Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1p32a- CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEE--CCEEEEEEEECCEEEEEEEECCCCCCCCCCCCEEEEEEEHHHCCEEEEEEEECCCCCCCCCCCEEEEEEEEECCCC---------CCCCCCC-EEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC >P1;d1yqfa1 ---CHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEECCCC--CEEEEEEEEEC-----CEEEEEEEEEECCHHHHHCCCHHHHHHHHHCCCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-- >P1;d3jv1a- C--HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEECCCCCCCCEEEEEECCEEEEEEEEEECCCCCCCCEEEEEEEEEC-C--EEEEEEEEEEC-----CEEEEEEEEEECCHHHHHCCCHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-- PSA >P1;d1p32a- 925aa2684186027316724870885a628097b08252a--b350401263b80400020508b046a7020803030166b4595020020203bb8b954501043006152d2a---------9459939-23608a08a852771173047150547005201610201234250660373289167a >P1;d1yqfa1 ---7a767524505641671693a823a51932b90716458b42302042737b160102050867b96692270400005a84--5010020005a-----860405311609636302659a816560784850581a729996268135306714036800700250062041444176077328908-- >P1;d3jv1a- a--88678527606821641685bb32a51a32ba062516655740203173ca140001042559b3b651030300016c-a--5021040004a-----260404400408709203567a7067516748504718819984367257305715046800600360142072423266035337919-- Translating the sequences C**HHHHHHHHHHHHHHHHHH**CCCCCCCCCCCCCEEEE*--CCEEEEEEEECCEEEEEEEECCCCCCCCCC**EEEEEEE*****EEEEEEEE**C*****C**EEEEEEEE*C***---------***CCCC-******CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*** ---*HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEE*C*C--*EEEEEEEEEC-----CEEEEEEEEEECCHHHHHCCCHHHHHHH**CCCCCCHHHCCHHHHHHHHHHHH*CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-- C--HHHHHHHHHHHHHHHHH*CCCCCCCCCCCCCCCEEE*CCCCC**EEEEEECCEEEEEEEE**CCCCCCCCEEEEEEEEEC-C--EEEEEEEEEEC-----CEEEEEEEEEECCHHHHHCCCHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-- 54529.tem _________________________________ C--HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEEEC*C--EEEEEEEEEEC-----CEEEEEEEEEECCHHHHHCCCHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-- Structural block scores 1 2 - 4.0 M 3.5 75.0 75.0 3 20 H 4.9 H 4.9 5.0 5.1 21 35 C 4.9 H 6.0 5.8 6.3 36 39 E 4.8 H 4.2 4.5 3.5 40 44 C 4.4 M 35.0 6.1 5.8 45 52 E 4.8 H 2.6 2.6 2.5 53 54 C 5.0 H 9.8 9.2 11.5 55 62 E 5.0 H 1.4 1.9 1.2 63 72 C 4.8 H 4.9 6.5 5.9 73 81 E 4.7 H 2.3 2.0 1.4 85 86 - 4.0 M 7.0 75.0 75.0 87 96 E 4.7 H 1.4 1.3 1.6 98 102 - 4.0 M 9.0 75.0 75.0 104 113 E 4.8 H 2.0 2.6 2.2 114 115 C 4.5 M 3.5 7.5 7.5 116 120 H 4.0 M 35.2 2.8 2.8 121 123 C 4.0 M 75.0 6.7 6.0 124 130 H 4.0 M 45.4 5.2 5.2 131 138 C 4.2 M 14.5 5.6 5.1 139 141 H 4.0 M 6.2 6.2 5.7 142 143 C 5.0 H 4.0 5.5 5.0 144 155 H 5.0 H 4.6 4.8 4.9 156 160 C 4.8 H 3.6 3.0 3.4 161 190 H 5.0 H 3.0 3.4 3.3 192 193 - 4.0 M 8.8 75.0 75.0 >>>>>>