Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1e6yc- ------------------------------------------------------------------------------------CCCCCCCCCCCHHHHHHHHHHHC--CCCCCCCCCHHHHHHHHCCCCCCC---------CCCCCCCCHHHHCCCC-CHHHHCCCCHHHHHCCCEEEEEEEECC------------CCCCCCHHHHHHHHHHHCC----CCEEEECC--CCEEEEEEHHHHH------HHHHHHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEC-------CEEEEEECCCCCEEEEEEECCCCCCHHHHHHHCCCCCCCC-CCHH----------HCHHHHHHHHHHHHHHHHHHHCCC----- >P1;d5a0ya1 CCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCC------CEEEHHHHCHHHCHHHHHHHHHHHC-----EEEEECHHHHHHHHH-----CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCEEEEEECCHHHHHHCCHHHCCCHHHHCCHHHHHHHHHHHC-------------CCEEEEEECCHHHHHHC-CCCHHHHHHHHHHHHHHHH----HCCCCCCC-----HHHHHHHHHHC----CCEECCC----------------C---------------------------------------------------------------CCCC >P1;d5a0yb1 -------------------------------------------------------------CCCCCEEEEEC----CCCCEEEEEEEHHHHCCCCCHHHHHHHHHHHH-----EEEEEHHHHHHHHHHCCCCCCCCCCC-------------------------------------------------CCCC---CCCCHHH-HHHHHHHHHHHHCCCCCCCCEEEEEHHHCEEEEECCHHHHHCCCCCCHHHHHHHHHHHHHHHH----HHCCCC-------CCHHHHHHHHHCCCCCCCCCCCCCEECCCCCHHHC-CCC------------------------------------------------------------------- >P1;d7b1sb1 -------------------------------------------------------------CCCCCEEEEEC----CCCCEEEEEEEHHHHCCCCCHHHHHHHHHHHH-----EEEEEHHHHHHHHHHCCCCCCCCCCCCCCCHHHCC------------------CCCCHHHCCCCCCCC-------CCCC---CCCCCCC-HHHHHHHHHHHHCCCCCCCCEEEEEHHHCEEEEECCHHHHCCCCCCCHHHHHHHHHHHHHHHH----HCCCCC-------CHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCC-CCC------------------------------------------------------------------- >P1;d7b1sc- ------------------------------------------------------------------------------------CCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCC---------CCCCCCCCHHHCCCCCCCCHHHCCCCHHHHHCCCEEEEEEEECC------------CCCCCCHHHHHHHHHHHCC----CCEEEECC--CCEEEEEEHHHHH------HHHHHHHHCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEC-------CEEEEEECCCCCEEEEEEEEECCCCHHHHHHHCCCCCHHHCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHCHHHHCCC PSA >P1;d1e6yc- ------------------------------------------------------------------------------------b8a69212072500501350101--806521807961002002018375---------b24453541a748378-885686941702520034310000005------------3200012700140052226----a0716049--2401040203101------80034000100000000000063270153925b57004063600223b-------71000320031761b7606067106984028200103972-2159----------7096036557737558775a8579----- >P1;d5a0ya1 b77a618135503a351959948577392261082146307507842894a78545288ba6604532225249a4a------6132323367642994358604420-----002000450151049-----41667051940360061025001223137a939447876084030302003392177047710330476469a6067418718-------------83020002002510485-7472006200510330003----00916464-----90394059104----411543a----------------a---------------------------------------------------------------a89c >P1;d5a0yb1 -------------------------------------------------------------476b7543355----b8884676615415436962883787643331-----30604043016103505020894458-------------------------------------------------a442---8170274-09600740483014789350406268c043030200453089294212004200600150027----21a058-------84260042000043792751450208283602745-a7a------------------------------------------------------------------- >P1;d7b1sb1 -------------------------------------------------------------b7577544453----b8984775823325327843894657823430-----004040250370033050057b343515763573c------------------57319c277818285-------6402---7040183-0950073048202468a1b0307268a0530301006610789a6422025300610150026----11a178-------70660031000033692640340106163821457-b7a------------------------------------------------------------------- >P1;d7b1sc- ------------------------------------------------------------------------------------a8858113023300622340012949065218076730010011164b6---------a27564642a73c3693784777632702530025030000004------------3100031700150062115----90706049--4300020203101------90032000110000000000065170254924964005012600315c-------73010331020680b7506066226695047300202881a31444bb06b26497015112642548628521a6589438c4 Translating the sequences ------------------------------------------------------------------------------------*******CCCC*HHHHHHHHHH*--*********HHHHHHHH**CCCCC---------C***CC**HHH*CCCC-C****CCCC*HHHHCCCEEEEEE****------------CCCCCCHHHHHHHHHHHCC----CCEEEE**--C*EEEE**HHHHH------HHHHHHHH*************CCCCCCC*****CC************C-------C*EEE**CCCCC****************************-****----------************************----- *************************************************************CCCCC***EE*****C------*EEEHHHHC***CHHHHHHHHHHH*-----EEEEE*HHHHHHHHH-----CCCCCC***********HHH*CCCC*C****CCCC*HHHHCCCEEEEEE********CC***CCC****CCHHHHHHHHHHHC-------------***EEEEECCHHHHH*C-CCCHHHHHHHHHHHHHHHH----HCCCCCCC-----**HHHHHHHH*----CC**CCC----------------C---------------------------------------------------------------**** -------------------------------------------------------------CCCCC***EE*----C*******EEEHHHHCCCCCHHHHHHHHHHH*-----EEEEEHHHHHHHHHHCCCCCCCCCCC-------------------------------------------------**CC---CCCC***-*HHHHHHHHHHHCC****CCEEEE****CEEEEECCHHHHH*C*CCCHHHHHHHHHHHHHHHH----H*CCCC-------CCHHHHHHHH****CCC**CCCC*EE***CC****-**C------------------------------------------------------------------- -------------------------------------------------------------CCCCC***EE*----C*******EEEHHHHCCCCCHHHHHHHHHHH*-----EEEEEHHHHHHHHHHCCCCCCCCCCC***C***CC------------------CC**HHHCCC*****-------**CC---CCCCCCC-*HHHHHHHHHHHCC****CCEEEE****CEEEEECCHHHH**C*CCCHHHHHHHHHHHHHHHH----HCCCCC-------C*HHHHHHHH****CCC**CCCC*EEE**CCCCC*-**C------------------------------------------------------------------- ------------------------------------------------------------------------------------*******CCCC*HHHHHHHHH*************HHHHHHHH**CCCCC---------C***CC**HHH*CCCC*C****CCCC*HHHHCCCEEEEEE****------------CCCCCCHHHHHHHHHHHCC----CCEEEE**--C*EEEE**HHHHH------HHHHHHHH*************CCCCCCC*****CC************C-------C*EEE**CCCCC************************************************************************ 55088.tem _________________________________ -------------------------------------------------------------CCCCC***EE*----C------*EEEHHHHCCCCCHHHHHHHHHHH*-----EEEEEHHHHHHHHHHCCCCCCCCCCC---C***CC**HHH*CCCC-C****CCCC*HHHHCCCEEEEEE****--**CC---CCCCCCCCCHHHHHHHHHHHCC----CCEEEE****CEEEEECCHHHHH*C-CCCHHHHHHHHHHHHHHHH----HCCCCCCC-----CCHHHHHHHH****CCC**CCCC*EEE**CCCCC*-**C------------------------------------------------------------------- Structural block scores 0 60 - 4.5 M 75.0 5.4 75.0 75.0 75.0 61 65 C 4.2 M 75.0 4.2 7.1 7.5 75.0 66 68 * 3.0 P 75.0 2.3 4.0 4.3 75.0 69 70 E 4.2 M 75.0 3.5 4.0 4.5 75.0 72 75 - 4.5 M 75.0 6.9 75.0 75.0 75.0 77 82 - 3.8 M 75.0 75.0 6.8 7.2 75.0 84 86 E 3.8 M 10.0 2.0 4.0 4.3 8.8 87 90 H 3.8 M 4.5 2.8 3.5 3.2 3.8 91 95 C 4.5 M 3.2 5.0 5.2 4.8 2.2 96 106 H 4.8 H 1.5 4.9 5.5 5.4 1.8 108 112 - 3.9 M 18.8 75.0 75.0 75.0 4.8 113 117 E 3.8 M 3.6 0.4 2.6 1.6 3.6 118 127 H 4.7 H 2.0 2.9 2.3 2.3 1.9 128 138 C 4.3 M 43.1 36.3 4.1 4.0 43.5 139 141 - 3.8 M 75.0 5.0 75.0 4.3 75.0 143 145 * 2.1 P 3.3 3.0 75.0 5.0 4.7 146 147 C 4.1 M 4.0 0.0 75.0 7.8 5.0 148 149 * 3.0 P 4.5 3.5 75.0 75.0 5.0 150 152 H 4.2 M 6.2 2.3 75.0 75.0 6.5 154 157 C 4.2 M 6.5 1.2 75.0 75.0 7.6 160 163 * 3.0 P 6.8 7.4 75.0 75.0 6.5 164 167 C 4.3 M 5.0 5.0 75.0 40.5 4.5 169 172 H 4.4 M 2.2 5.2 75.0 6.1 2.5 173 175 C 4.5 M 1.0 4.0 75.0 7.3 0.7 176 181 E 4.1 M 1.3 1.3 75.0 16.5 1.3 182 185 * 3.0 P 1.2 3.8 75.0 75.0 1.0 186 187 - 4.5 M 75.0 1.5 75.0 75.0 75.0 188 189 * 3.0 P 75.0 7.0 7.2 5.0 75.0 190 191 C 4.2 M 75.0 2.0 3.0 1.0 75.0 192 194 - 4.5 M 75.0 5.0 75.0 75.0 75.0 195 203 C 4.1 M 25.7 3.7 11.6 10.9 25.8 204 214 H 5.0 H 2.1 5.4 3.7 3.5 2.1 215 216 C 4.8 H 4.0 41.5 2.5 3.0 3.0 217 220 - 3.8 M 75.0 75.0 6.8 6.4 75.0 221 222 C 4.5 M 5.2 75.0 2.5 5.8 4.5 223 226 E 4.5 M 3.5 75.0 3.0 3.0 3.2 227 230 * 2.5 P 40.8 40.2 6.6 6.1 40.8 232 236 E 4.8 H 1.8 0.8 1.6 1.4 1.0 237 238 C 3.8 M 1.0 0.0 0.0 0.0 1.0 239 243 H 4.9 H 1.0 2.4 4.0 4.0 1.0 247 249 C 4.2 M 75.0 6.0 2.3 4.0 75.0 250 265 H 4.4 M 1.0 1.6 1.8 2.1 1.0 266 269 - 3.8 M 0.0 75.0 75.0 75.0 0.0 271 277 C 4.7 H 3.4 4.3 24.9 25.4 3.7 278 282 - 3.8 M 6.1 75.0 75.0 75.0 5.6 283 284 C 4.2 M 6.0 4.5 6.0 3.5 5.0 285 292 H 3.8 M 2.4 3.9 1.8 2.0 1.8 293 296 * 1.8 P 1.8 57.2 1.8 1.5 2.2 297 299 C 4.3 M 53.8 26.7 6.0 5.7 54.2 300 301 * 3.0 P 75.0 3.0 6.0 5.0 75.0 302 305 C 4.3 M 58.0 23.1 2.5 1.8 58.0 307 309 E 4.4 M 0.0 75.0 3.3 2.3 0.3 310 311 * 2.1 P 2.5 75.0 5.5 4.5 3.0 312 316 C 4.3 M 2.2 75.0 3.8 4.0 1.8 319 320 * 2.1 P 9.2 75.0 8.8 9.2 9.2 322 388 - 3.9 M 21.5 71.1 75.0 75.0 4.6 >>>>>>