Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3w2wa2 -------------------------------------CHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCEECCEECCHHHHCHHHHHH-------------CCCHHHHHHHHCCCCCCC-- >P1;d3w2wa4 -----CHHHHHHHCCHHHHHHH---------CCCHHHHHHHHHHHHCCCCCC-CCCCCHHHHHHHHCCCC-CH---HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCC >P1;d4uw2a4 CCCCHHHHH-HHHH-HHHHHH-EEECCEECHHHCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-------CCCCCCHHHHCCCHHHHCC---CCCCHHHHCHHHHHHHC-C-CCC >P1;d6ifka4 CCCCIIIIIIIHHH-HHHHHH-H-----CCCCCC--HHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHCCC-C----CCCCHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHHHHHHH-CCC PSA >P1;d3w2wa2 -------------------------------------a368306787027504873260264047237930889705614101163069-------------8502a1057008288016-- >P1;d3w2wa4 -----95176107703037106---------72621950062014405961a-98160067006500508-69---94178136602700360183193a504304600530672259a759 >P1;d4uw2a4 aa299b336-6148-500520-225a5704c808827c0065005005305645b434008503720473-------9069105404962872587---a5312022011005601-6-17b >P1;d6ifka4 9b645740665006-403700-6-----618319--4900750061057278-61166048106401650-5----8813a405801530460013---a585218001400330164-36a Translating the sequences -------------------------------------*HHHHHHHHHH*******CCCHHHHHHHH*CCC*******C**HH*HHHHHH-------------C**HHHHHHHH**C*C*C-- -----******HH**HHHHHH*---------**C**HHHHHHHHHH******-**CCCHHHHHHHH*CCC-**---****HH*HHHHHH*HHHHCC***CCC**HHHHHHHHHHHC*C*CCC *********-*HH*-HHHHHH-***********C**HHHHHHHHHHHH*******CCCHHHHHHHH****-------C*****HHHH***HHHHCC---CCCC*HHH*HHHHHHHC-C-CCC ***********HH*-HHHHHH-*-----*****C--HHHHHHHHHHHH****-*****HHHHHHHH*CCC-*----*C**HH*HHHHHH*HHHHCC---CCCC*HHHHHHHHHHH***-CCC 418771.tem _________________________________ ***********HH*-HHHHHH-*-----*****C**HHHHHHHHHHHH*******CCCHHHHHHHH*CCC-**---*C**HH*HHHHHH*HHHHCC---CCCC*HHHHHHHHHHHC*C*CCC Structural block scores 0 10 * 3.0 P 75.0 36.7 13.2 5.8 11 12 H 4.3 M 75.0 3.5 2.5 0.0 15 20 H 4.3 M 75.0 2.3 2.0 2.3 23 27 - 4.3 M 75.0 75.0 5.9 75.0 28 32 * 3.0 P 75.0 46.8 4.9 3.8 34 35 * 3.5 M 75.0 1.5 5.0 75.0 36 47 H 4.8 H 11.1 3.0 3.4 3.1 48 54 * 1.4 P 4.7 16.9 4.9 15.1 55 57 C 4.3 M 3.7 2.3 3.7 4.3 58 65 H 5.0 H 3.1 3.0 3.1 2.9 67 69 C 4.3 M 6.3 4.3 4.7 3.7 71 72 * 2.9 P 8.0 7.5 75.0 40.0 73 75 - 4.3 M 5.3 75.0 75.0 75.0 78 79 * 1.0 P 2.5 4.0 3.0 2.0 80 81 H 4.3 M 0.5 4.5 5.0 7.2 83 88 H 4.8 H 4.2 3.5 4.7 3.7 90 93 H 4.3 M 75.0 2.5 5.5 2.5 94 95 C 4.3 M 75.0 5.5 7.5 2.0 96 98 - 4.3 M 75.0 4.3 75.0 75.0 99 102 C 4.3 M 58.2 4.9 4.9 7.1 104 114 H 4.7 H 3.2 3.0 1.5 1.8 119 121 C 4.5 M 52.0 7.0 6.5 6.5 >>>>>>