Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2o70a1 CHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH--CCCC-CHHHHHHHHHHHHH-HCCHHHHHHHHHCCCCCCCHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHC-- >P1;d2o8ia1 -------CCHHHHHHHHCCCCCCCHHHHHHHHHCCHHHCCCCHHHHHHHHHHHHH-HCCHHHHHHHHHHCCCHHHHHHHHH-----------CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC >P1;d2q37a1 ------------CCCHHHCCC-CCHHHHHC-CCCC----CCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCC-----------CCCHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCHHHHHHCCCCHHHHHHHHCCC--CHHHHC-CCCCCC PSA >P1;d2o70a1 7397128276860384012000515800430275--4709-62820353037207-72787511600440120039304686028405810460403808993355087105604940801000002628492036305503748494018400510250032005537-- >P1;d2o8ia1 -------284a50264009102805300440266a03a29210730292006106-807894138005302403721877a-----------778099039a3475078217603950601000038b3627401731880282899602840082016003230191765 >P1;d2q37a1 ------------977625800-00530173-285a----85856522652471056508681145007413310666-----------b218403-8627a92374066208505930811001104a4206-61730371284756401740010--601363-675486 Translating the sequences *******CCHHHHHHHHCCCCCCCHHHHHHHHH*--**CC-CHHHHHHHHHHHHH-HCCHHHHHHHHHCCCCCCCHHHHH***********HHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC***CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH**C-- -------CCHHHHHHHHCCCCCCCHHHHHHHHHCC***CCCCHHHHHHHHHHHHH-HCCHHHHHHHHH*CCC***HHHHH*-----------*CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHHCCCCC ------------***HH*CCC-CCHHHHH*-**CC----CCCHHHHHHHHHHHHH**CCHHHHHHHHHCCCCCCC**-----------***HH**-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC**-**HHHHHHCCCCHHHHHHHH***--*HHHH*-*CCCCC 158694.tem _________________________________ -------CCHHHHHHHHCCCCCCCHHHHHHHHHCC-**CCCCHHHHHHHHHHHHH-HCCHHHHHHHHHCCCCCCCHHHHH*-------***HHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC Structural block scores 0 6 - 4.0 M 5.3 75.0 75.0 7 8 C 4.0 M 4.5 5.0 75.0 9 16 H 4.2 M 4.4 3.9 32.0 17 23 C 4.7 H 1.3 2.9 12.6 24 32 H 4.6 H 3.2 2.7 11.6 33 34 C 4.0 M 40.0 8.2 7.8 36 37 * 2.7 P 5.5 6.8 75.0 38 41 C 4.5 M 22.5 3.5 24.0 42 54 H 5.0 H 3.2 2.8 3.8 57 58 C 5.0 H 4.5 3.5 4.0 59 67 H 5.0 H 3.6 4.2 3.6 68 74 C 4.4 M 1.4 2.7 2.6 75 79 H 4.0 M 4.4 5.0 47.4 81 87 - 4.0 M 3.6 75.0 75.0 88 90 * 2.7 P 3.0 75.0 4.8 91 92 H 4.0 M 5.0 41.0 6.0 93 99 C 4.6 H 3.3 5.1 14.4 100 117 H 5.0 H 4.3 4.8 4.4 118 129 C 4.8 H 2.2 3.2 2.7 130 140 H 4.5 M 3.4 3.7 9.9 141 144 C 4.8 H 5.5 5.0 5.2 145 165 H 4.6 H 2.5 3.0 13.2 166 170 C 4.2 M 33.0 5.6 6.0 >>>>>>