Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1hp1a1 ---CCEEECCCCCCCHHHHCCCCCHHHHHHHHHHHHHH-----CCCEEEEEHHHCCCCCCCEEECHHHHHHHCCCCCEEEEEEEEHHHHHHHHHHHCCCCC-CCCCCEEEE---CEEEEEE-----C----------------------CEEEEEEEC----CEECCCCCEEEEEEEHHHHCCHHHCCCCCCC---CCEEEE-EEEHHHHHHHHHHHHCCCCHHHHCCCCCEEEE--- >P1;d2z1aa1 CCCEEEEECCCCCCCHHHHCCCCCHHHHHHHHHHHHHCH--HHCCCEEEEEHHHCCCCCCCEEEEHHHHHHHCCCCCEEEEEEEEHHHHHHHHHHHHCCHHHCCCCCEEEE---CEEEEEECCCCCC----------------------CCEEEEEEEECCEEEECCCCCEEEEEEEHHHHCCHHHCHHHHCC--CCCEEEE-EEEHHHHHHHHHHHHCEECC---CCCCCEEEECCC >P1;d3c9fa1 -CCEEEEECCCCCCCC-CCCCCCCCHHHHHHHCCHHHCCCCCCCCEEEEEEHHHCCCCCCCEEEEHHHHHHHCCCCCCEEEEEEEHHHHCCHHHHHHCCCCC----CCCCCHHHHCCCCCCCCCCEECCCCCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCC----CEEEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEECCCHHHHHHHHHHC--------------------C PSA >P1;d1hp1a1 ---41040743020467401470010010002001520-----a020000001403300758604495057003562100103060660360035005284-752100000---4030404-----9----------------------570580305----9860459661300003500423390350255---971551-85500400231056217060571417a40428--- >P1;d2z1aa1 9a7500404560407673012300100000030022206--93a0400000010031206656022420560035723000010508203500120024058221200000---2040001055748----------------------7003501063a98267064a441300003600704250620570--9653552-83210600131046375081---966a00503736 >P1;d3c9fa1 -a74236082302003-1338474000200265003506389a10000000000045105656025622650024724011040406103500820371a0b----860206502829aa998357483556ba94992a5924428257021003032276976----3702000055036104300442a292a481671284400400263029--------------------a Translating the sequences ---**EEECCCCCCCHHHHCCCCCHHHHHHHHHHHHH*-----CCCEEEEEHHHCCCCCCCEEE*HHHHHHHCCCCCEEEEEEEEHHHHHHHHHHH*CCCC-CCCCCEEEE---CEEEEEE-----C----------------------C*EEEEEE*----CEECCCCCEEEEEEEHHHHCCHHHC***CCC---CCEEEE-EEEHHHHHHHHHHHHC**C****CCCCCEEEE--- *CCEEEEECCCCCCCHHHHCCCCCHHHHHHHHHHHHHC*--**CCCEEEEEHHHCCCCCCCEEEEHHHHHHHCCCCCEEEEEEEEHHHHHHHHHHHHCC***CCCCCEEEE---CEEEEEECCCC*C----------------------CCEEEEEEEECC**EECCCCCEEEEEEEHHHHCCHHHCHHH*CC--CCCEEEE-EEEHHHHHHHHHHHHC**C*---CCCCCEEEE**C -CCEEEEECCCCCCC*-**CCCCC*HHHHHHH**HHHC*****CC*EEEEEHHHCCCCCCCEEEEHHHHHHHCCCCC*EEEEEEEHHHH**HHHHHHCCCC*----C**************CCCC************************CC**EEEEEECC*C**----CEEEEEEEHHHH**HHH*HHHCCC**CCC*EEE****HHHHHHHHHH*--------------------C 55816.tem _________________________________ -CCEEEEECCCCCCCHHHHCCCCCHHHHHHHHHHHHHC*--**CCCEEEEEHHHCCCCCCCEEEEHHHHHHHCCCCCEEEEEEEEHHHHHHHHHHHHCCCC*CCCCCEEEE---CEEEEEECCCC*C----------------------CCEEEEEEEECC*CEECCCCCEEEEEEEHHHHCCHHHCHHHCCC--CCCEEEE-EEEHHHHHHHHHHHHC**C*---CCCCCEEEE--C Structural block scores 1 2 C 4.0 M 75.0 8.8 8.8 3 7 E 4.6 H 1.8 1.8 3.0 8 14 C 5.0 H 2.9 3.7 2.1 15 18 H 4.0 M 4.2 4.0 20.5 19 23 C 5.0 H 2.4 1.2 5.2 24 36 H 4.8 H 0.9 0.8 1.8 39 40 - 4.0 M 75.0 75.0 5.5 41 42 * 2.7 P 75.0 6.0 9.8 43 45 C 4.7 H 4.2 4.8 0.3 46 50 E 5.0 H 0.0 0.0 0.0 51 53 H 5.0 H 1.7 0.3 0.0 54 60 C 5.0 H 2.6 2.6 3.0 61 64 E 4.8 H 4.5 3.2 3.2 65 71 H 5.0 H 4.3 2.7 3.7 72 76 C 5.0 H 3.2 3.4 3.0 77 84 E 4.9 H 1.4 1.1 1.8 85 96 H 4.8 H 2.4 1.8 2.3 97 100 C 4.5 M 4.8 2.8 4.6 102 106 C 4.2 M 3.0 1.4 61.6 107 110 E 4.0 M 0.0 0.0 2.0 111 113 - 4.0 M 75.0 75.0 3.7 115 120 E 4.0 M 1.8 0.8 8.2 121 124 C 4.0 M 75.0 4.2 6.2 127 148 - 4.0 M 75.0 75.0 6.1 149 150 C 4.5 M 6.0 3.5 3.5 151 158 E 4.5 M 12.0 2.2 1.4 159 160 C 4.0 M 75.0 9.8 4.5 163 164 E 4.0 M 7.0 6.5 6.5 165 169 C 4.2 M 4.8 4.9 60.6 170 176 E 5.0 H 1.4 1.1 1.3 177 180 H 5.0 H 2.0 2.2 3.2 181 182 C 4.0 M 3.0 3.5 3.5 183 185 H 5.0 H 5.0 3.7 2.3 187 189 H 4.0 M 2.7 2.7 2.7 190 192 C 4.7 H 4.0 4.0 4.8 193 194 - 4.0 M 75.0 75.0 5.5 195 197 C 4.7 H 30.3 6.7 7.5 198 201 E 4.8 H 3.0 3.8 3.8 203 205 E 4.0 M 6.0 4.3 5.3 206 217 H 4.8 H 1.9 2.1 8.4 219 220 * 2.7 P 3.5 2.5 75.0 223 225 - 4.0 M 4.3 75.0 75.0 226 230 C 4.0 M 5.3 6.3 75.0 231 234 E 4.0 M 3.5 2.0 75.0 235 236 - 4.0 M 75.0 5.0 75.0 >>>>>>