Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4emta1 -CHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCC---CCC--CEEEEEEECCC---------CCCCEEEEEEEECCEEEEEEEEEECCHHHHHHCCCCHHHC-CCHHHHHHHHHHHHHHHHHHHHHCHHHHCCEEEEEECCCCCCCCCCHHHHHHHHHCCCC----- >P1;d5cfla1 CCHHHHHHHHHHCCHHHHCCCHHHHHCCCHHHHH--C-CCEEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEECCCEEEEECCEEEEECCCCCCCEEEEEEECCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHCCCEEEEEECC--C---CCHHHHHHHHHHCCCCCCCC PSA >P1;d4emta1 -707b20680148205500540880057006738c80aa60342000000160714b805---309--5064135067b---------791701001023b97323000020071066047077974b-168941472053017105700591680573030021553b897b140051006214728----- >P1;d5cfla1 6304a10580052204200240570044376058--1-520012000000620505a70121900467205424405436543c8865450502002051cb8520000020061055037206776c70558604710630163037007928707a313004053--9---51004001630580a2987c Translating the sequences -CHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH****C*CC****EEEEEECCCCCCCCCC---CCC--CEEEEEEECC*---------***CEEEEEEEECCEEEEEEEEEECCHHHHHH****HHHC-CCHHHHHHHHHHHHHHHHHHHHHCHHHHCCEEEEEECC**C***CCHHHHHHHHH*CCC----- *CHHHHHHHHHH*CHHHH***HHHHH***HHHHH--C-CCEEEEEEEEEECCCCCCCCCC***CCC**CEEEEEE*CCE*********EEEC*EEEEE**CC***EEEEEEECC*HHHHHHHHHH**C*CCHHHHHHHHHHHHHHHHHHHH*CHHH*CCEEEEEECC--C---CCHHHHHHHHHHCCC***** 254144.tem _________________________________ -CHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH--C-CCEEEEEEEEEECCCCCCCCCC---CCC--CEEEEEEECCE---------EEECEEEEEEEECCEEEEEEEEEECCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHCHHHHCCEEEEEECC--C---CCHHHHHHHHHHCCC----- Structural block scores 2 12 H 4.8 H 4.3 3.2 14 33 H 4.2 M 3.5 3.0 34 35 - 3.0 P 10.2 75.0 38 39 C 5.0 H 8.2 3.5 40 49 E 4.2 M 0.9 0.3 50 59 C 5.0 H 4.3 3.6 60 62 - 3.0 P 75.0 4.0 63 65 C 5.0 H 4.0 1.3 66 67 - 3.0 P 75.0 6.5 69 75 E 4.7 H 2.7 2.7 76 77 C 5.0 H 6.5 4.5 79 87 - 3.0 P 75.0 6.4 88 90 E 3.0 P 5.7 3.0 92 99 E 4.2 M 0.9 1.2 100 101 C 5.0 H 10.2 12.0 102 111 E 4.4 M 1.7 1.7 112 113 C 5.0 H 3.5 3.0 114 126 H 3.9 M 4.5 3.8 129 130 C 5.0 H 3.5 2.5 131 151 H 4.9 H 3.7 3.6 153 156 H 4.5 M 4.8 5.5 157 158 C 5.0 H 5.0 6.8 159 164 E 5.0 H 1.0 1.3 165 166 C 5.0 H 5.0 4.0 167 168 - 3.0 P 7.2 75.0 170 172 - 3.0 P 9.2 75.0 173 174 C 5.0 H 2.5 3.0 175 184 H 4.8 H 1.9 1.9 185 187 C 5.0 H 5.7 6.2 188 192 - 3.0 P 75.0 7.7 >>>>>>