Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1mr1c1 --------CEEECCCCCEEEEECHHHCC--CCCCCCEEECCCCCEECHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCEECCCCCCC--CHHHHHHHHHHHHHHHCC------ >P1;d1oqja- -----CCCEEEEEEC-CEEEEEEHHHCCCCCCCCCCEEEC--CEEECHHHHHHHCC----------CHHHCCHHHHCEEC------CEEHHHHHHCCCCCCCCCCCCCCCCC >P1;d1ufna1 CCCHHHCCEEEEEEC-CEEEEEEHHHHHH-CCCCEEEEEC-CCCEEEHHHHHHHHC----------CCCCCCHHHHEEEC------CEEHHHHHHCCCCC------------ PSA >P1;d1mr1c1 --------50105130507030439508--567330020243673100450051135a5aa95829c263760272041196178a--744763565056017526------ >P1;d1oqja- -----a551380404-b28050124503030473700419--87400066007508----------44a5930150041c------85304620667802036298534982 >P1;d1ufna1 8b764756303030a-8160302173168-5494400429-757212044008409----------63a09914420608------9440650485a304------------ Translating the sequences --------*EEE**C*CEEEEE*HHHCC--CCCCCCEEEC*CCCEECHHHH***CC**********CCCH**HHHHCEEC******--*HHHHHH*********CC------ -----*CCEEEEEEC-CEEEEEEHHHCC**CCCCCCEEEC--C*EECHHHHHHHCC----------C**HCCHHHHCEEC------CEEHHHHHHCCCCC****CC****** ******CCEEEEEEC-CEEEEEEHHH***-CCCC**EEEC-CCCEE*HHHHHHH*C----------CCC*CCHHHH*EEC------CEEHHHHHHCCCCC------------ 63763.tem _________________________________ -----*CCEEEEEEC-CEEEEEEHHHCC*-CCCCCCEEEC-CCCEECHHHHHHHCC----------CCCHCCHHHHCEEC------CEEHHHHHHCCCCC****CC------ Structural block scores 0 4 - 4.0 M 75.0 75.0 7.3 6 7 C 4.0 M 75.0 5.0 5.5 8 13 E 4.5 M 2.0 2.7 1.5 17 22 E 4.8 H 2.3 2.7 2.0 23 25 H 5.0 H 5.7 3.7 3.7 26 27 C 4.0 M 4.0 1.5 3.5 30 35 C 4.7 H 4.0 3.5 4.3 36 38 E 5.0 H 0.7 1.7 2.0 41 43 C 4.3 M 5.3 30.0 6.3 44 45 E 5.0 H 2.0 2.0 1.5 47 53 H 4.6 H 2.1 3.4 2.9 54 55 C 4.5 M 2.0 4.0 4.5 56 65 - 4.0 M 7.5 75.0 75.0 66 68 C 4.3 M 6.8 6.2 6.5 70 71 C 4.0 M 6.5 6.0 9.0 72 75 H 5.0 H 2.8 1.5 2.8 77 78 E 5.0 H 2.5 2.5 3.0 80 85 - 4.0 M 6.9 75.0 75.0 87 88 E 4.0 M 41.0 4.0 4.0 89 94 H 5.0 H 4.8 3.0 3.8 95 99 C 4.0 M 4.4 4.6 4.5 100 103 * 2.7 P 3.2 2.8 75.0 104 105 C 4.0 M 4.0 8.5 75.0 106 111 - 4.0 M 75.0 5.2 75.0 >>>>>>