Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gqea- CCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCHHHHHHHHC-CCCCHHHHHHCCCEEEEEEEEECCCCCEEEEEEEEECCCHHHHHHHHCEEEEEEEECCCCCCCCEEEEEEEEEEEECCCCCCCCCCCHHHEEEEEECCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCHHHHHHHCCC-CHHHHHH-CCHHHHHCCCCCCCCCCCCCCEEEEEEHHHCEEEECCCCCEECCHHHHHCCCCHHHHHHHHHCCC-------- >P1;d1zbta1 -----CHHHHHHHHHCCCCC---------------------------------------CCCCHHHHH---HHHHHHHHHHHHCC-----CCCCCCCHHHHCC-HHHHCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHCCCCCC-CCCCCCCC-CCCCCCCCCC-EEEE-CCC-CHHHHHHHHCEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHC--CCCHHHEEEEEECCC---------CCCEEEEEECCCCEEEC-CCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHCCCCCC----CCCCCCEEEECCCCEEEECCCCEEECCHHHHHCCCCHHHHHHHHHHHHHHHHHHCC PSA >P1;d1gqea- 8572573166046216702b4072a62583196046508787166767507704343521430052056783176049408606869589228703760561385045031050a591041100020605b6920012002-01503400970a091730024608731042000203432010002001020300260533b978532040301000101461b87278841635414056ab848626701003111544835110133835850571030-2002413-63676287669ab5a76a46840020223563050421532158194033050440031006595-------- >P1;d1zbta1 -----834750473064698---------------------------------------ba2119404---5036046515715a-----ab59828258336-2396012307648417230100031492b71013004301604600-52c07072-32774c7c01-4010-047-5011301001010202130b929787454020302011156953--70579416123374a---------81300202043092504-555984-80474041020201244725667798b038----662840000033632010310b2418408501606055007302641344457878 Translating the sequences *****HHHHHHHHHHHHHHH***************************************HHHHHHHHH***HHHHHHHHHHHHHH*****HHHHHHHHHHHHH*HHHHHHHHCCCCCCCCCCEEEEEEECCCHHHHHHHH*-**CCHHHH*HCCCEEEE*EEEECCCCCE*EEEE*EEC*CHHHHHHHHCEEEEEEEECCCCCCCCEEEEEEEEEEEECC***C**CCCHHHEEEEEECCC*********CCCEEEEEECCCC*EEE*CCCCCH*HHHHHCC*-*HHHHHH-**HHHHHCCCCCC****CCCCEEEEEEHHHCEEEECCCC*EECCHHHHHCCCCHHHHHHHHH***-------- -----*HHHHHHHHH*****---------------------------------------****HHHHH---HHHHHHHHHHHH**-----*******HHHH**-HHHH****CCCCCCCCCC**EEEEECCC*HHHHHHHH*HHCC****-*CCC****-****CCCCC*-EEEE-**C-CHHHHHHHHCEEEEEEE*CCCCCCCC*EEEEEEEE***CCHHHC--CCCHHHEEEEEECCC---------CCCEEEEEECCCCEEE*-CCCCC*-*****CCH*HHHHHHH*HHHHHHHCCCCCC----CCCC**EEEE***CEEEECCCCEEECCHHHHHCCCCHHHHHHHHHHHH******** 75620.tem _________________________________ -----HHHHHHHHHHHHHHH---------------------------------------HHHHHHHHH---HHHHHHHHHHHHHH-----HHHHHHHHHHHHH-HHHHHHHHCCCCCCCCCCEEEEEEECCCHHHHHHHHH-HHCCHHHH-HCCCEEEE-EEEECCCCCE-EEEE-EEC-CHHHHHHHHCEEEEEEEECCCCCCCCEEEEEEEEEEEECCHHHC--CCCHHHEEEEEECCC---------CCCEEEEEECCCCEEEE-CCCCCH-HHHHHCCH-HHHHHHH-HHHHHHHCCCCCC----CCCCEEEEEEHHHCEEEECCCCEEECCHHHHHCCCCHHHHHHHHHHHH-------- Structural block scores 0 4 - 3.0 P 5.4 75.0 5 19 H 4.2 M 4.2 4.9 20 58 - 3.0 P 4.7 75.0 59 67 H 4.1 M 2.2 4.8 68 70 - 3.0 P 7.0 75.0 71 84 H 4.7 H 4.4 4.2 85 89 - 3.0 P 7.4 75.0 90 102 H 3.6 M 3.8 6.2 104 111 H 4.0 M 2.2 3.2 112 121 C 5.0 H 3.6 4.2 122 128 E 4.4 M 1.1 0.7 129 131 C 5.0 H 7.5 5.0 132 140 H 4.6 H 1.8 3.1 142 143 H 3.0 P 0.5 0.5 144 145 C 5.0 H 2.5 3.0 146 149 H 3.0 P 1.8 2.5 152 154 C 5.0 H 3.5 4.8 155 158 E 3.0 P 5.0 4.0 160 163 E 3.0 P 3.0 4.8 164 168 C 5.0 H 3.8 7.2 171 174 E 5.0 H 0.5 1.2 176 177 E 3.0 P 1.5 2.0 181 188 H 5.0 H 0.4 0.8 190 197 E 4.8 H 1.6 1.1 198 205 C 5.0 H 5.8 6.7 206 217 E 4.3 M 1.5 1.8 218 219 C 5.0 H 0.5 3.0 220 222 H 3.0 P 3.7 6.7 224 225 - 3.0 P 9.8 75.0 226 228 C 5.0 H 5.3 4.0 229 231 H 5.0 H 6.7 6.7 232 237 E 5.0 H 3.3 2.7 238 240 C 5.0 H 3.0 7.2 241 249 - 3.0 P 6.9 75.0 250 252 C 5.0 H 2.7 4.0 253 258 E 5.0 H 1.0 0.7 259 262 C 5.0 H 5.2 4.0 263 266 E 4.0 M 2.5 2.8 268 272 C 5.0 H 3.6 6.4 275 279 H 3.0 P 3.6 4.6 280 281 C 5.0 H 1.5 2.0 284 290 H 4.7 H 1.7 1.6 292 298 H 4.4 M 5.4 5.7 299 304 C 5.0 H 8.3 6.6 305 308 - 3.0 P 7.1 75.0 309 312 C 5.0 H 7.1 5.5 313 318 E 4.3 M 1.3 0.7 319 321 H 3.0 P 3.3 4.0 323 326 E 5.0 H 2.0 0.8 327 330 C 5.0 H 3.0 3.9 331 333 E 4.3 M 2.0 2.3 334 335 C 5.0 H 6.5 6.0 336 340 H 5.0 H 3.4 2.8 341 344 C 5.0 H 2.0 3.0 345 356 H 4.5 M 3.1 3.0 357 364 - 3.0 P 75.0 5.9 >>>>>>