Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c8ba- CCCCCCCCCCCCCCCCCEECCCCEEEECCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHCHHHHHHHCC---CCCHHHHCCCCCCEEEECCHHHCCCCCCHHHHHHHCCCCCCCEEEEEEECC-CCCHHHCCCCEEEE--CCCCCCC--------CCCCCC----------CCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-------- >P1;d1cfza- -----------------------------------------------------------------------CCEEEEEECCCCCHHHHHHHHHHHHHHHHEECCC-------CEEEEEE---EC----CCHHHHHHHC-CCCEEEEEEECCCCCC--CCCCEEEEECCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC------------------CCCCCC----HHHHCCHHHHHHHHHHHHHCCCCCCEEHHHC PSA >P1;d1c8ba- b897a01303868baa86966931143749a1997253010427a673642371034204210543b068403000000055754120000300850---530367266b501010320435aa3a6722511794183805010000023-04489211400000--0003232--------824616----------6400000001767ba9dffb986728497718945623a7174106400600040031007b9d3-------- >P1;d1cfza- -----------------------------------------------------------------------440000000427400100003005006741403b-------5050350---54----335804b402-60300000000114a5--8414111156760171062a618105601600830595a31062000000104447------------------776701----850682163007301510551a060545978 Translating the sequences ***********************************************************************CCEEEEE*CCCCCHHH*HHHHHHH**---**CHH*******CEEEE******C****HHHHHHH**C*CCCEEEEEEECC-CCC**HCCC*EEEE--******C--------******----------C*EEEEEECCCCCC******************CCCCCC****HHHHHHHHHHHHHHHHH**CCCC-------- -----------------------------------------------------------------------CCEEEEEECCCCCHHHHHHHHHHHHH***EEC**-------CEEEEEE---EC----**HHHHHHHC-CCCEEEEEEECC*CCC--*CCCEEEEE**HHHHHHC********HHHHHH**********CEEEEEEECCCCCC------------------CCCCCC----HHHH**HHHHHHHHHHHHHCCCC******** 53163.tem _________________________________ -----------------------------------------------------------------------CCEEEEEECCCCCHHHHHHHHHHHHH---EECHH-------CEEEEEE---EC----HHHHHHHHHC-CCCEEEEEEECC-CCC--HCCCEEEEE--HHHHHHC--------HHHHHH----------CEEEEEEECCCCCC------------------CCCCCC----HHHHHHHHHHHHHHHHHHHCCCC-------- Structural block scores 0 70 - 3.0 P 4.9 75.0 71 72 C 5.0 H 1.5 4.0 73 78 E 4.7 H 0.0 0.0 79 83 C 5.0 H 4.4 3.4 84 96 H 4.5 M 1.8 0.7 97 99 - 3.0 P 75.0 5.7 100 101 E 3.0 P 4.0 2.5 103 104 H 3.0 P 4.5 7.2 105 111 - 3.0 P 5.4 75.0 113 118 E 4.3 M 1.0 2.2 119 121 - 3.0 P 4.0 75.0 124 127 - 3.0 P 6.6 75.0 128 136 H 4.1 M 3.6 4.3 139 141 C 5.0 H 4.3 3.0 142 148 E 5.0 H 0.1 0.0 149 150 C 5.0 H 2.5 0.5 152 154 C 5.0 H 2.7 6.5 155 156 - 3.0 P 8.5 75.0 158 160 C 5.0 H 2.0 3.0 161 165 E 4.6 H 0.0 1.8 166 167 - 3.0 P 75.0 6.5 168 173 H 3.0 P 1.3 2.5 175 182 - 3.0 P 75.0 4.2 183 188 H 3.0 P 4.5 2.2 189 198 - 3.0 P 75.0 4.5 200 206 E 4.7 H 0.6 0.3 207 212 C 5.0 H 5.4 3.3 213 230 - 3.0 P 9.2 75.0 231 236 C 5.0 H 4.8 4.7 237 240 - 3.0 P 6.4 75.0 241 259 H 4.6 H 1.9 3.2 260 263 C 5.0 H 9.2 4.1 264 271 - 3.0 P 75.0 5.5 >>>>>>