Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3jcla1 -------CCCCCCCHHHHHCCCCCCCCCCCEEEEECCEEECHHHHCCCCEEEEEEEECCCHHHHCCCEECEEEEEEEECCHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEE-EEEEEEEEECCCCCCCCCCCHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCEEEEEEEEEEEC----CCCCEEEEEEEECCCC-CCEEECCCCCCC >P1;d7eama- CCCCCCCCCCCCCCHHHHHCCCCCCCHHHCEEEEECCEECCCHHHHCCCCCCEEEEECCCCCCCCCCEECEEEEEEEEEEHHHHHHCCCCCCCHHHHHCCCCCCCCCEEEEEEEC-HH----HHCCCCCCCCCEEECCCC---------------CCCCCCCCCCCC------------CCEECCCCCCCCC-CC--------------------CCEECCEEECCCCCCCCHHHCEEEEEEEEEECCCCCCCEECC------ PSA >P1;d3jcla1 -------9c17526137103548000001054430570304142117506147170361736703541022110000000483481072a495400300040157310000101065a568302333800-000240903030a428673420680280626506006004551046606040044-5055516035409952890500595010820101030310606----4000000011059394-63030216789b >P1;d7eama- b969885a9496040770094a9020013063550170302057049298152170291635702684101020000002040171011748650022002019a0300000130-2a----5006ab007802002328---------------870842442666------------912424b560a88-69--------------------93044006101053a3a8561010000010376b39330303------ Translating the sequences -------CCCCCCCHHHHHCCCCCCC***CEEEEECCEEECHHHH*CCCEEEEEEEECCCHHHHCCCEECEEEEEEEE**HHHHHHHCCCCCC*****CCCCCCCCCEEEEEEEC*********CEEEEE-EEEEEEEEE***************CCCCCCCCCHHH************CC**CCC-CCCCC*CC********************CC*EEEEEEEEEEEC----*C**EEEEEEEECCCC-CCEEEC****** *******CCCCCCCHHHHHCCCCCCCHHHCEEEEECCEE*C*HHHHCCC***EEEEECCC****CCCEECEEEEEEEEEEHHHHHH*CCCCCCHHHHHCCCCCCCCCEEEEEEEC-HH----HHC********EEE****---------------CCCCCCCCC***------------CCEECCC*CCCCC-CC--------------------CCEE**EEE*****C****HCEEEEEEEEEECCCC*CCEE*C------ 143587.tem _________________________________ -------CCCCCCCHHHHHCCCCCCCHHHCEEEEECCEEECHHHHHCCCEEEEEEEECCCHHHHCCCEECEEEEEEEEEEHHHHHHHCCCCCCHHHHHCCCCCCCCCEEEEEEEC-HH----HHCEEEEE-EEEEEEEEE---------------CCCCCCCCCHHH------------CCEECCC-CCCCC-CC--------------------CCEEEEEEEEEEEEC----HCEEEEEEEEEECCCC-CCEEEC------ Structural block scores 0 6 - 3.0 P 75.0 8.1 7 13 C 5.0 H 6.1 6.1 14 18 H 5.0 H 2.4 2.8 19 25 C 5.0 H 2.9 4.9 26 28 H 3.0 P 0.3 1.3 30 34 E 5.0 H 3.2 3.8 35 36 C 5.0 H 6.0 4.0 37 39 E 4.3 M 1.0 1.0 41 45 H 4.2 M 1.8 3.2 46 48 C 5.0 H 4.0 6.7 49 56 E 4.2 M 3.6 3.2 57 59 C 5.0 H 4.7 5.3 60 63 H 3.0 P 4.0 3.8 64 66 C 5.0 H 4.0 5.3 67 68 E 5.0 H 0.5 2.5 70 79 E 4.6 H 0.4 0.5 80 86 H 4.7 H 4.0 1.9 87 92 C 5.0 H 6.2 4.5 93 97 H 3.0 P 1.4 1.8 98 106 C 5.0 H 2.3 2.8 107 113 E 5.0 H 0.3 0.6 116 117 H 3.0 P 7.8 6.2 118 121 - 3.0 P 5.5 75.0 122 123 H 3.0 P 1.0 2.5 125 129 E 3.0 P 2.8 5.6 131 139 E 3.7 M 2.0 2.8 140 154 - 3.0 P 4.2 75.0 155 163 C 5.0 H 3.2 4.3 164 166 H 3.0 P 2.0 6.0 167 178 - 3.0 P 3.1 75.0 179 180 C 5.0 H 3.0 5.0 181 182 E 3.0 P 2.0 3.0 183 185 C 5.0 H 2.7 5.8 187 191 C 5.0 H 4.0 6.5 193 194 C 5.0 H 3.0 7.5 195 214 - 3.0 P 4.0 75.0 215 216 C 5.0 H 5.0 6.0 217 228 E 3.7 M 1.2 2.0 230 233 - 3.0 P 75.0 6.6 236 245 E 4.6 H 0.7 0.5 246 249 C 5.0 H 6.2 6.9 251 252 C 5.0 H 4.5 3.0 253 255 E 4.3 M 1.0 1.0 257 262 - 3.0 P 7.1 75.0 >>>>>>