Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1i42a- CCCCCCCCCCCCCCEEEEEEEC--CC-CCEEEEECC-CCCCCHHHHHHHHCCC-CHHHCCEEEEC--CCCC----CCCCCCC------CCCHHH--CCCCC-EEEEEEC---- >P1;d1j0ga1 -----------CCEEEEEEEECCCCCCCEEEEEEEC-CCCHHHHHHHHHHHCCCCCCCEEEE--C--HHH------CCCCCC------CCHHHHHHHCCCEEEEEECCCCCCC >P1;d1wspa1 -----------CCCEEEEEEECCCCCCEEEEECCC--CCCHHHHHHHCC-----CCCCEEEEEEEECCCCCCCEEEEEECCCCCCCCCCC---------CCEEEEEEEC---C >P1;d2m17a- -----------C-CCCEEEEC-C--CCCEEECCCCC-CCCHHHHHHHHHHHCCCCCCCCEECCCC--CCC------CCCCCC------CCHHHH--CCCCCCEEEEECCCCCC >P1;d5y3ba- ------------CCEEEEEEECCEEEEEEEEECCCCCCCCHHHHHHHHC-----CCCCEEEEEEEEECCC--EEEEEECCCCCCCCCCCC---------CEEEEEEEEC---- >P1;d6iw3a- ------------CCEEEEEEECCCCCCEEEEECCCCCCCCHHHHHCCCC-----CCCCCEEEEEEEECCC--EEEEEECCCCCCCCCCCC---------CEEEEEEECC---- >P1;d6mdha1 -----------CCCCCCCCCC----------------CCCHHHHHHHHHHHHCCCHHHEEEEECC----------------CCCCCCCCCCHHHCCCCCCCCEEEEECC---C PSA >P1;d1i42a- a44280736ba48001060728--9c-283501041-6140521641055447-518a0926120--472a----673091c------a40571--a2215-4040706---- >P1;d1j0ga1 -----------a551504022266885371415144-8440640164007419262640202--0--992------950a35------3600701861537050464a87aab >P1;d1wspa1 -----------692020214129589366431654--602035038307-----6a98051202480b86bb9323421796a4601417---------9401030464---e >P1;d2m17a- -----------a-42302031-9--b9645085044-9330630063015520025840722946--26c------660669------250140--71747151506477689 >P1;d5y3ba- ------------950403142663a93553608573b602062028209-----398a050202063888--655652077395502038---------8501030556---- >P1;d6iw3a- ------------6503011244a5a936425072109602033027309-----93a9160305164988--6635531775a4602199---------4502020668---- >P1;d6mdha1 -----------298191725b----------------704074016104751814681060115b----------------78830889530471b099c37230627a---8 Translating the sequences ***********CCCEEEEEEEC--*C-**EEE**CC-CCC**HHHHHH*****-C*****EEE**--CCC*----***CCCC------CC****--***C*-EEEEE*C---- -----------CC*EEEEEEECC**C**EEEE***C-CCCHHHHHHHH******CCCC*EEE--*--***------**CCCC------CC*********C**EEEE**C**** -----------CCCEEEEEEECC**C**EEEE**C--CCCHHHHHHH**-----CCCC*EEEE****CCC*********CCC******CC---------C**EEEEE*C---* -----------C-C**EEEE*-C--C**EEE***CC-CCCHHHHHHHH******CCCC*EE****--CCC------**CCCC------CC****--***C**EEEEE*C**** ------------CCEEEEEEECC*****EEEE**CC*CCCHHHHHHHH*-----CCCC*EEEE****CCC--******CCCC******CC---------C**EEEEE*C---- ------------CCEEEEEEECC**C**EEEE**CC*CCCHHHHH****-----CCCC*EEEE****CCC--******CCCC******CC---------C**EEEEE*C---- -----------CCC*******----------------CCCHHHHHHHH******C****EEEE**----------------C******CC*********C**EEEEE*C---* 54236-1.tem _________________________________ -----------CCCEEEEEEECC**C**EEEE**CC-CCCHHHHHHHH******CCCC*EEEE****CCC--******CCCC******CC****--***C**EEEEE*C---* Structural block scores 0 10 - 4.6 H 6.0 75.0 75.0 75.0 75.0 75.0 75.0 11 13 C 4.5 M 4.0 6.8 5.7 29.8 29.7 28.7 6.3 14 20 E 4.4 M 2.3 2.0 1.4 1.6 2.0 1.6 5.2 21 22 C 4.4 M 41.5 4.0 5.5 42.0 6.0 7.2 75.0 23 24 * 2.8 P 42.0 7.0 6.5 75.0 6.8 7.8 75.0 26 27 * 2.1 P 38.5 4.0 4.5 7.5 4.0 4.5 75.0 28 31 E 4.4 M 4.0 3.2 3.5 4.2 3.5 2.8 75.0 32 33 * 1.8 P 0.5 3.0 5.5 2.5 6.5 4.5 75.0 34 35 C 4.3 M 2.5 4.0 39.5 4.0 5.0 0.5 75.0 37 39 C 5.0 H 3.7 5.3 2.7 5.0 2.7 2.7 3.7 40 47 H 4.7 H 2.4 2.6 2.8 2.2 2.5 2.2 2.4 48 53 * 2.8 P 16.7 3.8 63.7 2.2 64.0 64.0 4.3 54 57 C 4.4 M 6.1 4.5 8.4 4.8 7.6 7.9 4.8 59 62 E 4.6 H 4.5 19.8 2.0 5.0 1.8 2.2 2.0 63 66 * 2.5 P 38.0 56.2 3.5 40.0 2.8 4.0 41.6 67 69 C 4.3 M 4.3 6.7 8.5 6.8 8.0 8.3 75.0 70 71 - 4.4 M 42.8 75.0 11.5 75.0 75.0 75.0 75.0 72 77 * 3.0 P 40.2 52.3 3.8 52.0 4.8 4.7 75.0 78 81 C 4.6 H 5.6 4.6 5.8 5.2 4.2 5.0 58.0 82 87 * 3.1 M 75.0 75.0 4.2 75.0 3.5 3.9 5.8 88 89 C 5.0 H 7.2 4.5 4.0 3.5 5.5 9.0 7.0 90 93 * 3.1 M 3.2 1.8 75.0 1.2 75.0 75.0 3.5 94 95 - 4.2 M 75.0 4.5 75.0 75.0 75.0 75.0 6.2 96 98 * 3.1 M 4.8 4.0 75.0 5.0 75.0 75.0 6.0 100 101 * 1.4 P 40.0 3.5 2.0 4.0 2.5 2.5 5.0 102 106 E 4.9 H 3.0 3.8 1.6 3.4 1.8 2.0 2.6 109 111 - 4.2 M 75.0 9.3 75.0 7.0 75.0 75.0 75.0 >>>>>>