Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ew0a1 -----------CCCCEEEECCCCCCCCCCCCEEEEEEEECCEEEEEECCCEEEEEHHHHHHHCCCCCCCCC------CCEEEECCCEEEEEEEEEEEC-----CCCCCCEEEEECCEEEECCCHHHHHHHCCCCCCCEEEEEEEEEECCCHHHHHHHCCCCEEEECCCCCCCCCHH-HHHHHHHHHHHHCCCCCCC- >P1;d2gs5a1 CCHHHHCCCCCCCCCCCEEECCCCCCCCCCCEEEEEEECCCCEEEEECCCEEEEEHHHCC-------H-HHHHHCCCCCEEEECCCEEEEEEEEEEEECCCCCHHHCCCCCCCCCCEECCC-CCCHHHH--HHHEEE-EEEEEEEEECCCHHHHHHHCCCEEECCCCHHHHHCCCCCCHHHHCCCCCCHHHHCCCCC >P1;d2hafa1 ----------CCCCCEEEEECCCCCCCC-CCEEEEEEEC-CEEEEEECCCEEEEEHHHHHHHCCCCCCCCCCCCCHHHCEEEECCCEEEEEEEEEECC-----CCCCCCEEECCCCCEEECCHHHHHHCCCCCCCCCEEEEEEEEEEEC-CCHHHHHCCCEECCC-HHHHHCCCHH-HHHHHHHHHCC-----CCC- PSA >P1;d2ew0a1 -----------623130000148b6a32680000017038800300000222a340461048491b08a08------724003003566743200029-----936286085049900104172016200738b0b610002020209665046128684021070560005362a-50173017211697b2918- >P1;d2gs5a1 0788318a92691630000013a97a5344000001544b800200101541a5508732-------4-60260039230004012574a7130000029b070881b3086039400071-a071950--562060-00010103075a5067216814010060537002163923000402308513861574a >P1;d2hafa1 ----------670234000026816941-7000000506-a00200000333b440330098491a34692736831664002004446863100021-----46908525503950000417301310008200820000202020a8-604742868103206-1610050529-4014400572a-----583- Translating the sequences -----------CCCCEEEE*CCCCCCCCCCCEEEEEEE*CCEEEEEECCCEEEEEHHHHHHHCCCCCCCCC------CCEEEECCCEEEEEEEEEEEC-----CCCCCCEEE**CCEEEECCCHHHHHH*CCCCCCCEEEEEEEEEECCCHHHHHHHCCC*EE**CC****CCCHH-HHHHHHHHH**H***CCCC- **********CCCCC**EEECCCCCCCCCCCEEEEEEECCC*EEEEECCCEEEEEHHH**-------*-*****C**CCEEEECCCEEEEEEEEEEE*********CCC***CCCCEE**C-C**HHHH--******-EEEEEEEEECCCHHHHHHHCCCEEECCCCHHHH*CC****HHHH****CCH***CCCC* ----------CCCCCEEEEECCCCCCCC-CCEEEEEEEC-CEEEEEECCCEEEEEHHHHHHHCCCCCCCCC***C***CEEEECCCEEEEEEEEEE*C-----CCCCCCEEECCCC*EEECC*HHHHH**CCCCCCCEEEEEEEEEE*C-**HHHHHCCCEE*CC-*HHHHCCCHH-HHHHHHHHHCC-----CCC- 143456.tem _________________________________ ----------CCCCCEEEEECCCCCCCCCCCEEEEEEECCCEEEEEECCCEEEEEHHHHHHHCCCCCCCCC***C**CCEEEECCCEEEEEEEEEEEC-----CCCCCCEEECCCCEEEECCCHHHHHH*CCCCCCCEEEEEEEEEECCCHHHHHHHCCCEEECCCCHHHHCCCHH-HHHHHHHHHCCH***CCCC- Structural block scores 0 9 - 4.0 M 75.0 5.7 75.0 10 14 C 4.8 H 17.4 5.0 3.6 15 19 E 4.4 M 0.6 0.0 0.8 20 30 C 4.9 H 5.5 5.2 10.8 31 37 E 5.0 H 1.1 1.4 0.7 38 40 C 4.3 M 6.3 7.8 30.5 41 46 E 4.8 H 0.5 0.5 0.3 47 49 C 5.0 H 0.7 2.0 1.0 50 54 E 5.0 H 4.3 5.1 5.1 55 61 H 4.4 M 3.3 24.3 3.3 62 70 C 4.0 M 5.8 51.1 5.4 71 73 * 2.7 P 75.0 2.7 5.3 75 76 * 2.7 P 75.0 6.0 2.0 77 78 C 4.5 M 4.5 2.5 6.0 79 82 E 5.0 H 1.8 1.0 1.5 83 85 C 5.0 H 1.0 1.0 1.3 86 96 E 4.9 H 3.2 3.4 3.1 98 102 - 4.0 M 75.0 5.9 75.0 103 108 C 4.5 M 5.7 5.2 5.3 109 111 E 4.0 M 4.3 4.7 4.0 112 115 C 4.5 M 5.5 4.0 4.2 116 119 E 4.2 M 0.2 1.8 0.0 120 122 C 4.3 M 4.0 28.8 4.0 123 128 H 4.5 M 1.8 3.7 1.3 130 136 C 4.0 M 6.7 13.4 2.9 137 146 E 4.9 H 0.7 8.0 0.6 147 149 C 4.3 M 7.0 7.5 31.2 150 156 H 4.7 H 3.7 3.9 4.4 157 159 C 5.0 H 6.0 4.3 5.0 160 162 E 4.3 M 1.0 0.3 1.7 163 166 C 4.0 M 3.0 2.8 20.5 167 170 H 4.0 M 1.5 2.5 1.8 171 173 C 4.7 H 4.7 3.0 3.3 174 175 H 4.0 M 6.2 6.0 5.5 177 185 H 4.4 M 2.9 1.3 2.8 186 187 C 4.0 M 1.0 6.5 6.2 189 191 * 2.7 P 9.2 5.7 75.0 192 195 C 4.8 H 5.0 4.2 22.8 >>>>>>