Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d8ba- ------------------------------------------------CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCC-CCC--HHHHHHCHHHHHHHHHHHHHCCCC---------- >P1;d1go3f- CCCCCCCCCCCCCHHHHCCHHHHHHHCCCC---------------------------HHHHHHHHHHHHHCCCC--HH-HHCCHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHCC---CCCCCCCCCCCCC---------- >P1;d1wuda1 --------------------------------------------------CCCHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHC-CCCCCCC---CCCCCCCCC--CHHHHHCCCCC-HHHHHHCCC------------- >P1;d1y14a- -------CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHH-HHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHCHHHCCCCCHHHHHHHHHHHHHHCCCC- >P1;d1yt3a2 --------------------------------------------CCHHHCCCHHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHCCCCCCCCCCHHHCH--HHHHHHHHHHHHHHCCCCC--------------- >P1;d2cpra1 -----------------------------CCCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCHHHHHHHHHHCCCCCHHHHHCCCCCC--HHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCC >P1;d2e1fa- --------------------------------------CCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHCCCCHHHHCCCC-CCC--HHHHHHCHHHHHHHHHHHHHC----CCCCCCCCC >P1;d2hbja1 -----------------------------------CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHCCCCHHHHHCCCCCCC--HHHHHCHHHHHHHHHHHHHHHHHHC--------- >P1;d2ma1a- ---------------------------------------------------CCHHHHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHCCCCCHHHHCCCCCCCC--HHHHHCCHHHHHHHHHHHC--------------C PSA >P1;d1d8ba- ------------------------------------------------bb845630055047209730a83a842c8001571053002410695a408708-c06--862481054029203402724898---------- >P1;d1go3f- 7aba77998553020021626831578a07---------------------------99455526615661428--59-40301850482a1646000500252096483058008---752318701201b---------- >P1;d1wuda1 --------------------------------------------------a25770263058207710784b34574006680033-0372466---95580b91b--7339611a405-315514697------------- >P1;d1y14a- -------998230201202623860484274667884277138607601830199a58a24640350046010047a1-05304820881b05660215001550a6094017506705b4177a40360074058240a7- >P1;d1yt3a2 --------------------------------------------87058385198029305720661177482659600676001300130080591ba604004c--4108202a40581087099--------------- >P1;d2cpra1 -----------------------------896193a53671266c66a05313230053018012600783b48276002781015002511563a502800a912--6006741a3026001504726288498589a895 >P1;d2e1fa- --------------------------------------b7948---a926711750385048105720763a273770047700510052002658203409-a08--9a2064063007304800975----9292240ba >P1;d2hbja1 -----------------------------------920393206764b13952560023016105710763a3345500317000000460126595037093902--610572075006105504563977b--------- >P1;d2ma1a- ---------------------------------------------------a47621831562068019618642750178732730175622318809419d249--9546601860493179269--------------f Translating the sequences ------------------------------------------------*****HHHHHHHHHHHHHHHHH*CCC****CCHHHHHHHHH*CCCC**HH**CC-CCC--HHHHHHCHHHHHHHHHHH******---------- ******************************---------------------------HHHHHHHHHHHHH*CCC--HH-*H**HHHHHH*CCC**HHH*****CCC**HHHHHHC*---*************---------- --------------------------------------------------***HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHH*-***CCCC---***CC*CCC--*HHHHHC****-HHHHHH***------------- -------**************************************************HHHHHHHHHHHHH*CCC*HHH-*HHHHHHHH**CCC**HHH*****CCC**HHHHHHCHHH*****HHH***************- --------------------------------------------*********HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH**CCC******C***C*--HHHHHH*HHHHHHH*****--------------- -----------------------------************************HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH*CCCC*HHH**CC*CCC--HHHHH**HHHHHHHHHHH**************** --------------------------------------*****---*******HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH*CCCC*HHH**CC-CCC--HHHHHHCHHHHHHHHHHH***----********* -----------------------------------******************HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH*CCCC*HHH**CC*CCC--HHHHH**HHHHHHHHHHH*******--------- ---------------------------------------------------**HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH*CCCC*HHH**CC*CCC--HHHHH*CHHHHHHHHHHH*--------------* 47819.tem _________________________________ --------------------------------------*****-*********HHHHHHHHHHHHHHHHH*CCCHHHHCCHHHHHHHHH*CCCC*HHH**CC*CCC--HHHHHHCHHHHHHHHHHH******---------- Structural block scores 0 37 - 4.4 M 75.0 20.0 75.0 17.3 75.0 58.7 75.0 69.4 75.0 38 42 * 3.6 M 75.0 75.0 75.0 5.2 75.0 4.4 7.9 3.4 75.0 44 52 * 2.7 P 37.8 75.0 51.9 2.9 5.0 5.2 20.7 5.4 59.9 53 69 H 4.9 H 4.1 21.7 4.1 5.1 4.3 2.7 4.0 2.9 4.2 71 73 C 5.0 H 7.5 4.7 6.2 0.3 5.3 7.8 6.5 5.5 6.0 74 77 H 4.5 M 5.6 41.0 4.0 5.6 5.0 3.8 4.2 3.5 3.5 78 79 C 4.5 M 0.5 39.5 3.0 37.5 3.0 1.0 2.0 1.5 4.0 80 88 H 4.8 H 2.6 3.2 10.9 4.2 2.0 2.7 2.8 1.3 4.2 90 93 C 4.8 H 4.0 5.4 4.5 5.6 2.0 3.2 2.0 2.2 3.2 95 97 H 4.4 M 4.8 0.0 53.0 1.0 7.2 5.2 3.3 4.7 5.3 98 99 * 1.0 P 7.5 2.5 5.0 2.5 8.2 5.0 3.5 5.0 6.5 100 101 C 4.2 M 4.0 1.0 4.0 0.5 2.0 0.0 4.5 4.5 5.0 103 105 C 4.8 H 6.2 3.7 7.2 5.2 5.5 4.0 6.2 3.7 5.0 106 107 - 4.4 M 75.0 5.0 75.0 3.0 75.0 75.0 75.0 75.0 75.0 108 113 H 4.8 H 4.8 4.0 4.8 4.3 2.5 3.8 5.2 3.5 5.0 115 125 H 4.3 M 2.8 24.2 10.3 5.7 4.8 2.9 2.8 3.0 5.0 126 131 * 2.5 P 6.3 2.6 41.2 2.7 64.0 5.5 41.0 6.2 64.0 132 141 - 4.0 M 75.0 75.0 75.0 11.6 75.0 7.5 12.5 68.7 69.8 >>>>>>