Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n10a2 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCC---------CCCCCCCC----CCEEEEEEEEC----------------------CCCC--CCCCCC----------------------------------CCCCC-CCEEEECHH-HHHHHCCCCCEEEEEECC-CCCCCC---CCEEEEEEEECCCCCCCCEEEEEHHHHHCCCCC------------------------------------CCHHHHHCCCCEEEEEEECCCCCCCC---------------- >P1;d2enga- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEEEEEECCCCCCHHHCCC---------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE-----CCEEEEEEEEE-CCCCCHHHHCCCEEEEEECC-HHHC-C---CEEEEEEEECCEEEEECCCCCCCCCCCHHHHHCCCCCCCCCCCCCHHHHHHCCHHHHH--------HHHHHHCCCCCCCCCEEEEEEECCCHHHHHHHCCCCCCHHHCCCC >P1;d2g5da1 CCCCCCCCCCCCCEEEEC---------------CEEEEECCHHHCCCCCCC-CHHHHHHHHHHHHHHHCCCC------------CCHHHHHHHHCC-CCCHHHHHHHHHHHEEEEEEEE-CCCCCEEEEEEEECEEEEECCCCCCCCEEEECCCCCCEEEECCCEEECCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCEEEECCCHHHHHCCCCCCCCCEEEEECCHHHHHHHHHHCCEEEECCCC-CEEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHCH-HHHHHHHCCCCCCEEEEEC---CCCCCCCCCCC--CCCCEEEECC-----CCCCCCCEEEEEEE---CCCC-CCEEEEEEEEEEECC----------------------------CCC------------CCCEEEEEEEEC-HHHHHHHHHC-EEEEEEEEEEECCCCCCCCC------------ >P1;d2pi8a- ------------------CCCCCCCCCCCCCCCCCCCEECC--CCCCCCCCCCHHHHHHHHHHHHHHCHHHHH-----------HCHHHHHHHHHHH---HHCCCCCCCCCCEEEEECCCCCCCCEEEEEEEECEEEEECCCCCCCCEEEECCC--------------------------HHHHH--------------------CCHHHHHHCCCCH-HHEEEEECCC-CCCC-CCCCCEEEECCCCCCCEEEEEEEECCCCCCCHHHHHHHCCCC------CCHHHHHHHHCCHHHHHHHHCCCCCCEEEEECC-CCCCCCCCCCCC--CCCCCEECCC-----CCCCCCCCEEEEEEEECCCCCEEEEEEEECCEEECCC----------------------------CCC------------C-CEEEEEEEEC-HHHHHHHHHC-EEEECEEEEEECC------------------- >P1;d2pnwa1 ----------------------------------CEEEECCHHHCCCHHHC-CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHEEEEEEEE-----EEEEEEEEECEEEEECCCCCCCCEEEECCCCCEEECCC---------CCCCC-CCCC-------CCC--EEEEECCEEECCCCHHHHHCCCCCCCCCEEEEECCHHHHHHHHHHCEEEEECCCC-CEEEEEEEEECCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHCH-HHHHHHHCCCCCCEEEEEE----CCCCCCCCCC--CCCCEEECCC-----CCCCCCCEEEEEECCCCCCCC-CCCEEEEEEEEECCC----------------------------CCC------------CCCEEEEEEEEC-HHHHHHHHCC-EEEEEEEEEEEHHHHHHHC------------- >P1;d3czba- -----------------------------------CCCCCCHHHCCCCCCC-CHHHHHHHHHHHHCCCC-------------CCHHHHHHHHHHHCCCCCHHHHHHHHHHHEEEEE---HHHHCCEEEEEECCCEEECCCCCCCCCCEEECCCCCCCEEEECCCCC--------------HHHCC-----CEEEEEEECCEEEECCCHHHHCCCCCC----CCEEE-CHHHHHHHHHHCEEEEECCCC-CEEEEEEEEECCCCCCCCHHHHHCCCCCC------HHHHHHHHHCCCHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCC--CCCCEEECCC-----CCCCCCCEEEEEEE--------CCCEEEEEEEEECCC----------------------------CCC------------CCCEEEEECCCC-HHHHHHHCCC-EEEEEEEEEEECC------------------- >P1;d4jp6a- --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CEEEEEEEEECCCCHHHCCCCC---------CCCCCCHHHHCCCC----------------------------------HHHHCCCEEEEECCCCCCCHHHHCCCEEEEEECC-----CC---CEEEEEEEEEC---CCC-CEEEEHHHHHHHCCC------------------------------------C---HHHHHCCEEEEEEEECCC---C---------------- >P1;d5xbxa1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCEEC---------CCCCEEEC----CEEEEEEEEECCCCCCCCCCCC---------C-----------------CCCCCCHHHH-HCCEEEECHHHHCCCCCCCCCCCCCCCEEEEE-ECCCCCCC-----CCCCCCC------C---CCEEEEECCCCCCC------------------C---CHHHHCCCCCCCCCCCCCCCCCCEEEEE--CCCCHHHHH-CCCCCCEEEEEECCCHHHHHHHC-CCCCCCC---- PSA >P1;d1n10a2 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------c99889a---------aa6b76a9----82470302347----------------------c350--939628----------------------------------66415-410010083-014a38026000202075-280013---73330000231892429300202160002005a------------------------------------9349602829506040222a1955ac---------------- >P1;d2enga- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------68160312010100300349---------30417310100449184297281520169b070020040003448-----a8200000006-18c48255000000103055-7504-9---1500000014230200000011486200640282011957700955940670395036--------002000500550860504052040287018303030830a82564 >P1;d2g5da1 b74739a52868352653---------------805030162750460780-40250050024007505839------------605500300540-6363740340026100002022-9a644350301100107015773b7053200030730021728a56084579450626043970229b7061000116c860320130660494308c205300101010210200323000041674-723201402301165510072019431195b625184038106826-7439300040210100572---71131305040--2240000005-----41000000000103---2045-48500200000136b----------------------------906------------700101000231-8901720b60-71604000000052506348------------ >P1;d2pi8a- ------------------b7588501168185195543628--50507560504a404600630672279117-----------6239005101601---76a0507637250202010854100030201101214026856b9142100404--------------------------99337--------------------2104601663068-7101010441-2203-041311003046b56320025353074955606500966745------444448137627696245002301000017238-635041427000--1330010017-----84053010001000305c908146712000000155b----------------------------a06------------7-2100000242-7900630720-7110000105448------------------- >P1;d2pnwa1 ----------------------------------36063161950440690-40470170074008205a3760730705040910340045058781743760151036100004043-----4040201000407007847b51622005307203707a---------9423b-c057-------816--00342b8a0440320640452408c4a0100205432500000303003020598-6443004102000922502620077931669711134127107636-9604a10150500100551----1032305040--2531000005-----81001000000104804403b-885011000001175----------------------------608------------410201000123-8800340150-4270500000047007513------------- >P1;d3czba- -----------------------------------9901a70a80610780-70430060023006219-------------6841770194058479285850371037106052---06b076430101410506034956a4031101442b60553410666--------------88489-----65510177bb7237023047037791c----23010-110100200222201020568-6411035132043715606740766823a------971361037333870351045021000061580973041408370--2421000014-----a50a2070000205--------b45032000000232----------------------------407------------63010100113a-a902740b60-7160200303146------------------- >P1;d4jp6a- --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------4179040225504087381306---------60904017300847----------------------------------6821132200000056536278000400401067-----18---24010000141---b38-002002800660054------------------------------------7---406877103040623a26---e---------------- >P1;d5xbxa1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3150933---------9670233a----9520000141646601100007---------8-----------------a566027002-53300000020004376745107000400403-0020205b-----5045046------5---8412000010033b------------------b---48410007241a4452062300000100--145510872-60510000064090497056216-6040394---- Translating the sequences ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*******---------**C*****----**EEEEEEEE*----------------------****--******----------------------------------CC**C-CCEEE*C**-*****C*CCCEEEEEE**-******---**EEEEEEE*CC*********************------------------------------------**HHHH**C**EEEEEEE***C****---------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*EEEEEEE*CCCCC******---------*********************************************-----******EEE**-*********CCCEEEEEE**-****-*---*EEEEEEEE*C******************************CC***************--------****HH*****C***EEEEEEE**C******************** ******************---------------******************-********************------------************-**********************-**********************************************************************************************************************C*********-*EEEEEEEE*CCCCC*C*****************************-*******************---*********CC--CCCCEEE*C*-----**C*CCCEEEEEE*---****-****EEEEEEEE*CC----------------------------*CC------------************-**HHHHH**C-*EEEEEEEE**C********------------ ------------------***********************--******************************-----------*************---******************************************************--------------------------*****--------------------*************-**********-****-***C************EEEEEEE*CCCCC*C***********------*********************************-**********CC--CCCC*EE*C*-----**C*CCC*EEEEE*************EEE**EEE*CC----------------------------*CC------------*-**********-**HHHHH**C-*EEE*EEEE**C*------------------- ----------------------------------*****************-*******************************************************************-----**************************************---------*****-****-------***--*********************************************C*********-*EEEEEEEE*CCCCC*C*****************************-*******************----********CC--CCCCEEE*C*-----**C*CCCEEEEEE********-****EEEEEEEE*CC----------------------------*CC------------************-**HHHHH**C-*EEEEEEEE**********------------- -----------------------------------****************-*****************-------------**********************************---***********************************************--------------*****-----***************************----*****-***********C*********-*EEEEEEEE*CCCCC*C************------*******************************************CC--CCCCEEE*C*-----**C*CCCEEEEEE*--------****EEEEEEEE*CC----------------------------*CC------------************-**HHHHH**C-*EEEEEEEE**C*------------------- --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------**EEEEEEEE*CCC***C****---------**************----------------------------------****CCC*EEE*C**********CCCEEEEEE**-----**---*EEEEEEEE*C---***-***************------------------------------------*---HH*****EEEEEEEE**C---*---------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*******---------**C*****----**EEEEEEEE*CCCCC*C****---------*-----------------**********-*******************CC**CCCCEEE**-*******C-----*******------*---**EEEEE***CC**------------------*---*****CC*********************--****HHHHH-*C****EEEEEE**C********-*******---- 50685.tem _________________________________ ----------------------------------*****************-********************------------***********************************-******************************************------------------*****-----*--*************************-*******************C***********EEEEEEEE*CCCCC*C************-************************************************CC**CCCCEEE*C********C*CCCEEEEEE**-**********EEEEEEEE*CC*****-***************-------*CC------------************-**HHHHH**C**EEEEEEEE**C********------------ Structural block scores 0 33 - 4.7 H 75.0 75.0 36.4 42.2 75.0 75.0 75.0 75.0 34 50 * 3.5 M 75.0 75.0 3.2 12.4 3.7 8.9 75.0 75.0 52 71 * 3.5 M 75.0 75.0 3.0 3.6 3.5 13.4 75.0 75.0 72 83 - 4.6 H 75.0 75.0 75.0 69.3 3.4 63.7 75.0 75.0 84 118 * 3.5 M 75.0 75.0 4.4 9.2 2.9 10.1 75.0 75.0 120 161 * 3.5 M 75.0 75.0 3.1 16.4 10.0 3.5 75.0 75.0 162 179 - 4.4 M 75.0 75.0 5.0 75.0 44.3 59.3 75.0 75.0 180 184 * 3.8 M 75.0 75.0 4.2 6.2 61.4 7.4 75.0 75.0 185 189 - 4.5 M 75.0 75.0 5.9 75.0 46.8 75.0 75.0 75.0 191 192 - 4.3 M 75.0 75.0 0.5 75.0 75.0 5.0 75.0 75.0 193 217 * 3.7 M 75.0 75.0 3.8 37.7 3.9 7.5 75.0 75.0 219 237 * 3.0 P 44.1 75.0 1.1 9.5 1.9 12.6 75.0 41.5 239 249 * 2.7 P 32.2 75.0 9.5 3.4 9.8 9.5 61.8 30.2 250 257 E 4.9 H 2.9 3.4 1.8 2.5 2.0 2.2 3.6 1.0 259 263 C 4.6 H 75.0 0.4 2.6 5.0 2.2 3.0 3.8 3.4 266 277 * 2.9 P 75.0 51.3 3.1 10.2 3.6 5.0 50.8 50.6 279 326 * 2.5 P 60.6 7.7 9.2 10.8 10.4 10.8 54.1 30.0 327 328 C 4.4 M 6.0 75.0 2.0 0.0 2.0 3.5 7.0 3.0 329 330 * 3.4 M 2.5 9.2 75.0 75.0 75.0 75.0 1.5 3.5 331 334 C 4.5 M 21.2 0.5 2.0 1.8 2.8 2.2 2.0 1.0 335 337 E 4.9 H 0.3 0.0 0.0 0.3 0.0 0.0 0.0 1.3 340 347 * 2.7 P 13.1 14.4 48.1 49.2 48.6 49.3 4.2 10.5 350 352 C 4.7 H 2.7 0.0 0.0 1.3 0.3 3.0 1.3 75.0 353 358 E 4.6 H 0.7 0.7 0.2 0.2 0.2 0.3 0.8 14.8 359 360 * 1.6 P 6.0 5.0 39.0 1.5 6.0 40.0 6.5 5.0 362 371 * 2.9 P 24.6 32.6 17.8 5.3 11.8 47.0 53.6 61.3 372 379 E 4.8 H 1.4 0.8 0.4 0.4 0.4 0.6 0.8 1.0 381 382 C 4.7 H 4.5 2.5 8.8 8.2 6.0 2.5 38.0 1.5 383 387 * 3.9 M 5.2 0.4 75.0 75.0 75.0 75.0 34.5 47.9 389 403 * 3.9 M 1.9 2.8 75.0 75.0 75.0 75.0 2.2 70.8 404 410 - 4.5 M 75.0 3.6 75.0 75.0 75.0 75.0 75.0 34.6 412 413 C 4.5 M 75.0 0.0 3.0 3.0 4.0 3.5 75.0 0.0 414 425 - 4.3 M 75.0 5.2 75.0 75.0 75.0 75.0 75.0 4.0 426 437 * 2.8 P 75.0 50.8 1.2 7.8 1.2 2.2 75.0 12.9 439 440 * 1.6 P 42.0 1.0 8.5 8.0 8.0 9.8 41.0 5.0 441 445 H 4.6 H 4.4 1.0 2.0 1.8 1.4 2.6 45.8 3.6 446 447 * 1.4 P 5.0 5.0 8.8 4.5 3.0 8.8 7.0 40.5 449 450 * 2.2 P 7.0 7.0 41.0 41.0 39.5 41.0 4.0 3.0 451 458 E 4.8 H 2.0 2.0 1.4 0.4 1.8 1.5 2.2 1.2 459 460 * 1.0 P 5.8 2.0 0.0 4.5 0.0 2.0 6.2 4.5 462 469 * 3.0 P 41.6 3.8 4.1 66.6 12.2 66.4 67.4 4.5 470 481 - 4.5 M 75.0 4.1 75.0 75.0 75.0 75.0 75.0 33.4 >>>>>>