Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2c1wa1 CCCCHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCCCCCCCCEEEECHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCEEEEEEEEC--CCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEEEECCEEEEEEEEEECCEEEEEEEEEEECCCC >P1;d6wlca2 ---------------------------------CCCCCCCCC---CCCCCCCC----HHHHHHHHCC----------------HHHHHHHC----------CCC------------------------------------CCCHHHHCCCCCC-CCCCCCCCCHHHHHHHHHHCCEEEECCCCC--------CCCCEEEEEEECCCCCEEEEEEECC-CCHHHHHHHHCCCCCC--CCEEEEEEEECCEEEEEEEEEECCEEEEEEECCC----- PSA >P1;d2c1wa1 da23850171045018017350507a0060412140b5ba08850055026710966010230150041127394714543982462046006200714004201820384830666586016302500042009b684400000100100342637201010000001005692060400213b97a8175512001020105--96818450000000000000000000122b7931521040530301000302c8100302030331925 >P1;d6wlca2 ---------------------------------b13512907---18708253----7104001727----------------49600852----------807------------------------------------5220530000407-8a8030000100002136707081743466--------b310201505057380317500001-0203201600361717--6824405030384602010407977051030454----- Translating the sequences *********************************CCCCCCCCC***EEEECHHH******HHHHHHHH****************HHHHHHHH**********HHH************************************CCHHHHHCCCCCC*CCCCCCCCCHHHHHHHHH*CCEEEEEECCC********CCCEEEEEEEEC--CC****EEEEC*CCHHHHHHHHHHHHHC**CCEEEEEEEECCEEEEEEEEEECCEEEEEEEEEE***** ---------------------------------CCCCCCCCC---****C***----HHHHHHHH**----------------HHHHHHH*----------***------------------------------------CC*HHHHCCCCCC-CCCCCCCCCHHHHHHHHHHCCEEEE**CCC--------CCC*EEEEEEEC**CCEEEEEEE*C-CCHHHHHHHH*****C--CCEEEEEEEECCEEEEEEEEEECCEEEEEEE***----- 142877.tem _________________________________ ---------------------------------CCCCCCCCC---EEEECHHH----HHHHHHHHHH----------------HHHHHHHH----------HHH------------------------------------CCHHHHHCCCCCC-CCCCCCCCCHHHHHHHHHHCCEEEEEECCC--------CCCEEEEEEEEC--CCEEEEEEEEC-CCHHHHHHHHHHHHHC--CCEEEEEEEECCEEEEEEEEEECCEEEEEEEEEE----- Structural block scores 0 32 - 3.0 P 3.7 75.0 33 41 C 5.0 H 5.7 4.4 42 44 - 3.0 P 4.3 75.0 45 48 E 3.0 P 2.5 4.0 50 52 H 3.0 P 4.7 3.3 53 56 - 3.0 P 5.2 75.0 57 66 H 4.2 M 1.2 2.9 67 82 - 3.0 P 4.5 75.0 83 90 H 4.8 H 3.0 4.2 91 100 - 3.0 P 2.0 75.0 101 103 H 3.0 P 2.0 5.0 104 139 - 3.0 P 3.9 75.0 140 141 C 5.0 H 0.0 3.5 142 146 H 4.6 H 0.2 2.0 147 152 C 5.0 H 1.3 1.8 154 162 C 5.0 H 2.2 3.3 163 172 H 4.8 H 1.2 2.0 173 174 C 5.0 H 5.5 3.5 175 180 E 4.3 M 1.7 3.8 181 183 C 5.0 H 2.0 5.3 184 191 - 3.0 P 7.4 75.0 192 194 C 5.0 H 2.7 5.2 195 202 E 4.8 H 0.5 1.6 204 205 - 3.0 P 75.0 5.0 206 207 C 5.0 H 7.5 4.0 208 215 E 3.8 M 3.2 2.0 218 219 C 5.0 H 0.0 1.0 220 232 H 4.2 M 0.1 2.3 234 235 - 3.0 P 6.8 75.0 236 237 C 5.0 H 8.0 7.0 238 245 E 5.0 H 2.0 2.2 246 247 C 5.0 H 4.0 5.5 248 257 E 5.0 H 0.9 2.4 258 259 C 5.0 H 10.2 8.0 260 269 E 4.4 M 1.2 2.9 270 274 - 3.0 P 4.0 75.0 >>>>>>