Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dj0a- ---------------------------CCCEEEEEEEEECCCCCCCCCCC----------CCC-----CCHHHHHHHHHHHHHCCCCC-EEECCCCCCCCEEEEEEEEEEECCCCCHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEEEECCC------CCCCCCCCCCEECCCCCCHH--HHHHHHHHHC-------------EEEE----CHHHCCCCCCCC-----------CCEEEEEEEEEEEE-----CCEEEEEEEECCCCCCHHHHHHHHHH------HHHCCCC--CCCHHHHHHHHC-----CHHHCCCCCCCCCEEEEEEECC----HHHCCCCCCCCCCCCCC------------------------------ >P1;d1k8wa5 -----------------------------CCEEEEEEECC-----CCCHH-------------------HHHHHHHHHCCCC-------EEECCCCCCCCEEEEEEEE-----H-HHHHHHHHHH-----------------------CCCEEEEEEEEECEECCCCCC------CC-CCEECCC-CCC-CCHHHHHHCCCEEEEECCCCCCCCCC-CCCHHHHHH-----------CCCCCCCCCEEEEEEEEEEEEEEC----CEEEEEEEECCC--CCHHHHHHHHHHHC----------------------------------CCCEEEEEEEEEEEC---CCHHH-------CEEHHHHHHHHHHCCCCCCCHHHHHHHCCCCCHHHC-C >P1;d1s71a1 -----------------------CC----CCEEEEEEECC-----CCCHH-------------------HHHHHHHHHCCCC------CEEECCCCCCCCEEEEEEEE-----H-HHHHHHHHCC-----------------------CCCEEEEEEEEECEEECCCCC------CCCEEEECCCCCCCHHHHHHHHHHCCCCC-----------------------------------------CCCCCEEEEEEEEEEEECCEEEEEEEEEECCC--CCHHHHHHHHHHHC----------------------------------CCCEEEEEEEEEEEC--CEEHHH-------CCCHHHHHH---------C--CCCC---EEHHHHHHHC >P1;d1sb7a1 -----------------CCHHHCCCCCCCCCCCCCCCCCHHHEEEEEECCCCCCCCCCEEEEEEEEECCCHHHHHHHHCC-CCCCHHH-CCCCCCCCCCCEEEEEEEECCCC-CCCCCCCC---------CEEEEEEEEECCCCCC-CCCCEEEEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCC--------CCCCCCHHHHHHHHHHHHHHHHHHHCCC----CCCCCCCCCCEEECC-----C-CCCEEECCCCHHHHHHHHHCCCCC-CEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHCCCCEEECCCCCEEEEEEEEE-C-CEEEEEEEEECCCCHHHHHCCCCCC-------------------- >P1;d1v9fa- ----------------CCCCCCCCCEEEECCCEEEEEECC-----CCCCCCC-----------CCCCCCCHHHHHHHHCHHHHHCHHHH--CCCCCCCCCEEEEEEEC-----CHHHHHHHHHHHH--------------------CCCCEEEEEEEEE-CCCC-----------------------------------------CCEEEECCEEE--C---CCCC-----------CCEEECC-CCCCCEEEEEEEEEC----CCEEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-------HHHHHHHH----HCCCCCEEEEEEE--EECCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH----------HHCCC >P1;d1v9ka- ------------------------CCCCCCCCEEEEEECC-----CCCCCCC-----------CC-CCCCHHHHHHHHCCCCC----CC-EECCCCCCCCEEEEEEEC-----CHHHHHHHHHHHH--------------------CCC-CEEEEEEEE-CCCCC----------------------------------------CCCEECCCEEEEEC---CCCC-----------EEEEECC-CCCCCCEEEEEEEEC----CCEEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCC----------------HHHHHHHHHCCCCCCCCCEEEEEEC--CCCCCCC-CCCEECCC-HHHHHHHHCCCCC--------------------- >P1;d1vioa1 ----------------------------CCCCEEEEEECC-----CCCCC---------------CCCCCHHHHCC-------CHHHHC-EECCCCCCCCEEEEEEEC-----C--HHHHHHHHCC--------------------CCCCCEEEEEEEC-CCCCC------------------------------------------------------CHHHHHH-----------HCCCCCCCCCCCCCCEEEECC------CC--EEEEEECCCCCCHHHHHHHHC--------------------------------------CCCEE--EEEEEEEC--CEECCCCCCCC-EEECCHHHHHHCC-------------------------- >P1;d2ab4a2 ------------------------C----CCEEEEEEECC-----CCCHH-------------------HHHHHHHHHCCCC------CEEECCCCCCCCEEEEEEEE-----H-HHHHHHHHHC-----------------------CCCEEEEEEEEECEEECCCCC------CCCEEEECCC-CCCHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCHHHHHH-----------CCCCCCCCCEEEEEEEEEEEEEEC----CEEEEEEEECCC--CCHHHHHHHHHHHC----------------------------------CCCEEEEEEEEEEEC--CEECCC-------CCCCCCCC------------HHHHHHHCEEHHHCCC-C >P1;d2apoa2 CCCCCCCCCCCCCCCCHHHCCHHHH----HCEEEEEEEC------CCCHH-------------------HHHHHHHHHCCCC------CEEECCCCCC-CEEEEEEEE-----H-HHHHHHHHCC-----------------------CCCEEEEEEEEEC-------------------------CCCHHHHHHHHHHHCCCC------------------------------------------CCCCCCEEEEEEEE--CC--EEEEEEEECCC--CCCC-CHHHHHHHC----------------------------------CCCEEEEEEEEEEEC--CEEHHH-------CCCHHHHHHHHHHHHCCCC--CCHHHHEEEHHHHH--C PSA >P1;d1dj0a- ---------------------------a6531000004050170510236----------b4b-----50012400500361083906-0510360454000130000050618397630296047303c305021037059703066107012100001057------9718a447000217360408--1035003404-------------7610----030022a91a3a-----------52513033040435-----a4400010204400420010000000------3000553--537105601835-----529602a206140000030403----b709039371106a298------------------------------ >P1;d1k8wa5 -----------------------------34000001036-----82507-------------------6003303700a05-------0620450251020000000-----3-4016426604-----------------------523020301030013051003------61-4546481-707-a7088106504881705011206255-c63034206-----------7a57082a338020540443237c----540101020257--02000001400340----------------------------------600000240203202---05594-------0160740451494096b2736720462016481048-9 >P1;d1s71a1 -----------------------b3----74000002046-----92508-------------------6006604910929------40420570341020000000-----4-602611a805-----------------------927020401030023045304------81a468563057076a505710792257b-----------------------------------------b5715143050451465951000303030510--65022004400650----------------------------------901000160403302--504294-------035096058---------8--4501---2429605942 >P1;d1sb7a1 -----------------2939703111960826051337370030304025a1467362000103036250460053003-0926475-01104526561102000003799-b3706703---------9070253410695078-a60601502000370643a2036005304900000007314ac65135205700667--------8187917730300102000101030053----b62250120000226-----b-69734206873b503520653500-0001003a1205670272067007a38602700642380501410205a0717046-8-6001050204380305000100034-------------------- >P1;d1v9fa- ----------------595472807223239100002053-----7020309-----------bb576500000014436505905500--00050242000000001-----4650175044217--------------------6650200000001-5408-----------------------------------------82740732035--2---7858-----------a213157-807701041401240----25002020303334320000002429210000521b044920ac06-------a8035217----8060000001003--060036775131608227403500610461267447----------8568d >P1;d1v9ka- ------------------------a635249200003050-----6440509-----------8a-b6801038158836a2a----10-510240153000000002-----4730174055137--------------------556-722130004-65067----------------------------------------82610613044844---b714-----------3107239-807803050513341----3200004020314310001000452710002082003----------------570165076280b081000001214--1410257-76636086-980650163483a--------------------- >P1;d1vioa1 ----------------------------674311001016-----70207---------------8a56200520c-------a32860-400370426010000001-----2--6900730408--------------------9562611040403-6506a------------------------------------------------------8056305-----------80160aa29550570806337------85--30101021a184004200631--------------------------------------90704--60303204--70503a08505-2260788117405-------------------------- >P1;d2ab4a2 ------------------------6----53000002025-----82606-------------------4003200621927------70521760350020000000-----0-5017118608-----------------------815120202020001051202------5095454490-a186950590034139425040012054537845034006-----------69661818455040260350608c----520103030126--02000002300950----------------------------------801000040202102--514285-------01202805------------4850494035397037-4 >P1;d2apoa2 ba7a897a76788c44267108601----3300000104------b1508-------------------5003404710909------6041056075-140000000-----2-4018127507-----------------------6230103020308-------------------------526595055008514881------------------------------------------8254055050381a--84--4040203041a--0906-006500730----------------------------------a36050480301400--204570-------0171940550155147787--33036001024103--5 Translating the sequences ---------------------------**C**EEEEEE*C*****CCC**----------***-----**HHHHHHHH**********-*EECCCCCCCCEEEEEEEE********HHHHHHHH************************CCCEEEEEEEEEC**------*****************C**--*HHHHHH***-------------****----************-----------CC****EEEEEEEE-----*CEEEEEEEECCC**C*HHHHHHH**------*******--************-----*****CCC*****EEEEEE***----*********CCC*****------------------------------ -----------------------------CC*EEEEEECC-----CCC**-------------------*HHHHHHHHCC*C-------*EECCCCCCCCEEEEEEEE-----*-HHHHHHHHH*-----------------------CCCEEEEEEEEEC********------**-*******-C**-**HHHHHH******************-*********-----------********C*****EEEEEEEE**----CEEEEEEEECCC--C*HHHHHHH****C----------------------------------CCCEE***EEEEEEC---*****-------C***HHHHHH**************************-* -----------------------**----CC*EEEEEECC-----CCC**-------------------*HHHHHHHHCC*C------**EECCCCCCCCEEEEEEEE-----*-HHHHHHHH**-----------------------CCCEEEEEEEEEC********------***********C*****HHHHHH******-----------------------------------------CCCCC*EEEEEEEE*******EEEEEEEECCC--C*HHHHHHH****C----------------------------------CCCEE***EEEEEEC--*E****-------CCC*HHHHH---------*--****---********** -----------------************CC*******C*******************************HHHHHHHHCC-C******-***CCCCCCCCEEEEEEEE****-********---------****************-*CCCEEEEEEEEEC*************************C*****HHHHHH******--------****************************----*CCCCC****EEE**-----*-***EEE**CC*****HHHH*****-************************************CCCEE******EEE****E*-*-**************HHH********-------------------- ----------------*************CC*EEEEEECC-----CCC****-----------*******HHHHHHHHC**********--*CCCCCCCCEEEEEEE*-----**HHHHHHHHH**--------------------**CC*EEEEEEEE-C***-----------------------------------------***********--*---****-----------*******-CCCCC*EEEEEEEE*----*CEEEEEEEECCC**C*HHHHHHH****C*****************-------********----******EEEEEE*--*E***********CCC*HHHHHH*************----------***** ------------------------*****CC*EEEEEECC-----CCC****-----------**-****HHHHHHHHCC*C*----**-EECCCCCCCCEEEEEEE*-----**HHHHHHHHH**--------------------**C-CEEEEEEEE-C****----------------------------------------**************---****-----------*******-CCCCC*EEEEEEEE*----*CEEEEEEEECCC**C*HHHHHHH****C********----------------**********CCC*****EEEEEEC--*******-*****CCC-HHHHHH*******--------------------- ----------------------------*CC*EEEEEECC-----CCC**---------------*****HHHH**-------******-EECCCCCCCCEEEEEEE*-----*--HHHHHHHH**--------------------**CCCEEEEEEE*-C****------------------------------------------------------*******-----------********CCCCC**EEEE**------*C--EEEEEECCC**C*HHHHHHH*--------------------------------------CCCEE--*EEEEEEC--*E*********-***C*HHHHHH**-------------------------- ------------------------*----CC*EEEEEECC-----CCC**-------------------*HHHHHHHHCC*C------**EECCCCCCCCEEEEEEEE-----*-HHHHHHHHH*-----------------------CCCEEEEEEEEEC********------**********-C*****HHHHHH****************************-----------********C*****EEEEEEEE**----CEEEEEEEECCC--C*HHHHHHH****C----------------------------------CCCEE***EEEEEEC--*E****-------CCC*****------------****************-* *************************----*C*EEEEEEC------CCC**-------------------*HHHHHHHHCC*C------**EECCCCCC-CEEEEEEEE-----*-HHHHHHHH**-----------------------CCCEEEEEEEEEC-------------------------C*****HHHHHH******------------------------------------------CCCC**EEEEEEE*--**--EEEEEEEECCC--C***-*HHH****C----------------------------------CCCEE***EEEEEEC--*E****-------CCC*HHHHHH*********--**************--* 55120.tem _________________________________ -----------------------**--**CC*EEEEEECC-----CCC**----------------****HHHHHHHHCC*C********EECCCCCCCCEEEEEEEE-----**HHHHHHHHH**--------------------**CCCEEEEEEEEEC********------**********-C*****HHHHHH******-*********************-----------********CCCCC*EEEEEEEE*----*CEEEEEEEECCC**C*HHHHHHH****C---*****---------------------***--CCCEE***EEEEEEC--*E***********CCC*HHHHHH*********--****---********-* Structural block scores 0 22 - 4.5 M 75.0 75.0 75.0 56.7 53.9 75.0 75.0 75.0 7.0 23 24 * 3.2 M 75.0 75.0 7.2 2.0 3.5 42.8 75.0 40.5 0.5 25 26 - 4.0 M 75.0 75.0 75.0 1.0 2.0 4.5 75.0 75.0 75.0 27 28 * 3.4 M 8.2 75.0 75.0 7.5 2.5 3.5 40.5 75.0 75.0 29 30 C 4.7 H 4.0 3.5 5.5 4.0 6.0 6.5 5.5 4.0 3.0 32 37 E 4.7 H 0.7 0.2 0.3 3.0 0.3 0.5 0.5 0.3 0.2 38 39 C 4.6 H 2.5 4.5 5.0 5.0 4.0 2.5 3.5 3.5 39.5 40 44 - 4.4 M 2.6 75.0 75.0 2.0 75.0 75.0 75.0 75.0 75.0 45 47 C 4.7 H 1.0 5.0 5.3 2.3 3.0 4.7 3.0 5.3 5.8 48 49 * 1.0 P 4.5 3.5 4.0 1.0 1.5 2.5 3.5 3.0 4.0 50 65 - 4.4 M 62.6 75.0 75.0 3.0 53.9 58.0 70.8 75.0 75.0 66 69 * 2.9 P 38.8 57.8 57.8 4.0 4.5 6.4 5.9 57.2 57.5 70 77 H 4.9 H 1.5 2.0 3.2 2.2 1.1 4.2 21.2 1.6 2.4 78 79 C 4.3 M 1.5 5.2 4.5 1.5 4.5 4.5 75.0 5.0 4.5 82 89 * 3.3 M 12.6 65.6 56.8 13.5 12.4 48.3 22.4 57.1 57.0 90 91 E 4.5 M 3.0 4.0 3.0 1.0 37.5 3.0 2.0 3.5 2.5 92 99 C 5.0 H 2.8 2.1 2.5 3.6 1.6 1.9 2.8 2.8 12.4 100 107 E 4.9 H 0.5 0.2 0.2 0.4 0.1 0.2 0.2 0.2 0.5 108 112 - 4.5 M 2.4 75.0 75.0 20.6 75.0 75.0 75.0 75.0 75.0 113 114 * 2.3 P 5.5 39.0 39.5 7.2 5.0 5.5 38.5 37.5 38.5 115 123 H 4.6 H 4.7 3.2 3.8 27.6 3.1 2.9 11.6 3.2 3.1 124 125 * 2.6 P 5.5 39.5 40.0 75.0 4.0 5.0 4.0 41.5 41.0 126 145 - 4.5 M 3.2 75.0 75.0 18.3 75.0 75.0 75.0 75.0 75.0 146 147 * 3.4 M 6.0 75.0 75.0 42.8 6.0 5.0 7.0 75.0 75.0 148 150 C 4.8 H 2.7 3.3 6.0 4.0 2.3 29.3 4.7 4.7 3.7 151 159 E 4.9 H 0.6 1.0 1.1 1.2 8.4 9.7 9.8 1.0 1.0 161 168 * 2.8 P 57.8 1.6 2.6 3.6 48.4 39.8 40.2 1.4 75.0 169 174 - 4.4 M 6.6 75.0 75.0 2.3 75.0 75.0 75.0 75.0 75.0 175 184 * 3.2 M 3.0 11.4 5.2 2.0 75.0 75.0 75.0 4.5 75.0 187 191 * 3.0 P 31.8 19.9 5.7 7.6 75.0 75.0 75.0 5.8 5.4 192 197 H 4.4 M 1.8 3.8 3.3 2.7 75.0 75.0 75.0 2.8 3.0 198 203 * 2.9 P 38.8 4.3 6.1 4.3 75.0 75.0 75.0 3.8 4.5 205 225 * 3.2 M 47.2 6.6 75.0 27.6 21.2 14.3 51.3 2.9 75.0 226 236 - 4.5 M 24.9 75.0 75.0 0.6 75.0 75.0 75.0 75.0 75.0 237 244 * 3.1 M 75.0 6.2 75.0 39.9 13.1 12.5 4.8 5.6 75.0 245 249 C 4.2 M 3.2 3.2 5.9 3.0 4.4 4.6 4.8 3.6 18.8 251 258 E 4.6 H 2.8 3.1 2.8 1.5 2.0 2.6 12.8 2.8 3.4 260 263 - 4.4 M 75.0 59.4 6.2 75.0 75.0 75.0 75.0 59.4 40.5 266 273 E 4.8 H 0.9 1.0 1.1 4.6 0.9 0.8 19.4 1.1 1.6 274 276 C 4.9 H 2.7 4.7 2.0 6.0 3.0 2.7 4.5 3.0 5.2 277 278 * 3.2 M 2.0 75.0 75.0 8.2 3.5 2.0 4.5 75.0 75.0 281 287 H 4.7 H 0.1 0.7 1.7 3.7 0.9 1.4 2.1 0.7 13.1 288 291 * 1.9 P 37.5 1.8 2.8 18.8 3.5 2.5 56.5 3.5 2.5 293 295 - 4.0 M 75.0 75.0 75.0 0.3 0.0 0.7 75.0 75.0 75.0 296 300 * 3.6 M 1.6 75.0 75.0 3.3 3.9 2.6 75.0 75.0 75.0 301 321 - 4.2 M 27.5 75.0 75.0 4.1 28.5 58.0 75.0 75.0 75.0 322 324 * 3.6 M 5.3 75.0 75.0 2.0 3.3 4.0 75.0 75.0 75.0 325 326 - 4.0 M 3.0 75.0 75.0 3.0 75.0 4.0 75.0 75.0 75.0 327 329 C 4.7 H 4.8 2.0 3.3 3.7 52.7 6.5 5.3 3.0 6.5 330 331 E 4.0 M 3.0 0.0 0.0 2.5 3.0 4.0 2.0 0.0 2.5 332 334 * 1.4 P 1.7 2.0 2.3 2.0 0.0 0.3 52.0 1.3 4.0 335 340 E 4.9 H 0.5 1.2 1.7 2.9 0.2 0.7 1.3 0.8 1.3 342 343 - 4.4 M 1.5 75.0 75.0 4.0 75.0 75.0 75.0 75.0 75.0 346 356 * 2.7 P 18.1 49.8 49.5 16.0 3.5 10.7 10.3 49.5 49.2 357 359 C 4.3 M 0.7 2.3 2.7 2.0 3.3 4.7 2.7 1.0 2.7 361 366 H 4.2 M 29.9 3.5 17.2 2.7 3.2 4.7 4.8 27.5 3.8 367 375 * 3.2 M 75.0 5.8 67.6 9.2 2.9 20.6 58.9 75.0 5.0 376 377 - 4.2 M 75.0 4.5 75.0 75.0 5.5 75.0 75.0 39.5 75.0 378 381 * 3.4 M 75.0 3.2 2.5 75.0 40.2 75.0 75.0 4.2 2.2 382 384 - 4.0 M 75.0 2.7 75.0 75.0 75.0 75.0 75.0 4.3 2.0 385 392 * 3.5 M 75.0 4.0 4.6 75.0 49.2 75.0 75.0 4.6 10.8 >>>>>>