Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1xdpa2 CEEECHHHCCCCHHHHHHHHHHHHCHHHCCCEECCCCCCCCCCCCCCCEEEEEEEEE---CCEEEEEEEECCCCCCCCEEECCCCCCCCCCEEEEHHHHHHHHHHHHHCC-CCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECC----CCCHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHCCCCCCHHHCCC >P1;d2hw4a1 ---------------------------------CHHHCCCE-EECCCEEEEEEEEEEECC--CEEEEEEECCCCC--------------------CHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECC-------------------------CCEEEEECCCCCCCCCCHHHHHHHHHHHCC---CCEEEECC---------------------- >P1;d2o8ra2 CEEECCCCCCHHHHHHHHHHHHHCCHHHCCCCCCCCCCCC--CCCCCCCEEEEEECCCCCCCCCEEEEEECCCCCCCCEEEECCCCCCCCCEEEEHHHHHHCCHHHHCC----CCC-CCEEEECCCCCCCCCCC----------------------CCCCEEEC----C-CHHHHHHHCCCCCCCCC-CEEEECCCCCHHHH-CCCCCCCCCCCC- PSA >P1;d1xdpa2 343121750296027404710466067208223058a25049505543000000026---bb4341000200356060007024475a9350000000000200600058-91907604010011455a8279656809a848916794688363221502106----80387015304910905950514436220166338a344148a956ba >P1;d2hw4a1 ---------------------------------71780650-503666502000030333--8222000014507--------------------71540296029416869060502000502054a-------------------------5540402470a5266090420072058526---71706468---------------------- >P1;d2o8ra2 25215930a57806830751056404540934041a7574--3062720100020349797984300002002861600050528a93842100000200251073007----b29-1600001030963569a----------------------a4750101----8-377016302423a0788-40666b41104735-92531398756c- Translating the sequences CEEEC***CC**HHHHHHHHHHH*CHHHCCC**CCCCCCC**CCCCCCEEEEEEEEE---CC*EEEEEEECCCCCCCCEEE*CCCCCCCCCEEEEHHHHHHHHHHHHHC*-CCCCCEEEEEEEEEE*CCCCCCC*******************CC*CEEEEECC----CCCHHHHHHHHHHCCCCCCCEEEECCCCCCHHHH**CCCCCC***CC* ---------------------------------C***CCC*-**CCC*EEEEEEEEE*CC--CEEEEEEECCCCC--------------------*HHHHHHHHHHHH***CC***EEEEEEEEEECC-------------------------CC**EEE**CC****CC*HHHHHHHHHHCC---CCEEEECC---------------------- CEEEC***CC**HHHHHHHHHHH*CHHHCCC**CCCCCCC--CCCCCC*EEEEEE***CCCCC*EEEEEECCCCCCCCEEE*CCCCCCCCCEEEEHHHHHH**HHHH*C----CCC-**EEEE***CCCCCCCC----------------------C***EE*C----C-CHHHHHHH***CCCCCC-*EEE*CCCCCHHHH-*CCCCCC***CC- 143724.tem _________________________________ CEEEC***CC**HHHHHHHHHHH*CHHHCCC**CCCCCCC*-CCCCCCEEEEEEEEE*CCCCCEEEEEEECCCCCCCCEEE*CCCCCCCCCEEEEHHHHHHHHHHHHHC*-CCCCCEEEEEEEEEECCCCCCCC-------------------CC*CEEEEECC----CCCHHHHHHHHHHCCCCCCCEEEECCCCCCHHHH-*CCCCCC***CC- Structural block scores 1 3 E 4.0 M 2.7 75.0 2.7 5 7 * 2.7 P 4.3 75.0 4.0 8 9 C 4.0 M 1.0 75.0 7.8 10 11 * 2.7 P 7.5 75.0 7.5 12 22 H 4.0 M 3.2 75.0 3.7 25 27 H 4.0 M 5.0 75.0 4.3 28 30 C 4.0 M 3.3 75.0 4.0 31 32 * 2.7 P 2.5 75.0 2.0 33 39 C 4.6 H 4.4 4.9 5.5 42 47 C 4.5 M 3.7 4.3 3.3 48 56 E 4.7 H 0.9 1.1 1.1 58 62 C 4.0 M 35.4 32.8 8.0 63 69 E 4.9 H 1.4 0.9 1.3 70 77 C 4.6 H 2.5 30.2 2.9 78 80 E 4.0 M 2.3 75.0 1.7 82 90 C 4.0 M 5.5 75.0 5.7 91 94 E 4.0 M 0.0 75.0 0.2 95 107 H 4.7 H 0.6 3.8 1.5 111 115 C 4.0 M 5.2 4.0 34.5 116 125 E 4.4 M 1.7 1.4 8.6 126 133 C 4.1 M 6.6 58.1 6.1 134 152 - 4.0 M 6.3 75.0 75.0 153 154 C 4.0 M 4.5 5.0 75.0 157 161 E 4.0 M 1.8 3.4 3.4 162 163 C 4.5 M 3.0 5.2 0.5 164 167 - 4.0 M 75.0 4.8 75.0 168 170 C 4.3 M 3.7 3.0 28.7 171 180 H 4.7 H 3.8 3.3 3.2 181 187 C 4.4 M 4.0 34.4 15.9 188 191 E 4.8 H 3.5 4.2 4.0 192 197 C 4.2 M 2.3 52.3 3.9 198 201 H 4.0 M 4.5 75.0 4.8 204 209 C 4.0 M 4.0 75.0 3.8 210 212 * 2.7 P 8.2 75.0 6.7 213 214 C 4.0 M 8.8 75.0 9.2 >>>>>>