Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2biba1 CCCCEEEECCCCCEEEECCCCCCCCCCEEEEECCEEEEECC-----CCCCCCCEEEEECCEEEEECCCCCCCC-CCEEECCEEECCCCCCCCCC-EEEECCCCEEEECCCCCCCCEEEECCCCEEEECCCCCCCCEEEEECCEEEEECC---CCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCCEECCCCCEECCCCCCCCCCCCCC >P1;d2j8ga1 -----------------------------------------CCCCC--CCCCEEEEECCCCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEEECHHHCCEEEEEEEE---------------------CCEEEECCCCCCCCCCCCCC-----------------CCCCCEEECC------------ PSA >P1;d2biba1 b293521549965331136a292851541350a85410039-----804012652255a95401018701005-52350a75411028713035-511519a441104a802123521538964110188020445205299341204a---80204554153a95411049802026422448a440104a8001065215299641105a702014764065033037800247b5a577 >P1;d2j8ga1 -----------------------------------------a8a99--4834062354b55530528965406641240244411046701014551243a9611003980100450051d9540105a800024430136830040328917050321226---------------------c9001435b95834a93326-----------------a31b35518b------------ Translating the sequences *****************************************-----**CCCC*EEEEECCEEEEE*CCCCCCC-**EEECCEEE**CCCCCCCC-EEEE*CC*EEEECCCCCCCCEEEE*CC*EEEECCCCCCCCEEEEECCEEEEE*C---CC****EEEE*********************CCEEEEECCCCCCCCEEEEE*****************ECCCC*EECC************ -----------------------------------------*****--CCCCEEEEE*CC*EEEEECCCCCCC*EEEEECCEEEEECCCCCCCC*EEEEECCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEEEC***CCEEEEEEEE---------------------CCEEEE*CCCCCCCC*****-----------------*CCCCEEECC------------ 69360.tem _________________________________ ------------------------------------------------CCCCEEEEEECCEEEEEECCCCCCC-EEEEECCEEEEECCCCCCCC-EEEEECCEEEEECCCCCCCCEEEEECCEEEEECCCCCCCCEEEEECCEEEEEEC---CCEEEEEEEE---------------------CCEEEEECCCCCCCCEEEEE-----------------ECCCCEEECC------------ Structural block scores 0 47 - 3.0 P 11.8 68.2 48 51 C 5.0 H 1.8 4.8 52 57 E 4.3 M 4.2 3.3 58 59 C 5.0 H 9.8 8.2 60 65 E 4.3 M 1.8 3.3 66 72 C 5.0 H 3.0 5.4 74 78 E 4.2 M 3.0 2.2 79 80 C 5.0 H 8.8 3.0 81 85 E 4.2 M 2.2 2.0 86 93 C 5.0 H 3.6 2.9 95 99 E 4.6 H 2.6 3.0 100 101 C 5.0 H 9.8 9.8 102 106 E 4.6 H 2.0 1.6 107 114 C 5.0 H 3.8 3.1 115 119 E 4.6 H 3.2 2.2 120 121 C 5.0 H 8.5 11.2 122 126 E 4.6 H 2.4 2.0 127 134 C 5.0 H 3.4 3.7 135 139 E 5.0 H 2.8 2.2 140 141 C 5.0 H 9.0 7.0 142 147 E 4.7 H 2.3 1.7 149 151 - 3.0 P 75.0 6.0 152 153 C 5.0 H 4.0 3.5 154 161 E 4.0 M 3.2 2.6 162 182 - 3.0 P 3.8 75.0 183 184 C 5.0 H 9.2 10.8 185 189 E 4.6 H 1.8 1.6 190 197 C 5.0 H 3.7 7.0 198 202 E 3.0 P 3.0 4.6 203 219 - 3.0 P 4.3 75.0 221 224 C 5.0 H 2.8 4.6 225 227 E 4.3 M 2.0 3.7 228 229 C 5.0 H 5.0 9.8 230 241 - 3.0 P 5.6 75.0 >>>>>>