Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1pg6a- C-CEEECCCCCCCEEEEECCCCCEEEECCCEEECCCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEECCC--CEEEEECCCCC-CCEEEEEEC---CCCEEECCCCEEEEECCCEECCCCCCCCCCCCCEECCEEEEEECCCCEEEEEEECCC-CEEHHHEEEEECCCEEEEECCCCCCHHHHCCCCEEEEECEEEEEEEC-CCHHHHHHHHHHHC-------- >P1;d1yoxa1 CCEEEEE-CCCCEEEEEECCCCEEEECCCCEE-CCCEEEEC--------------------CCEEEECCCCCEEEEECCCCC-EEEEEEE-HHHHCCEEEEEHHHEEEEECCCCCCCCC---CCCEEEEECCCEEEEEEECCEEEEEEEEEEEEEEHHHEEEECCCEEEEEEECC---------CEEEEEEEEEEEEEEC-CCHHHHHHHHHHCCHHHHHCCC >P1;d3zzsa- -----------------------------------------------------------------------CCEEEEEECCCCEEEEEEECCC--------------------------CCCEEEEEEECCCCEEEEECCC------------------------------------------CEEEEEEECCEEEEECCEEEC------------------- PSA >P1;d1pg6a- 5-735269b9614060308796302015b04645a408574468d898362088729464491130086--90700030616-140210802---b40020169010001050617661c93d544020776010000002707536192a6-3220420000045081703355b9717b5969300107471100217-51696664758877-------- >P1;d1yoxa1 5073724-7aa220203043a2101048c065-5b405769--------------------91222062a582300020607-0201004-0772b340100550100006a0839828---b320120268210000004734456089532604131000015a08353766a---------8550103475100104-304754496775657983589a >P1;d3zzsa- -----------------------------------------------------------------------655120403577020122249a--------------------------a576363470676533626359------------------------------------------813506164703153789378------------------- Translating the sequences C-*EEE**CCCC*EEEEECCCC*EEE*CCCEE*CCC****C********************C*EEE*CC--CEEEEECCCCC-**EEEEE*C---CC*EEE****EEEEECCC**CCCCCCCCCC***EECC*EEEEECCCCEEEEEEE***-*EEHHHEEEE*CC*EEEEE*CC********CC*EEEEECEEEEEEEC-CCHHHHHHHHHH*C-------- C**EEE*-CCCC*EEEEECCCC*EEE*CCCEE-CCC****C--------------------C*EEE*CC**CEEEEECCCCC-EEEEEEE-****CC*EEE****EEEEECCC**CCCC---CCCEEEEECCCEEEEE**CCEEEEEEE*****EEHHHEEEE*CC*EEEEE*CC---------CEEEEEE*EEEEEEEC-CCHHHHHHHHHH*C******** -----------------------------------------------------------------------C*EEEE**CCC*EEEEEEE*C*--------------------------CCC***EEEE*CCCEEEEECCC------------------------------------------C*EEEEEEC*EEEEE*C****------------------- 51219.tem _________________________________ C-*EEE*-CCCC*EEEEECCCC*EEE*CCCEE-CCC****C--------------------C*EEE*CC--CEEEEECCCCC-EEEEEEE*C*--CC*EEE****EEEEECCC**CCCCCCCCCCEEEEECCCEEEEECCCCEEEEEEE***-*EEHHHEEEE*CC*EEEEE*CC--------CCEEEEEECEEEEEEEC-CCHHHHHHHHHH*C-------- Structural block scores 3 5 E 4.0 M 3.3 4.0 75.0 8 11 C 4.0 M 6.9 7.5 75.0 13 17 E 4.0 M 1.8 1.0 75.0 18 21 C 4.0 M 7.5 4.9 75.0 23 25 E 4.0 M 0.7 0.3 75.0 27 29 C 4.0 M 5.5 6.8 75.0 30 31 E 4.0 M 5.0 5.5 75.0 33 35 C 4.0 M 6.5 6.8 75.0 36 39 * 2.7 P 5.0 4.5 75.0 41 60 - 4.0 M 6.0 75.0 75.0 63 65 E 4.0 M 1.3 2.0 75.0 67 68 C 4.0 M 7.0 4.0 75.0 69 70 - 4.0 M 75.0 7.8 75.0 72 76 E 4.8 H 1.4 1.0 2.6 77 81 C 4.6 H 3.2 3.0 3.8 83 89 E 4.7 H 2.3 1.0 1.3 93 94 - 4.0 M 75.0 4.5 75.0 95 96 C 4.0 M 7.8 7.2 75.0 98 100 E 4.0 M 0.7 0.3 75.0 101 104 * 2.7 P 4.0 2.5 75.0 105 109 E 4.0 M 0.4 0.2 75.0 110 112 C 4.0 M 1.7 5.5 75.0 113 114 * 2.7 P 3.5 5.5 75.0 115 124 C 4.0 M 6.7 26.9 33.8 125 129 E 4.2 M 2.6 1.0 4.0 130 132 C 4.7 H 4.3 5.3 6.0 133 137 E 5.0 H 0.2 0.2 4.0 138 141 C 4.2 M 2.2 2.8 23.0 142 148 E 4.0 M 4.4 4.3 75.0 149 151 * 2.7 P 6.2 5.7 75.0 154 155 E 4.0 M 2.0 2.0 75.0 156 158 H 4.0 M 2.0 1.7 75.0 159 162 E 4.0 M 0.0 0.0 75.0 164 165 C 4.0 M 4.5 7.8 75.0 167 171 E 4.0 M 3.8 5.2 75.0 173 174 C 4.0 M 5.0 8.2 75.0 175 182 - 4.0 M 7.6 75.0 75.0 183 184 C 4.0 M 7.5 41.5 4.5 185 190 E 4.8 H 1.8 2.3 3.5 192 198 E 4.7 H 1.7 2.0 3.7 201 202 C 4.0 M 3.0 1.5 5.0 203 212 H 4.0 M 6.5 5.8 68.3 215 222 - 4.0 M 75.0 7.4 75.0 >>>>>>