Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1tkea2 C-CHHHHHHHHHHHHHHHHHHHHHHC-CC-CEECCCCEECCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHCCCHHHHHHHHHHCCCCC-CCEEEEECC-EEEEECCCCCCCHHHCCCEEEEEEEEEEHHHCCCCCEEEEEEEEECC >P1;d1v4pa- ---CCCHHHHHHHHHHHHHHHHHHHHCHHHCCEEEEEEECCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHH---HHHHCCCC---CCCCCCCEEEEEEECCCEEEECCCCCCCCHHHCCCEEEEEEEEEC-----C-CCEEEEEEEEC- >P1;d2e1ba2 CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCEEEEEEECCCCH-HHHHHHHHHHHHHHHHHCCCEEEEECC--------------------------C---CEEEEECCCCEECCCCCCCCCHHHCCCEEEEEEEEEEC-------CEEEEEEEEC- PSA >P1;d1tkea2 a-8a8736211200000000001322-66-030050314b9001000109590579106602730350055417074570407403720482a0610131045526696-601003047-000019060071054035040492642413956a354022030205a >P1;d1v4pa- ---a3536220100000010003310887023045261983500010307550599316401510460097615034361406604851---77501327---537894560400107a11310196800830240360204605138-----a-74000020204- >P1;d2e1ba2 8766535311020000002100140067a708346461556305000207560-57129702820161075038052366b--------------------------b---72201039034162746009205206306605145289-------b303010208- Translating the sequences C-*HHHHHHHHHHHHHHHHHHHHHH*-CC-CEE**CCEECCEEEEEEECCCCCCHHHHHHHHHHHHHHH**CCCCEEEECCHHHHHHHH*****HH********CCCCC-*CEEEEECC-EEEE*CCCCCCCHHHCCCEEEEEEEEEE*****C*C*EEEEEEEEC* ---***HHHHHHHHHHHHHHHHHHHHC***C*EEE**EECCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE**HHHHHHHH---**HH****---*CCCCC***EEEEECCCEEEECCCCCCCCHHHCCCEEEEEEEEE*-----C-CCEEEEEEEEC- C**HHHHHHHHHHHHHHHHHHHHHHHCCC*CEEEECC**CCEEEEEEECCCC*-HHHHHHHHHHHHHHHHHCCC*EEEECC--------------------------C---CEEEEECCC*EE*CCCCCCCCHHHCCCEEEEEEEEEE*-------CEEEEEEEEC- 55186.tem _________________________________ C-*HHHHHHHHHHHHHHHHHHHHHHHCCC*CEEEECCEECCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHH---**HH****---*CCCCC-*CEEEEECCCEEEECCCCCCCCHHHCCCEEEEEEEEEE*----C-CCEEEEEEEEC- Structural block scores 3 25 H 4.8 H 2.1 1.8 1.5 26 28 C 4.0 M 29.0 7.7 7.8 31 34 E 4.2 M 2.0 3.0 5.2 35 36 C 4.0 M 1.5 4.0 5.0 37 38 E 4.0 M 2.5 5.0 3.0 39 40 C 5.0 H 10.2 5.5 5.5 41 47 E 5.0 H 0.3 1.3 1.4 48 53 C 4.7 H 4.7 3.7 15.5 54 70 H 4.9 H 3.5 3.8 3.7 71 74 C 4.8 H 3.0 3.0 2.8 75 78 E 5.0 H 5.8 4.0 4.0 79 80 C 4.0 M 2.0 2.5 8.8 81 88 H 4.0 M 2.9 3.8 75.0 89 91 - 4.0 M 4.7 75.0 75.0 92 93 * 2.7 P 5.2 7.0 75.0 94 95 H 4.0 M 3.5 2.5 75.0 96 99 * 2.7 P 1.2 3.2 75.0 100 102 - 4.0 M 3.0 75.0 75.0 104 108 C 4.2 M 5.8 6.2 62.3 112 116 E 5.0 H 0.8 1.0 1.0 117 119 C 4.7 H 28.7 6.2 4.0 120 123 E 4.5 M 0.0 1.2 3.5 124 131 C 4.9 H 3.0 4.4 3.8 132 134 H 5.0 H 3.0 2.0 2.3 135 137 C 5.0 H 2.7 3.0 3.0 138 147 E 4.9 H 3.5 2.9 3.7 149 152 - 4.0 M 5.8 75.0 75.0 155 156 C 4.0 M 4.5 5.5 43.2 157 164 E 5.0 H 1.1 0.5 1.1 >>>>>>