.7 115 118 E 4.5 M 2.0 4.2 119 120 C 5.0 H 7.8 10.5 122 125 C 5.0 H 1.2 2.5 126 136 H 4.5 M 0.1 2.5 137 140 - 3.0 P 5.6 75.0 141 144 C 5.0 H 2.8 3.2 147 152 E 4.0 M 0.2 0.0 153 154 C 5.0 H 2.5 4.0 155 158 - 3.0 P 4.2 75.0 159 160 C 5.0 H 3.0 5.0 161 166 H 4.7 H 3.2 1.5 168 177 H 4.2 M 2.4 2.8 178 183 - 3.0 P 4.2 75.0 184 190 E 3.9 M 0.0 1.1 191 197 C 5.0 H 1.7 1.9 198 202 - 3.0 P 75.0 4.5 203 207 C 5.0 H 6.0 5.6 208 223 H 4.0 M 3.0 2.9 224 225 - 3.0 P 75.0 6.0 227 228 H 5.0 H 4.0 4.5 229 230 - 3.0 P 75.0 3.5 231 232 H 3.0 P 3.0 1.0 233 234 C 5.0 H 3.5 2.0 235 244 H 4.0 M 3.3 3.5 246 259 H 4.1 M 0.4 1.1 260 264 C 5.0 H 3.8 3.4 265 275 E 3.4 M 0.8 2.9 276 277 - 3.0 P 2.0 75.0 279 287 E 3.7 M 0.1 0.3 288 307 - 3.0 P 4.8 75.0 >>>>>>