Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ig0a2 CCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHCCEEEEECCHHHHHHHHCCCCHHHHCCCCCCEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHCHHHHHHHCCCCHHHCCCCCHHHHHHHHHHCCCCHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECC >P1;d1ig3a2 C------------------CCCCCCCHHHCCCCCCCEEEEECCCCCC---CCHHHHHHHCCEEEEECCHHHHHHHCCC---CCHHHCCCCEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHC----------------------------------CCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCC-CCEEEECC PSA >P1;d1ig0a2 b9a7a5798487a6a94b49986788634506aa03000000437061727403700520701000000023017106659931550205000021950696048206819010040408a244030000000020116904731862a22706555001641771289172980430000002129688851620550386078804006020146 >P1;d1ig3a2 a------------------a7a36673026797b1500000052602---a304300750302000100013015508---b42770204000051b4049504810662a05026175a8441000006101510774----------------------------------92a06000000232778742520570383079108-13010107 Translating the sequences C******************CCCCCCHHH*CCCCCCEEEEEECCCCCC***HHHHHHHHHCCEEEEECCHHHHHHHHCC***HHH**CCCCEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHH*H**********************************HCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC*EEEEEECC C------------------CCCCCC*HHHCCCCCC*EEEEECCCCCC---**HHHHHHHCCEEEEECCHHHHHHH*CC---**HHHCCCCEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHH*----------------------------------*CCC*EEEEECCCCCCHHHHHHHHHHHHHHHH*CC-**EEEECC 63999.tem _________________________________ C------------------CCCCCCHHHHCCCCCCEEEEEECCCCCC---HHHHHHHHHCCEEEEECCHHHHHHHHCC---HHHHHCCCCEEEECCCCCCHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHHH----------------------------------HCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC-EEEEEECC Structural block scores 1 18 - 3.0 P 7.8 75.0 19 24 C 5.0 H 7.8 7.2 25 28 H 4.0 M 5.2 3.0 29 34 C 5.0 H 5.3 6.9 35 40 E 4.7 H 0.5 0.8 41 46 C 5.0 H 3.3 2.5 47 49 - 3.0 P 3.3 75.0 50 58 H 4.6 H 3.1 3.6 59 60 C 5.0 H 3.5 1.5 61 65 E 5.0 H 0.2 0.4 66 67 C 5.0 H 0.0 0.5 68 75 H 4.8 H 1.8 1.9 76 77 C 5.0 H 3.0 4.0 78 80 - 3.0 P 6.7 75.0 81 85 H 3.4 M 4.6 6.3 86 89 C 5.0 H 1.8 1.5 90 93 E 5.0 H 0.0 0.0 94 99 C 5.0 H 3.8 4.2 100 108 H 5.0 H 4.8 4.3 109 111 C 5.0 H 3.3 4.2 112 115 E 5.0 H 1.2 3.2 116 122 C 5.0 H 4.1 5.6 123 138 H 4.8 H 1.1 2.1 139 172 - 3.0 P 4.3 75.0 174 176 C 5.0 H 2.3 4.2 177 182 E 4.7 H 0.0 1.0 183 188 C 5.0 H 4.7 3.5 189 205 H 4.9 H 4.7 4.2 206 207 C 5.0 H 2.0 4.0 209 214 E 4.3 M 1.5 1.0 215 216 C 5.0 H 5.0 3.5 >>>>>>