Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1vf7a- --CCEEEEEEECEECC--EEEECCCCCEEEEECCCCCCEEECCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC------HHHHHHHHHHHHHHHH-HHHHHHHHHH---------CCEEECCCCEEECCCCCCCCCEECCCCCCCCEEEECCCEEECCEEEEHHHHHHHHHHHHCCCCCEEECCEEECCEECCCCCEECCCCEEECCCCCCCCCCCEEEECCEEECCCCCCCCCCEEEEEEECC >P1;d3lnnb- CCCCCEEEEEEEEECCCCEEECCCCCCEEEC-CCCCCCCEE-CCCCCEEEECH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCCCEEEECCCCCEEEEECCCCCCCEECC-CCCCCCEEECCCEEEEEECCC-------HHHH--HHCCC----CCCEEEECCCCCC-CEEECCCC-CCCCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEC-C PSA >P1;d1vf7a- --97643061605025--52504050745046330835370846520010438825762682586287346416416942788416------9852671474268057-6167142325---------3050503152309906195738066b29a10030320620202051659117305600757506403b70030303168466063404030808585ab9c2120203040492406373604020618 >P1;d3lnnb- b948526050504014742460501020504-061954360-39620020209-5127245507727773771567166186a9847538747714652871277073573792584a073554a9143001406382202529186747186-384100000206301000415-------6803--b6066----20a0507077299-55650653-18933a86610402010815646041565040306-7 Translating the sequences --CCEEEEEEE*EECC--EEEECCCCCEEEE*CCCCCCEEE*CCCEEEEE*CH*HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC------HHHHHHHHHHHHHHHH-HHHHHHHHHH---------**EEECCCCEEE**CCCCCCCEECC*CCCCCEEEECCCEEE**EEEE*******HHHH****CCE****EEE**EECCCCCE*C***EEEC*CCCCCCCCCEEEE**EEECCCCCCCCCCEEEEEEE*C **CC*EEEEEEEEECC**EEE*CCCCCEEE*-CCCCCC*EE-CCC**EEEECH-HHHHHHHHHHHHHHHHHHHHHHHHH**CCCCC******HHHHHHHHHHHHHH*****HHHH*************EEEE*CCCCEEEEECCCCCCCEECC-CCCCC*EEECCCEEEEEE***-------HHHH--HHCC*----***EEEECCCCC*-CEEE***C-CCCCCCCCC****EEEEECCCCCCCCCCEEEEEE*-C 111369.tem _________________________________ --CCEEEEEEEEEECC--EEEECCCCCEEEE-CCCCCCEEE-CCCEEEEEECH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC------HHHHHHHHHHHHHHHH-HHHHHHHHHH---------EEEEECCCCEEEEECCCCCCCEECC-CCCCCEEEECCCEEEEEEEEE-------HHHH--HHCCE----EEEEEEECCCCCE-CEEEEEEC-CCCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEE-C Structural block scores 0 1 - 3.0 P 75.0 10.2 2 3 C 5.0 H 8.0 6.0 4 13 E 4.6 H 3.1 2.7 14 15 C 5.0 H 3.5 2.5 16 17 - 3.0 P 75.0 5.5 18 21 E 4.5 M 3.0 3.0 22 26 C 5.0 H 3.2 1.6 27 30 E 4.5 M 3.2 2.2 32 37 C 5.0 H 3.7 4.2 38 40 E 4.3 M 3.3 3.0 42 44 C 5.0 H 5.0 6.0 45 50 E 4.0 M 1.2 1.0 54 80 H 4.9 H 4.9 4.7 81 85 C 5.0 H 5.4 7.5 86 91 - 3.0 P 75.0 5.7 92 107 H 4.8 H 5.1 4.6 109 118 H 3.8 M 3.7 5.5 119 127 - 3.0 P 75.0 5.4 128 132 E 3.8 M 2.6 1.6 133 136 C 5.0 H 2.2 4.2 137 141 E 4.2 M 4.6 2.2 142 148 C 5.0 H 4.4 5.3 149 150 E 5.0 H 4.0 4.0 151 152 C 5.0 H 6.0 7.0 154 158 C 5.0 H 4.5 3.2 159 162 E 4.5 M 1.5 0.0 163 165 C 5.0 H 2.7 2.7 166 174 E 3.9 M 2.0 1.6 175 181 - 3.0 P 3.7 75.0 182 185 H 5.0 H 2.8 4.2 186 187 - 3.0 P 6.0 75.0 188 189 H 3.0 P 6.0 8.8 190 191 C 5.0 H 3.0 3.0 193 196 - 3.0 P 5.4 75.0 197 203 E 3.6 M 1.3 3.5 204 208 C 5.0 H 5.0 5.0 212 217 E 3.0 P 2.3 4.5 220 228 C 5.0 H 7.7 6.1 229 237 E 3.7 M 1.6 1.8 238 247 C 5.0 H 3.8 3.8 248 254 E 4.7 H 2.6 2.6 >>>>>>