Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ddga1 ----------------------------CCCCCCCC-CCCEEEEEEEEEECCC-------CCCCCEEEEEEEECCCCC-CCCCCCCEEEECCCCCHHHHHHHHHHC--CCCCCCEEEEC--------------------CEEEEHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCCCHHHCCCC--------HHHHHHHH--HCCHHHHHHHCC-CCCCHHHHHH-HCCCCCCEEEECCCCCC---CCCCEEEEEEEECEEEEC-C--EEEE----CHHHHHHHHCCCCC---CEEEEEEECCCCCC >P1;d1f20a1 ---------CCCCCCEEEEECCCCCCHHHHHHHHHC-CCCEEEEEEEEEECCC-------CCCCCCEEEEEEECCCCHHHCCCCCCEEEECCCCCHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCC----CCHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHH-HCCCCCCEEEECCCCCC---CCCCEEEEEEECCEEECHHHCCCEEE----CHHHHHHCCCCC----CCEEEEEEECCC--- >P1;d2rc5a1 -----------------------CCC--CCCCCCEE-EEEEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEECCCC-CCCCCCCCEEEEECCCCCHHHHHC-------------------------------------------------------------------------------------------------------------------------CCCCCCCCCEEEECCCCCCCHHHCCCEEEEEEECCCCCC-----CCCC--CCCHHHHHHHCCCC----CCEEEEEEEECCCCC >P1;d3lo8a1 --------------CCCCCCCHHHHCCCCCCCCCCCCCCCEEEEEEEEEECCCC----CCC---CCEEEEEEECCC--CCCCCCCCEEEEECCCCCCCCC-----------------------------------------------------------------------------------------------------------------------------C-CCCCCEEEECCCCCCCCCCCCCEEEEEEECCCCCCC--CCCCCCHHHCCHHHHHHHCCCC----CCEEEEEEEECCC-- >P1;d3qfta1 CCEEEEECCCCCHHHCCCCCCCCCCCCCCCCCCCCC-CCCEEEEEEEEEECCC-------CCC-CCEEEEEEECCCCC-CCCCCCCEEEECCCCCHHHHHHHHHHH--CCCCCCEEEEEECCC--------CCCCCCCCCCCEEHHHHHHHCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHH-HCCCCCCEEEECCCCCC---CCCCEEEEEEECCEEECCCC--CEEE----CHHHHHHHCCCCCC-CCCEEEEEEECCCC-- >P1;d4dqla1 --------------------------------------CCEEEEEEEEEECCC-------CCCCCCEEEEEEECC---CCCCCCCCEEEECCCCCHHHHHHHHHHH--CCCCCCEECCC----------------------CEEHHHHCC-CCCCCCCCCHHHHHHHHHCCC-CHHHHHHHHCCC-----HHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHH-CCCCCCCEEEECCCCCC---CCCCEEEEEEECCEEECCCCCC-EEE----CHHHHHHHHCCC----CCEEEEEEECCC--- >P1;d5gxub1 ------------------------------CCCCCC-CCCEEEEEEEEEECCC-------CCC-CCEEEEEEECCCCC-CCCCCCCEEEECCCCCC-CHHHHHHHH--CCCCCCCCC-------------------CCCC-CCCHHHHHC-CCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCC----CCCCIIIIIICCCCHHHHHHHCCCCCCCHHHHHHHCCCCCCCEEEECCCCCC---CCCCEEEEEEECC-CCCCCC--CCCC----CHHHHHHHHCCCCCCCCCEEEEEEECCCC-- PSA >P1;d1ddga1 ----------------------------8a946275-961140403416442a-------ab3a71113020408b15-050662020002020458107100720--60718270609--------------------a76140640024400014-022900250054081a803623738--------86078208--501000004313-1808183019-00460502419031319---918630105020634607-9--3902----40000000411a56---86040005658b82 >P1;d1f20a1 ---------8066a20404629a2282140006017-4400403024278436-------993a84203030204648608096a130000000358506401820570261852030132656aa39b55462451730030002500120020361063830630080066792364044005----07a30480478340100300540520500010000-2082070331703043a---846510005081635604b5905315----510010033096----855000105639--- >P1;d2rc5a1 -----------------------079--92538327-a72150605406233586b74a476023121401040709-300015302000106961671486-------------------------------------------------------------------------------------------------------------------------94a428172351903031306887451000405170617-----2945--76530002006086----8440201002a69a2 >P1;d3lo8a1 --------------ca7b3738715869822474374a9025030330844479----a29---832020102013--602034b020000069615988-----------------------------------------------------------------------------------------------------------------------------b-261923618030710046540500004071414538--9568638853650112008075----755050010298c-- >P1;d3qfta1 360624328a18a85017001483301772938065-930110205306332a-------a8a-71301020304a08-190663030001010797105600930--51706320004046a--------a3c77200102010400013001017206480074005209577237304400587b906821562045041100000330620604010000-10330814317031418---74572000514054560818--2514----4101210482636a-b71200010582b9-- >P1;d4dqla1 --------------------------------------e32615034064329-------9b3a83212020503---b16076b030003050198006300910--a3847662646----------------------641055101-710012206470062007306-875485056118-----7621576057431000000350680606053008-20490532518043309---966530004081649908093b-833----300001016187----94804021373c--- >P1;d5gxub1 ------------------------------967143-8722805002164348-------9a4-c2201010205c0b-09077302000307039-107401710--74748421a-------------------b506-824045003-30202620858006200530958921840650049----8191582067262000300360620405073007800430713218041339---9175302040816-662514--2525----11001304705349ab13203000582ca-- Translating the sequences ----------------------------**CCCC*C-CCCEEEEEEEEEECCC-------CCC*C*EEEEEEECCCC*-CCCCCCCEEEECCCCC*HHHHHHH***--CCCCCC*****--------------------*****HHHH****CCCCC-CCHHHHHHHH***C****HHH****--------********--*CCHHHHHHHCC-CCCCHHHHHH-*CCCCCCEEEECCCCCC---CCCCEEEEEEE*C****C-*--****----CHHHHHHH*CCC**---CEEEEEEECCCC** ---------**************************C-CCCEEEEEEEEEECCC-------CCC*CCEEEEEEECCCC***CCCCCCEEEECCCCC*HHHHHHH*****CCCCCC******************************HHHH****CCCCC*CCHHHHHHHH***C****HHH******----*************CCHHHHHHHCC*CCCCHHHHHH-*CCCCCCEEEECCCCCC---CCCCEEEEEEECC***C*****C***----CHHHHHH**CCC----CCEEEEEEECCC--- -----------------------***--**CCCC**-***EEEEEEEEEECCC*******CCC*CCEEEEEEECCCC-*CCCCCCCEEEE*CCCC*HHHHH*-------------------------------------------------------------------------------------------------------------------------***CCCCCCEEEECCCCCC****CCCEEEEEEECC***C-----C***--**CHHHHHHH*CCC----CCEEEEEEE*CCC** --------------****************CCCC*C*CCCEEEEEEEEEECCC*----**C---CCEEEEEEECCC--*CCCCCCCEEEE*CCCC*****-----------------------------------------------------------------------------------------------------------------------------*-CCCCCEEEECCCCCC***CCCCEEEEEEECC***CC--**C*******CHHHHHHH*CCC----CCEEEEEEE*CCC-- ******************************CCCC*C-CCCEEEEEEEEEECCC-------CCC-CCEEEEEEECCCC*-CCCCCCCEEEECCCCC*HHHHHHH***--CCCCCC*********--------*************HHHH****CCCCC*CCHHHHHHHH***C****HHH***********************CCHHHHHHHCC*CCCCHHHHHH-*CCCCCCEEEECCCCCC---CCCCEEEEEEECC***CC**--C***----CHHHHHHH*CCC**-*CCEEEEEEECCCC-- --------------------------------------CCEEEEEEEEEECCC-------CCC*CCEEEEEEECC---*CCCCCCCEEEECCCCC*HHHHHHH***--CCCCCC*****----------------------***HHHH**-*CCCCC*CCHHHHHHHH***C-***HHH******-----************CCHHHHHHHCC*CCCCHHHHHH-*CCCCCCEEEECCCCCC---CCCCEEEEEEECC***CC****-***----CHHHHHHH*CCC----CCEEEEEEECCC--- ------------------------------CCCC*C-CCCEEEEEEEEEECCC-------CCC-CCEEEEEEECCCC*-CCCCCCCEEEECCCCC*-*HHHHH***--CCCCCC***-------------------****-***HHHH**-*CCCCC*CCHHHHHHHH***C****HHH*******----************CCHHHHHHHCC*CCCCHHHHHH**CCCCCCEEEECCCCCC---CCCCEEEEEEECC-**CC**--C***----CHHHHHHH*CCC****CCEEEEEEECCCC-- 63380-1.tem _________________________________ --------------****************CCCC*C-CCCEEEEEEEEEECCC-------CCC*CCEEEEEEECCCC**CCCCCCCEEEECCCCC*HHHHHHH***--CCCCCC*****-----------------********HHHH****CCCCC*CCHHHHHHHH***C****HHH******-----************CCHHHHHHHCC*CCCCHHHHHH-*CCCCCCEEEECCCCCC---CCCCEEEEEEECC***CC****C***----CHHHHHHH*CCC**--CCEEEEEEECCCC-- Structural block scores 0 13 - 4.5 M 75.0 50.4 75.0 75.0 5.1 75.0 75.0 14 29 * 3.4 M 66.8 3.5 53.2 6.8 3.1 75.0 75.0 30 33 C 4.3 M 5.2 1.5 4.8 4.2 5.0 75.0 5.8 37 39 C 4.5 M 5.3 2.7 6.5 6.5 4.0 30.8 5.7 40 49 E 5.0 H 2.7 3.0 2.9 2.8 2.1 3.1 2.8 50 52 C 5.0 H 5.5 4.3 3.7 5.0 5.2 4.7 5.0 53 59 - 4.4 M 75.0 75.0 7.3 45.9 75.0 75.0 75.0 60 62 C 4.7 H 8.3 7.0 4.3 53.0 9.7 7.8 7.8 64 65 C 4.8 H 4.0 6.0 2.0 5.5 4.0 5.5 7.2 66 72 E 5.0 H 1.6 1.4 1.7 1.0 1.3 1.7 0.9 73 76 C 4.8 H 5.1 3.5 4.0 19.8 3.6 38.2 4.4 77 78 * 3.1 M 40.0 7.0 39.0 40.5 41.5 43.2 43.2 79 85 C 4.9 H 2.7 4.9 1.3 2.9 3.6 4.5 3.7 86 89 E 5.0 H 0.5 0.8 0.5 0.5 0.8 0.8 0.5 90 94 C 4.8 H 1.6 0.6 4.4 4.2 1.8 1.8 2.6 96 102 H 4.4 M 2.4 3.4 15.3 36.4 2.7 2.4 12.6 103 105 * 2.5 P 3.0 3.3 75.0 75.0 4.0 3.3 2.7 106 107 - 4.6 H 75.0 6.0 75.0 75.0 75.0 75.0 75.0 108 113 C 4.4 M 4.0 3.7 75.0 75.0 3.7 6.4 5.7 114 118 * 2.7 P 4.4 1.2 75.0 75.0 1.2 4.8 32.7 119 135 - 4.4 M 75.0 5.7 75.0 75.0 38.9 75.0 75.0 136 143 * 3.2 M 31.7 1.8 75.0 75.0 0.8 48.2 13.9 144 147 H 4.4 M 2.5 1.8 75.0 75.0 1.0 2.8 2.2 148 151 * 2.8 P 2.5 0.8 75.0 75.0 1.0 20.8 20.2 152 156 C 4.4 M 1.0 2.2 75.0 75.0 1.8 0.8 2.0 158 159 C 4.4 M 1.0 3.0 75.0 75.0 3.0 3.0 4.0 160 167 H 4.4 M 2.2 2.9 75.0 75.0 2.9 2.4 2.6 168 170 * 2.5 P 3.0 2.7 75.0 75.0 2.3 3.3 2.7 172 175 * 2.6 P 4.9 6.0 75.0 75.0 5.2 23.8 6.0 176 178 H 4.4 M 3.7 4.3 75.0 75.0 4.3 5.7 4.3 179 184 * 2.7 P 28.5 2.2 75.0 75.0 2.2 3.5 2.5 185 189 - 4.4 M 75.0 60.0 75.0 75.0 7.1 75.0 61.8 190 201 * 2.7 P 22.4 4.9 75.0 75.0 3.6 4.4 4.6 202 203 C 4.4 M 0.5 0.5 75.0 75.0 1.0 0.5 1.0 204 210 H 4.4 M 1.0 1.7 75.0 75.0 0.9 1.1 1.7 211 212 C 4.4 M 2.0 2.5 75.0 75.0 3.0 3.0 3.0 214 217 C 4.4 M 4.2 1.2 75.0 75.0 2.5 3.0 2.2 218 223 H 4.4 M 3.7 0.2 64.0 75.0 0.2 2.7 2.8 226 231 C 4.9 H 2.5 2.8 4.0 15.8 2.5 3.5 2.5 232 235 E 5.0 H 4.0 3.5 4.5 4.5 3.8 4.0 3.5 236 241 C 5.0 H 2.8 3.4 1.7 1.8 2.8 3.2 3.3 242 244 - 4.2 M 75.0 75.0 4.7 3.3 75.0 75.0 75.0 245 248 C 4.9 H 6.0 5.8 6.0 3.5 5.8 6.5 5.5 249 255 E 5.0 H 1.6 2.0 1.4 1.6 1.7 2.1 2.4 256 257 C 4.8 H 3.0 3.5 4.0 2.5 2.5 3.5 3.5 258 260 * 1.3 P 4.3 4.7 2.3 3.3 5.0 7.3 29.0 261 262 C 4.4 M 3.5 2.0 41.0 5.5 4.0 4.0 3.5 263 266 * 3.2 M 58.5 6.4 75.0 41.0 39.8 5.9 38.8 268 270 * 1.0 P 3.7 3.0 6.0 5.7 3.3 4.7 4.0 271 274 - 4.4 M 75.0 75.0 40.8 6.0 75.0 75.0 75.0 276 282 H 4.9 H 0.0 0.7 0.7 1.3 1.3 0.3 1.3 284 286 C 5.0 H 4.2 5.0 4.7 4.0 3.7 5.3 2.7 287 288 * 3.7 M 5.5 75.0 75.0 75.0 8.2 75.0 6.5 289 290 - 4.4 M 75.0 75.0 75.0 75.0 43.2 75.0 11.0 291 292 C 4.8 H 41.5 6.5 6.0 6.0 4.0 6.5 2.0 293 299 E 5.0 H 2.1 1.6 1.0 1.6 1.1 2.6 1.4 300 303 C 4.7 H 7.6 23.2 6.9 7.9 7.6 24.4 8.2 304 305 - 4.2 M 5.0 75.0 6.2 75.0 75.0 75.0 75.0 >>>>>>