Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1kcma- ----------------------------------CEEEEEEEEECCCHHHHHHHHHHHHHHHHC-------------------------CCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEECHHHCC-------------------------HHHHCCCC------------CCCCEEEEEEEEECCEEEEEEEEC---CCHHHEEEEEEEEEECCCCCCCCCCCCCHHHHCCCEEEEECCCCHHHCCHHHCCHHHCCCCCCCCCCCCCCCCCCHHHHHCCCC----------------------CCCCEEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHHHHHCCCC-- >P1;d1z02a2 ---CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEECCHHHHHHHH-CCCCCH--HHHCCCHHHHHCCCCCCCEEEECC-------CC---CEEEECC-CCCC--CEEEEC----CCCCCEEEECEEC------------------------CCCEECC--CCCC-CCC--EEEEE-CCCEEEEECCCCC-------CCEEEEEEEECC-------------CCEEEEEEEEEEEC-C-CHHHHHHHHHHHHHCHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHCCCC------------------------HHHHHHHHHHHHHHHHCCCCCCC--CCCCCCCCCCCHHHHHHHHCCCCCCCCCCCC >P1;d2b1xa2 -CCCHHHHHHHHHHHHHHHHCCCCCCEE------ECCCCEEEEECCCCHHHHHHHHHCCCCHH-HHCH--HHHHC-CCCCCC----C------CHHH---CEEEEECC-CCC--EEEEECCCC-----C--------CCCCCHHHCCH--HHHHHHHHHCC-------HHHHHHHCCCCEEEEEE-CCCEEEEEEEECCCCCCCCEEEEEEEEEEEEE-------------CCEEEEEEEEEEEC-CCCHHHHHHHHHHHHHHCCCC--CCCHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCC-CCCCCCCCEEECCCCCCHHHHHHHHHHHHHH------HCC--CCC------------------------- >P1;d2ckfa2 CCCCHHHHHCCHHHHHHHHHCCCCCCEE------EEEEEEEEEECCCCHHHHHHHHHCCCCHH-HHCH--HHHHHHCCHHHH----HCCCCCC---C---CEEEEECC-CCC--EEEEECCCCCCCCC---------CC-HHHHHHHH--HHHHHHHHHHC-------HHHHHHHC--CEEEEEE-CCCEEEEEC------------CCEEEEEEECC-------------CCCEEEEEEEEEEC-CCCHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHCHHHHCCCCCCCCCCCCEEC-CC--CCCCEEEECCCCCHHHHHHHHHHHHHH------HCC--CHHHHHCCCCCCCCCCCCCCHHHHHCCC >P1;d3gzya2 CCCCHHHHCCCCHHHHHHHHCCCCCCEE------ECCCCEEEEECCCHHHHHHHHHHCCHHHHCCCCH--HHHHHHCCC-------CCCHHHCCCCC---CEEEEECCCCCC--EEEEEECCCHHHHHH---------HHHHHHHHHHCCHHHHHHHHHCC---------CCC-HHHEEEEEEEE-CCCEEECCC------------CCEEEEEEECC-------------CCCEEEEEEEEEEC-CCCHHHHHHHHHHHHHHCCCC--CCCHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCCCC--CCCCEEE-ECCCCHHHHHHHHHHHHHH------HCC--CHHHHCC--------------------- >P1;d4hjla2 CCCCHHHHHCCHHHHHHHHHCCCC-CEE------EEEEEEEEEECCCCHHHHHHHHHCCCCHH-HHCH--HHHHHHCCCCHH----HHHHCCCCCCC---CEEEEECC-CCC--EEEEECCCCCCCCCC--------CCHHHHHHHHH--HHHHHHHHHHC-------HHHHHHHC--CEEEEEE-CCCEEEECC------------CCEEEEEEEEE-------------CCEEEEEEEEEEEC-CCCHHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEECCC--CCCCEEECCCCCCHHHHHHHHHHHHHH------CCC--CHHHHHHHCCCHHHHHCCC--------- >P1;d7buga2 --CCHHHHCCC-----------------CCCCCCEEEEEEEEEECCCHHHHHHHH-HCHHHH--HHHCCCHHHHHCCCCCCCEEECCCC-----HHH---CEEEECCCCCCC--CEEEEC----HHH-HCEEECEEEE-----------------------CCEEEEE--CCCCCCCCCCEEEEE-CCCEEEEECCCCC-------CCEEEEEEEEEE-------------CCEEEEEEEEEEEC-C-CHHHHHHHHHHHHHCHHHHIIIIICHHHHHHHHHHHHHHCCCCHHHHCCCC------------------------HHHHHHHHHHHHHHHHCCCCCCHHHHCC---------------------------- PSA >P1;d1kcma- ----------------------------------63210000000041a202003320683348-------------------------a6b3688615434667164c8628542213142349326-------------------------88458825------------b22213223217114131413314---528a512132103026220847300829875266062150200449306b71356820015260a52510408a7026705a6a----------------------a12200001001022659853a8205610851436003100200010240172728305735667798598-- >P1;d1z02a2 ---87423000307713506175032000233a6023102231331124000110-031222--830581700665804222215144-------a7---0032037-9910--100002----035a305334549------------------------9795628--c363-253--01000-1500001000036-------600000204423-------------64100030000330-5-767447705840461044300352142038305841b50587502871a28------------------------92230141027027533799a97--58c7b216474a847757869586638a79a >P1;d2b1xa2 -947787315603201400440044504------35b72351406021320021000206213-8105--70166-900274----6------6004---3100010a-300--000002128-----c--------5937600400a--40271046306-------86006003600100101-04230000110024682942000020304435-------------87501010201004-503970263043003400057--04005402650474198389aa367796726238c9186-17a1703250043010100051026136636------92a--987------------------------- >P1;d2ckfa2 9627866213504200400450025105------33291344426022210020000106220-7104--b1099077603a----13627b7---7---40000001-100--00000280011003---------80-95057105--61364057218-------75114000--0001001-042200000------------00010204458-------------66202030200003-50799025203600440006a--060264159503550554988a55989882636577002-05--502000023030100110031037136------617--517404775a8116608548107734a5 >P1;d3gzya2 9518875201403101300340073715------42bb444250501122002100030523258205--702542149-------8363853a516---900002071000--000002943520431---------02740171018694062037305---------603-03500100001-041400100------------00010403548-------------77402030321002-50687015204510530023a--03006302770154158278893575a6758334a47a4638--6034601-3010210010036035236------729--4287054--------------------- >P1;d4hjla2 95178671153002002003720a-304------44391344515022210021000137220-7102--700671602139----112675818b7---20000002-100--002020400000026--------80274038204--70286038718-------84204001--0002001-042300000------------00020203557-------------61103030100005-60687016301600350004a--040162049612661468678946b69a7284730905372a--522000156020100110030037036------608--6295049407803650269--------- >P1;d7buga2 --577223002-----------------5144b6032212445080224000000-020222--5202605006605030102262666-----775---10641482a451--200202----056-6084425348-----------------------d983535--026294702762000-1500001310023-------501000104436-------------79104050000240-7-779535703840785024100340063016204734a51668702861937------------------------8011003102702882379875786586---------------------------- Translating the sequences ----------------------------------*EEEEEEEEECCC*HHHHHHHHH****HH*-------------------------*******C****EEEEE*C*CCC**EEEEE***C*****-------------------------HHHH***C------------**C***EEEEEE*CC*EEEEE***---*********EEEEEE*****************C**EEEEE*******CCHHH**HHH*******CCC**CCC***HHHHH****----------------------***C*******EEE**CCCCHHHHHHHHHHHHHH******H****C*************************-- ---CHHHH*CC*********CCCC*C********EEEEEEEEEE*CC*HHHHHHH-*CC**H--HH****HHHHH*CCC*********-------*C---CEEEE*C-*CCC--*EEEEC----*************------------------------*******--****-C**--EEEEE-CCCEEEEEC****-------*C*EEEEEEE**-------------CC*EEEEEEEEEEC-C-CHHHHHHHHHHHHH*******CCC*HHHHHHHHHHHHH*CCC*HH**CCCC------------------------***HHHHHHHHHHHHH*******--C**C*************************** -*CCHHHH************CCCC*C**------E****EEEEECCC*HHHHHHHHHCC**HH-HH**--HHHH*-CCC***----*------****---CEEEEECC-CCC--EEEEEC**C-----*--------***********--***HHHH***C-------*******C***EEEEEE-CCCEEEEE***************EEEEEEE**-------------CC*EEEEEEEEEEC-CCCHHHHHHHHHHHHH**CCC--CCC*HHHHHHHHHHHHH*CCC*HH**CCCC*********-C*******EEE**CCCCHHHHHHHHHHHHHH------H*C--C**------------------------- **CCHHHH*CC*********CCCC*C**------EEEEEEEEEECCC*HHHHHHHHHCC**HH-HH**--HHHHH*CC****----*******---C---CEEEEECC-CCC--EEEEEC**C*****---------**-********--***HHHH***C-------*******C--*EEEEEE-CCCEEEEEC------------C*EEEEEEE**-------------CC*EEEEEEEEEEC-CCCHHHHHHHHHHHHH**CCC--CCC*HHHHHHHHHHHHH**C**HH**CCCC*********-C*--****EEE**CCCCHHHHHHHHHHHHHH------H*C--C*************************** **CCHHHH*CC*********CCCC*C**------E****EEEEECCC*HHHHHHHHHCC**HH*****--HHHHH*CCC-------**********C---CEEEEECC*CCC--EEEEE***C******---------***************HHHH***C---------***-*****EEEEEE-CCCEEE**C------------C*EEEEEEE**-------------CC*EEEEEEEEEEC-CCCHHHHHHHHHHHHH**CCC--CCC*HHHHHHHHHHHHH*CCC*HH**CCCC**********C*--****EEE-*CCCCHHHHHHHHHHHHHH------H*C--C******--------------------- **CCHHHH*CC*********CCCC-C**------EEEEEEEEEECCC*HHHHHHHHHCC**HH-HH**--HHHHH*CCC***----**********C---CEEEEECC-CCC--EEEEEC**C******--------***********--***HHHH***C-------*******C--*EEEEEE-CCCEEEE*C------------C*EEEEEEE**-------------CC*EEEEEEEEEEC-CCCHHHHHHHHHHHHH**CCC--C***HHHHHHHHHHHHH*CCC*****CCCC**********C*--****EEE**CCCCHHHHHHHHHHHHHH------**C--C******************--------- --CCHHHH*CC-----------------******EEEEEEEEEECCC*HHHHHHH-HC***H--HH****HHHHH*CCC**********-----***---CEEEE*CC*CCC--*EEEEC----***-**********-----------------------*******--*****C****EEEEE-CCCEEEEEC****-------*C*EEEEEEE**-------------CC*EEEEEEEEEEC-C-CHHHHHHHHHHHHH***********HHHHHHHHHHHHH*CCC*HH**CCCC------------------------***HHHHHHHHHHHHH*******H****---------------------------- 55961-2.tem _________________________________ **CCHHHH*CC*********CCCC*C**------EEEEEEEEEECCC*HHHHHHHHHCC**HH-HH**--HHHHH*CCC***----**********C---CEEEEECC*CCC--EEEEEC**C******--------***********--***HHHH***C-------*******C***EEEEEE-CCCEEEEEC****-------*C*EEEEEEE**-------------CC*EEEEEEEEEEC-CCCHHHHHHHHHHHHH**CCC**CCC*HHHHHHHHHHHHH*CCC*HH**CCCC**********C*--****EEE**CCCCHHHHHHHHHHHHHH******H*C**C*************************-- Structural block scores 0 1 * 3.4 M 75.0 75.0 42.0 7.5 7.0 7.0 75.0 2 3 C 4.5 M 75.0 41.5 5.5 4.5 4.5 4.0 6.0 4 7 H 4.6 H 75.0 4.0 6.2 5.5 5.5 5.5 3.5 9 10 C 4.3 M 75.0 0.0 5.5 4.0 2.5 4.0 1.0 11 19 * 2.5 P 75.0 3.6 1.6 1.6 1.2 0.8 75.0 20 23 C 4.4 M 75.0 3.2 2.0 1.8 2.8 4.9 75.0 26 27 * 2.5 P 75.0 0.0 2.0 2.5 3.0 2.0 75.0 28 33 - 4.2 M 75.0 4.1 75.0 75.0 75.0 75.0 5.2 34 43 E 4.6 H 1.2 1.7 4.2 3.5 4.8 3.8 2.3 44 46 C 4.9 H 1.3 1.7 2.7 2.7 2.0 2.3 3.3 48 56 H 4.9 H 2.5 9.0 0.9 0.6 0.8 0.7 8.8 57 58 C 4.4 M 3.0 2.0 1.0 0.5 1.5 2.0 1.0 59 60 * 1.0 P 5.5 2.0 4.0 4.0 3.5 4.5 2.0 61 62 H 4.7 H 3.5 38.5 2.0 1.0 2.5 1.0 38.5 64 65 H 4.3 M 75.0 5.5 4.5 4.0 5.0 4.0 3.5 66 67 * 1.8 P 75.0 2.5 2.5 2.0 2.5 1.0 1.0 68 69 - 4.2 M 75.0 4.5 75.0 75.0 75.0 75.0 3.0 70 74 H 4.5 M 75.0 3.8 4.0 6.1 3.6 4.0 3.4 76 78 C 4.5 M 75.0 4.0 3.0 6.7 4.7 2.7 2.7 79 81 * 2.5 P 75.0 2.0 4.3 4.5 75.0 4.3 0.3 82 85 - 4.2 M 75.0 2.2 75.0 75.0 75.0 75.0 3.0 86 95 * 2.7 P 27.8 54.4 46.2 26.2 5.2 5.0 40.7 97 99 - 4.6 H 3.3 75.0 75.0 75.0 75.0 75.0 75.0 101 105 E 4.8 H 4.8 1.6 0.4 0.0 0.4 0.0 3.0 106 107 C 4.6 H 5.0 41.0 5.2 0.5 3.5 1.0 5.0 109 111 C 5.0 H 5.3 3.3 1.0 0.3 0.0 0.3 3.3 112 113 - 4.6 H 6.5 75.0 75.0 75.0 75.0 75.0 75.0 114 118 E 4.8 H 2.4 0.2 0.0 0.0 0.0 0.8 0.8 120 121 * 2.5 P 3.0 75.0 1.5 4.0 6.5 2.0 75.0 123 128 * 2.2 P 16.5 16.1 64.6 13.3 2.5 1.3 27.8 129 136 - 4.2 M 75.0 4.1 75.0 75.0 75.0 75.0 3.8 137 147 * 3.2 M 75.0 75.0 4.0 10.5 8.9 3.5 68.9 148 149 - 4.6 H 75.0 75.0 75.0 75.0 7.0 75.0 75.0 150 152 * 3.1 M 75.0 75.0 2.0 3.3 4.3 3.0 75.0 153 156 H 4.4 M 6.2 75.0 3.0 3.8 2.8 4.2 75.0 157 159 * 2.5 P 6.0 75.0 3.0 3.3 3.3 5.3 75.0 161 167 - 4.2 M 75.0 6.6 75.0 75.0 75.0 75.0 6.6 168 174 * 2.3 P 55.5 35.6 2.9 2.6 33.4 2.6 24.1 176 178 * 2.3 P 2.0 27.7 2.0 50.0 1.7 50.0 3.0 179 184 E 4.9 H 2.8 12.7 0.5 0.3 0.3 0.5 2.5 186 188 C 4.9 H 2.0 2.0 2.0 2.0 1.7 2.0 2.0 189 193 E 4.8 H 2.4 0.2 0.6 0.4 1.0 0.6 0.8 195 198 * 3.4 M 38.8 2.2 0.8 75.0 75.0 75.0 1.2 199 205 - 4.3 M 15.2 75.0 5.0 75.0 75.0 75.0 75.0 209 215 E 4.9 H 2.0 1.4 1.9 1.6 1.9 1.7 1.3 216 217 * 1.0 P 2.0 2.5 4.0 6.5 6.0 6.0 4.5 218 230 - 4.6 H 4.7 75.0 75.0 75.0 75.0 75.0 75.0 231 232 C 4.8 H 4.0 5.0 7.5 6.0 7.0 3.5 8.0 234 243 E 4.8 H 2.0 0.9 0.5 0.7 1.1 0.7 1.5 246 248 C 4.7 H 3.0 29.0 2.7 4.0 3.7 4.0 29.7 249 261 H 4.8 H 4.0 4.8 3.2 3.4 3.2 3.1 5.1 262 263 * 1.0 P 3.0 0.5 0.0 0.0 0.0 0.0 2.5 264 266 C 4.2 M 5.8 3.7 4.0 5.5 5.2 4.8 2.3 267 268 * 3.7 M 3.0 0.0 75.0 75.0 75.0 75.0 0.0 269 271 C 4.3 M 1.3 3.3 1.3 2.0 1.0 1.3 2.3 273 285 H 4.8 H 16.5 4.2 4.2 4.1 3.8 4.1 4.0 287 289 C 4.4 M 75.0 6.7 9.2 8.3 7.7 7.0 6.7 291 292 H 4.3 M 75.0 1.0 4.5 5.0 4.0 5.0 1.0 293 294 * 1.8 P 75.0 7.5 7.0 8.5 6.0 8.8 7.0 295 298 C 4.6 H 75.0 5.4 6.0 6.8 7.1 7.1 5.0 299 308 * 3.0 P 53.9 75.0 13.1 11.1 6.0 4.6 75.0 311 312 - 4.2 M 0.0 75.0 5.8 75.0 75.0 75.0 75.0 313 316 * 2.5 P 0.2 75.0 3.0 1.8 3.2 2.2 75.0 317 319 E 4.4 M 1.0 75.0 1.7 0.0 2.3 0.3 75.0 320 321 * 2.8 P 4.0 75.0 3.5 2.5 39.0 5.5 75.0 322 325 C 4.2 M 6.8 22.0 0.5 1.0 0.8 0.8 21.0 326 339 H 4.9 H 4.0 2.7 2.8 1.9 2.1 1.7 2.6 340 345 * 3.7 M 1.7 8.6 75.0 75.0 75.0 75.0 7.2 349 350 * 3.7 M 0.0 10.2 75.0 75.0 75.0 75.0 7.0 352 376 * 3.1 M 4.8 6.4 69.6 4.6 58.0 24.2 75.0 377 378 - 4.2 M 75.0 9.8 75.0 7.8 75.0 75.0 75.0 >>>>>>