Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2r31a2 --------------------CHHHHC--CCCCCCEEEEEEC-CEEEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHHEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEECCCCCCCCHHHHHHHHHHHHCCC-HHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC >P1;d2r6ia1 CHHHHHHHCHHHCCCHHHHHHHCCCCCCCCCCCCEEEEECCCCCEEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCC-CCHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECC-CCCCCHHHHHHHHHHHHCCCCHHHHHHHHC-CCCCCCHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHCCC-CHHHHHHHHHC PSA >P1;d2r31a2 --------------------799664--415096081654b-9120010588315068855020325600620181157089426697021152022012603462a82044006203703004026658703640383054017102750705053044b783804860474057205705-4100000340013040000000002940603501710114432517679475a43880782374064116006103 >P1;d2r6ia1 9704800260141747934750336440710086060381a9902102158661500534603051640053036202617940407-500130016021904874671163027305903006016859713640677035007101860808044187a-69a049a02720291066147300000032-03315000010010294182a501700014651516379689753771774442-71114007017 Translating the sequences --------------------*HHHHC--CCCCCCEEEEEEC-CEEEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHH*CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHHEECCCCHHHHHHHHHHHHHHHHHHHHH*CCCCCCEECC*CCCCCHHHHHHHHHHHHCCC-HHHHHHHHH*HHCCCCHHHHHHHHCCCCCHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHH*HHHHHHHHH*C ********************HH***C**CCCCCCEEEEE*C*C*EEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCC**-C*HHHHHHHHHHCCHHHHHHHHHHHHHHHHCC***EECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECC-CCCCCHHHHHHHHHHHHCCC*HHHHHHHH*-**CCCCHHHHHHHHCCCCCHHHHHHH*CHHHHHHHHHHCCCHHHHHHHHHH***-*HHHHHHHHHC 160909.tem _________________________________ --------------------HHHHHC--CCCCCCEEEEEEC-CEEEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCHH-CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHHEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECC-CCCCCHHHHHHHHHHHHCCC-HHHHHHHHH-HHCCCCHHHHHHHHCCCCCHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHC Structural block scores 0 19 - 3.0 P 75.0 4.2 20 24 H 3.4 M 7.4 3.4 26 27 - 3.0 P 75.0 2.0 28 33 C 5.0 H 4.2 3.7 34 39 E 4.7 H 4.0 3.0 43 48 E 4.7 H 0.7 1.0 49 50 C 5.0 H 6.5 6.5 51 52 E 5.0 H 5.5 6.0 53 65 C 5.0 H 3.5 2.5 66 77 H 5.0 H 2.9 2.6 78 84 C 5.0 H 5.1 4.4 85 86 H 3.0 P 7.5 3.5 89 99 H 4.8 H 1.6 1.3 100 101 C 5.0 H 3.0 4.5 102 117 H 5.0 H 3.4 4.0 118 119 C 5.0 H 3.5 4.5 120 122 H 3.0 P 1.0 1.0 123 124 E 5.0 H 2.0 3.0 125 128 C 5.0 H 4.8 5.0 129 150 H 4.9 H 3.4 3.7 151 156 C 5.0 H 3.3 4.0 157 158 E 5.0 H 2.0 4.5 159 160 C 5.0 H 7.8 8.8 162 166 C 5.0 H 4.6 5.9 167 178 H 5.0 H 4.0 4.0 179 181 C 5.0 H 4.0 3.7 183 191 H 4.8 H 1.3 0.9 193 194 H 3.0 P 0.5 1.5 195 198 C 5.0 H 1.8 2.2 199 206 H 5.0 H 0.0 0.2 207 211 C 5.0 H 4.2 4.8 212 219 H 4.8 H 2.1 3.2 221 230 H 5.0 H 4.0 3.9 231 233 C 5.0 H 6.7 7.7 234 246 H 4.5 M 5.3 5.2 248 257 H 4.6 H 2.5 2.2 >>>>>>