Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1zdya- CHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCHHHCCCCCCCEEEEEECHHHCCCCEEEEEECHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCEEEEEEEECCCCCCCCHHHHHCCCCCCHHHHHCHHHHHHCCCCCEEEEEEECCCCEEEEEEC-----CCCHHHHCHHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCCEEEEEEEEEECCHHHHHHHHHHC >P1;d4ee6a- ---CCHHHHHHHC-CCHHHCCCCCHHHHHHHHHHCHHHHC--CCEEEEECCCHHHHHCCEEEEEEECC-CCHHHHHHHCCCCC-CCCCHHHHC-CHHHHCCEEEEEEEEECCCEEC-CEEEECCC-CCCHHHHC-CCCCCCHHHHCHHHHCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCHHHCCHHHHHHHHHHCCCCCCCHHHHHHHCCCCEEEEEEECCCCCCCEEEEEEEECCHHHCCCC---CCHHHHHHHHHCCCCC---CCCEEEEEEECCCCEEC-CEEEEEC------------ PSA >P1;d1zdya- 8891063007005600720a0a035a5024004003700749a020103010a73292040200032938200530386921852b45017006204731605300000204410110103037a7001195017051006005614a108517063032000004541010002-----707a700559104500840a04608a501700640110100011872702200000003426100097a916940540036002117b58200200000239411130001000198038319641 >P1;d4ee6a- ---a278016105-00720708037950240060066109--a0100030134b7592020101406e-05006204749019-3b2300600-2028405062000100038002-01020538-00504502-08000a00651390052801610110003057410102003a817804a601659104500960a0380583006006405100000009378033000005048049030a---02830440057041a1---d3503020102584141-0001137------------ Translating the sequences ***HHHHHHHHHH*HHHH*CCCCCHHHHHHHHHHCHHH*C**CC*EEEEEECHHH**CCEEEEEE*HH*CCHHHHHHHCCCCC*CCCCHHHHH*HHHHHCC**EEEEEEECCCEEE*EEEE*CCC*CCCHHHHH*CCCCCHHHHHCHHHHHHCCCCCEEEEEEECCCCEEEEEEC-----CCCHHHHCHHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEEEEECCCCCCCEEEEEEEECC***CCCC***HHHHHHHHHHHCCCCC***CCCEEEEEEECCCCEEE*EEEEEEC************ ---**HHHHHHH*-**HHHCCCCCHHHHHHHHHHCHHHHC--CCEEEEE**CHHHHHCCEEEEEEE**-CCHHHHHHHCCCCC-CCCCHHHH*-*HHHHCCEEEEEEEEECCCEE*-*EEEECCC-CCCHHHH*-CCCCC*HHHHCHHHH**CCCCCEEEEEEECCCCEEEEEEC*****CCCHHH*CHHHHHHHHHH*CCCCCCHHHHHHH**CCEEEEEEECCCCCCCEEEEEEEECCHHHCCCC---**HHHHHHHHHCCCCC---CCCEEEEEEECCCCEE*-*EEEEEC------------ 143492.tem _________________________________ ---HHHHHHHHHH-HHHHHCCCCCHHHHHHHHHHCHHHHC--CCEEEEEEECHHHHHCCEEEEEEEHH-CCHHHHHHHCCCCC-CCCCHHHHH-HHHHHCCEEEEEEEEECCCEEE-EEEEECCC-CCCHHHHH-CCCCCHHHHHCHHHHHHCCCCCEEEEEEECCCCEEEEEEC-----CCCHHHHCHHHHHHHHHHHCCCCCCHHHHHHHHHCCEEEEEEECCCCCCCEEEEEEEECCHHHCCCC---HHHHHHHHHHHCCCCC---CCCEEEEEEECCCCEEE-EEEEEEC------------ Structural block scores 0 2 - 3.0 P 8.3 75.0 3 12 H 4.4 M 2.2 4.0 14 18 H 3.8 M 1.8 1.8 19 23 C 5.0 H 4.8 3.6 24 33 H 5.0 H 3.0 3.3 35 38 H 4.5 M 2.5 3.2 40 41 - 3.0 P 6.5 75.0 42 43 C 5.0 H 5.2 5.2 44 50 E 4.1 M 1.0 0.7 52 56 H 4.2 M 6.3 7.3 57 58 C 5.0 H 1.0 1.0 59 65 E 4.7 H 1.3 1.1 66 67 H 3.0 P 5.5 10.2 69 70 C 5.0 H 5.0 2.5 71 77 H 5.0 H 2.7 2.7 78 82 C 5.0 H 5.2 4.6 84 87 C 5.0 H 5.6 4.9 88 92 H 4.6 H 1.6 1.2 94 98 H 4.6 H 3.2 3.2 99 100 C 5.0 H 3.5 2.5 101 109 E 4.6 H 1.1 1.0 110 112 C 5.0 H 2.7 3.7 113 115 E 4.3 M 0.7 0.7 117 121 E 4.2 M 0.8 0.6 122 124 C 5.0 H 6.8 5.3 126 128 C 5.0 H 0.3 1.7 129 133 H 4.6 H 3.2 2.2 135 139 C 5.0 H 1.2 1.6 140 144 H 4.6 H 3.4 4.3 146 151 H 4.3 M 4.8 3.2 152 156 C 5.0 H 3.4 3.2 157 163 E 5.0 H 0.7 0.7 164 167 C 5.0 H 3.2 4.0 168 173 E 5.0 H 0.3 0.7 175 179 - 3.0 P 75.0 5.9 180 182 C 5.0 H 4.7 4.0 183 186 H 4.5 M 4.4 4.4 188 198 H 4.8 H 3.3 3.5 199 204 C 5.0 H 4.8 4.4 205 213 H 4.6 H 3.7 3.0 214 215 C 5.0 H 0.5 2.5 216 222 E 5.0 H 0.4 0.1 223 229 C 5.0 H 3.9 4.3 230 237 E 5.0 H 0.2 1.0 238 239 C 5.0 H 3.5 6.0 240 242 H 3.0 P 3.0 4.3 243 246 C 5.0 H 2.2 3.4 247 249 - 3.0 P 8.8 75.0 250 260 H 4.6 H 3.5 3.0 261 265 C 5.0 H 0.8 3.3 266 268 - 3.0 P 7.8 75.0 269 271 C 5.0 H 3.3 7.2 272 278 E 5.0 H 0.3 0.9 279 282 C 5.0 H 4.5 4.8 283 285 E 4.3 M 1.0 2.0 287 292 E 4.7 H 0.2 0.8 294 305 - 3.0 P 4.4 75.0 >>>>>>