Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1svba2 CHHHHCCCCEEEEECCCCC--EEEEEEECCCCEEEEEC------CEEEEEEEEEEEEEECCEEEEEEECCEEEEEEEEEECCCCCCCCCCHHHHCCCEEEEEEEEEECHHH----------CCCCCEEEEEEEEEEEEECC---CCEEEEEECCCCCCEEEEEEEECCCCC--CCCCCCCC----CCEEEEECCCCCEEEEECHHHCEEEEEEEHHHCCCCCCEEEEECCCCCCCCCCEEEEEHHHHHC-----CCCCEEC-CCCCCCCCHHHHEEECCCCCC--CCCEEECCCCHHHHHHHCC--------CCCEEEEECCEEECCCCEEE-EEEECC----CCCCCCC >P1;d3n40f1 ----------------CCEEEEEEEECCCCCCEEEEECCCCCCCEEEEEEEEEEEEEE-EEEEEEEEC-CEEEECCCCEEECC--CCCCCC--CCCCCCCEEEEEE-----CCCCEECCEECCCCCCCCEEEEEEEEEECHHHHCCCEEEEEEE--EEEEEEEEEEEEC---------------CEEEEEEEECC-CCCEEEECC-EEEEECCCCCCCCCCCCEEEEEC-------CEEEECCCCCCCCCCCCCCCCEECCCCCCCCCEECC-CCEECCCCCCCCCCCEECCCCHHHHHHHHCCCCHHHHCHHHCEEECC--CCEEECCCCCEEEEEEEECHHHCCCCCC >P1;d3p54a1 CCCCCCCCEEEEECCCCCC--EEEEEEECCCEEEEECC------CCCCEEEEEEEEEECCCEEEEEEEEEEEEEEEEEEECCCCCCCCCCHHHHCCCEEEEEEEEEECHHH----------CCCCCEEEEEEEEEEEEEE-----EEEEEEECCCCCEEEEEEEEECCCCCCCCCCCHHHHHHCCCEEEEEECCCCCEEEEECHHHCEEEEEEEHHHCCCCCCEEEEEECC------EEEEEECCCCCC-----CCCCEEE-CCEEEEECHHHHEEEEEEECC--EEEEEECCCCHHHHHHHCC--------CCEEEEEC-CCEEECCCEEE-EEEECC----CCCCCCC PSA >P1;d1svba2 220412b526637089b36--50606050b00000507------92020000032010580833200003061664523042076870618118592011544608007c3----------90b7775020000050603a---734000030567702010200032c76--247a6a0b----524405033974535160b813402010408402907510001024759934200105473039-----1810217-6b5a40641630060390745--70506347322a7039508--------c2650407a64010571403-020005----70736b8 >P1;d3n40f1 ----------------c03515250504265426160717a14515010103302140-716230000-3140315a160423--370928--b4c4121205107-----813056a67140a398900010201041184088330002405--b071204010406---------------a7604060506-094324368-0402006142b340078100116-------73002290262450702600000066393a902040-80605507b153402360280006402742b500366064b05031b--50302304164020104016a00667a7 >P1;d3p54a1 0007a3c526537099b34--41606042800000406------91020002023030680543200003040663605052075a707093395a5000635608018c4----------a097696000000040605-----34020120536305040000021a17aa416639405965002312020a74425180790720105050570191542000207a------500008393048-----1810211-5949716626400615c0934--8150513a343a9038508--------c2550919-a1040870504-040304----70745b8 Translating the sequences C****CCC*EEEE*CCCCC--EEEEEEECCCCEEEEEC------CEEEEEEEEEEEEE*CCEEEEEEE*CEEEEEEEEEECCCCCCCCCCHHHHCCCEEEEEEEEEECHHH----------CCCCCEEEEEEEEEEEEEC*---CCEEEEEECCCCC*EEEEEEEECCCCC--CCCC****----C*EEEEECCCCCEEEEECHHHCEEEEEEEHHHCCCCCCEEEEECCC*****C*EEEEE*****C-----CCCCEEC-CCCCCC*CHHHHEEECCCCCC--CCCEEECCCCHHHHHHHCC--------CCCEEEE**C*EE*CCCEEE-EEEECC----CCCCCCC ----------------CC***EEEEE**CCCCEEEEEC*******EEEEEEEEEEEEE-**EEEEEE*-CEEEE****EE*CC--CCCCC*--*CCC***EEEEEE-----**********CCCCC***EEEEEEEEEEC****CC*EEEEE**--*EEEEEEEEE**C---------------C*EEEEEE*CC-C**EEE***-*EEEE******CCCCCCEEEEEC-------CEEEE**CCCCCC*****CCC*E*C*CCCCCCE***-**EECCCCCC**CCCEE*CCC*HHHHHHHCC**********CEEE*C--C*EE*CC****EEEE*******CCCCCC C****CCC*EEEE*CCCCC--EEEEEEECCC*EEEE*C------C***EEEEEEEEEE*CCEEEEEEE**EEEEEEEEEECCCCCCCCCCHHHHCCCEEEEEEEEEECHHH----------CCCCCEEEEEEEEEEEEE*-----*EEEEEECCCCCEEEEEEEEECCCCC**CCCC*******CCEEEEEECCCCCEEEEECHHHCEEEEEEEHHHCCCCCCEEEEE*CC------EEEEEECCCCCC-----CCCCEE*-CC****ECHHHHEEE****CC--***EEECCCCHHHHHHHCC--------CC*EEEEC-CCEEECCCEEE-EEEECC----CCCCCCC 56983.tem _________________________________ C****CCC*EEEE*CCCCC--EEEEEEECCCCEEEEEC------CEEEEEEEEEEEEE*CCEEEEEEE*CEEEEEEEEEECCCCCCCCCCHHHHCCCEEEEEEEEEECHHH----------CCCCCEEEEEEEEEEEEEC*---CCEEEEEECCCCCEEEEEEEEECCCCC--CCCC****---CCEEEEEECCCCCEEEEECHHHCEEEEEEEHHHCCCCCCEEEEECCC-----CEEEEEECCCCCC-----CCCCEEC-CCCCCCECHHHHEEECCCCCC--CCCEEECCCCHHHHHHHCC--------CCCEEEEC-CCEEECCCEEE-EEEECC----CCCCCCC Structural block scores 1 4 * 2.7 P 1.8 75.0 4.4 5 7 C 4.0 M 6.2 75.0 6.8 9 12 E 4.0 M 5.5 75.0 5.2 14 18 C 4.4 M 7.5 33.1 7.3 19 20 - 4.0 M 75.0 3.0 75.0 21 27 E 4.7 H 3.1 3.0 3.0 28 31 C 4.8 H 2.9 4.2 2.5 32 36 E 4.8 H 1.0 3.0 0.8 38 43 - 4.0 M 75.0 4.8 75.0 45 57 E 4.8 H 0.8 1.5 1.0 59 60 C 4.0 M 4.0 4.0 4.0 61 67 E 4.9 H 2.3 1.6 2.0 70 79 E 4.6 H 3.3 3.1 3.0 80 89 C 4.7 H 4.1 18.0 4.3 90 93 H 4.0 M 4.5 42.4 6.0 94 96 C 5.0 H 5.3 6.8 6.8 97 106 E 4.6 H 2.9 9.4 2.8 108 110 H 4.0 M 7.5 75.0 8.2 111 120 - 4.0 M 75.0 4.8 75.0 121 125 C 5.0 H 6.9 5.3 6.5 126 138 E 4.8 H 1.9 2.0 1.9 141 143 - 4.0 M 75.0 4.0 75.0 144 145 C 4.0 M 5.0 5.5 39.0 146 151 E 4.8 H 1.2 1.5 1.5 152 156 C 4.0 M 5.0 33.3 3.4 157 165 E 4.9 H 0.6 1.7 1.0 166 170 C 4.2 M 6.1 32.0 4.3 171 172 - 4.0 M 75.0 75.0 10.5 173 176 C 4.0 M 5.9 75.0 4.2 177 180 * 2.7 P 7.0 75.0 4.0 181 183 - 4.0 M 75.0 75.0 6.7 184 185 C 4.0 M 40.0 8.8 2.5 186 191 E 4.8 H 2.5 2.7 1.3 192 196 C 4.6 H 5.2 17.2 4.7 197 201 E 4.6 H 4.0 4.4 4.0 203 205 H 4.0 M 6.8 29.7 5.3 207 213 E 4.6 H 1.6 1.9 1.9 214 216 H 4.0 M 4.0 5.8 4.0 217 222 C 5.0 H 3.8 3.7 3.3 223 227 E 5.0 H 0.4 0.6 0.8 228 230 C 4.0 M 2.0 52.0 5.8 231 235 - 4.0 M 6.6 75.0 75.0 237 242 E 4.5 M 1.3 2.7 2.2 243 248 C 4.2 M 4.3 3.2 4.5 249 253 - 4.0 M 75.0 3.0 75.0 254 257 C 4.8 H 2.5 0.0 2.5 258 259 E 4.5 M 1.5 0.0 1.5 262 267 C 4.3 M 6.2 5.8 5.8 270 273 H 4.0 M 2.5 21.8 3.0 274 276 E 4.7 H 2.0 2.0 2.3 277 282 C 4.3 M 4.7 4.9 5.6 283 284 - 4.0 M 75.0 4.0 75.0 285 287 C 4.0 M 4.0 2.0 4.7 288 290 E 4.7 H 3.0 3.0 2.0 291 294 C 4.8 H 4.0 2.5 5.1 295 301 H 5.0 H 5.2 3.3 5.5 302 303 C 5.0 H 4.0 6.8 4.0 304 311 - 4.0 M 75.0 3.2 75.0 312 314 C 4.0 M 6.8 5.2 6.5 315 318 E 4.8 H 2.2 2.2 3.8 321 322 C 4.0 M 5.0 40.0 5.8 323 325 E 4.3 M 0.3 1.0 1.3 326 328 C 4.7 H 4.3 1.7 5.0 329 331 E 4.0 M 2.3 3.7 3.0 333 336 E 5.0 H 0.5 0.8 1.8 337 338 C 4.0 M 2.5 2.0 2.0 339 342 - 4.0 M 75.0 4.4 75.0 343 349 C 4.9 H 6.1 5.2 6.1 >>>>>>