Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1jr1b1 -----CCCCCCCCCHHHHHCC-------CCCCCHHHEEECCCCC--CCCHHHCCCCEECCC-------CCEECCCEEECCCCCCCCHHHHHHHHHHCCEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHC--CCEEEECCCCCCCHHHHHHHHHHHHHCC-CCEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCC-CHHHHCCCCCCHHHHHHHHHHHHHHH------CCCEEEECCCCCHHHHHHHHHHCCCEEEECHHHHCCCCCCCCEEECCCCEEEEEECCCCCCCCC------------CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCEEECCHHHHHHHCCCCCCCCCCCCC >P1;d1mwfa1 CCCCC-----------------------CCCCCHHHEEECCCCCCCCCCHHHCCCCEECCCEECCCCCCCEECCCEEECCCCCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCC------------CCCCEEEECC-CCHHHHHHHHHHHC--CCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCEECCEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCCCCCCEEEECCEEEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHH-----HCCEEECCHHHHHHHCCCCCCCC----- >P1;d2c6qa1 -------------------------------CCHHHEEECCCCCCCC-CHHHCCCCEEEE--CCCCCCEEEE-CCEEECCCCCCCCHHHHHHHHHCCCEEECCCCCC----HHHHHHHHH--------HCHHHCCCEEEEECCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHCC-CCEEEEEEECCHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHC------CCEEEEECCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCCEEEECCEEEEEEECCCCHHHHHHHCCCCCC---CCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHH-----HCCEEEC--------------------- >P1;d6d4ra- ----------------CCCCCCCCCCCCCCCCCHHHEEECCCCC--CCCHHHCCCCEECCC-------CCEECCCEEECCCCCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCCC-----------CCCCEEEECCCCCHHHHHHHHHHHC--CCEEEEECCCCCC--CHHHHHHHHHHHC-CCEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHH------CCCEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCCCCCCEECCC--CEEEEECCCCCCCCC-------------CCCCCEEEEEC-CCHHHHHHHHHHHHHHHHHHHCCCCHHHHCC------CCEEECCCCCC---------------- PSA >P1;d1jr1b1 -----b996981320750044-------c560306405026694--507186060404004-------61505000000010100218001000100000000252727401500540162895840142a883000000022888026104201818--0200002465024680270053028426-91000000004481054016070000000011551-31483486024000000300230464------a010001340571800110000001000001000006201391465bb541050202406703b------------662306392272252036104201540163016000430840271017270206419994388693595a8497865 >P1;d1mwfa1 8795b-----------------------87425064060654945b606495070401002257b79071308100000012000148001100421000001112729502720650065------------7340000000-33057003303916--03000011140437505500710185288810000000222700330060300000001024511303833840110020054016106603853431000001330562400000000000000003000104203073353aa65200010000730701221172a966185400454405224607720760077025300700024064018-----405144089a45889a65a6a7a----- >P1;d2c6qa1 -------------------------------2408206156392908-578504042807--0310737060-0000001200000170051027240000004217----395058019--------725a10810000011aa8226602610630660500003298035870061047017405-720000010022710450050100000001015702213843970340030034008104a2------9010001330852810010000200000012100004105184355aa7410100125054016524c324a---856220534217335503720580066033101700055062046-----4051574--------------------- >P1;d6d4ra- ----------------2978ba67887758124073051566b2--b18498060203004-------6130910000001110031600120062200000034173a5015106302729-----------b130000013bb7037101304708--0200002297048--02a1066025400-b1000001007580052019160000000101441121483476023001005202310656------a0000014305738000100001010000011001031027a4474b--530502025066036-------------83406465172-5508730880165035200800053055018------1915519aa86---------------- Translating the sequences -----****************-------CCCCCHHHEEECCCCC--CCCHHHCCCCEECCC-------CCEECCCEEECCCCCCCCHHHHHHHHH*CCEEEECCCCCHHHHHHHHHHHHCC************CCCCEEEECCCC*HHHHHHHHHHHC--CCEEEE*CCCCCCHHHHHHHHHHHHH*C-CCEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCC-CHHHHCCCCCCHHHHHHHHHHHHHHH------CCCEEEECCCCCHHHHHHHHH*CCCEEEECHHHHCCCCCCCCEEE*CC*EEEEEECCCCCCCCC------------CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHH******CCEEECC******************** *****-----------------------CCCCCHHHEEECCCCC**CCCHHHCCCCEECCC*******CCEECCCEEECCCCCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCC------------CCCCEEEECC-C*HHHHHHHHHHHC--CCEEEE*CCCCCCHHHHHHHHHHHHH****C*EEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHH*******CCEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCCCCCCEEE*CC*EEEEEECCCCCCCCC************CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHH*CCCCHHHHHH-----*CCEEECC***************----- -------------------------------CCHHHEEECCCCC**C-CHHHCCCCEE**--********EE-CCEEECCCCCCCCHHHHHHHHHCCCEEE*CCCCC----HHHHHHHH*--------*****CCC*EEEECCC**HHHHHHHHHHHC**CCEEEE*CCCCCCHHHHHHHHHHHHH*C-CCEEEEEEECCHHHHHHHHH*CCCEEEECCCCCCCCCHHHH*CCCCCHHHHHHHHHHHHHH*------CC*EEEECCCCCHHHHHHHHHCCCCEEEEC****CCCCCCCCEEE*CC*EEEEEECCCC*************---*CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHH-----*CCEEEC--------------------- ----------------************CCCCCHHHEEECCCCC--CCCHHHCCCCEECCC-------CCEECCCEEECCCCCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCC*-----------CCCCEEEECCCC*HHHHHHHHHHHC--CCEEEE*CCCCCC--*HHHHHHHHHH*C-CCEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHH------CCCEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCCCCCCEE**C--*EEEEECCCCCCCCC-------------CCCCCEEEEEC-CCHHHHHHHHHHHHHHHHHHHCCCCHHHH**------CCEEECC****---------------- 51412.tem _________________________________ ----------------*****-------CCCCCHHHEEECCCCC**CCCHHHCCCCEECCC-******CCEECCCEEECCCCCCCCHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCC*------*****CCCCEEEECCCC*HHHHHHHHHHHC--CCEEEE*CCCCCCHHHHHHHHHHHHH*C-CCEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHH------CCCEEEECCCCCHHHHHHHHHCCCCEEEECHHHHCCCCCCCCEEE*CC*EEEEEECCCCCCCCC********---*CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHH-----*CCEEECC***************----- Structural block scores 0 15 - 4.3 M 27.5 54.1 75.0 75.0 16 20 * 3.5 M 2.6 75.0 75.0 7.5 21 27 - 4.3 M 75.0 75.0 75.0 7.6 28 32 C 4.6 H 5.3 5.2 46.2 4.0 33 35 H 5.0 H 3.3 3.3 3.3 3.3 36 38 E 5.0 H 1.7 2.0 2.3 2.0 39 43 C 5.0 H 5.4 5.6 5.0 6.1 44 45 * 3.5 M 75.0 8.2 4.5 75.0 46 48 C 4.8 H 4.0 4.0 29.3 6.8 49 51 H 5.0 H 5.0 6.0 6.7 7.0 52 55 C 5.0 H 2.5 2.8 2.0 2.0 56 57 E 5.0 H 2.0 0.5 5.0 1.5 58 60 C 4.3 M 1.3 0.7 27.3 1.3 62 67 * 3.5 M 75.0 6.6 2.3 75.0 68 69 C 4.3 M 3.5 4.0 3.5 3.5 70 71 E 5.0 H 2.5 1.5 3.0 1.5 72 74 C 4.8 H 1.7 3.0 25.0 3.3 75 77 E 5.0 H 0.0 0.0 0.0 0.0 78 85 C 5.0 H 0.5 0.5 0.4 0.8 86 94 H 5.0 H 1.2 2.0 2.6 1.8 95 97 C 4.8 H 0.0 1.0 2.0 1.3 98 101 E 4.8 H 0.0 0.0 0.0 0.0 102 106 C 5.0 H 3.2 2.4 2.8 3.0 107 118 H 4.8 H 2.4 3.2 27.6 3.0 119 120 C 4.3 M 4.0 5.5 42.0 4.5 122 127 - 4.3 M 4.5 75.0 75.0 75.0 128 132 * 3.5 M 6.5 75.0 5.1 75.0 133 136 C 4.8 H 0.8 3.5 2.2 3.9 137 140 E 5.0 H 0.0 0.0 0.0 0.0 141 144 C 4.7 H 5.0 19.5 5.8 6.8 146 156 H 5.0 H 2.3 2.8 3.1 2.4 158 159 - 4.3 M 75.0 75.0 6.0 75.0 160 161 C 5.0 H 1.0 1.5 2.5 1.0 162 165 E 5.0 H 0.0 0.0 0.0 0.0 167 172 C 5.0 H 3.5 2.2 4.5 5.0 173 185 H 4.8 H 3.5 3.4 3.5 14.3 189 190 C 4.7 H 5.0 4.5 4.5 6.2 191 197 E 4.9 H 0.0 0.0 0.1 0.1 198 199 C 5.0 H 2.0 2.0 1.0 3.5 200 209 H 4.9 H 2.9 2.1 2.4 3.1 210 212 C 5.0 H 2.3 1.0 0.3 2.0 213 216 E 5.0 H 0.0 0.0 0.0 0.0 217 225 C 4.9 H 10.1 1.9 2.0 1.6 226 229 H 5.0 H 4.0 3.5 4.0 4.0 230 235 C 4.9 H 4.0 2.8 4.3 3.7 236 250 H 5.0 H 1.5 2.1 2.4 2.1 251 256 - 4.3 M 75.0 4.3 75.0 75.0 257 259 C 4.5 M 3.8 0.3 3.3 3.5 260 263 E 5.0 H 0.2 0.2 0.2 0.2 264 268 C 5.0 H 3.8 3.4 3.8 3.8 269 277 H 5.0 H 1.2 0.7 1.3 1.3 278 281 C 4.8 H 0.2 0.0 0.5 0.5 282 285 E 5.0 H 0.0 0.0 0.0 0.0 287 290 H 4.3 M 0.2 0.8 0.8 0.5 291 298 C 5.0 H 2.6 2.1 2.4 3.1 299 301 E 4.8 H 3.7 3.7 4.0 5.0 303 304 C 4.7 H 11.5 10.5 10.5 43.2 306 311 E 4.9 H 2.0 1.3 1.0 2.5 312 320 C 4.6 H 3.7 1.9 2.7 3.1 321 328 * 3.5 M 75.0 3.3 5.4 75.0 329 331 - 4.3 M 75.0 7.0 75.0 75.0 333 338 C 4.9 H 3.8 3.5 3.3 16.0 339 343 E 5.0 H 4.6 3.6 3.4 4.6 344 347 C 4.8 H 2.8 3.5 4.0 21.8 348 366 H 5.0 H 2.3 3.2 2.7 3.4 367 370 C 5.0 H 1.8 1.5 2.5 2.0 371 376 H 4.8 H 3.5 3.2 3.0 3.2 377 381 - 4.3 M 2.2 75.0 75.0 75.0 383 384 C 5.0 H 1.0 2.5 2.5 5.0 385 387 E 5.0 H 3.3 3.0 4.3 3.7 388 389 C 4.7 H 5.0 4.0 39.5 5.0 390 404 * 3.2 M 6.7 8.0 75.0 57.3 405 409 - 4.3 M 7.0 75.0 75.0 75.0 >>>>>>