Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fm0d- -----CEEEEECHHHHHHHC---CCEEEECCC---CCCHHHHHHHHHCCCH--------------------HHHHHHCCC----------CCEEEECCEEC-CCC-----CCCCCCCEEEEECCCCCC >P1;d1ryja- -CCCCEEEEEEE---CC-------EEEEEEEC--CCCCHHHHHHHH---------------------------------CCCC------CCCEEEECCEEC-CCC-----CCCCCCCEEEEECCCCCC >P1;d1tygb- --------CEEECC------------EEECCC--CCCCHHHHHHHC---------------------------------CCCC------CCCEEEECCEEE-CHH-HCCCCCCCCCCEEEEECCCCC- >P1;d1v8ca1 ------CEEEECCHHHHHHC---CCEEECCCC-----CHHHHHHHHHHHC---HHHHHHHEEC----------------------CEECCCCEEEECCEE--HHHCCHHHCCCCCCCEEEEECCCCCC >P1;d1vjka1 -----CEEEECCCHHHHHHC---CCCEEEECC--CCCCHHHHHHHHHHHCC--------------------CCCCCCCCCCCC------CCCEEEECCCCC-CCC-----CCC-CCCCEEEECCC--- >P1;d1zud2- --------CEEECC------------EEECCC--CCCCHHHHHHHH---------------------------------CCCC------CCEEEEECCEEC-CHH-HCCCCCCCCCCEEEEEECCCCC >P1;d2cu3a1 ------------------------CEECCEECCCCCCCHHHHHHC----------------------------------------CCCHHHEEEEECCEEEEHHH--CCCCCCCCCCEEEEEECC--C >P1;d2hj1a1 --CEEEEEEEEEEC-------CEEEEEEEEEEC--CCCHHHHHHHHCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------------------------- >P1;d2k9xa- CCCCCCCEEEEECCCCCCCC--CCCEECCCCCCCCCCCHHHHHHHHHHHHCCCC--CCCCCCC--------------------CCCCCCCCEEEEECCCC--HHHHCCCCCCCCCCCEEEEEECCCCC >P1;d2qjla- ---CEEEEEEEECCHHHHCC--CCCEEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHEEC----------------------CEECCCEEEEECCEE--HHHHCHHHCCCCCCCEEEEEECCCCC >P1;d4idia- ---CEEEEEEEECCHHHHCCCCCCCEEEEEECC-CCCCHHHHHHHHHHHCCCCC---CCCCCCCCCCEEEECCCCCEEEEECCCCCCCCCCEEEEECCEE--HHHCCHHHCCCCCCC-CEEEEC---- PSA >P1;d1fm0d- -----504020668047306---472461528---273033016400756b--------------------61380066c----------80401067761-829-----4608781301011489bf >P1;d1ryja- -9a710500143---96-------8666451a--643406620667---------------------------------8354------971202088a62-826-----35065923011566a98f >P1;d1tygb- --------305167------------87281a--b91104500555---------------------------------926b------590303159670-779-4076270927250416587cc- >P1;d1v8ca1 ------0402046505940a---464161717-----3025004200643---6606a3008b----------------------a70298020316962--0392752806088a1303040198cb >P1;d1vjka1 -----240500675048109---566260808--aa040450072038329--------------------60a18004364b------04000106a741-634-----470-7a260301329--- >P1;d1zud2- --------603048------------853805--a82104500572---------------------------------9492------970500057950-559-508a4407980504057799bf >P1;d2cu3a1 ------------------------052596549167420560096----------------------------------------c38374020404a5626067--01856089815041585b--d >P1;d2hj1a1 --944835121728-------856145726086--b1858511660802a5076053984a396666958a96a69ba486395a989---------------------------------------- >P1;d2k9xa- 97c98405020385037024--75934617a383a9140230063106782748--484004a--------------------94550480062205775--07727726270c4202020326988b >P1;d2qjla- ---3060403036801700c--86551806086966030220073027510a67a2284016b----------------------870263030305a36--1573843916087a04010323980b >P1;d4idia- ---825040303680373065583340306082-a5050300000015100567---8200637965426004c66266020447070488040306965--186293291706480-010426---- Translating the sequences -----**EEEE*********---**EEEE**C---CCCHHHHHHHH*****--------------------*********----------C*EEEECCEE*-***-----CCCCCCCEEEEE*CC*** -******EEEE*---**-------*EEEE**C--CCCCHHHHHHHH---------------------------------****------CC*EEEECCEE*-***-----CCCCCCCEEEEE*CC*** --------*EE***------------EEE**C--CCCCHHHHHHH*---------------------------------****------CC*EEEECCEE*-***-****CCCCCCCEEEEE*CC**- ------*EEEE*********---**EEE***C-----CHHHHHHHH****---**********----------------------****CC*EEEECCEE--********CCCCCCCEEEEE*CC*** -----**EEE**********---***EEE**C--CCCCHHHHHHHH*****--------------------************------CC*EEEECC***-***-----CCC-CCC*EEEE*CC--- --------*EE***------------EEE**C--CCCCHHHHHHHH---------------------------------****------CC*EEEECCEE*-***-****CCCCCCCEEEEE*CC*** ------------------------*EE****C**CCCCHHHHHH*----------------------------------------*******EEEECCEE*****--***CCCCCCCEEEEE*CC--* --*****EEEE***-------****EEEE****--CCCHHHHHHHH******************************************---------------------------------------- *******EEEE*********--***EE****C**CCCCHHHHHHHH********--*******--------------------******CC*EEEECC**--********CCCCCCCEEEEE*CC*** ---****EEEE*********--***EEEE**C**CCCCHHHHHHHH*****************----------------------****CC*EEEECCEE--********CCCCCCCEEEEE*CC*** ---****EEEE**************EEEE**C*-CCCCHHHHHHHH********---********************************CC*EEEECCEE--********CCCCCCC-*EEE*C---- 54285.tem _________________________________ ---****EEEE*********--***EEEE**C*-CCCCHHHHHHHH********--*******--------************--****CC*EEEECCEE*-********CCCCCCCEEEEE*CC*** Structural block scores 0 2 - 4.5 M 75.0 31.5 75.0 75.0 75.0 75.0 75.0 53.0 9.5 75.0 75.0 3 6 * 3.1 M 38.8 3.2 75.0 56.2 39.0 75.0 75.0 4.8 5.2 2.2 3.8 7 10 E 4.6 H 1.5 1.2 20.8 1.5 1.2 21.0 75.0 2.2 1.8 1.8 1.8 11 19 * 2.7 P 4.4 52.0 51.6 4.8 4.4 51.3 75.0 51.9 3.6 4.2 4.0 20 21 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 41.5 75.0 75.0 5.0 22 24 * 2.9 P 28.7 52.7 75.0 28.3 28.7 75.0 50.0 4.0 7.0 6.3 4.7 25 28 E 4.5 M 3.2 5.5 23.0 3.0 3.5 22.8 5.2 4.5 3.5 3.5 1.8 29 30 * 1.0 P 3.5 3.0 4.5 4.0 4.0 4.0 5.5 3.0 8.8 3.0 3.0 34 37 C 4.8 H 21.8 4.2 5.6 57.0 6.2 5.4 4.8 23.9 6.1 3.8 5.1 38 45 H 4.9 H 2.1 4.1 3.0 1.6 2.2 2.9 12.6 4.0 1.9 1.8 0.4 46 53 * 3.2 M 31.8 75.0 75.0 30.5 31.2 75.0 75.0 4.8 5.2 4.8 3.1 54 55 - 4.2 M 75.0 75.0 75.0 3.0 75.0 75.0 75.0 2.5 75.0 6.2 75.0 56 62 * 3.6 M 75.0 75.0 75.0 5.6 75.0 75.0 75.0 6.6 4.4 4.6 13.4 63 70 - 4.5 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.1 75.0 75.0 4.9 71 82 * 3.6 M 22.3 51.7 52.4 75.0 4.5 52.0 75.0 7.7 75.0 75.0 4.0 83 84 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.8 6.5 75.0 5.5 85 88 * 3.3 M 75.0 75.0 75.0 4.9 75.0 75.0 6.6 25.2 3.5 4.2 2.8 89 90 C 4.5 M 41.5 8.0 7.0 8.5 2.0 8.0 5.5 75.0 4.0 4.5 8.0 92 95 E 4.8 H 1.2 1.0 1.8 1.5 0.2 1.2 1.5 75.0 2.5 1.5 1.8 96 97 C 4.8 H 6.5 8.0 7.0 7.5 8.2 6.0 7.2 75.0 6.0 7.8 7.5 98 99 E 4.3 M 6.5 8.2 6.5 4.0 5.5 7.0 5.5 75.0 6.0 4.5 5.5 102 109 * 2.5 P 49.2 48.9 14.4 4.5 48.5 14.7 21.5 75.0 4.8 5.0 5.0 110 116 C 4.8 H 4.9 4.3 4.1 4.8 15.1 4.6 5.3 75.0 3.9 4.6 3.7 117 121 E 4.7 H 1.0 2.0 3.2 2.0 2.0 2.8 3.0 75.0 1.4 1.6 16.0 123 124 C 4.7 H 6.0 8.2 7.5 5.0 5.5 8.0 8.2 75.0 7.5 6.0 40.5 125 127 * 2.8 P 14.3 13.2 33.3 10.7 75.0 14.3 54.5 75.0 9.2 6.5 75.0 >>>>>>