Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f0la2 ------------------------------------------------------------------------------------CHHHHCCHH-------HCEEEECCEEEEEECCCCCCHHHHCCCCCCCCCCCCCHHHCCEEEECCHHHHHCCCCCCCCC----------CCCCCEEEEEECC-C-----EEEEEECCCCCHHHHHHHCCCCCCCCHHHHHCCHHHHHHHCCCCCEEEEEEECCCCCCCEEEEECCCHHHHCEEEE-EEEHHHHCCCCCHHHHHHHHHHHC--------- >P1;d1s21a- --------------------------------------------------------------------CCCCCCCCCCCCHHHCCHHHHHHHHHHHCHHHHCCCCCCCEEEEECCHHHHC---CCEEECCCCCCCEE---EEEEEEEECCCCCC-----------CCCCCCCHHH---EEEEEEEHHHHCCCEEEEEEC-------CCCCCCCEEEEEHHHHHCC----------CCCEEECCC---CCCCEEEEEECC--CCCEEECEECC------------------------------ >P1;d1wfxa- ----CCHHHHHHHHHHCCCHHHCCCCCCCCCEEHHHHHHHHHHCC-CCCCCHHHHHHHHHHCCCCCEEEEC--CEEEECCCCCC--CCCCC---------CCCCCCCCEEEECCCHHHCCCC-CCCCC-C--------CCCCEEEECCHHHHHHHHCCCC---C-------------CCEEEEEEHHHHHHCCCCCCCC-C------------------------------------CEEEECCCCHHHEEEEEECCC-------------------------------------------- >P1;d2o0qa1 -----------------------------------------------------------------------------------------------------------CEEEEEEEHHHHHHHHHHCEECCCHHHH---HHCCEECEE-HHHHHHHHHHHCCCCC-------------CEEEEEEECCCC--CCEEEEECHHH---------------------------------CEEEEECCCEEHHHEEEEEECCCCC-------------------------------CCCCCCHHHHC >P1;d3ki2a1 ------------------------------------------------------------------CEEEC--CEEECCCHHHHHHHHHHHHH-------CCEE---EEEEEEECHHHHHHHHHCCCCCC-------CCCCCEEECCCHHHHHCCCCCCCCCCHHHCCCHHHHHCCCEEEEEEEE-HHHHHHEEECCCCHHHCHHHHHHHHCCC---CCCC----------------CCEEEEECCCCC-CEEEEECHHHHCCCEEEEEEEECCCC--CCCCCCHHHHHHHHHHCCCCCCCC >P1;d6e3aa- CCCHHHHHHHHHHHHHCCHHHHCCCCCCCCCEEHHHHHHHHCCCHHHCCCCHHHHHHHHHHCCCCCEEEEC--CEEEECCCCCCCCCCCCC---------CC--CCCCCEEEEECHHHHHHHHHHCCCCC--------CCCCEEEECCHHHHHHHHHCCC---C-------------CCEEEEECHHHHHHCCCCEEECCC------------------------------------CEEEECCCCHHHEECC------------------------------------------------- PSA >P1;d1f0la2 ------------------------------------------------------------------------------------94a601299-------6041676020120041b709712850746bb7244a5711200200443230056013a67a----------9250000030205-8-----500000044770640063090549520071006a80194108b06000001625bc2b032000118204507073-202058595981610670275499--------- >P1;d1s21a- --------------------------------------------------------------------76715b5082530650888125501662102433a07472301271766707---97417055a38260---11154053066047-----------5305263070---03134350862a210060205-------a405931203030020272----------a07012246---ba6013000003--7c450508228------------------------------ >P1;d1wfxa- ----b71472013001031972a0906a40005064005104739-196056720452068082820425c--91000010013--80707---------3396813830220011741761-87005-c--------7334010123692055506569---9-------------6001020305104748180320-8------------------------------------300107400170054274547-------------------------------------------- >P1;d2o0qa1 -----------------------------------------------------------------------------------------------------------720000033940570487840502a706---759104000-3910572044626757-------------90000004070a--a40534552d9---------------------------------560000324053920464370924a-------------------------------841060aa418 >P1;d3ki2a1 ------------------------------------------------------------------06035--61159172a50473145157-------7123---0000201318405712780257a-------a41400400050520078012770758977157915403000000003-7a1183021094207804a502930928---0506----------------5100001468c3-51200003600460301001050002--965a05891376089008607054 >P1;d6e3aa- b153860182025001200671a0a067501040870171038486056064810520276294620306b--640100100208940607---------74--40482022000565286156700429--------c310020035472035404541---9-------------70220203045055591400301b------------------------------------621002404360051a------------------------------------------------- Translating the sequences ------------------------------------------------------------------------------------*********-------*C****CCEEEEEEC*****HHHHCCCCCC**********CCEEEECCHHHHH****CCC**----------******EEEEE**-*-----*EEEEEC***************************************EEEE**CC*****EEEE*CC**********-************************--------- --------------------------------------------------------------------**C**C****CC*********************C****CCEEEEE*CHHHH*---*C***CC*******---**EEEE********-----------**********---EEEEEEE*HHH**C*EEEEEC-------*******************----------**CEEE*CC---****EEEE**C*--***********------------------------------ ----*****************************************-************************C--C****CC****--*****---------*C****CCEEEE**CHHH****-*CCCC-C--------**CCEEEECCHHHHH****CCC---*-------------**EEEEEE*HHH**C******C-*------------------------------------CEEEECCCC*****EEEE*CC-------------------------------------------- -----------------------------------------------------------------------------------------------------------CEEEEEE*HHHH*HHHH*C**CC*****---**CCEE*E*-HHHHH******C****-------------*EEEEEEE****--C*EEEEEC***---------------------------------***EEE*CC*******EEEE*CC**-------------------------------*********** ------------------------------------------------------------------****C--C****CC*************-------*C**---*EEEEEECHHHH*HHHHCCCCCC-------***CCEEE*CCHHHHH****CCC******************EEEEEEE-HHH****EE***C***************---****----------------C*EEE**CC***-*EEEE*C*******************--************************ **********************************************************************C--C****CC***********---------*C--**CC*EEEEECHHHH*HHHH*CCCCC--------**CCEEEECCHHHHH****CCC---*-------------**EEEEE**HHH**C***EEEC**------------------------------------CEEEECCCC*******------------------------------------------------- 56399-2.tem _________________________________ ------------------------------------------------------------------****C--C****CC*************-------*C****CCEEEEEECHHHH*HHHHCCCCCC*****---**CCEEEECCHHHHH****CCC**-*--------***--*EEEEEEE*HHH**C*EEEEEC***----********---****--------------**CEEEECCCC*****EEEE*CC**-*******-***-------------------**--------- Structural block scores 0 65 - 4.1 M 75.0 75.0 9.1 75.0 75.0 3.7 66 69 * 3.0 P 75.0 40.8 2.8 75.0 2.2 2.2 71 72 - 4.5 M 75.0 3.0 75.0 75.0 75.0 75.0 74 77 * 2.7 P 75.0 3.8 0.2 75.0 4.0 1.2 78 79 C 4.3 M 75.0 4.0 0.5 75.0 4.0 0.5 80 92 * 2.5 P 27.0 3.8 25.1 75.0 4.2 14.3 93 99 - 4.5 M 75.0 3.0 75.0 75.0 75.0 75.0 102 105 * 2.7 P 4.5 5.4 6.0 75.0 38.8 38.5 106 107 C 4.4 M 3.0 4.5 5.5 41.0 37.5 6.0 108 113 E 4.7 H 0.8 2.3 1.2 0.3 0.5 1.0 115 118 H 4.4 M 4.9 4.8 3.2 4.0 3.2 4.5 120 123 H 4.2 M 4.5 58.5 22.5 4.8 4.2 4.5 124 129 C 4.4 M 5.6 4.0 16.6 4.0 5.4 3.7 130 134 * 3.4 M 5.7 5.7 75.0 5.1 75.0 75.0 135 137 - 4.1 M 7.5 27.0 75.0 75.0 53.5 75.0 138 139 * 1.9 P 1.0 75.0 5.0 6.0 2.5 7.8 140 141 C 4.5 M 1.0 1.0 3.5 5.0 2.0 0.5 142 145 E 4.8 H 0.5 2.5 0.5 1.0 1.0 0.5 146 147 C 4.2 M 4.0 4.0 2.5 37.5 2.5 4.0 148 152 H 4.5 M 1.6 3.2 4.4 3.6 1.4 3.2 153 156 * 1.7 P 3.0 58.0 4.0 3.2 4.0 3.2 157 159 C 4.3 M 6.5 75.0 6.7 4.0 5.3 3.3 160 161 * 3.4 M 8.8 75.0 75.0 6.5 3.5 75.0 164 171 - 4.2 M 75.0 12.4 75.0 75.0 5.8 75.0 172 174 * 3.4 M 5.3 2.3 75.0 75.0 3.0 75.0 175 176 - 4.1 M 0.0 75.0 75.0 75.0 1.5 75.0 178 184 E 4.7 H 1.4 2.7 0.9 0.6 0.4 1.3 186 188 H 4.2 M 52.7 5.3 2.0 5.8 6.2 3.0 189 190 * 2.7 P 75.0 6.2 5.5 75.0 4.5 5.0 193 197 E 4.1 M 0.0 1.6 2.8 3.4 3.2 1.6 199 201 * 2.7 P 5.0 75.0 52.7 8.2 5.0 29.2 202 205 - 4.1 M 4.2 75.0 75.0 75.0 4.9 75.0 206 213 * 3.4 M 2.9 4.3 75.0 75.0 4.1 75.0 214 216 - 4.1 M 6.0 1.0 75.0 75.0 75.0 75.0 217 220 * 3.4 M 2.2 1.2 75.0 75.0 2.8 75.0 221 234 - 4.4 M 4.3 54.4 75.0 75.0 75.0 75.0 235 236 * 3.4 M 3.0 5.2 75.0 5.5 75.0 75.0 238 241 E 4.7 H 0.0 1.2 0.2 0.8 0.2 0.8 242 245 C 4.1 M 3.5 40.0 2.8 2.8 2.8 2.5 246 250 * 1.4 P 7.5 20.6 2.6 3.6 20.7 2.8 251 254 E 4.5 M 1.2 1.0 4.2 5.0 0.8 40.4 256 257 C 4.2 M 1.0 0.0 5.5 5.5 1.5 75.0 258 259 * 3.0 P 5.0 39.0 75.0 7.2 3.0 75.0 261 267 * 3.4 M 3.7 4.8 75.0 75.0 2.0 75.0 269 271 * 3.4 M 1.3 4.0 75.0 75.0 2.0 75.0 272 290 - 4.1 M 4.6 75.0 75.0 75.0 11.7 75.0 291 292 * 3.4 M 9.0 75.0 75.0 6.0 8.5 75.0 293 301 - 4.1 M 75.0 75.0 75.0 4.6 3.3 75.0 >>>>>>