Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1v8da- --------CHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECC------HHHCCCEEEEHHHHHHC--CCCEEC---CCCCCCCCCHHHHHHHHHCC-----------------------CEEEECCCC-----CCC----CEEEEECC---CCCHHHCCC-----------------------CEEEECCCCC--------------------------------EECCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCC----- >P1;d3ijwa1 CHHHHCCCCCCCHHHHHHHHHHH----CCCCC-CEEEEECCHHHC---CCCCHHHHHHHHC-CCCCC-CCEEE-CCCCHHHCCHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC---CHHHHHHHCCCCCEECCCCCCCCEEEECCHHHHHCCCCCC-CCCCCCHHHHHHHCCCEEEEECCCHHHCCCHHHHHHHH---CCCCCEEEEEEEECCEEEEEEEEECCCC-------------CCHHHHHHHHCCCCCE-EEECCEEEEE-C-------------HHHHHHHHHHHHHCC---- >P1;d6np3a- --------CCCCHHHHHHHHHHH----CCCCCCEEEEEECHHHHC---CCCCCHHHHHHHHHHHHCC-CCEEEEECCCCCCCHHHHCC----CCCCCHHHHHHCCCCCCCCCCCCHH-HCCHHHHHHCCCCCEECCCCCCCEEEECCCHHHHHCCCCCCCCCCCCCHHHHHHCCCCEEEEECCCHHHCCCHHHHHHHCCCCCCCEEEEEEEEEECCEEEEEEEEEECCCCCCHHHCCCCCCCHHHHHHHHHHHHCCCEEEEECCEEEEEEE-------------HHHHHHHHHHHHHHHCC-C >P1;d7kesa- -------CCCCCHHHHHHHHHHH----CCCCCCEEEEEECHHHHC---CCCCCCHHHHHHHHHHHCC-CCEEEEECCCC-CCHHHHC---------CHHHHHHCCCCCCCCCCCCHH-HCHHHHHHHCCCCCEECCCHHHCEEEEECCHHHHHCCCCCCCCCCCCCHHHHHHHCCCEEEEECCCHHHCCHHHHHHHHCCCCCCCEEEEEEEEECCCCEEEEEEEEECCCCCCCCCC----CCHHHHHHHHHHHCCCCEEEEECCEEEEEEE-------------HHHHHHHHHHHHHHHHHHC PSA >P1;d1v8da- --------45a146105500830095260877100000030250449711470060003000520594802000005------871a2000035701731--a0753a---48062720500011026309-----------------------410005305-----430----30000007---370840036-----------------------4426170804--------------------------------505607040120597687bba32557854455576969----- >P1;d3ijwa1 ca57870a840458400620590----60863-000000427300---4059616000400-60038-60000-10405602004428876157862672267280043a706037---97023211637905009001100002162086005a0526-00247000320152304000012505400001000320---a129731000244ba8231380616263-------------906700840285a516-a504508030-4-------------043006201621589---- >P1;d6np3a- --------a53548500720290----40663100001041a405---8049623000300250019-80000010005300185038----5a603a923a816003388020468-437004400528b0500700100000025405500640702201047000110073a02000011616200001100030907b144130000135b88341221403028001860069a2520014006302763a057560070a01006-------------06600620280037417-8 >P1;d7kesa- -------c831559500730580----70693210001041a606---806763610030044003a-90000010204-177a417---------488538808002398260398-386002000529a0400500400000035509400670124200066000110373702000000613501000001240905b143461200137b883603703021286118a08----87112700650186a5165660150600002-------------0340073016202620777 Translating the sequences --------C***HHHHHHHHHHH****CCCCCCEEEEEECHHHH****CC***HHHHHHHHHHHH*C*CCEEEEECC------HHHCC*********HH*--*CC**C---CCCC****CHHHHHHH**CC-----------------------C****CCCC-----***----CEEEEECC---*CC*HH***-----------------------*EEEE***CC--------------------------------EECCEEEEEEE**************HHHHHHHHH****----- ********CCCCHHHHHHHHHHH----CCCCC-*EEEEEC*HHHC---CCCC*HHHHHHH*-***CC-CCEEE-*CCC***C*HHHCC*********HHHHHHCCCCCCCCCCCC*---CHHHHHHHCCCCCEECCC***C*EEE*CCHHHHHCCCCCC-CCCCCCHHHHHH*CCCEEEEECCCHHHCC*HHHHHHH*---CCC**EEEEEEE*CC*EEEEEEEE*CCC-------------**HHHHHHHH**CCCE-EEECCEEEEE-*-------------HHHHHHHHHHHHH**---- --------CCCCHHHHHHHHHHH----CCCCCCEEEEEECHHHHC---CCCC*HHHHHHHHHHHHCC-CCEEEEECCC***C*HHHCC----*****HHHHHHCCCCCCCCCCCC**-*C*HHHHHHCCCCCEECCC***C*EEE*CCHHHHHCCCCCCCCCCCCCHHHHHH*CCCEEEEECCCHHHCC*HHHHHHH****CCC**EEEEEEE*CC*EEEEEEEE*CCC***************HHHHHHHH**CCCE*EEECCEEEEEEE-------------HHHHHHHHHHHHH****-* -------*CCCCHHHHHHHHHHH----CCCCCCEEEEEECHHHHC---CCCC**HHHHHHHHHHHCC-CCEEEEECCC*-*C*HHHC---------*HHHHHHCCCCCCCCCCCC**-*CHHHHHHHCCCCCEECCC***C*EEE*CCHHHHHCCCCCCCCCCCCCHHHHHH*CCCEEEEECCCHHHCC*HHHHHHH****CCC**EEEEEEE*CC*EEEEEEEE*CCC*******----****HHHHHHHH**CCCE*EEECCEEEEEEE-------------HHHHHHHHHHHHH****** 110710.tem _________________________________ -------*CCCCHHHHHHHHHHH----CCCCCCEEEEEECHHHHC---CCCC*HHHHHHHHHHHHCC-CCEEEEECCC***C*HHHCC*********HHHHHHCCCCCCCCCCCC**-*CHHHHHHHCCCCCEECCC***C*EEE*CCHHHHHCCCCCCCCCCCCCHHHHHH*CCCEEEEECCCHHHCC*HHHHHHH****CCC**EEEEEEE*CC*EEEEEEEE*CCC*******----****HHHHHHHH**CCCE*EEECCEEEEEEE-------------HHHHHHHHHHHHH****-* Structural block scores 0 6 - 4.3 M 75.0 7.1 75.0 75.0 8 11 C 4.5 M 5.1 4.0 5.9 4.2 12 22 H 5.0 H 2.9 3.5 3.4 3.8 23 26 - 4.3 M 4.0 75.0 75.0 75.0 27 32 C 4.9 H 4.8 16.3 3.3 4.5 33 38 E 4.9 H 0.0 0.0 0.2 0.3 40 43 H 4.8 H 1.8 3.0 3.9 4.4 45 47 - 4.3 M 6.7 75.0 75.0 75.0 48 51 C 4.7 H 3.2 4.5 5.2 5.2 53 64 H 4.6 H 1.3 7.7 1.2 1.8 65 66 C 4.7 H 7.0 5.5 5.0 6.8 68 69 C 5.0 H 4.0 3.0 4.0 4.5 70 74 E 4.7 H 0.4 15.2 0.2 0.2 75 77 C 4.8 H 26.7 1.3 0.0 0.7 78 80 * 2.7 P 75.0 3.7 2.7 26.7 83 85 H 5.0 H 5.3 2.7 4.3 5.2 86 87 C 4.7 H 6.2 5.0 5.5 41.0 88 96 * 2.7 P 1.8 5.6 36.1 67.1 97 102 H 4.5 M 28.6 5.0 7.2 6.7 103 114 C 4.7 H 22.4 3.6 2.9 3.4 115 116 * 1.6 P 4.5 41.0 7.0 8.5 120 126 H 4.9 H 0.6 2.3 2.1 1.1 127 131 C 4.6 H 18.6 5.0 5.3 5.3 132 133 E 4.3 M 75.0 2.5 2.5 2.0 134 136 C 4.3 M 75.0 3.0 2.3 1.7 137 139 * 2.3 P 75.0 0.7 0.3 1.3 142 144 E 4.3 M 75.0 0.7 0.0 0.0 146 147 C 4.3 M 75.0 4.0 4.5 5.0 148 152 H 4.3 M 75.0 2.8 2.0 2.6 153 165 C 4.5 M 24.5 9.0 2.5 2.6 166 171 H 4.3 M 38.7 1.0 0.3 0.8 173 175 C 4.5 M 51.0 1.7 4.5 3.3 176 180 E 5.0 H 0.0 0.8 0.4 0.4 181 183 C 4.8 H 27.3 2.7 2.7 2.0 184 186 H 4.3 M 51.0 3.0 3.0 3.0 187 188 C 5.0 H 3.5 0.0 0.0 0.5 190 196 H 4.5 M 23.3 0.9 0.7 1.0 197 200 * 3.2 M 75.0 56.2 4.0 3.5 201 203 C 4.3 M 75.0 4.5 5.5 5.5 204 205 * 2.3 P 75.0 8.0 2.5 3.5 206 212 E 4.3 M 75.0 1.4 1.0 1.9 214 215 C 4.3 M 75.0 11.0 9.8 9.8 217 224 E 4.6 H 12.4 3.0 2.1 2.8 226 228 C 4.8 H 26.3 3.7 3.3 3.7 229 235 * 3.5 M 75.0 75.0 2.1 4.9 236 239 - 4.3 M 75.0 75.0 6.9 75.0 240 243 * 2.9 P 75.0 39.8 1.8 4.2 244 251 H 4.3 M 75.0 3.4 2.0 2.6 252 253 * 2.3 P 75.0 6.5 6.5 7.0 254 256 C 4.3 M 75.0 5.5 4.5 5.5 259 261 E 4.8 H 26.7 5.2 3.7 4.0 262 263 C 5.0 H 5.5 4.5 3.5 3.0 264 270 E 4.8 H 2.0 12.9 2.5 1.1 271 283 - 4.3 M 6.6 75.0 75.0 75.0 284 296 H 4.8 H 5.8 2.3 2.5 2.2 297 300 * 2.6 P 58.5 41.8 4.8 3.8 >>>>>>