Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1z1wa1 ------------------CCEEEEEEEEEEECC-----CCEEEEEEEEEECC-----EEEEEECCCCEEE----EEEECCC--------EECCEEC--CC-EEEEEEEC------CCCEEEEEEEEECCC-CCCEEEEECC---------CCCEEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEECCC--CEEEECCCEEEEEEC-----CCEEEEECCCCCCCHHHCCEEEECC >P1;d3u9wa1 CCCCCCCCCCCC-----CEEEEEEEEEEEEECC-----CCEEEEEEEEEEEECCCCEEEEEEEECCCEEE----EEEECC------EECCEEECCCCHHHCEEEEEEEEEEECCCCEEEEEEEEECCC---CCCCEEEEC---HHHCCCCCCCEEEECCCCCCHHHCCCCCCCCCCCEEEEEEEEEECC--CEEEECCEEEE-EEECCCCCCEEEEEEEEEEEECHHHCCEEEEC- >P1;d4fkea1 CCCHHHC-----CCCCCCEEEEEEEEEEEECCCCCCCCCCEEEEEEEEEEEECCC-EEEEEEECCCCEECCCCCCCEEEECCCCCCCCEEEEEEEC--CC-CEEEEEEEEEECCCCEEEEEEEEEEECCC-CCCEEEEEEEEECC----EEEEEEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEEECC--CEEEECCCCCCCCEECCCCCCEEEEECCCCCCCCHHHCCEEEECC >P1;d4qmea1 C-----CCCCHHHCCCCCEEEEEEEEEEEEC-C-----C-CEEEEEEEEEEECCCCC-CEEEECC-CEEE----EEEECC------EECCCEEE------CCEEEEC--CCCC--CCEEEEEEEEECHHHCCCCCEEEEC----------C--EEEECCCCCCHHHCCCCCCCCCC-CEEEEEEEEECCCCCEEEECCEEEE-EEECC--CCEEEEEEECCCCCCHHHCCEEEE-- >P1;d6q4ra1 CCCCCCC-----CCCCCCEEEEEEEEEEEEECC-----CCEEEEEEEEEEEECCC-CCEEEEECCCCEEE----EEEEECC---CEEEC-EEEEEC--CC-CEEEEECCCCCCCCCCEEEEEEEEEECCC-CCCEEEEEEEECCC---CCEEEEEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEECCC--CEEEECCCEEE-EEEEEC--CEEEEEECCCCCCCHHHCCEEEECC PSA >P1;d1z1wa1 ------------------160730504040407-----73408040302054-----98040201b0905----4030599--------71a1816--66-10506059------970503010218058-964001049a---------981300040785102400001055735020101010257--160502263574649-----a313030440751004603000053 >P1;d3u9wa1 b83850101628-----2040330305040319-----54003420202010148606402000030707----302079------96172627a458620220505038207675416040102035---704005015---4951bb6822404070671300000000005605020302010165--0505040876a-56807747713104052875100250503005- >P1;d4fkea1 9762265-----78028204041070302021936a8750204050303030455-161000002709060ba43030503cb1a2180350432a--80-20000105840639420201050315026-482001143467cb----7520101060575100000000016a15020401010259--0506033645aa376098469112050450761003604040047 >P1;d4qmea1 c-----8895b86588010404304040303-7-----5-30206050302033664-4050203-1703----404156------880b3848------c640208--c026--850302020214077287600125c----------b--50306057520240000003640-0501020104596046050439446-0664b--782021314149601036050300-- >P1;d6q4ra1 a8032a7-----970092040610302020407-----72407020304030766-14200000280907----6010328---74260-721737--91-30000204860749670200040429016-5a5001243462a8---76442001050576000100000016905020303031346--05050337346-35627a--7120030550971002505020045 Translating the sequences ------------------**EEEEEEEEEEECC-----CCEEEEEEEEEE**-----EEEEEECCCCEEE----EEEECCC--------*E**EEC--CC-*EEEEEE*------CC*EEEEEEEEECCC-CCCEEEEEC*---------C**EEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEE*CC--CEEEECCCEEE*EE*-----C*EEEEECCCCCCCHHHCCEEEECC CCC***C*****-----CEEEEEEEEEEEEECC-----CCEEEEEEEEEEEECCC**EEEEEE*CCCEEE----EEEECC------EEC*EEE**C******EEEEEE****CCCC*EEEEEEEE**C---CCC*EEEEC---*******C**EEEE*CCCCCHHHCCCCCCCCCCC*EEEEEEEEECC--CEEEECC*EEE-EEECCC*CCEEEEEE******CHHHCCEEEEC- CCC***C-----*CCCCCEEEEEEEEEEEE*CC*****CCEEEEEEEEEEEECCC-*EEEEEECCCCEE*******EE**C*********EEEEEC--CC-CEEEEEE****CCCC*EEEEEEEEEECCC-CCCEEEEE******----****EEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEEECC--CEEEECCC*****EECCC*CCEEEEE*CCCCCCCHHHCCEEEECC C-----C******CCCCCEEEEEEEEEEEE*-C-----C-*EEEEEEEEEEECCC**-*EEEECC-CEEE----EEEECC------EEC**EEE------*CEEEE*--***C--CCEEEEEEEEE*****CCC*EEEEC----------C--EEEE*CCCCCHHHCCCCCCCCCC-CEEEEEEEEECC**CEEEECC*EEE-EEECC--CCEEEEEE*CCCCCCHHHCCEEEE-- CCC***C-----*CCCCCEEEEEEEEEEEEECC-----CCEEEEEEEEEEEECCC-**EEEEECCCCEEE----EEEE*CC---**EEC-EEEEEC--CC-CEEEEE*****CCCCCEEEEEEEEEECCC-CCCEEEEE******---*****EEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEE*CC--CEEEECCCEEE-EEE**C--CEEEEEECCCCCCCHHHCCEEEECC 63737.tem _________________________________ CCC***C-----*CCCCCEEEEEEEEEEEEECC-----CCEEEEEEEEEEEECCC-*EEEEEECCCCEEE----EEEECCC-----EEC*EEEEEC--CC-CEEEEEE****CCCCCEEEEEEEEEECCC-CCCEEEEEC*--**----*C**EEEEECCCCCHHHCCCCCCCCCCCCEEEEEEEEECC--CEEEECCCEEE-EEECCC-CCEEEEEECCCCCCCHHHCCEEEECC Structural block scores 0 2 C 4.3 M 75.0 7.5 7.3 54.2 6.2 3 5 * 3.0 P 75.0 4.3 3.3 75.0 5.2 7 11 - 3.8 M 75.0 3.4 75.0 8.3 75.0 13 17 C 4.3 M 75.0 60.4 4.0 4.4 3.6 18 30 E 4.8 H 2.6 1.9 1.8 1.9 1.7 31 32 C 4.8 H 3.5 5.0 5.0 41.0 3.5 33 37 - 4.5 M 75.0 75.0 6.9 75.0 75.0 38 39 C 4.8 H 5.0 4.5 2.5 40.0 4.5 40 51 E 4.9 H 2.5 1.2 1.7 1.8 1.9 52 54 C 4.5 M 75.0 4.3 4.7 4.0 6.3 57 62 E 4.8 H 3.8 2.0 1.2 14.3 1.0 63 66 C 4.8 H 3.1 0.8 2.2 19.8 2.5 67 69 E 4.8 H 4.7 4.7 5.0 3.3 5.3 70 73 - 4.5 M 75.0 75.0 6.5 75.0 75.0 74 77 E 4.8 H 1.8 1.2 1.5 2.2 1.8 78 80 C 4.2 M 7.7 30.3 2.7 28.7 4.3 81 85 - 4.2 M 75.0 75.0 7.5 75.0 47.2 86 87 E 4.1 M 75.0 7.5 4.5 8.0 4.0 90 94 E 4.4 M 4.3 5.5 2.8 19.6 4.0 96 97 - 4.5 M 75.0 6.5 75.0 75.0 75.0 98 99 C 4.1 M 6.0 4.0 4.0 75.0 5.0 102 107 E 4.8 H 2.7 2.0 0.2 14.8 0.3 108 111 * 2.1 P 58.5 3.2 4.2 22.4 4.5 112 116 C 4.3 M 48.2 5.8 4.8 33.8 6.6 117 126 E 4.8 H 2.0 1.7 1.7 1.4 2.1 127 129 C 4.2 M 4.3 51.7 2.7 4.7 2.3 131 133 C 5.0 H 6.3 3.7 4.7 7.0 6.8 134 138 E 4.8 H 1.0 1.2 1.2 1.6 1.4 141 142 - 3.8 M 75.0 75.0 6.5 75.0 4.0 143 144 * 3.0 P 75.0 6.5 12.0 75.0 9.2 145 148 - 4.3 M 75.0 7.2 75.0 75.0 58.0 151 152 * 2.1 P 4.5 2.0 1.0 75.0 3.0 153 157 E 4.8 H 1.4 3.0 1.6 2.8 1.2 158 162 C 5.0 H 4.2 3.4 3.6 3.8 3.6 163 165 H 5.0 H 2.0 0.0 0.0 2.0 0.3 166 177 C 4.9 H 2.2 1.3 2.0 7.3 1.8 178 186 E 4.9 H 0.8 1.0 1.1 1.4 1.7 187 188 C 5.0 H 6.0 5.5 7.0 7.0 5.0 189 190 - 4.5 M 75.0 75.0 75.0 3.0 75.0 192 195 E 5.0 H 2.8 2.5 2.8 2.8 2.5 196 198 C 4.6 H 3.3 4.0 4.0 5.3 4.3 199 201 E 4.5 M 5.0 7.8 6.5 4.7 4.3 203 205 E 4.7 H 6.3 6.3 5.3 4.0 4.7 206 208 C 4.1 M 75.0 4.7 5.7 30.2 6.5 210 211 C 4.6 H 42.8 7.0 7.5 7.5 41.0 212 217 E 4.8 H 1.7 1.5 1.5 1.5 1.0 218 224 C 4.5 M 3.0 4.0 3.3 3.6 3.9 225 227 H 5.0 H 3.3 2.3 3.0 3.0 2.3 228 229 C 5.0 H 1.5 2.5 2.0 2.5 2.5 230 233 E 5.0 H 0.0 0.8 1.0 0.8 0.5 234 235 C 4.3 M 4.0 40.0 5.5 75.0 4.5 >>>>>>