Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m2oa2 ---------------------------------------CHHHHHHHHCEEECCCEEECCHHHHHHCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEECCCEEEEEEECCCEECCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEECC---CCEEEEEEEEEEEECCCEEEEEEEEEEEEEECCCCHHHHHCC >P1;d1pd0a2 CCCCCCCCCCHHHCCCCCHHHHHCCCCCCCCCHHHCCCCCHHHCCCCCCEEECCCCEECCHHHHHHHCCCCEEEECCCCC-------CCCCEEEEEEEEECCCEEEEEEECCCCCC----------------CCCCEEEEECCCCCCEEEEEEECCCCCCCEEEEEEEEEEECCCCCEEEEEEEEEEEEECC-HHHHHHCC PSA >P1;d1m2oa2 ---------------------------------------a47733772004041320043382189394400060200253c3a7a574505904020503a302010053906127a2b1c01085534406001050a7020733020201028---a84050303050511196955341413050279738508815 >P1;d1pd0a2 380275885789836965896897712711026951a936ba22154730503000002359119708270105030018-------69405803030604900501606480718----------------a653050a70317450404050585087610404010402085b5556340502000064-36205102 Translating the sequences ---------------------------------------CHHHHHHHHCEEECCCEEECCHHHHHH*CCCCEEEECCCCC*******CCCEEEEEEEEEECCCEEEEEEECCCEEC****************CCCEEEEEEECCCCCEEEEEEECC---CCEEEEEEEEEEEECCCEEEEEEEEEEEEEECC**HHHHHCC ***************************************CHHH*****CEEECCC*EECCHHHHHHHCCCCEEEECCCCC-------CCC*EEEEEEEEECCCEEEEEEECCC**C----------------CCC*EEEEE*CCCCCEEEEEEECC***CCEEEEEEEEEEE*CCC*EEEEEEEEEEEEECC-HHHHHHCC 81995.tem _________________________________ ---------------------------------------CHHHHHHHHCEEECCCEEECCHHHHHHHCCCCEEEECCCCC-------CCCEEEEEEEEEECCCEEEEEEECCCEEC----------------CCCEEEEEEECCCCCEEEEEEECC---CCEEEEEEEEEEEECCCEEEEEEEEEEEEEECC-HHHHHHCC Structural block scores 0 38 - 3.0 P 75.0 5.6 40 47 H 3.8 M 5.0 5.4 49 51 E 5.0 H 1.3 1.7 52 54 C 5.0 H 2.7 1.0 55 57 E 4.3 M 0.7 0.0 58 59 C 5.0 H 3.5 2.5 60 66 H 4.7 H 4.9 4.6 67 70 C 5.0 H 4.2 4.2 71 74 E 5.0 H 1.5 1.5 75 79 C 5.0 H 1.8 2.4 80 86 - 3.0 P 7.4 75.0 87 89 C 5.0 H 5.3 6.3 90 99 E 4.8 H 2.5 2.5 100 102 C 5.0 H 5.5 4.3 103 109 E 5.0 H 1.1 2.6 110 112 C 5.0 H 4.0 4.0 113 114 E 3.0 P 3.5 4.0 116 131 - 3.0 P 4.7 75.0 132 134 C 5.0 H 2.0 7.2 135 141 E 4.4 M 3.4 3.6 142 146 C 5.0 H 3.0 4.0 147 153 E 5.0 H 0.7 1.9 154 155 C 5.0 H 5.0 6.5 156 158 - 3.0 P 75.0 4.3 159 160 C 5.0 H 9.2 6.5 161 172 E 4.8 H 2.2 1.3 173 175 C 5.0 H 3.7 8.2 176 189 E 4.9 H 3.4 2.5 190 191 C 5.0 H 8.0 5.0 193 198 H 4.7 H 5.3 2.8 199 200 C 5.0 H 3.0 1.0 >>>>>>