Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ijqa1 CCEEEEECCCCEEEEECC-----CCCCEEEECC-CCCEEEEEEECCCCEEEEEECCCCEEEEEECC----EEEECCCCCCCCEEEEECCCCEEEEEECCCCEEEEEECCCCCEEEEEECCCCCEEEEEEECCCCEEEEEECCC-CCEEEEEECCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCCCCCEEEEECCCCCCCEEEEEEECCEEEEEECCCCEEEEEECCCCCCCEEEECC-CCCCCCEEEECHHHCCCC >P1;d1npea- CEEEEEEEEEEEEEEEECCCCCCHHHCEEEEEEEEEEEEEEEEECCCCEEEEEECCCCEEEEEECCCCCCEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCCCCCEEEECCCCCCEEEEEEECCCCEEEEEECCCCCCEEEEEECCCCCCEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCEEEEEEEEEC---CCCEEEEEEECCEEEEEECCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCCC---- PSA >P1;d1ijqa1 701000004510320028-----465454104a-05500001000645300000236420111524----8400488042011000011653000001640000103080782720156ac140120200036740000030a-8010000219079362005890640010104076410000005420000033817927402628950230100001874000002635000004269079064004a-043022020128731296 >P1;d1npea- 912000005110010207735034a507201618a1300101001363100000334200030507c4927100597002011000126833000000734100104150782630159a06201202001656300000227981100004070782530059905000100024a5510000003352000031883c915216a---0530010102970000002633000000186465342150b765401101004683---- Translating the sequences C*EEEEE****EEEEE*C-----***CEEEE**-***EEEEEEECCCCEEEEEECCCCEEEEEECC----EEEECCCCCC**EEEEECCCCEEEEEECCCCEEEEEECCCCCEEEEEECCCCCEEEEEEECCCCEEEEEECCC-CCEEEEEECCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECC****EEEEEC***CCCEEEEEEECCEEEEEECCCCEEEEEECCCC***EEEECC-CCCCCCEEEECHHH**** CEEEEEEEEEEEEEEEEC*****HHHCEEEEEE*EEEEEEEEEECCCCEEEEEECCCCEEEEEECC****EEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCCCC*EEEE*CCCCCEEEEEEECCCCEEEEEECCC*CCEEEEEECCCCC*EEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCEEEEEEEEEC---CCCEEEEEEECCEEEEEECCCCEEEEEECCCCEEEEEE*CC*CCCCCCEEEEC***---- 63825.tem _________________________________ CEEEEEEEEEEEEEEEEC-----HHHCEEEEEE-EEEEEEEEEECCCCEEEEEECCCCEEEEEECC----EEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCCCCEEEEEECCCCCEEEEEEECCCCEEEEEECCC-CCEEEEEECCCCCEEEEECCCCCCEEEEEEECCCCEEEEEECCCCEEEEEECCEEEEEEEEEC---CCCEEEEEEECCEEEEEECCCCEEEEEECCCCEEEEEEECC-CCCCCCEEEECHHH---- Structural block scores 1 16 E 4.2 M 1.1 0.8 18 22 - 3.0 P 75.0 3.6 23 25 H 3.0 P 5.0 6.5 27 32 E 4.3 M 4.1 2.8 34 43 E 4.4 M 1.1 1.6 44 47 C 5.0 H 3.8 3.2 48 53 E 5.0 H 0.5 0.2 54 57 C 5.0 H 3.8 3.0 58 63 E 5.0 H 1.7 1.3 64 65 C 5.0 H 3.0 3.5 66 69 - 3.0 P 75.0 6.9 70 73 E 5.0 H 3.0 2.0 74 79 C 5.0 H 4.3 3.8 80 86 E 4.4 M 0.3 0.4 87 90 C 5.0 H 3.2 4.8 91 96 E 5.0 H 0.5 0.5 97 100 C 5.0 H 2.8 3.5 101 106 E 5.0 H 0.7 1.0 107 111 C 5.0 H 4.6 4.2 112 117 E 4.3 M 2.8 2.8 118 122 C 5.0 H 6.8 5.5 123 129 E 5.0 H 0.7 0.7 130 133 C 5.0 H 4.0 4.5 134 139 E 5.0 H 0.7 0.5 140 142 C 5.0 H 4.5 3.7 144 145 C 5.0 H 4.0 4.5 146 151 E 5.0 H 0.5 0.8 152 156 C 5.0 H 5.2 4.4 157 161 E 4.6 H 2.2 2.0 162 167 C 5.0 H 5.3 4.7 168 174 E 5.0 H 0.9 0.4 175 178 C 5.0 H 4.2 6.1 179 184 E 5.0 H 0.2 0.2 185 188 C 5.0 H 2.8 2.8 189 194 E 5.0 H 0.5 0.8 195 196 C 5.0 H 5.5 4.5 197 205 E 4.1 M 4.2 5.3 207 209 - 3.0 P 7.3 75.0 210 212 C 5.0 H 1.7 2.7 213 219 E 5.0 H 0.3 0.6 220 221 C 5.0 H 7.5 8.0 222 227 E 5.0 H 0.7 0.0 228 231 C 5.0 H 4.0 3.5 232 237 E 5.0 H 0.7 0.0 238 241 C 5.0 H 4.2 4.8 242 248 E 3.9 M 3.7 3.7 249 250 C 5.0 H 7.2 5.8 252 257 C 5.0 H 1.8 2.8 258 261 E 5.0 H 0.8 0.2 263 265 H 3.0 P 6.0 5.7 266 269 - 3.0 P 4.5 75.0 >>>>>>