Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1u04a1 -----------------CEEEECCEEECC--HHHCCCCEEEEECC----------CHHHHHHHCCEEEEECCCCEEEECC----------------CCCCCCCCEEEEEECHHHCC--HHHHHHHHHHHHHHCCCCHHHHHHHHCCCC---CCEEEC----------------CEEEEEEEE-EEEECCC-CEEEEEEEEEEEECC-CHHHHCCCCHH-----------HHHHHCCCCCCCCEEC----CCCCCCCEEECCCCCC---CCCCEECCHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHCC--CCCCCCEEEEEECCCCCCEEECCCCEECEEEHHHCCC-----HHHHHHCC---CHHHHHHHHHHHHHCC----------CCCCCCCCCEEEECC >P1;d1yvua1 -------------------CCEECEEEEEECCCCC--EECCCEECCCCCHHHHHHHHHHHHHHHCCCEEEECCEEEECCCCCCCCCEEEECCCCCEEEEECCCEECCCCC-----C--HHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHEEECC--------------CCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEECCCHHHHHHHC-----------------CCCCCCCEEEEC----CC--CCCEEEE-----------EEEECCCCCHHHHHHC-CCC-C----CHHHHHHHHHHHHCHHHHHHCEEEEEC-----CCCEEECCCEEECCC-----C-----CHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH----CCCEEECCCCEECC--C >P1;d3mj0a1 -------------------------------------------------------------------------------------------------------------------CEEHHHHHHHHCCC----------------------------------------------------------------------CCCCC-CCCHHHCHH-----------------HHHHHHCCCEEEECCCHHHCCCCEEEECCEEEEEECCCCEEECC------------------CCEEE--HHHHHHC-CCCCCCCCCCEEEECCCCCC--CCEECHHHEEECC---------------------------------------------------------------- >P1;d4krea1 CCCCCCCCCCCCCCCCEEEEEEECEEEEECCC--CEEEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCC---CCCCEECCCCEEEECCCCCCCCEEEEEECCEEEEEEEEE---EEEEHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCEEECCEEECCCCCCCCEEECCEEEEEEEEEEEEECCCCEEEEEEEEEEEEECCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCEEEECCCC-----CCEEEEEEEEEEECCCCEEEEECC-------------CCCEEEEE--HHHHHHHHHCCCCCCCCCEEEEEC------CEEEEHHHEEECCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCHHHCHHHHHCCCEECCCCEEEEEEE PSA >P1;d1u04a1 -----------------645423410404--96031950211416----------5176005611010234864100006----------------a092b592653a62618606--761015005010345702773015202632---72552c----------------434020106-7062678-301010402030206-10051085438-----------4046108437400101----0038434060105896---8603146769205730631166235----68a34670465079--024900002043196a741200000000117055389-----71781070---a96337104300840b----------28005a803645478 >P1;d1yvua1 -------------------b825420303070783--1000051459669a3173002000350530001193400003629a283170304965623056756709706-----4--4300200040005627-0277036303763587011749--------------94511020206050542874510030206133004120051045a-----------------a5b368250206----80--9110407-----------61260573a6930752-721-1----373066005501757a20550200304-----674200021020129-----a-----8387624828798643720350081028206----65106016702548--b >P1;d3mj0a1 -------------------------------------------------------------------------------------------------------------------3150141015401a----------------------------------------------------------------------88079-82504822a-----------------5024305616020500a409494552505000532056133538------------------84612--0262077-39250624200002007a96--5300001002287---------------------------------------------------------------- >P1;d4krea1 ba8a9998789968a48659544230305024--44021030305659256611150033016545106---b2500010552000175050b656160517506020444---440305503500246849309601500300010210263331c7100561ac36330930010023120004345740101031401000141402600330084aa77607893165027306712010315c-----57416046018620361313375b-------------77844611--027305a5293907432000030b------5510001002006314084817aa04742781173797735630553078351571410520807057702855447 Translating the sequences -----------------****E*CEEE**--***C***E***E**----------*HHHHHHH*C*******C***E*CC----------------****CC**E**********C--HHHHHHHHHH****CC**HHHHHHHH****---**EE*C----------------*EEEEEEEE-EEEECCC-*EEEEEEEEEEEE*C-CHHHH******-----------**HHH***CCC**EEC----*C**CC*EEE******---CC**EE*C****************C----***HHHHHHHHHCC--CCCCC*EEEE*******C*EE****EE*********C-----*HHHH***---*HHHHHHHHHHHHH**----------C***CCCC*E***** -------------------**E*CEEE*******C--*E***E*************HHHHHHH*C*******C***E*CC********************CC**E*****-----C--HHHHHHHHHH****CC-*HHHHHHHH*********EE*C--------------***EEEEEEEE*EEEECCC**EEEEEEEEEEEE*CCCHHHHHH**-----------------****CCCEEEEC----*C--CC*EEE*-----------EEE*C***********-***-C----***HHHHHHHHH*C******CEEEEEC-----*C*EE****EEECC*-----C-----*HHHH*******HHHHHHHHHHHHH******----**C***CCCC*E**--* -------------------------------------------------------------------------------------------------------------------C**HHHHHHHH***----------------------------------------------------------------------*****-CCCHHH*HH-----------------HHH***CCCEEEEC*****C**C**EE**********CC*EE**------------------*****--HHHHHH*-*CC**CCCCCEEEE*C****--C*EE****EEECC---------------------------------------------------------------- *********************E*CEEE*****--C***E***E*************HHHHHHH*C****---C***E*CC********************CC**E******---****HHHHHHHHHH****CC**HHHHHHHH*********EE*C*****************EEEEEEEE*EEEECCC**EEEEEEEEEEEE*CCCHHHHHH*****************HHH***CCCEEEEC***-----CC*EEE*********CC*EEE*C*-------------**C*****--HHHHHHHHHCC**CCCCCEEEEEC------C*EE****EEECC******C******HHHH*******HHHHHHHHHHHHH************C***CCCC*E***** 101690.tem _________________________________ -----------------****E*CEEE*******C***E***E*************HHHHHHH*C*******C***E*CC********************CC**E******---*C**HHHHHHHHHH****CC**HHHHHHHH*********EE*C--------------***EEEEEEEE*EEEECCC**EEEEEEEEEEEE*CCCHHHHHH****-----------**HHH***CCCEEEEC***-*C**CC*EEE*********CC*EEE*C***********-****C*******HHHHHHHHHCC**CCCCCEEEEEC****-*C*EE****EEECC******C-----*HHHH*******HHHHHHHHHHHHH******----**C***CCCC*E***** Structural block scores 0 16 - 4.3 M 75.0 75.0 75.0 8.5 17 20 * 2.9 P 4.8 42.4 75.0 6.2 24 26 E 4.3 M 1.7 1.7 75.0 2.0 27 33 * 3.0 P 24.1 3.6 75.0 23.0 35 37 * 3.1 M 5.0 50.3 75.0 2.0 39 41 * 2.3 P 1.3 0.0 75.0 1.0 43 55 * 3.2 M 58.6 5.0 75.0 4.0 56 62 H 4.3 M 3.6 1.4 75.0 1.9 65 71 * 2.8 P 2.6 2.0 75.0 33.9 73 75 * 2.3 P 1.7 1.3 75.0 2.3 78 79 C 4.3 M 3.0 4.5 75.0 0.5 80 99 * 3.3 M 61.1 4.3 75.0 3.5 100 101 C 4.3 M 8.2 6.5 75.0 4.0 102 103 * 2.3 P 5.5 5.5 75.0 2.5 105 110 * 2.5 P 5.4 16.2 75.0 2.3 111 113 - 4.3 M 5.0 75.0 75.0 75.0 116 117 * 3.5 M 75.0 75.0 3.0 1.5 118 127 H 4.9 H 2.5 1.3 1.7 2.4 128 131 * 2.0 P 2.0 2.8 58.9 6.8 132 133 C 4.3 M 6.0 4.5 75.0 1.5 134 135 * 2.9 P 1.0 37.5 75.0 7.5 136 143 H 4.3 M 3.1 3.5 75.0 1.1 144 152 * 2.7 P 27.4 4.4 75.0 1.7 153 154 E 4.3 M 5.0 4.0 75.0 3.0 157 170 - 4.3 M 75.0 75.0 75.0 4.1 171 173 * 3.1 M 51.3 6.0 75.0 4.0 174 181 E 4.3 M 2.0 1.5 75.0 1.1 183 186 E 4.3 M 3.8 3.5 75.0 1.8 187 189 C 4.3 M 7.0 5.7 75.0 5.3 190 191 * 2.9 P 39.0 4.5 75.0 2.0 192 203 E 4.3 M 1.1 1.6 46.4 0.9 205 207 C 4.8 H 27.3 2.3 5.0 3.0 208 213 H 4.7 H 2.3 1.7 4.4 1.8 214 217 * 2.9 P 5.0 41.4 75.0 2.8 218 228 - 4.3 M 75.0 75.0 75.0 6.5 229 230 * 3.5 M 2.0 75.0 75.0 3.5 231 233 H 4.3 M 3.7 53.5 2.3 2.3 234 236 * 1.0 P 4.0 6.5 2.3 3.3 237 239 C 5.0 H 4.7 5.3 4.0 4.7 240 243 E 4.7 H 0.2 1.8 2.0 0.8 245 247 * 3.5 M 75.0 75.0 3.5 6.2 251 252 * 3.5 M 5.5 75.0 6.5 75.0 253 254 C 4.7 H 3.5 5.0 4.5 6.0 256 258 E 4.8 H 2.0 1.3 2.3 2.3 259 267 * 2.6 P 28.2 67.4 2.2 3.3 268 269 C 4.3 M 7.0 75.0 3.5 3.5 271 273 E 4.5 M 2.7 3.0 3.7 2.3 276 286 * 3.4 M 3.8 5.2 75.0 69.2 288 291 * 3.2 M 4.2 21.2 75.0 41.0 293 299 * 3.1 M 46.4 44.7 24.4 23.7 300 308 H 4.8 H 3.9 2.6 11.3 3.8 309 310 C 4.7 H 8.0 6.0 5.5 6.0 311 312 * 2.3 P 75.0 8.8 2.5 4.5 313 317 C 4.4 M 3.0 2.4 2.8 3.2 318 322 E 4.7 H 0.4 1.0 0.4 0.6 324 327 * 3.5 M 4.8 75.0 8.1 75.0 332 333 E 5.0 H 1.0 1.0 0.0 0.5 334 337 * 1.0 P 0.0 0.8 0.2 0.2 338 340 E 4.8 H 0.0 0.7 1.3 0.7 341 342 C 4.3 M 1.0 1.5 7.5 3.0 343 348 * 3.3 M 4.7 64.0 75.0 3.3 350 354 - 4.3 M 75.0 75.0 75.0 5.8 356 359 H 4.3 M 4.2 6.0 75.0 5.0 360 366 * 2.8 P 34.6 5.7 75.0 5.1 367 379 H 4.3 M 3.7 3.6 75.0 4.5 380 385 * 3.1 M 51.9 3.0 75.0 3.7 386 389 - 4.3 M 75.0 75.0 75.0 2.5 390 391 * 3.5 M 75.0 5.5 75.0 1.0 393 395 * 2.3 P 2.7 2.0 75.0 2.3 396 399 C 4.3 M 5.9 3.5 75.0 4.8 402 406 * 2.8 P 5.6 34.7 75.0 5.0 >>>>>>