Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1m5ya1 ----------------------------------------------------CCCEEEEECCCEEEHHHHHHHHHHHHHHHHCCCC---------CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECC >P1;d1w26a1 CCHHHHCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-----------CCCHHHHHHHHHHHHHHHHC---CCCCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHC-CCCCC-CHHHHHHHHHHC----CCCCC--CHHHHHHHHHHHHHCCCCCCCC-----------------------------CCCCCCCCCCC------ PSA >P1;d1m5ya1 ----------------------------------------------------b48300303b640336507a3166337818a696---------b258786036700361013200212099481907795057303630876b0749614861696858197216513462115603452068407---478824772497ab8547514561279227503862258061645b >P1;d1w26a1 79696057690990469328737745667365053664376115a1187595-----------b0589515730460156208---76c458740873647614a5054611284105612763927136931473267-0687a-548732763584----98368--47602521004122784b5aa8-----------------------------b386961548d------ Translating the sequences ----------------------------------------------------***********EEEHHHHHHHHHHHHHHHHC***---------CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH*HHHCC*CHHHHHHHHHHH****HHHHH**HHHHHHHHHHHHHHHHCCC---*****************************HHHHHHHHHHC****** ****************************************************-----------***HHHHHHHHHHHHHHHHC---*********CCCCHHH*HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH*-***CC-CHHHHHHHHHH*----*****--*HHHHHHHHHHHHH**CCC***-----------------------------**********C------ 109998.tem _________________________________ ---------------------------------------------------------------EEEHHHHHHHHHHHHHHHHC------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHHCC-CHHHHHHHHHHH----HHHHH--HHHHHHHHHHHHHHHHCCC--------------------------------HHHHHHHHHHC------ Structural block scores 0 62 - 3.0 P 62.7 17.4 63 65 E 3.0 P 2.3 5.5 66 81 H 5.0 H 4.8 3.9 83 94 - 3.0 P 58.0 23.2 95 98 C 5.0 H 6.6 6.0 99 122 H 4.9 H 3.2 4.0 123 128 C 5.0 H 4.8 4.2 129 138 H 4.8 H 4.5 4.8 140 142 H 3.0 P 5.0 4.7 143 144 C 5.0 H 8.8 8.8 147 157 H 4.8 H 5.5 5.2 158 161 - 3.0 P 5.5 75.0 162 166 H 3.0 P 5.0 6.8 167 168 - 3.0 P 3.0 75.0 169 184 H 4.6 H 3.5 3.2 185 187 C 5.0 H 3.7 6.8 188 219 - 3.0 P 12.0 68.9 220 229 H 3.0 P 4.6 6.2 231 236 - 3.0 P 5.6 75.0 >>>>>>