Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3hhya- ------------------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC------------CCHHHHHHHHC-HHHHHHHHHHCC------CCCCCCCCCCCCCCCC-CEECCEEECCCCCCHHHC----CEEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCCCCCC--CC-----CCCCEEEEECCC-CCEEEEEEECCCCEECCCCCHHHHHHHHCCCCCEECCCEEEEEECCC-EECEEEEEEECCC-CCCCCCCCCCCC------HHHEECCEEC----CCC-----CEEEECCEECEEC----------------- >P1;d4whsa- ------------------------------------------------------------------------CCCCCCCCCCC----CCCC----CHHHHHCHHHHCCCCC------------CCCCCC--CCCCC-------------CCCCCEEEEEEEEECCCCCCCCCCEEEEECCCCCCCCCC-------CCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCC------C-------CCCCCCCEEEEEECCCCCCCEEEEEEEHHHHHHHHCCCCHHHCCCHHHHHHHEEEEEEEC----------CEEEEECCEECCC---------CCCCCCCCC >P1;d4whsb- ------------------------------------------------------------------------CCCCCEEECCCCCCCCCCC----CCCCCHHHCC-CCCCCCCC-CCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC--CCCCEEEEECCC-CCEEEEEEECCCCEEEC----CCC-------CEEECCEEEEEECCCCCCCCEEEEEEECCC-CCHHHCCCHHHCCCHHHHHCCEEEE--CHHHC----CCCCCEEEECCEEECCEEECCCCCC--------- >P1;d5umha- CCCCCCHHHHHHHHHHCCCCCCCCC------HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC------------CCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEECC-CEEECEEECCCCC-CCCC----CEEEEEEEEEECCC-CCCCCEEEEECCCCCCCCCCCCCCCCCC-----CCCCEEEEECCC-CCEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEEECCC-CCCEEEEEECCCC-CCCCCCCCCCCC------HHHCCCEEEECCHHHHCCCCCCEEEEECCEEECCCCC--CCCCCCCCCCEEC PSA >P1;d3hhya- ------------------------ba8c369a77775599678667764886a3686656966614540586------------a1461152026-236717762870------80140004021127a0-462727160411970692----7300032100228781158040100000563500340a5--06-----620000003039-605040200203104043a3100740986b5623001000010306a-14402000006c5-821a60106012------7602051776----c59-----4241725030065----------------- >P1;d4whsa- ------------------------------------------------------------------------a989a8a9849----4233----8007940184194936------------b72331--60059-------------808452010102024098711510002040022906249-------a36394300030200065a7030402001035263b------8-------755100003020206a197322010004328b418901205819769437202084564a----------8410030104279---------b840012a9 >P1;d4whsb- ------------------------------------------------------------------------b682701048276843365----425a356159-8055aa69-a69165730125833a4b29952510042356a750937301000302054873045000404000380223688282918317--101080311068-60406020020141228----039-------9240000010101030610425220004b2-8206701204118478007521074--16b31----68930501305030103492694b7--------- >P1;d5umha- a66196891356048406393bb68------9772743277315635531479357a637795817720983------------90750130032612660662167178694aa1120000021104a0-545834150143b-1a70----700003020202a9-525204010000206030023067aa06-----610000005059-806020200106113047910015307a59240500000000032c8-10312000014a2-831670005002------7601181684790893a0567805105050301428a--817155a292465 Translating the sequences ------------------------************************************************------------CC*********-HHHHHHHHHHCC------*CCCCC***CCCCCCC-C**CC***CCCCC****C----CEEEEEEEEE*CCCCCCCCCEEEEECCCCCCCCCCCCCC--CC-----CCCCEEEEECCC-CCEEEEEEECCCC**CC**************CC**CC*EEEEEECCC-**CEEEEEEECCC-CC**CCCC***C------HHHEE**EE*----***-----*EEEECCEE****----------------- ------------------------------------------------------------------------***********----****----*HHHHH*HHHHCC**C------------CCCCCC--C**CC-------------****CEEEEEEEEE*CCCCCCCCCEEEEECCCCCCCCCC-------C*****CCCCEEEEECCC*CCEEEEEEECCCC**CC------*-------CC**CC*EEEEEECCC*CCCEEEEEEE********CCCC***C******HHHEE*EEE**----------C*EEEECCEE*CC---------********* ------------------------------------------------------------------------************CC*****----*****HHH**-CC**C***-CCCCC****CCCCCC*C**CC***CCCCC****C****CEEEEEEEEE*CCCCCCCCCEEEEECCCCCCCCCCCCCC**CC***--CCCCEEEEECCC-CCEEEEEEECCCC***C----***-------C***CC*EEEEE*CCC*CCCEEEEEEECCC-CC***CCC***C******H**EE*E--*****----***C*EEEECCEE*CC*********--------- *************************------*****************************************------------CC**********HHHHHHHHHH****C****CCCCC***CCC**CC-C***C***CCCCC-***C----CEEEEEEEEE*CCC-CCCCCEEEEECCCCCCCCCCCCCC**CC-----CCCCEEEEECCC-CCEEEEEEECCCC**CC**************CC**CC*EEEEEECCC-CCCEEEEEE*CCC-CC**CCCC***C------HHH***EEE************C*EEEECCEE*CC***--************* 49482.tem _________________________________ ------------------------*------****************************************************-CC**********HHHHHHHHHHCC**C****CCCCC***CCCCCCC-C**CC***CCCCC****C****CEEEEEEEEE*CCCCCCCCCEEEEECCCCCCCCCCCCCC**CC***--CCCCEEEEECCC-CCEEEEEEECCCC**CC**************CC**CC*EEEEEECCC*CCCEEEEEEECCC-CC**CCCC***C******HHHEE*EEE********-***C*EEEECCEE*CC***--************* Structural block scores 0 23 - 4.3 M 75.0 75.0 75.0 5.7 25 30 - 4.3 M 8.2 75.0 75.0 75.0 31 82 * 3.5 M 20.8 61.0 60.1 20.0 84 85 C 4.3 M 5.8 75.0 7.0 4.5 86 95 * 2.3 P 10.2 39.5 32.5 2.7 96 105 H 4.4 M 4.9 3.4 12.2 3.6 106 107 C 4.3 M 3.5 6.5 4.0 4.0 108 109 * 2.3 P 75.0 6.0 5.0 7.5 111 114 * 3.5 M 58.2 75.0 25.1 8.5 115 119 C 4.3 M 1.0 75.0 6.5 0.8 120 122 * 2.3 P 1.3 75.0 5.0 0.0 123 129 C 4.6 H 3.4 14.6 3.1 2.6 132 133 * 1.0 P 4.0 0.0 6.8 4.5 134 135 C 4.7 H 4.5 7.0 9.0 5.5 136 138 * 2.3 P 4.7 75.0 4.0 3.3 139 143 C 4.3 M 3.0 75.0 1.4 3.9 144 147 * 2.6 P 5.5 75.0 6.1 23.4 149 152 * 3.5 M 75.0 5.0 4.2 75.0 154 162 E 5.0 H 1.0 0.9 1.0 0.8 164 172 C 4.9 H 4.4 3.6 4.0 12.3 173 177 E 5.0 H 1.0 1.2 1.6 1.0 178 191 C 4.8 H 3.0 23.9 3.6 2.1 192 193 * 3.5 M 75.0 75.0 5.5 10.5 194 195 C 4.7 H 3.0 42.8 4.5 3.0 196 198 * 3.5 M 75.0 4.0 3.7 75.0 199 200 - 4.3 M 75.0 6.5 75.0 75.0 201 204 C 5.0 H 2.0 0.8 0.5 1.8 205 209 E 5.0 H 0.6 1.0 2.6 1.0 210 212 C 5.0 H 4.0 3.7 4.7 4.7 214 215 C 5.0 H 3.0 3.5 3.0 4.0 216 222 E 5.0 H 1.6 1.3 1.7 1.4 223 226 C 5.0 H 1.5 2.2 1.8 2.0 227 228 * 1.0 P 2.0 4.0 1.5 2.0 229 230 C 4.7 H 2.0 7.2 5.0 2.0 231 244 * 3.1 M 4.9 70.2 59.8 4.2 245 246 C 4.7 H 4.0 6.0 5.5 2.0 247 248 * 1.0 P 1.5 3.0 2.0 2.5 249 250 C 5.0 H 0.5 0.0 0.0 0.0 252 257 E 4.9 H 0.7 1.2 0.5 0.5 258 260 C 5.0 H 5.5 5.5 1.0 7.5 262 264 C 4.5 M 3.0 6.3 1.7 1.3 265 271 E 4.9 H 0.3 0.7 1.6 0.6 272 274 C 4.3 M 7.8 3.0 5.8 5.5 276 277 C 4.3 M 5.0 7.8 5.0 5.5 278 279 * 1.0 P 5.8 4.5 3.0 3.5 280 283 C 4.8 H 1.8 3.0 2.5 1.8 284 286 * 1.0 P 2.3 4.3 1.7 1.7 288 293 * 3.5 M 75.0 6.3 4.5 75.0 294 296 H 4.5 M 4.3 3.0 4.7 4.3 297 298 E 4.3 M 1.0 1.0 0.5 1.0 300 302 E 4.3 M 5.0 5.0 51.3 5.0 303 310 * 3.0 P 41.6 58.1 30.9 6.3 312 314 * 3.5 M 75.0 75.0 7.7 6.0 317 320 E 5.0 H 3.5 1.0 2.2 2.8 321 322 C 5.0 H 3.5 0.5 2.5 2.5 323 324 E 5.0 H 1.5 2.0 1.5 1.5 326 327 C 4.3 M 3.0 8.0 0.5 2.5 328 330 * 3.1 M 51.7 75.0 5.3 6.8 331 332 - 4.3 M 75.0 75.0 4.0 75.0 333 345 * 3.5 M 75.0 26.6 54.3 5.0 >>>>>>