Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2p6ra2 --CHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC----HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHC----CCCCCCCHHHHHH-HCCCHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHCHHHHHHHHC--HHHHHHHHHHHHHHC >P1;d2q0zx1 ------------------CCHHHHHHHHHCCHHHCCCCCCC---CCHHHHHHHHHHCCCCCCCCCCC----CHHHHHHHHHHHHHCC--------CCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHHCCCCCCCCCCC-HHHHHHHHCCCHHHHHHHHHHHCCCC >P1;d2xaua4 CCCHHHHHHHHHHHHH-CCHHHHHHHHHHH--CCCCCCCCCC--CCHHHHHHHHHCCCCC----------CCHHHHHHHHHHHHCCHHHHHHCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--------CCCC-------------------------------------------------------------------------- PSA >P1;d2p6ra2 --496047205300274705200000000102204107249808304820660385004216693a70950020000000022002136----396009407177b30750182036006401730592----a173053023105-20047400600517208194026016270434620565385008206--594064026317877 >P1;d2q0zx1 ------------------39336004500629607b03229---91593077117702371ba2709----3112001000012044--------b06-------a6057008402740491076048705859689117205148064206832702203407a7126505559164073089-7a625700808b93275067229828 >P1;d2xaua4 8178923830670378-9405520000003--2079005548--9249704614760348----------b3a6402240083044980874926600742202380035028315603740776--------a281-------------------------------------------------------------------------- Translating the sequences --CHHHHHHHHHH****CCCHHHHHHHHHHC*CCCCCCCCCC****HHHHHHHHHHCCCCCCCCCCC*****HHHHHHHHHHHHHCC**----HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH*----CCCC***H*****-*CCC****HHH*CCCCCHHHHHHHH*CCCCC*******HHHHHHHHC--HHHHHHHHHHH***C ------------------CCHHHHHHHHH*C***CCCCCCC---CCHHHHHHHHHHCCCCCCCCCCC----CHHHHHHHHHHHHHCC--------***-------HHHHHHHHHHHHHHHHHHHHHHH*****CC*****H*******CCC****HHH*CCCCCHHHHHHHH*CCCCC******-HHHHHHHHC**HHHHHHHHHHH***C **CHHHHHHHHHH***-CC*HHHHHHHHHH--CCCCCCCCCC--CCHHHHHHHHH*CCCC----------*CHHHHHHHHHHHH*C*******HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH*--------CCCC-------------------------------------------------------------------------- 158702.tem _________________________________ --CHHHHHHHHHH***-CCCHHHHHHHHHHC*CCCCCCCCCC--CCHHHHHHHHHHCCCCCCCCCCC---*CHHHHHHHHHHHHHCC**----HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH*----CCCC***H*****-*CCC****HHH*CCCCCHHHHHHHH*CCCCC******-HHHHHHHHC--HHHHHHHHHHH***C Structural block scores 0 1 - 4.0 M 75.0 75.0 4.5 3 12 H 4.0 M 3.6 75.0 4.6 13 15 * 2.7 P 3.0 75.0 6.0 17 19 C 4.3 M 4.0 29.0 4.3 20 29 H 4.9 H 0.3 2.7 1.5 32 41 C 4.7 H 3.7 11.6 4.0 42 43 - 4.0 M 4.0 75.0 75.0 44 45 C 4.0 M 1.5 5.0 5.5 46 55 H 4.9 H 4.2 4.7 4.8 56 66 C 4.4 M 4.4 4.8 49.1 67 69 - 4.0 M 4.7 75.0 75.0 72 84 H 4.9 H 0.5 0.6 3.3 85 86 C 4.5 M 1.5 4.0 6.5 87 88 * 2.7 P 4.5 75.0 4.0 89 92 - 4.0 M 75.0 75.0 7.0 93 99 H 4.0 M 4.4 45.4 3.6 100 103 C 4.0 M 3.8 75.0 1.5 104 127 H 4.8 H 3.7 7.0 12.6 129 132 - 4.0 M 75.0 4.5 75.0 133 136 C 4.5 M 5.4 8.0 5.4 137 139 * 2.7 P 2.7 3.0 75.0 141 145 * 2.7 P 2.2 3.6 75.0 148 150 C 4.0 M 1.3 2.0 75.0 151 154 * 2.7 P 2.8 4.8 75.0 155 157 H 4.0 M 2.0 3.0 75.0 159 163 C 4.0 M 3.6 2.8 75.0 164 171 H 4.0 M 2.9 4.6 75.0 173 177 C 4.0 M 3.2 5.0 75.0 178 183 * 2.7 P 3.8 4.5 75.0 185 192 H 4.0 M 3.2 4.7 75.0 194 195 - 4.0 M 75.0 4.0 75.0 196 206 H 4.0 M 3.6 5.0 75.0 207 209 * 2.7 P 7.3 6.3 75.0 >>>>>>