Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1exta1 CCCCCCEEECCCCCCCEEECCCC--CEEEEECCCCCCCCCEEEECCCCCCCC----CCCCCC-----CCC-------------- >P1;d1exta2 ----------------CCCCCCHHHCCEEEECC-CCCCCCEEE-CCCCCEEEEEECCEEEEE---------------------- >P1;d1exta3 ----------------CCCCCC---CEEEEECC-CCCCCCEEEECCC-EEEEC------CEEEEHHHCCCCCCCHHHHCCCCCC >P1;d1sg1x2 ----------------CCCCCCC--CEEEEECC-CCCCCCEEE-ECCCCEECCCCC---CEE---------------------- >P1;d1sg1x3 ----------------CCCCCCC--CEEEEECC-CCCCCCEEEECCCCCCCC----CCCCCC-----CCC-------------- >P1;d1xu1r- -----------------CCCCCHHHCEEEEC--------------------------CCCEEEEHHHHCC--CCCHHHHHHHC- >P1;d1xu2r- --------------------CC--CCEEEEC--------------------------CCCEEEEHHHCCCCCCCCHHHHHHHHC >P1;d2heyr1 ----------------CCCCCCHHHCEEEEECC-CCCCCCEEEECCC-EEECC-CCCCCCCEEECCCCCCCCCCCCCCC----- >P1;d2heyr3 CCCCCCEEEEC---CEEEECCCC--CEEEEECC-CCCCCCEEEECCCCCCCC----CCCCC------CCC-------------- >P1;d3wvta1 CCCCCCEEEEC---CEEEECCCC--CEEEEECC-CCCCCCEEEECCCCEECC----CCCCCC-----CCEEC-----------C >P1;d3wvta2 -------------------CCCHHHCEEEEECC-CCCCCCEEEECCC-EEEEEEECCEEEEEEEC------------------- >P1;d4i9xc1 -------------------CCCCCCCEEECCC------CCEEECCCCCCCCCCCC--CCCCCC--------------------- >P1;d4i9xc2 ----------------CCCCCCC--CEEEEECC-CCCCCCEEE-ECCCCCCCCCCC---CCC---------------------- >P1;d4i9xc3 ----------------CCCCCCCC---CCCCCC-CCCCCCCC------------------------------------------ PSA >P1;d1exta1 6a06a840414957712072075--82106710517c690614807bb2608----851455-----906-------------- >P1;d1exta2 ----------------b5690668280355261-5b9560510-079a3745457aa31204---------------------- >P1;d1exta3 ----------------b50807---60546581-5a956050705a9-30439------37034197079949079516977ac >P1;d1sg1x2 ----------------b56818c--42551461-7b9850607-03b947539a65---605---------------------- >P1;d1sg1x3 ----------------b364076--81013741-798470425905bb3607----743474-----506-------------- >P1;d1xu1r- -----------------b8706558050428--------------------------967722506733a--a24a5047408- >P1;d1xu2r- --------------------28--a520518--------------------------968631407732b6b8129804a409b >P1;d2heyr1 ----------------b4390589300855672-6a97301030768-03166-9964015037049c47040716708----- >P1;d2heyr3 3809b611533---a43082084--83005550-289691428707ac6606----72218------706-------------- >P1;d3wvta1 a509974153c---a42041064--74305641-7a9680423607982505----941049-----90573-----------a >P1;d3wvta2 -------------------b0578420545674-7a95a100215ab-2523568c830530569------------------- >P1;d4i9xc1 -------------------b050347311285------8625607ba62707861--647906--------------------- >P1;d4i9xc2 ----------------955808b--41654461-6b8760506-05bb47328888---616---------------------- >P1;d4i9xc3 ----------------35b608ac---857874-38854018------------------------------------------ Translating the sequences *******************CCC*--CEEEEECC*CCCCCCEEE**CC*****----***C**-----***-------------- ----------------***CCC***C*EEEECC-CCCCCCEEE-*CC***************---------------------- ----------------***CCC---CEEEEECC-CCCCCCEEE**CC-*****------C************************ ----------------***CCC*--CEEEEECC-CCCCCCEEE-*CC*********---C**---------------------- ----------------***CCC*--CEEEEECC-CCCCCCEEE**CC*****----***C**-----***-------------- -----------------**CCC***CEEEE*--------------------------**C**********--***********- --------------------CC--*CEEEE*--------------------------**C************************ ----------------***CCC***CEEEEECC-CCCCCCEEE**CC-*****-*****C*******************----- ***********---*****CCC*--CEEEEECC-CCCCCCEEE**CC*****----***C*------***-------------- ***********---*****CCC*--CEEEEECC-CCCCCCEEE**CC*****----***C**-----*****-----------* -------------------CCC***CEEEEECC-CCCCCCEEE**CC-*****************------------------- -------------------CCC***CEEE**C------CCEEE**CC********--**C***--------------------- ----------------***CCC*--CEEEEECC-CCCCCCEEE-*CC*********---C**---------------------- ----------------***CCC**---****CC-CCCCCC**------------------------------------------ 57586.tem _________________________________ ----------------***CCC***CEEEEECC-CCCCCCEEE**CC************C*****--***-------------- Structural block scores 0 15 - 4.5 M 5.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 18.1 19.1 75.0 75.0 75.0 75.0 16 18 * 2.2 P 3.0 7.5 5.5 7.5 6.8 31.5 75.0 6.2 3.7 2.0 75.0 75.0 6.3 6.5 19 21 C 4.9 H 3.0 5.0 5.0 5.7 3.7 4.3 28.3 4.7 3.3 2.3 5.5 5.5 5.3 4.7 22 24 * 3.1 M 51.7 5.3 75.0 54.2 52.0 6.0 53.5 6.7 51.3 51.3 6.3 2.3 53.8 32.7 26 30 E 4.6 H 3.2 3.0 4.0 3.4 2.4 3.8 3.2 4.8 2.6 3.6 4.0 3.0 4.0 20.6 31 32 C 4.6 H 0.5 3.5 4.5 3.5 2.5 75.0 75.0 4.5 2.5 2.5 5.5 40.0 3.5 5.5 34 39 C 4.6 H 5.9 6.1 5.9 6.8 5.8 75.0 75.0 5.9 5.8 6.8 7.2 52.3 6.4 4.7 40 42 E 4.5 M 3.7 2.0 4.0 4.3 3.7 75.0 75.0 1.3 4.7 3.0 0.7 4.3 3.7 28.0 43 44 * 2.6 P 4.0 37.5 2.5 37.5 4.5 75.0 75.0 3.5 3.5 3.0 3.0 3.5 37.5 75.0 45 46 C 4.5 M 9.2 8.0 9.8 7.2 8.2 75.0 75.0 7.0 8.8 8.0 11.0 11.0 8.2 75.0 47 58 * 2.9 P 28.5 5.9 45.3 23.6 28.5 63.8 63.8 16.2 28.5 27.8 10.8 16.4 23.7 75.0 60 64 * 2.9 P 47.0 45.8 3.0 46.0 47.2 3.2 2.8 3.0 61.6 47.6 4.6 33.0 46.4 75.0 65 66 - 4.2 M 75.0 75.0 8.0 75.0 75.0 6.5 7.0 6.5 75.0 75.0 75.0 75.0 75.0 75.0 67 69 * 3.1 M 5.0 75.0 5.3 75.0 3.7 5.5 5.5 7.8 4.3 4.7 75.0 75.0 75.0 75.0 70 83 - 4.3 M 75.0 75.0 6.9 75.0 75.0 20.0 6.0 29.1 75.0 60.4 75.0 75.0 75.0 75.0 >>>>>>