Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1go3e2 -----------------------CEEEEEEEEEE-CCHHHC-CCCCCCCCCHH-HHHCCCEEC--CEEEEEEEECCCCCCCC---------------CCCCCCEEEEEEEEEEC >P1;d1y14b2 -----------------------CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCEEECC-CEEEEEECC-------------HHHCCCC---------CEEEEEEEEEC >P1;d4c2mg1 CCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECHHHC-CCHHHHHHHHCCHHHCCCEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEC PSA >P1;d1go3e2 -----------------------96542638350-043835-b6a45204304-95226676b--4041340450918167b---------------b3921416050303054 >P1;d1y14b2 -----------------------865457142809086954698276301630375038446d8-416046037-------------5970607---------23060503045 >P1;d4c2mg1 c9675687877936748a68837253537242502013725-a7355004523065336754a9130203416907040547928a94ba271942995640405050403061 Translating the sequences -----------------------CEEEEEEEEEE-CCHHHC-CC*******HH-HHHCCCEEC--CEEEEEEEE***CCCCC---------------CCCC**EEEEEEEEEEC -----------------------CEEEEEEEEE**CC***C*CCHHHHHHHHH*HHHCC*EECC-CEEEEEE**-------------***CCCC---------*EEEEEEEEEC ***********************CEEEEEEEEEE**CHHHC-CCHHHHHHHH**HHHCCCEECC*CEEEEEEEE***CCCCC********CCCC***CCCC**EEEEEEEEEEC 88798.tem _________________________________ -----------------------CEEEEEEEEEE*CCHHHC-CCHHHHHHHHH*HHHCCCEECC-CEEEEEEEE***CCCCC-----***CCCC---CCCC**EEEEEEEEEEC Structural block scores 0 22 - 4.0 M 75.0 75.0 7.0 24 33 E 4.9 H 4.2 4.2 3.6 35 36 C 4.5 M 2.0 4.0 0.5 37 39 H 4.0 M 4.7 6.7 4.0 42 43 C 5.0 H 8.8 8.5 8.8 44 52 H 4.1 M 3.6 3.1 3.0 54 56 H 5.0 H 5.3 4.0 4.7 57 59 C 4.7 H 4.7 5.0 5.3 60 61 E 5.0 H 6.5 5.0 4.5 62 63 C 4.5 M 43.2 10.8 9.8 66 73 E 4.8 H 2.6 3.4 3.1 74 76 * 2.7 P 3.3 75.0 2.3 77 81 C 4.0 M 6.7 75.0 4.0 82 86 - 4.0 M 75.0 75.0 7.7 87 89 * 2.7 P 75.0 7.0 8.7 90 93 C 4.0 M 75.0 3.2 4.8 94 96 - 4.0 M 75.0 75.0 5.0 97 100 C 4.0 M 6.4 75.0 6.0 101 102 * 2.7 P 2.5 75.0 2.0 103 112 E 4.9 H 2.3 2.3 2.3 >>>>>>