Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ldja3 CCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCEEECCCCCCCCEEECCHHHHHHHHHHHCCCEEEHHHHHHHCCCCHHHHHHHHHHHHH--CCCEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCC---- >P1;d2hyec3 -----CHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCEEEEECCCCCCCCEEEEEHHHHHHHHHCCCCCCEEHHHHHHHCCCCHHHHHHHHHCCCCCCCCCEEECC--CCC---CCCCCCEEEECCCCCCCCCCEECHHHHHC PSA >P1;d1ldja3 a4a57347016004501720454b9929a970471057016606708338202640141006000364105890062007103a6297900460350281076057016405831a7-a38053a1612105aa0021940280311a62550361047105836a9271512123455514185076602030200000001308798212065006406043830371042005--360020479b1825838064834041477061878515039---- >P1;d2hyec3 -----975016105600630257b9175995058505810860671a32820153015100301104811489205301710593188920640420260165087116606851896b5b464927132147a40192940908157426624650381039649b590521141544617280992612030010010014107a46422074048503054920350042002b674105044--979---6079b050440770a19558131062117 Translating the sequences *****CHHHHHHHHHHHHHHCCC***CCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH**CCCCCCCCCCCHHHC**EEECCCCCCCCEEE**HHHHHHHHHHHCCCEEEHHHHHHHCCCCHHHHHHHHHHHHH--CCCEE*CC**CCC***CCCCCCEEEECCCCCCCCCC**C**---- -----CHHHHHHHHHHHHHHCCCHHHCC***HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH********HHHHHHHHHHHHHHHHHHHHHHHHHC*CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCEEEEECCCCCCCCEEEEEHHHHHHHHH**CCC*EEHHHHHHHCCCCHHHHHHHHH******CCCEEECC--CCC---CCCCCCEEEECCCCCCCCCCEECHH**** 75632.tem _________________________________ -----CHHHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCEEEEECCCCCCCCEEEEEHHHHHHHHHHHCCCEEEHHHHHHHCCCCHHHHHHHHHHHHH--CCCEEECC--CCC---CCCCCCEEEECCCCCCCCCCEECHH---- Structural block scores 0 4 - 3.0 P 7.4 75.0 6 19 H 5.0 H 2.6 2.9 20 22 C 5.0 H 4.3 4.7 23 25 H 3.0 P 9.8 7.2 26 27 C 5.0 H 5.5 6.0 28 42 H 4.6 H 4.2 4.6 43 47 C 5.0 H 4.8 5.5 48 64 H 5.0 H 2.2 1.9 65 70 C 5.0 H 3.2 3.0 71 115 H 4.6 H 3.8 3.9 118 146 C 5.0 H 3.7 4.8 147 161 H 4.7 H 3.7 3.8 162 172 C 5.0 H 5.0 5.6 173 175 H 5.0 H 2.0 2.0 177 181 E 4.2 M 4.0 4.4 182 189 C 5.0 H 4.1 4.6 190 194 E 4.2 M 1.4 1.0 195 205 H 4.6 H 1.1 1.4 206 208 C 5.0 H 8.0 6.8 209 211 E 4.3 M 1.7 2.7 212 218 H 5.0 H 3.0 4.0 219 222 C 5.0 H 2.5 2.0 223 235 H 4.4 M 2.8 2.4 236 237 - 3.0 P 75.0 8.8 238 240 C 5.0 H 3.0 4.0 241 243 E 4.3 M 0.7 1.7 244 245 C 5.0 H 5.5 4.0 246 247 - 3.0 P 10.2 75.0 248 250 C 5.0 H 3.7 8.3 251 253 - 3.0 P 5.3 75.0 254 259 C 5.0 H 4.8 5.6 260 263 E 5.0 H 2.2 3.2 264 273 C 5.0 H 5.3 5.2 274 275 E 3.0 P 3.0 2.0 277 278 H 3.0 P 6.0 3.0 279 282 - 3.0 P 75.0 2.8 >>>>>>