Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1p65a- -------------------------------------------CHHHHCCH-HHHHHHHHHH--HHHHHHC-CCEEEECCCC-CEEEECCCCCC------HHHHHHHHHHC--------- >P1;d2ge8a1 -------CCCCCHHHCCCCCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHCHHHHHHCCCCCCHHHHHHHCEEEEEEECCEEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC >P1;d2i9fa1 ----------------------------------------CCCCHHHHCCH-HHHHHHHHHH--HHHC-CC-CCEEEECCC--CEEEECCCCCC------HHHHHHHC------------ >P1;d5epwa- ------CCCCCCHHHCCCC-CCCHHHHCCCCCC---CCCCCCHHHHHHHHHCCCHHHHHCCCCCHHHHHHHEEEEEEEECCEEEEEEEECCCCCC-----CCCHHHHHHHCCHHHC---- >P1;d6zcoa- CCCCHHHHHHCCHHHCCCCCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHCCCCCHHHHHHHCEEEEEEECCEEEEEEECCCCCCCCCCCHHHHHHHHHHHCCHHHHCC-- PSA >P1;d1p65a- -------------------------------------------56684038-8057417534--7605778-6373665c97-967181a3915------98155408746--------- >P1;d2ge8a1 -------6895866729147a541240367036-98b3330033014404709118316716288943587082467849885537352838168a3862951560482044139751ad >P1;d2i9fa1 ----------------------------------------94766576078-8146418724--9725-6a-62637869b--975170a2815------77036616------------ >P1;d5epwa- ------b525545861513-a231650247159---753304a611840360a23750360529a74378707365796cb8665545183a17a-----a422732681430366---- >P1;d6zcoa- ba76495349565872603680213603880067a937530046016303408436503426389a425840927567497856446859392769387388048127605311692a-- Translating the sequences -------------------------------------------*HHHH**H-HHHHHHH***--HHHHHH*-**EEEE*CC*-*EEEECCCCCC------HHHHHHHHHHC--------- -------***CCHHHCCCC*CCC*****CCCCC-**CCCCCCHHHHHHHHHCHHHHHH*CCCCCHHHHHHH*EEEEEEECCEEEEEEECCCCCCC*****HHHHHHHHHHCC******** ----------------------------------------CC**HHHH**H-HHHHHHH***--HHH*-**-**EEEE*CC--*EEEECCCCCC------HHHHHHH*------------ ------****CCHHHCCCC-CCC*****CCCCC---CCCCCCHHHHHHHHHC**HHHHHCCCCCHHHHHHH*EEEEEEECCEEEEEEE*CCCCCC-----***HHHHHHHCC****---- **********CCHHHCCCC*CCC*****CCCCC***CCCCCCHHHHHHHHHC**HHHHHCCCCCHHHHHHH*EEEEEEECCEEEEEEECCCCCCC*****HHHHHHHHHHCC******-- 103068.tem _________________________________ -------***CCHHHCCCC-CCC*****CCCCC---CCCCCCHHHHHHHHHCHHHHHHHCCCCCHHHHHHH*EEEEEEECCEEEEEEECCCCCCC-----HHHHHHHHHHCC****---- Structural block scores 0 6 - 4.4 M 75.0 75.0 75.0 65.9 7.6 7 9 * 3.0 P 75.0 7.7 75.0 4.0 5.3 10 11 C 4.2 M 75.0 6.5 75.0 4.5 5.5 12 14 H 4.2 M 75.0 6.3 75.0 6.3 6.7 15 18 C 4.2 M 75.0 4.0 75.0 2.5 2.8 20 22 C 4.2 M 75.0 6.5 75.0 5.2 3.3 23 27 * 3.0 P 75.0 2.0 75.0 2.8 2.6 28 32 C 4.2 M 75.0 4.4 75.0 5.2 4.4 33 35 - 4.0 M 75.0 30.7 75.0 75.0 8.8 36 41 C 4.3 M 75.0 3.4 52.2 3.7 3.0 42 50 H 4.5 M 12.8 2.9 5.8 4.4 3.0 52 58 H 4.6 H 4.6 4.1 4.6 4.4 4.1 59 63 C 4.0 M 32.4 4.8 32.6 4.4 4.6 64 70 H 4.6 H 5.7 6.3 16.4 6.6 6.1 72 78 E 4.5 M 5.1 5.6 5.4 6.1 5.7 79 80 C 5.0 H 10.8 8.5 10.2 12.0 8.0 81 87 E 4.6 H 16.1 5.1 25.6 5.6 5.9 88 94 C 4.8 H 14.9 5.1 14.5 5.9 5.9 95 99 - 3.8 M 75.0 5.9 75.0 75.0 6.0 100 109 H 4.7 H 5.1 4.0 18.6 4.5 4.4 110 111 C 4.3 M 40.5 4.0 75.0 3.5 4.0 112 115 * 3.0 P 75.0 5.0 75.0 3.8 4.2 116 119 - 4.2 M 75.0 7.5 75.0 75.0 40.6 >>>>>>