Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fmta1 CCHHHHCCC---CCCCHHHHHHHHHHCC-CCCCEEEEECC---EEEEEEEEEEEC---CCCCCC-----------------CCCEEEEEC----CEEEEECCC--CEEEEEEEEECC--------------CCCEEHHHHHHHCH-HHCCCCCCCC----------------------------------------------------- >P1;d1xg9a4 -CCHHHCCC---CCCCHHHHHHHHCCCCCCCCCCEEEC-C---CEEEEEEEECC---------------------------------------------------CCCEEEEEEECC-------------------------------------------------------------------------------------------- >P1;d2blna1 ---CCCCCC---CCCCHHHHHHHHHHCCCCCCCEEEEECC---EEEEEEEEEEEC---CCCCCC-----------------CCCEEECC------CEEEECCC--CEEEEEEEEECC--------------CCCEEHHHHHHHHC---CCCCCCC------------------------------------------------------ >P1;d2bw0a1 CCHHHHCCC---CCCCHHHHHHHHHCCC-CCCCCEEEECC---EEEEEEEEECCCCCCCCCCEEECCC------------CCCCCEEEEC----CEEEEECCCC-CEEEEEEEECCC--------------CCEEEHHHCCC------------------------------------------------------------------- >P1;d3rfoa2 CCHHHHCCC---CCCCHHHHHHHHHHCC-CCCCCEEEECC---EEEEEEEEEEEE---CCCCCC-----------------CCCEEEECC----CCEEECCCCC-EEEEEEEEEECC--------------CCC-CHHHHHHHCC---CCCCCCCC----------------------------------------------------- >P1;d3ubya1 -----CCCCHHHHCCCHHHHHHHCCCC-----EEEEECCCCCEEEEEEEEEEEECCCC--CCCCCCHHHCCCCHHHHHHCCCCCEEEEEECCCEEEEEEECCCCCCEEEEEEEEEEECHHHHHHHHHCCHHHCCCCHHHHHHHCCCCHHHCCCCCCCCCCEEEECCCCCCHHHEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCCCC PSA >P1;d1fmta1 435860406---0643064025206704-86000103078---540403705239---691c25-----------------301025047----800100038--01010310205c--------------59316066028526-6004496506----------------------------------------------------- >P1;d1xg9a4 -57970404---8919585344206137bb74200468-d---5422238066c---------------------------------------------------a6161537648c-------------------------------------------------------------------------------------------- >P1;d2blna1 ---ab1504---06340750263066247777001042cc---540001506237---a92a36-----------------40003226------50100028--00010340214a--------------89517036007409---0869350------------------------------------------------------ >P1;d2bw0a1 494870508---0825073015306801-8910000504a---3400006023919c27486660607------------b04560101a----4000010344-810004203258--------------7741601603a------------------------------------------------------------------- >P1;d3rfoa2 585960506---0654056016204912-49300103079---440301305328---099849-----------------101024459----5000000438-10000220316c--------------6a4-6037107a37---09574503----------------------------------------------------- >P1;d3ubya1 -----b2136a0043504400340000-----10004088742020100000013039--0610205a45639506001461000001439a742000000598000000000203542820383289635700111240040030658002320072a201036088189640020403b76a913945000014b152005537b21 Translating the sequences *C*HHHCCC---CCCCHHHHHHHHH*CC-CCCC*EEEECC---EEEEEEEEEEEC---CCCCCC-----------------CCCEEEE**----**EEEECCC--CEEEEEEEEECC--------------CCC**HHHHHHH**-****CCCCC*----------------------------------------------------- -C*HHHCCC---CCCCHHHHHHHH**CC*CCCC*EEE*-C---*EEEEEEEE**---------------------------------------------------C**EEEEEEECC-------------------------------------------------------------------------------------------- ---***CCC---CCCCHHHHHHHHH*CC*CCCC*EEEECC---EEEEEEEEEEEC---CCCCCC-----------------CCCEEE**------*EEEECCC--CEEEEEEEEECC--------------CCC**HHHHHHH**---**CCCCC------------------------------------------------------ *C*HHHCCC---CCCCHHHHHHHHH*CC-CCCC*EEEECC---EEEEEEEEE**C***CCCC******------------*CCC*EEE**----**EEEECCC*-CEEEEEEEE*CC--------------CC***HHH***------------------------------------------------------------------- *C*HHHCCC---CCCCHHHHHHHHH*CC-CCCC*EEEECC---EEEEEEEEEEE*---CCCCCC-----------------CCCEEEE**----**EEE*CCC*-*EEEEEEEEECC--------------CCC-*HHHHHHH**---**CCCCC*----------------------------------------------------- -----*CCC****CCCHHHHHHH***C-----**EEE*CC***EEEEEEEEEEEC***--CCCC*****************CCCEEEE********EEEECCC**CEEEEEEEEE*****************CC**HHHHHHH*******CCCCC****************************************************** 50486.tem _________________________________ *C*HHHCCC---CCCCHHHHHHHHH*CC-CCCC*EEEECC---EEEEEEEEEEEC---CCCCCC-----------------CCCEEEE**----**EEEECCC*-CEEEEEEEEECC--------------CCC**HHHHHHH**---**CCCCC*----------------------------------------------------- Structural block scores 3 5 H 4.2 M 4.7 5.3 7.7 5.0 5.0 53.8 6 8 C 5.0 H 3.3 2.7 3.0 4.3 3.7 2.0 9 11 - 4.5 M 75.0 75.0 75.0 75.0 75.0 5.5 12 15 C 4.9 H 3.2 6.8 3.2 3.8 3.8 3.0 16 24 H 4.8 H 2.8 4.1 3.2 2.8 2.7 1.7 26 27 C 4.8 H 2.0 5.0 3.0 0.5 1.5 37.5 29 32 C 4.5 M 3.5 6.1 5.2 4.5 4.0 56.5 34 37 E 4.8 H 1.0 4.5 1.8 1.2 1.0 1.0 38 39 C 4.8 H 7.5 44.2 12.5 7.2 8.0 8.0 40 42 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.3 43 53 E 4.8 H 3.0 4.6 2.4 2.5 2.3 0.4 55 57 - 4.1 M 75.0 75.0 75.0 7.8 75.0 4.0 58 63 C 4.3 M 5.9 75.0 6.8 6.2 6.5 26.2 64 80 - 4.4 M 75.0 75.0 75.0 54.4 75.0 3.9 81 83 C 4.5 M 1.3 75.0 1.3 3.0 0.7 0.3 84 87 E 4.3 M 1.8 75.0 1.8 1.8 2.5 0.2 88 89 * 2.3 P 5.5 75.0 40.5 5.8 7.0 3.5 90 93 - 4.5 M 75.0 75.0 75.0 75.0 75.0 7.6 94 95 * 2.3 P 4.0 75.0 40.0 2.0 2.5 1.0 96 99 E 4.4 M 0.2 75.0 0.2 0.2 0.0 0.0 100 102 C 4.5 M 3.7 75.0 3.3 2.3 2.3 4.7 106 114 E 4.8 H 0.9 4.3 1.2 1.3 0.9 0.2 115 116 C 4.5 M 8.8 10.2 7.2 6.5 9.2 4.0 117 130 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.5 131 133 C 4.3 M 5.7 75.0 7.3 6.0 6.8 2.3 134 135 * 2.3 P 3.5 75.0 4.0 3.5 40.5 1.0 136 142 H 4.3 M 3.9 75.0 2.9 13.6 4.1 1.6 143 144 * 2.7 P 4.0 75.0 4.5 75.0 5.0 1.5 145 147 - 4.2 M 27.0 75.0 75.0 75.0 75.0 3.7 148 149 * 2.7 P 2.0 75.0 4.0 75.0 4.5 4.0 150 154 C 4.3 M 4.8 75.0 4.6 75.0 4.2 1.4 156 208 - 4.5 M 75.0 75.0 75.0 75.0 75.0 4.0 >>>>>>