Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fjgm- -----------------CCCCCCCCCCCCCHHHHHHH---CCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCC >P1;d1k3xa1 -CCCCCCC-CCCCHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCC---------------HHHHHHHHHHHHHHHHHHHHHC---------C------------------------------- >P1;d1r2za1 --CCCCCC--CCCCHHHHCCCC-----CCCHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCC-------------------CCCCCCHHHHHHHHHC-----------CCCCCCCCC----------------------- >P1;d1tdza1 --CCCC-C-CCCCHHHHHHHHCC----CCCHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHCC---------------HHHHHHHHHHHHHHHHHHC--C---------CCCCC--------------------------- >P1;d2hkja1 -CCCCHH---HCCHHHHHHHHH--CCCCCCHHHHHHH--HCCCCCHHHHHHHHHHHCCCCCCCHHHCC---------------HHHHHHHHHHHHHCCCC---------------------------------------------- >P1;d5itqa2 CCCCCCCCCHHHHHHHHHHCCC-CHHHHCCHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHH---CCCCCC-------------------------------- PSA >P1;d1fjgm- -----------------26009816067440030046---040056a4064008608073434046059721550463049214-0197257457754770257a37505115763018b66396903a33697889a98aa4889 >P1;d1k3xa1 -7135044-8a052850382044860474504900445400180875025501850a08294303608---------------a940450040006203828667---------d------------------------------- >P1;d1r2za1 --328043--970459404407-----443024003257003808842055009309084a3604409-------------------3160220450146278-----------c436868ab----------------------- >P1;d1tdza1 --4371-5-67062860354073----75502510345600390885206500840906464503608---------------7830550030006114727--8---------a64a8--------------------------- >P1;d2hkja1 -963406---a05375047219--8185010250034--20450a772055009609084a3406607---------------77104301710491970---------------------------------------------- >P1;d5itqa2 c62230274386025101740a-4600562015003334002808870275007427155755025106a25ba388965685579832004002500365589a---aa8b98-------------------------------- Translating the sequences -----------------****C*****CCCHHHHHH*---CCCCCHHHHHHHHH**CCCCCCC***CC****************-*HHHHHHHHHHHHHHHH************C******************************* -*CCCC*C-**CCHHHHHH********CCCHHHH**CCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCC---------------***HHHHHHHHHHHHHHHH***---------C------------------------------- --CCCC*C--*CC*HHHH***C-----CCCHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCC-------------------******HHHHHHHHH*-----------C********----------------------- --CCCC-C-**CCHHHHHH**C*----CCCHHHHHHCCCCCCCCCHHHHHHHHHH*CCCCCCCHHHCC---------------***HHHHHHHHHHHHHHH*--*---------C****--------------------------- -*CCC**---*CCHHHHHH***--***CCCHHHHHH*--*CCCCCHHHHHHHHHHHCCCCCCCHHHCC---------------***HHHHHHHHHH****---------------------------------------------- **CCCC*C*****HHHHHH**C-*****CCHHHH**CCCCCCCCCHHHHHHHHHHHCCCCCCCHHH***********************HHHHHHHHHHHHH***---******-------------------------------- 46946.tem _________________________________ -*CCCC*C-**CCHHHHHH**C*****CCCHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCC---------------***HHHHHHHHHHHHHHHH***---------C****--------------------------- Structural block scores 2 5 C 4.4 M 75.0 2.2 3.2 3.8 3.2 1.8 9 10 * 2.6 P 75.0 9.2 42.0 6.5 42.8 5.5 11 12 C 4.2 M 75.0 2.5 3.5 3.0 2.5 3.0 13 18 H 4.4 M 51.3 4.3 4.3 4.0 4.3 2.7 19 20 * 1.0 P 0.0 1.0 2.0 2.0 1.5 2.0 22 26 * 3.0 P 4.2 4.4 75.0 60.6 33.4 17.0 27 29 C 4.8 H 5.0 5.3 3.7 5.7 2.0 4.3 30 35 H 4.7 H 1.2 2.8 1.5 1.8 1.7 1.5 36 44 C 4.7 H 26.7 3.3 3.7 3.9 19.5 3.1 45 55 H 4.9 H 4.0 3.5 3.3 3.5 3.7 3.8 56 62 C 5.0 H 4.1 5.2 5.8 4.9 5.5 5.0 63 65 H 4.5 M 3.3 3.0 2.7 3.0 4.0 2.3 66 67 C 4.5 M 2.5 4.0 4.5 4.0 3.5 0.5 68 82 - 4.1 M 3.9 75.0 75.0 75.0 75.0 6.9 83 85 * 2.2 P 26.3 7.8 75.0 6.0 5.0 7.0 86 101 H 4.5 M 4.9 2.6 7.4 2.6 12.2 2.7 102 104 * 2.9 P 7.5 6.3 52.7 52.7 75.0 9.2 105 113 - 4.2 M 3.8 75.0 75.0 75.0 75.0 31.4 115 118 * 3.4 M 3.0 75.0 5.2 7.1 75.0 75.0 119 145 - 4.4 M 7.2 75.0 65.2 75.0 75.0 75.0 >>>>>>