Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1llqa2 CCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEEHHHCCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHCCCCCEEECC >P1;d7mf4a1 ------------------------------------CCHHHHCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHCHHHHCCCCCEEECHHHCC--CHHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC-CCCEEEECCCCCCCHHHHHHHHCCCCCEEECC PSA >P1;d1llqa2 b45a7557219c27917b8648532871967982a46468017323305321064840593405a4168640948510851057057277523204201801150180013004534a4033001650014004542509158101402073243860372029062840400000001207b27100000000001100121037a35242000000000033691173790403646035a970450031006000700766030000003881195037405961505042 >P1;d7mf4a1 ------------------------------------6458105422616311054940793704a5167831739601740283038476503205201601070070012005534a404500177001600153251056120140136459--6056305837288040000000022979520011000001110222009792425200000000006176008598071143611c7940150043007004310-57020000102780086019407a72605142 Translating the sequences ************************************CHHHHHCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHH**CHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHH****CCCCCEEEEHHHCC**HHHHHHH**CCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCHHHHHCCCCCCCCCCCCC*HHHHHHHHHHHHHHHHHH*CCCEEEECCCCHHHHHHHHHHHCCCCCEEECC ------------------------------------C*HHHHCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHCCCHHHHHHHH*HHHHCCCCCEEE*HHHCC--*HHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEE*CCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH*-CCCEEEECCCC***HHHHHHHHCCCCCEEECC 53223-2.tem _________________________________ ------------------------------------CHHHHHCCCCCCCHHHCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCEEEEHHHCC--HHHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-CCCEEEECCCCHHHHHHHHHHHCCCCCEEECC Structural block scores 0 35 - 3.0 P 6.2 75.0 37 41 H 4.6 H 3.8 3.6 42 48 C 5.0 H 3.3 3.7 49 51 H 5.0 H 2.0 1.7 52 53 C 5.0 H 3.0 2.5 54 59 H 5.0 H 5.0 5.5 60 72 C 5.0 H 4.7 4.8 73 85 H 5.0 H 3.8 3.5 86 89 C 5.0 H 5.8 6.2 90 103 H 4.7 H 2.4 2.3 105 114 H 5.0 H 2.2 2.0 116 123 H 5.0 H 3.1 3.4 124 126 C 5.0 H 4.0 5.0 127 139 H 4.2 M 2.6 1.8 140 144 C 5.0 H 3.0 2.8 145 148 E 4.5 M 1.8 1.5 149 151 H 5.0 H 3.3 4.3 152 153 C 5.0 H 3.0 7.0 154 155 - 3.0 P 5.5 75.0 156 164 H 4.3 M 3.2 4.0 165 170 C 5.0 H 4.0 4.8 171 175 E 5.0 H 0.0 0.0 176 186 C 5.0 H 2.9 3.3 187 205 H 5.0 H 0.8 1.4 206 208 C 5.0 H 6.2 5.0 209 211 H 5.0 H 2.7 3.0 212 218 E 4.7 H 0.0 0.0 219 223 C 5.0 H 1.2 1.4 224 228 H 5.0 H 4.8 4.2 229 241 C 5.0 H 3.8 4.5 242 260 H 4.8 H 2.8 2.5 262 264 C 5.0 H 4.0 4.0 265 268 E 5.0 H 0.8 0.5 269 272 C 5.0 H 0.8 0.8 273 283 H 4.5 M 4.2 3.9 284 288 C 5.0 H 5.2 6.5 289 291 E 5.0 H 1.7 2.0 292 293 C 5.0 H 3.0 3.0 >>>>>>