Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gwya- CCCCCEEEHHHCCHHHHHHHHHHCCCCCCEEEEEEEEEC-CCCEEEEEEEEEE---CCCCCCCCCEECCCEEEEEEEECCCCCCCCCEEEEEEEEECCCEEEEEEEEECCCCCCCCCEEEEEEEECCCCCCHHHHHHHHCC----CC--EECCCCEEEEEEECCEEEEEEECC--CCEEEEEEEEEC >P1;d2ofca- ---------------------------CEEEEEEEEECCCCCCEEEEEEEECCCCCCEEEEEEC--------CEEEEEEC----CCCCEEEEEEEECCCCEEEEEEEEEC----CEEEEEEEECCCCCCCHHHHHHHCCCCHHHHHHHHCCCC--EEEEECCCCCEEEEEEEECCCCEEEEEEEEC- PSA >P1;d1gwya- 740153250a60638206500930990710000001030-0450401313142---03262a0076043640000001058695640010000030676100000000135399640300030167656054a00550266----b1--25026643537085b040500014--715010205038 >P1;d2ofca- ---------------------------6040006152539807053323211752a32806569--------a2110403----515000002040a5701000000028----840000010706b93407400620074881341156233--63536086713020305627a6602020304- Translating the sequences ***************************C*EEEEEEEEEC-CCCEEEEEEEEEE---C******C********EEEEEE*C****CCCEEEEEEEEECCCEEEEEEEEE*C****C**EEEEEEEECCCCC*HHHHHHHHCC----**--EECC**EEEEEEECCEEEEEEE**--CCEEEEEEEEE* ---------------------------CEEEEEEEEE*C*CCCEEEEEEEE*****CEEEEEEC--------*EEEEEEC----CCC*EEEEEEEECCC*EEEEEEEEEC----CEEEEEEEE**CCCCCHHHHHHH**CC****HH****CC--EEEEE**CC*EEEEEEEE**CCEEEEEEEE*- 63724.tem _________________________________ ---------------------------CEEEEEEEEEEC-CCCEEEEEEEEEE---CEEEEEEC--------EEEEEEEC----CCCEEEEEEEEECCCEEEEEEEEEEC----CEEEEEEEEEECCCCCHHHHHHHHHCC----HH--EECC--EEEEEEECCEEEEEEEEE--CCEEEEEEEEE- Structural block scores 0 26 - 3.0 P 3.8 75.0 28 37 E 4.6 H 0.5 2.3 40 42 C 5.0 H 3.0 5.0 43 52 E 4.6 H 1.9 2.7 53 55 - 3.0 P 75.0 5.8 57 62 E 3.0 P 3.9 4.5 64 71 - 3.0 P 3.8 75.0 72 78 E 4.4 M 0.1 2.6 80 83 - 3.0 P 7.0 75.0 84 86 C 5.0 H 3.3 3.7 87 95 E 4.8 H 0.4 0.7 96 98 C 5.0 H 6.3 7.5 99 108 E 4.6 H 0.2 0.3 110 113 - 3.0 P 6.5 75.0 115 124 E 4.2 M 1.7 1.2 125 129 C 5.0 H 4.8 6.7 130 138 H 4.3 M 3.5 2.1 139 140 C 5.0 H 6.0 5.5 141 144 - 3.0 P 75.0 5.0 145 146 H 3.0 P 6.2 2.5 147 148 - 3.0 P 75.0 3.0 149 150 E 3.0 P 3.5 4.0 151 152 C 5.0 H 1.0 3.0 153 154 - 3.0 P 6.0 75.0 155 161 E 4.4 M 4.3 4.4 162 163 C 5.0 H 8.2 6.5 164 172 E 4.3 M 1.6 2.2 173 174 - 3.0 P 75.0 4.5 175 176 C 5.0 H 4.0 8.2 177 185 E 4.8 H 1.8 1.9 >>>>>>