Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1qtsa2 CEEECCCCHHHHHHHHCCCCCHHHEEEEEEECCCCCCHHHHHHHHHHH-CCEECCCCCCC----C-CCEEEEEEEECCCCEEEEEEEEEEEC-CCCEEEEEEEECCHHHHHHHHHHHHCCC-- >P1;d1r4xa2 CEEECCCC--CHHHHHHHH-CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCEECCCCCCCCCCCCEEEEEEEEEEC---CCEEEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHHC------ >P1;d2g30a2 CCCCCCCCHHHHHHHHHHC-CHHHCEEEEEC-CCCCCHHHHHHHHHHC-CCEEEEEEEEC----CEEEEEEEEEC--CC-CCEEEEEEEECC-CCCCEEEEEEECCHHHHHHHHHHHHHHHHC PSA >P1;d1qtsa2 a055281748404651771a58722234518055906686037306a1-400006a0087----8-80000003145986507010302067-9363050002065471056105400650-- >P1;d1r4xa2 70854528--708610690-67822445427279265076009712960803105813706ab5551302000306---b7430002050427910406000106345005301840------ >P1;d2g30a2 813a060768508812970-59912551406-8063809402730685-40210347679----92210200021--58-733000103038-b5510200000523820670265036103b Translating the sequences CEEECCCCHHHHHHHH**C*CHHH*EEEEEE*CCCCCHHHHHHHHHHH-CCEECCCCCCC----C-**EEEEEEE**CCC*EEEEEEEEEEC-CCCEEEEEEEECCHHHHHHHHHHHH***-- CEEECCCC--*HHHHHHH*-C***CEEEEEE*CCCCCHHHHHHHHHHH*CCEECCCCCCC****CEEEEEEEEEE*---CCEEEEEEEEEE**CC*EEEEEEEECCHHHHHHHHHH*------ C***CCCCHHHHHHHHHHC-CHHHCEEEEE*-CCCCCHHHHHHHHHH*-CCEE******C----CEEEEEEEEE*--CC-C*EEEEEEEE*C-CCC*EEEEEEECCHHHHHHHHHHHH***** 55711.tem _________________________________ CEEECCCCHHHHHHHHHHC-CHHHCEEEEEE*CCCCCHHHHHHHHHHH-CCEECCCCCCC----CEEEEEEEEEE*-CCCCEEEEEEEEEEC-CCCEEEEEEEECCHHHHHHHHHHHH***-- Structural block scores 1 3 E 4.0 M 3.3 4.3 4.8 4 7 C 5.0 H 4.5 4.8 3.2 8 17 H 4.5 M 4.6 18.7 5.4 21 23 H 4.0 M 5.7 5.7 6.3 25 30 E 4.8 H 3.8 4.3 3.5 32 36 C 5.0 H 5.0 5.8 5.0 37 47 H 4.9 H 4.6 4.3 4.0 49 50 C 5.0 H 2.0 4.0 2.0 51 52 E 5.0 H 0.0 2.0 1.5 53 59 C 4.1 M 4.5 3.4 5.1 60 63 - 4.0 M 75.0 8.2 75.0 65 74 E 4.6 H 8.7 1.4 1.0 77 80 C 4.0 M 7.0 42.1 23.8 81 90 E 4.8 H 1.9 1.8 1.3 93 95 C 4.7 H 6.0 3.3 7.2 96 103 E 4.9 H 1.2 1.4 0.4 104 105 C 5.0 H 5.5 4.5 3.5 106 117 H 4.8 H 2.8 8.8 3.5 118 120 * 2.7 P 3.7 75.0 2.3 121 122 - 4.0 M 75.0 75.0 7.2 >>>>>>