Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k2yx4 ---CCCEECCCEEEECC---------------CCCHHHHHHHHHHHC---CCC------------CCEEECC-------------CCEEEEEC-CEEEEEEECCC----CCEEEEEEEECC-----------CHHHHHHHHHHHHHHHHCC----CCCCCC >P1;d1wjwa1 CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCC----------------------------------------------CEEEEEECCCC----CCCEEEEEEECC----------HHHHHHHHHHHHHHHHHHCCCCCCCCCC-- >P1;d6y8ya4 ----CEEEEEEEEEEEC---------------HHHHHHHHHHHHHHHHCCCHHHCEEEECCEEEEEEEEEECCEECCCCCCEECCCCEEEEECCCEEEEEEECCCCCCCCEEEEEEEEEECCCHHHCCCCHHHHCHHHHHHHHHHHCHHHHHCCCCCCEEE PSA >P1;d1k2yx4 ---ba365093160707---------------7b4066005203680---90b------------b1a4449-------------70030308-51202020179----641010503045-----------a116501520361046258----906041 >P1;d1wjwa1 ab9a85152825060359869965a99781762642785085428626----------------------------------------------907083765cb----571250301075----------9a20460032003301a33607b97294-- >P1;d6y8ya4 ----4604030004706---------------38206601550385066a605847263cc450406503245663697672468400202055603010340a98a9a321020201131856952b384460052004002910503830a39415549 Translating the sequences ---CCCEE***EEEECC---------------CCCHHHHHHHHHHHC---C**------------**EEE*C-------------CCEEEEEC-CEEEEEEECCC----CCEEEEEEEECC-----------*HHHHHHHHHHHHHHHHCC----CCCC** ***CCC*EEEEEE**CC***************CCC*HHHHHHHHHHC*----------------------------------------------CEEEEEE*CCC----CC*EEEEEEECC----------HHHHHHHHHHHHHHHHHHCC*CCCCCCC-- ----C*EEEEEEEEE*C---------------***HHHHHHHHHHH****C****************EEE*C*************CCEEEEEC*CEEEEEEECCC****C*EEEEEEEE*C**********HHH*HHHHHHHHHHH*HH***CCCCCC*** 55957.tem _________________________________ ---CCCEEEEEEEEECC---------------CCCHHHHHHHHHHHC*--C**------------**EEE*C-------------CCEEEEEC-CEEEEEEECCC----CCEEEEEEEECC----------HHHHHHHHHHHHHHHHHHCC*CCCCCCC** Structural block scores 0 2 - 4.0 M 75.0 10.3 75.0 3 5 C 4.3 M 8.3 7.8 28.3 6 14 E 4.3 M 4.1 3.2 2.0 15 16 C 4.5 M 3.5 4.0 3.0 17 31 - 4.0 M 75.0 7.3 75.0 32 34 C 4.0 M 7.5 4.0 4.3 35 45 H 4.9 H 3.3 5.0 3.5 48 49 - 4.0 M 75.0 75.0 8.2 51 52 * 2.7 P 5.8 75.0 2.5 53 64 - 4.0 M 75.0 75.0 5.7 65 66 * 2.7 P 6.2 75.0 3.0 67 69 E 4.0 M 6.2 75.0 2.7 72 84 - 4.0 M 75.0 75.0 5.8 85 86 C 4.0 M 3.5 75.0 2.0 87 91 E 4.0 M 1.2 75.0 0.8 95 101 E 4.9 H 1.0 4.4 1.6 102 104 C 5.0 H 5.7 9.7 6.5 105 108 - 4.0 M 75.0 75.0 9.5 109 110 C 4.5 M 5.0 6.0 2.5 111 118 E 4.9 H 1.2 1.5 0.9 119 120 C 4.5 M 4.5 6.0 2.0 121 130 - 4.0 M 75.0 75.0 6.2 131 148 H 4.8 H 7.1 3.2 2.3 149 150 C 4.0 M 6.5 4.5 5.5 152 158 C 4.4 M 34.3 7.1 5.4 159 160 * 2.7 P 2.5 75.0 6.5 >>>>>>