Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d4ogca4 -----CCCCCC-------CCCCCEEEEHHH-CCCHHHHHCCCC---HHHHHHHHHCCCCCC--CCCCCCCCCCEEEECCEEEECCCEEEECCCCCCCCCCCCCCCCCEEEC-------CCEEECCCCEEEEEEEEECC--CCEEEEEEEHHHHHHHC---CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEEECCCCEEECCCCCCC--------------------------------------CHHHHHHHHCCCCCEEEEEECCC--CC-EEEEEECCCC-HHHCCCCHHHHHHHCC--------CCEEEEHH---HHHHCCCEEECCCCCCCCCCCCCCCCCEECC--- >P1;d4oo8a4 ----------------------------------------------------------------------------------------CCCCCCCCCCCCC-----CCEECCCCCC---CCEECCCCEEEEEEEEECCCCCEEEEEEEECCCHHHHC-----------CHHHHCCCCCC----------CCCCCEEECCCCEEECHHHCEEEECCCCCEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH--CCCCCC--HHHHH------HHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHCEEEEECCCCC------CEEEEEHHHHC >P1;d5axwa4 CCCCCCEEEEEECCCCEEEEEEECCCCCCCCCCCCCHHHCHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCCCCCCCCCEEEEC---------CCCCCEECHHHCCCCCCEEECCCCEEEEEEEEEC---CEEEEEEEEHHH----EEECCEEECCCCCCCCCCCC-------------CCEEEEEECCCCEEEECC-------------------------------------------------------EEEEEEEEEECCCC-EEEEECCCCCHHHHHHHCCCC-----C--------CCEEEECC---CC--CCEEEEEECCCCCEEECCCCCEE------- PSA >P1;d4ogca4 -----b6b996-------b35811522007-004241000014---5301200162a4157--990056578040618994250645040005386954077081100224-------c0014179603000013141--a5400110054105945---9873361903630000012750250455a504304203460004070871a--------------------------------------a1006017536913404035035--33-3010302827-1991c25a00330046--------60030304---6005240200132a77732792854302406--- >P1;d4oo8a4 ----------------------------------------------------------------------------------------da606a643875c-----8033375817---500346452100000105cc78314011022535a704-----------73671084a19----------80c432605461102178503010141920000170a0591680173016a7969517938237300830281--060053--9a318------504801962b2072055022007436155104838054279060270200544a638------93744404826 >P1;d5axwa4 7615a64240374977221035086018365010c43640114573560065036216637c68001724837743---5429b1753504112---------b08923422b748c36410225122300000309---941200003221----157465306842732a105b-------------907120003762102047-------------------------------------------------------71120340344743-401022493616530766a36-----8--------35122505---80--940411225a87846538a5564------- Translating the sequences -----C*****-------************-CCC**HHHC***---HHHHHHHHH****CC--CCCCCCCCCC**********CCC***ECCCCCCCCCCC**CCCC*EEC-------CCEEECCCCEEEEEEEEECC--C*EEEEEEEHHHHHHHC---C***CCCCCCCCCCCCCCC**********C*EEEEEECCCCEEECCC*C**--------------------------------------C*HHHHHHH*****EEEEEEC**--CC-EEEEE*CCCC-HHHCCCC***HHHH*C--------CCEEEE**---***HCCCEEE**CCCCC***CCCCC**EE**--- ----------------------------------------------------------------------------------------C*CCCCCCCCCCC-----CCEEC***CC---C*EECCCCEEEEEEEEECC**CEEEEEEEE***HHHHC-----------C****CCCCCC----------CC***EEECCCCEEEC***C****************************************C*HHHHHHH****--*****C--*****------****HHHHCCCCCCCHHHH*C********CC****CC***CC*H**CEEEEECCCCC------C*EEEE***** *****C*************************CCC**HHHC******HHHHHHHHH****CC**CCCCCCCCCC***---****CCC**CE***C---------CCCCCEEC***CC**CCEEECCCCEEEEEEEEEC---CEEEEEEEEHHH----****C***CCCCCCCCCCCC-------------CCEEEEEECCCCEEE*CC-------------------------------------------------------*EEEEEE*****CC-EEEEE*CCCCHHHH***CCCC-----C--------CCEEEECC---CC--CC*EEEEECCCCC***CCCCCEE------- 345926.tem _________________________________ -----C*****-------************-CCC**HHHC***---HHHHHHHHH****CC--CCCCCCCCCC***---****CCC**CECCCCCCCCCCC--CCCCCEEC***CC--CCEEECCCCEEEEEEEEECC--CEEEEEEEEHHHHHHHC---C***CCCCCCCCCCCCCCC----------CCEEEEEECCCCEEECCC*C**--------------------------------------C*HHHHHHH*****EEEEEEC****CC-EEEEE*CCCCHHHHCCCCCCCHHHH*C--------CCEEEECC---CC*HCCCEEEEECCCCC***CCCCCEEEE**--- Structural block scores 0 4 - 4.0 M 75.0 75.0 5.9 6 10 * 2.7 P 8.3 75.0 2.6 11 17 - 4.0 M 75.0 75.0 5.4 18 29 * 2.7 P 3.8 75.0 3.4 31 33 C 4.0 M 1.3 75.0 0.3 34 35 * 2.7 P 3.0 75.0 8.2 36 38 H 4.0 M 0.3 75.0 4.3 40 42 * 2.7 P 1.7 75.0 2.0 43 45 - 4.0 M 75.0 75.0 5.0 46 54 H 4.0 M 2.0 75.0 3.4 55 58 * 2.7 P 4.4 75.0 3.8 59 60 C 4.0 M 6.0 75.0 5.0 61 62 - 4.0 M 75.0 75.0 9.2 63 72 C 4.0 M 4.9 75.0 4.0 73 75 * 2.7 P 3.3 75.0 4.7 76 78 - 4.0 M 6.0 75.0 75.0 79 82 * 2.7 P 5.0 75.0 5.0 83 85 C 4.0 M 3.3 75.0 6.5 86 87 * 2.7 P 2.5 75.0 4.0 90 100 C 4.1 M 4.3 6.2 48.5 101 102 - 4.0 M 3.5 75.0 75.0 103 107 C 4.2 M 2.0 46.6 6.1 108 109 E 5.0 H 2.0 3.0 3.5 111 113 * 2.7 P 75.0 6.7 6.8 114 115 C 4.0 M 75.0 4.0 6.0 116 117 - 4.0 M 75.0 75.0 7.8 118 119 C 4.5 M 6.2 40.0 5.0 120 122 E 4.7 H 1.7 1.0 1.0 123 126 C 5.0 H 5.8 4.8 2.5 127 135 E 5.0 H 0.9 0.4 0.9 136 137 C 4.5 M 2.5 8.8 42.0 138 139 - 4.0 M 75.0 9.8 75.0 141 148 E 4.9 H 1.4 1.5 1.2 149 155 H 4.0 M 4.0 4.6 43.6 157 159 - 4.0 M 75.0 75.0 5.3 161 163 * 2.7 P 6.0 75.0 2.7 164 178 C 4.3 M 2.3 23.8 19.0 179 188 - 4.0 M 4.3 75.0 75.0 189 190 C 4.5 M 2.5 4.0 4.5 191 196 E 4.5 M 2.2 4.6 1.7 197 200 C 5.0 H 3.2 4.0 4.5 201 203 E 5.0 H 1.3 1.0 1.0 204 206 C 4.0 M 2.3 5.3 3.7 209 210 * 2.7 P 5.8 1.5 75.0 211 248 - 4.0 M 75.0 3.9 75.0 251 257 H 4.0 M 2.7 3.4 75.0 258 262 * 2.7 P 4.4 17.2 61.4 263 268 E 4.0 M 2.7 14.3 1.8 270 273 * 2.7 P 39.5 42.4 4.5 274 275 C 4.0 M 3.0 2.0 3.5 277 281 E 4.0 M 1.4 75.0 1.4 283 286 C 4.0 M 4.8 4.2 5.5 287 290 H 4.8 H 23.5 4.0 3.8 291 297 C 4.1 M 4.4 3.5 5.5 298 301 H 4.0 M 1.5 3.0 75.0 304 311 - 4.0 M 75.0 3.9 75.0 312 313 C 5.0 H 3.0 0.5 4.0 314 317 E 4.0 M 1.5 5.8 2.5 318 319 C 4.0 M 2.0 2.5 2.5 320 322 - 4.0 M 75.0 4.3 75.0 323 324 C 4.0 M 3.0 4.5 4.0 327 329 C 4.0 M 2.0 3.0 4.3 330 334 E 4.6 H 1.2 2.2 2.0 335 339 C 5.0 H 6.7 6.3 7.7 340 342 * 2.7 P 4.0 75.0 5.0 343 347 C 4.2 M 5.6 47.4 6.3 348 351 E 4.0 M 2.2 4.8 40.0 352 353 * 2.7 P 3.0 2.0 75.0 354 356 - 4.0 M 75.0 5.3 75.0 >>>>>>