Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1emsa2 CCCCEEEEEEECCCCC-C--CHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCH------HHHHHHH--HHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEC-CEEEEEEEEEEEECCCCCEEEEEECCCCCEEEEC-CCEEEE--HHHCCCCCCCCCCCEEEC-CEEECCCCHHHHHCHHHHHHHHH-C-----CCCEEECCCCCC---------HHHHHHHHHHHHHHHHHHHCCEEEECCCEEEEEC-------CEEEECCCEEECCCCCEEEECCC-CCCEEEEEEEHHHHHHHHH----HCCHHHCC------------------ >P1;d1uf5a- --CCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCHHHCCCCCHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCEEE-EEEEEEEEECCEEEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCEEEEC-CEEEEECCHHHHHCHHHHHHHHH-C-----CCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCEEEC--------CEEECCCCEEECCCCCEEEECCCCCCEEEEEEEEHHHHHHHHCC---CCCHHHHCCHHHCHHHHCC------- >P1;d2e11a- --CCCEEEEEEECCCCCC--CHHHHHHHHHHHHHHHCC-CCCEEECCCCCCCCC-CC------HHHH-HCEE--CCCHHHHHHHHHHHHHCCEEE-EEEEEEEC----CEEEEEEEEECCCCCE-EEEECCCCC----H-HH---C--CCCCCCCCC-CCCCEEEC-CEEEEEEEHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEECCC---------HHHH-HHHHHHHHHHHHHCCCEEEEEECEEECCC-------CCEEEEEEEEECCCCCEEEEEEC-CCEEEEEEECHHHHHHHHH----HCCHHHHCC------------CCCCC >P1;d2w1va- ----CEEEEEEECCCC-C--CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC-CC------CCHHHHC--CCCCCHHHHHHHHHHHHHCCEEECCCEEEEEC-C---EEEEEEEEECCCCCEEEEEECCCCCEEEEC-CCEEEE--HHHCCCCCCCCC-EEECC-CCEEEECCHHHHHCHHHHHHHHH-C-----CEEEEEEECCCC---------CCHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCC-------CCCCCCCCEEECCCCCEEEECCC-CCEEEEEEECHHHHHHHHH----HCCHHHCCCCC-------CCCCCC-- >P1;d3ivza- -----CEEEEEECCCCCC--CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCC-CH---HHHHHHCCC-CCCCHHHHHHHHHHHHHCCEEE-EEEEEEEC----CEEEEEEEEEECCE-EEEEEECCCCC------------HHHHHCCCCCCCCCCEEECC-CCEEEECC-CHHHCHHHHHHHHH-C-----CCCEEEEEECCCC-----C--------CHHHHHHHHHHHHCCEEEEEECCCEEC--------CEECCCCCEEECCCCCEEEECCCCCCEEEEEECCHHHHHC--CEEECCEEHHHHCCHHHCCC----------- >P1;d3p8ka1 ------CEEEEECCCCCC--CHHHHHHHHHHHHHHCCC-CCCEEECCC-CCCCC-CH------HHHHHHCEE--CCHHHHHHHHHHHHHHCCEEEEEEEEEEEC----CEEEEEEEEECCCCCEEEEEECCCCC----C--C---C--HHHCCCCCCCCCCCEECCCCCEEEEEEHHHHHCCHHHHHHHH-C-----CCCEEEEEECCC----------CCH-HHHHHHHHHHHHHHC-CEEEEECEEECC--------CCEEECCCEEECCCCCEEEECCC-CCEEEEECCCCHHHHHHHH----HCCHHHCCCCC-------CCC----- >P1;d5h8ia- CCCCEEEEEEEECCCCC---CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCC---HHHHHHCCC-CCCCHHHHHHHHHHHHHCCCEE-EEEEEEEC----CEEEEEEEEECCCCCEEEEEECCCCCEE------CCEE--HHHCCCCCCCCCCEEECC-CCEEEECCHHHHHCHHHHHHHHH-C-----CCCEEEEECCCEE-----CCCCCCCHHHHHHHHHHHHHHHCCCEEEECCEEEEEECCCCCCEEEEEECCCEEECCCCCEEEECCCCCCEEEEEEEEHHHHHHHHH---HH-CHHHHCCHHHCHHHHCCCCCCCCC PSA >P1;d1emsa2 8287613000000202-3--5156005303600340085904000000100000575------a213710--56078501640260036190000000114317-9445312100000038072424020130544558-aa5471--233413309842401403-00200000120033490032015-4-----802000000006---------4940554058203400540000000000066029-------94401030000106061313086-7410121501064076118----75441774------------------ >P1;d1uf5a- --8371400000013064a26276008202600560085703000000000100000230856960271006-7012840630073036350000-000000356d983210000000155083213010220231695376051010043004605381203802-70400000020035750034003-5-----601000000011345034485383136301620452045000000000000503--------a0400040000003072323085483201118030441560247---6230975265784b8696c------- >P1;d2e11a- --5940300000030423--53750191017206604a-700000000000101-03------8007-9026--3a2500710660075070000-00000429----8601000000017951-440102201----7-85---6--026503417-a1100615-901000000200334600303255218750000000000000---------2832-93035202400640000000000066056-------95501000000216081422146-8451321404095076117----87442594a------------b3a3d >P1;d2w1va- ----404000000515-7--7174008300620540174804000000000021-21------9303820--16073500740360066170100000000448-a---410000000038053222020230031648-c62615--03620350a730-20706-31300000010024570030004-4-----803000000000---------4300454037104300560000000001024684-------70202020000004062334063-9340131504195066028----56142765587-------667382-- >P1;d3ivza- -----2300000030512--4285018304600550196605000000000001208-53---820383035-0472700610350066070200-0000015b----930000000003a1-22110002202------------8406700460628140160a-40400000-20053550034003-5-----8000000000023-----6--------500720161054010000000002604--------7350103000000627232305557230101607193056--1656a952128516667489----------- >P1;d3p8ka1 ------200000030430--32970272057107828a-707000000-00011-01------750784007--70a60371047004528000000001012b----b6101000001570731130002212----6--6---7--045403408960610503761500000120033481034003-3-----602000000003----------964-830362055005400-000000008617--------837010200002060642341a6-93611307082a3077129----8543188164b-------86c----- >P1;d5h8ia- aa253020000004053---6685007102600440496902000000002120003033---970293055-3870500440380076060000-0000043b----c220000000005063241010120057------aa53--053005707292310605-30300000030013660023003-5-----8010000000103-----635985326601730390036000000000006504170578542240000000011608233406266421121501056158516---97-03276155763865809668876c Translating the sequences *****EEEEEE*CCCC-C--CHHHHHHHHHHHHHHHHHCCCCEEE*CCCCCCCC*C*------HHHHHH*--*****HHHHHHHHHHHH*CCEEE*EEEEEEEC-****EEEEEEEEECCCCCEEEEEECCCCC*****-******--HHHCCCCCCCCCC*EE*C-C*EE**CCHHHHHCHHHHHHHHH-C-----CCCEEE***CCC---------***H*HHHHHHHHHHHHHHCCEEEE**C*EE***-------C*EE*CCCEEECCCCCEEEECCC-CC*EEEEEE*HHHHHHHHH----HCCHHH*C------------------ --***EEEEEEECCCCCC**CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC*********HHHH**C**-*CCC***HHHHHHHHHHCCEEE-EEEEEEE******EEEEEEEEECCCCCEEEEEECCCCC**************HHH*CCCCCCCCC*EE*C-C*EEEECCHHHHHCHHHHHHHHH-C-----CCCEEEEE*CCC************H*HHHHHHHHHHHHHHCCEEEEE*C*EE*C--------C*EE*CCCEEECCCCCEEEECCC*CCEEEEEEE*HHHHHHHH**---*CCHHH*CC**********------- --***EEEEEEECCCCCC--CHHHHHHHHHHHHHHH**-CCCEEECCCCCCCCC-C*------HHHH-HC**--CCCHHHHHHHHHHHHHCCEEE-EEEEEEEC----*EEEEEEEEECCCCCE-EEEECCCCC----*-**---*--***CCCCCC-CCC*EE*C-C*EEEE**HHHHHC**********C*****CCCEEEEE*CCC---------***H-HHHHHHHHHHHHH*CCEEEEE*C*EE*C*-------C*EE****EEECCCCCEEEE**C-CCEEEEEEE*HHHHHHHHH----HCCHHH*CC------------***** ----*EEEEEEECCCC-C--CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC-C*------**HHHHC--**CCCHHHHHHHHHHHHHCCEEE***EEEEEC-*---EEEEEEEEECCCCCEEEEEECCCCC*****-******--HHHCCCCCCCCC-*EE*C-C*EEEECCHHHHHCHHHHHHHHH-C-----C**EEEEE*CCC---------***H*HHHHHHHHHHHHHHCCEEEEE*C****C*-------C****CCCEEECCCCCEEEECCC-CCEEEEEEE*HHHHHHHHH----HCCHHH*CC**-------******-- -----*EEEEEECCCCCC--CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC*C*-**---HHHHHHC**-*CCCHHHHHHHHHHHHHCCEEE-EEEEEEEC----*EEEEEEEEE*CC*-EEEEEECCCCC------------**HHHCCCCCCCCCC*EE*C-C*EEEECC-*HHHCHHHHHHHHH-C-----CCCEEEEE*CCC*-----*--------*HHHHHHHHHHHHCCEEEEE*C**E*C--------C*E**CCCEEECCCCCEEEECCC*CCEEEEEE**HHHHH*--********HHH*CC******----------- ------*EEEEECCCCCC--CHHHHHHHHHHHHHH***-CCCEEECCC-CCCCC-C*------HHHHHHC**--CC*HHHHHHHHHHHHHCCEEE*EEEEEEEC----*EEEEEEEEECCCCCEEEEEECCCCC----*--*---*--HHHCCCCCCCCCC*EE*C*C*EEEE**HHHHHC*HHHHHHHH-C-----CCCEEEEE*CCC----------**H-HHHHHHHHHHHHHHC-*EEEE*C*EE*C--------C*EE*CCCEEECCCCCEEEECCC-CCEEEEE****HHHHHHHH----HCCHHH*CC**-------***----- *****EEEEEEECCCCC---CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC*C****---HHHHHHC**-*CCCHHHHHHHHHHHHHCC*EE-EEEEEEEC----*EEEEEEEEECCCCCEEEEEECCCCC**------****--HHHCCCCCCCCCC*EE*C-C*EEEECCHHHHHCHHHHHHHHH-C-----CCCEEEEE*CC**-----********HHHHHHHHHHHHHHCC*EEEE*C*EE************EE*CCCEEECCCCCEEEECCC*CCEEEEEEE*HHHHHHHHH---*H-CHHH*CC***************** 56317.tem _________________________________ --***EEEEEEECCCCCC--CHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCC*C*-**---HHHHHHC**-*CCCHHHHHHHHHHHHHCCEEE*EEEEEEEC-*--*EEEEEEEEECCCCCEEEEEECCCCC*****-******--HHHCCCCCCCCCC*EE*C-C*EEEECCHHHHHCHHHHHHHHH-C-----CCCEEEEE*CCC*-----*--***H*HHHHHHHHHHHHHHCCEEEEE*C*EE*C*-------C*EE*CCCEEECCCCCEEEECCC*CCEEEEEEE*HHHHHHHHH----HCCHHH*CC******---******-- Structural block scores 0 1 - 4.2 M 5.0 75.0 75.0 75.0 75.0 75.0 10.5 2 4 * 2.9 P 7.0 6.0 6.0 51.3 75.0 75.0 3.3 5 11 E 4.8 H 0.6 0.7 0.4 0.6 0.7 11.0 0.3 12 17 C 4.8 H 13.7 2.3 2.0 15.5 1.8 1.7 14.5 18 19 - 4.6 H 75.0 6.2 75.0 75.0 75.0 75.0 75.0 21 37 H 4.9 H 2.6 3.1 3.7 2.8 3.4 4.6 3.3 38 41 C 4.8 H 4.5 3.8 20.5 4.0 4.2 22.2 4.2 42 44 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 45 53 C 4.9 H 0.1 0.1 0.2 0.3 0.1 8.6 0.6 58 59 * 3.7 M 75.0 1.5 75.0 75.0 4.0 75.0 3.0 60 62 - 4.6 H 75.0 6.3 75.0 75.0 75.0 75.0 75.0 63 68 H 4.7 H 4.1 4.2 16.5 4.2 4.0 5.2 5.0 70 71 * 2.5 P 75.0 3.0 4.0 75.0 4.0 3.5 5.0 74 76 C 4.5 M 5.0 1.0 5.2 3.3 4.3 5.8 5.0 77 89 H 4.9 H 2.6 3.3 2.8 2.9 2.6 3.0 2.8 90 91 C 5.0 H 4.5 2.5 3.5 3.5 3.5 4.0 3.0 92 94 E 4.9 H 0.0 0.0 0.0 0.3 0.7 0.0 0.0 96 102 E 4.9 H 1.4 0.4 0.9 1.1 0.9 0.6 1.0 106 107 - 4.2 M 4.0 8.5 75.0 75.0 75.0 75.0 75.0 109 117 E 5.0 H 0.8 0.3 0.8 0.6 0.3 0.9 0.4 118 122 C 4.8 H 3.6 3.8 4.4 3.2 17.9 4.0 2.2 123 128 E 4.9 H 2.3 1.7 14.2 1.8 1.0 1.3 1.8 129 133 C 5.0 H 1.8 1.2 1.0 1.0 1.2 1.4 0.6 134 138 * 3.2 M 5.2 4.8 61.4 4.4 75.0 61.2 47.4 140 145 * 2.8 P 6.3 3.2 40.7 5.4 75.0 52.2 29.8 146 147 - 4.2 M 75.0 0.5 75.0 75.0 6.0 75.0 75.0 148 150 H 4.6 H 2.7 2.3 2.7 3.0 4.3 3.0 2.7 151 160 C 4.9 H 3.8 2.9 10.8 10.6 3.1 4.0 3.5 162 163 E 5.0 H 2.5 5.5 3.0 3.5 3.5 2.5 3.0 169 172 E 4.8 H 0.5 1.0 0.2 0.8 1.0 1.2 0.8 173 174 C 4.2 M 0.0 0.0 0.0 0.0 0.0 0.0 0.0 175 179 H 4.8 H 1.2 1.0 1.0 0.6 16.4 1.2 0.8 181 189 H 4.6 H 2.7 2.4 2.6 2.1 2.2 2.6 2.2 192 196 - 4.6 H 75.0 75.0 4.2 75.0 75.0 75.0 75.0 197 199 C 4.7 H 3.3 2.3 0.0 3.7 2.7 2.7 3.0 200 204 E 4.8 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 206 208 C 4.9 H 2.0 0.7 0.0 0.0 0.7 1.0 0.3 210 214 - 4.6 H 75.0 3.2 75.0 75.0 75.0 75.0 75.0 216 217 - 4.2 M 75.0 6.5 75.0 75.0 75.0 75.0 4.0 218 220 * 2.0 P 5.7 4.7 4.3 2.3 75.0 30.0 7.3 223 236 H 4.9 H 2.9 2.7 2.7 2.7 7.6 2.9 3.1 237 238 C 4.8 H 0.0 0.0 0.0 0.0 0.5 37.5 0.0 239 243 E 4.8 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 247 248 E 4.4 M 6.0 2.5 6.0 3.0 4.0 7.0 5.5 252 258 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 5.1 261 262 E 4.4 M 2.0 2.0 2.5 1.0 2.5 3.5 2.0 264 266 C 4.6 H 1.0 1.3 0.0 0.7 1.0 0.7 0.0 267 269 E 5.0 H 0.0 0.0 0.0 0.0 0.0 0.0 0.0 270 274 C 5.0 H 2.6 2.0 3.4 2.0 3.0 2.8 3.2 275 278 E 5.0 H 2.0 2.5 2.2 3.0 2.5 3.2 3.0 279 281 C 4.7 H 4.7 4.3 3.7 3.0 3.3 5.8 2.7 283 284 C 5.0 H 5.5 5.5 6.0 6.0 4.5 6.0 5.0 285 291 E 4.8 H 1.4 1.9 2.3 2.0 1.6 2.6 1.7 293 301 H 4.7 H 3.7 2.9 4.0 4.1 19.4 4.6 4.1 302 305 - 4.4 M 75.0 58.0 75.0 75.0 6.9 75.0 58.5 307 308 C 4.4 M 4.5 2.5 5.5 3.5 3.5 4.5 37.5 309 311 H 5.0 H 4.0 5.3 3.7 4.3 3.7 4.0 4.0 313 314 C 4.8 H 39.5 4.0 7.2 5.0 3.5 3.5 3.0 315 320 * 3.3 M 75.0 7.2 75.0 52.5 6.7 52.6 5.8 321 323 - 4.2 M 75.0 7.0 75.0 75.0 75.0 75.0 4.3 324 329 * 3.6 M 75.0 64.6 41.7 5.3 75.0 41.9 7.3 330 331 - 4.2 M 75.0 75.0 8.2 75.0 75.0 75.0 9.2 >>>>>>