Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1coja2 --CCCCCCCH--HHHHHHHHHCCCHHHHHHHHHHHHHHCC--CEEEEEECCCC-CCEEEEEECCC------CCCCCCCCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCC-------- >P1;d1ix9a2 ----CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEEEC---CEEEEEEEECCCCHHHCHHHHCCCCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHC------------------- >P1;d2cw3a2 CCCCCCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEEECCC-CEEEEEEEECCCCHHHHC-----CCCEEEEEECCHHHCHHHHCCCHHHHHHHHHCCCCHHHHHHCC----------------------- >P1;d3ak2a2 ----CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCEEEEEEEECCC-CEEEEEEEECC------CCCCCCCCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHCHHHCC----------- >P1;d3ceia2 -----CCCCH--HHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEECCCC-CCEEEEEEECCCCHHHH------CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCC >P1;d3qvna2 CC-CCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEEEECCCCCC-CC-----CEEEEEEEECCHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHCC---------------------- >P1;d4h3ea2 ---CCCCCCC---HHHHHHHHHCCHHHHHHHHHHHHHCCCCCEEEEEEECHHH-CCCEEEEEECCCCHHHH------CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHC------------------- >P1;d6s0da2 -----CCCCH--HHHHHHHHHHCCHHHHHHHHHHHHHCCCCCEEEEEEE-CCC-CCCEEEEEECCCCC---C-----CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHHHCCHHHHHHHHHHHHC------------------ PSA >P1;d1coja2 --c2778159--7027105701725a50495036104638--02010002135-05030100236------9465594034003020277205a7378615310533186052650264067027526835868a-------- >P1;d1ix9a2 ----e2707b--704700460085197037504820482aa202010004b---970302104763206466a70903220010020376206a717a51641075117806076046306755------------------- >P1;d2cw3a2 a9b9169127--602830561186385036401640381a9303010112375-840404216594119659-----8542003020377205a72595154105711870607601640----------------------- >P1;d3ak2a2 ----2b6099--6035107611721870286006103709b202000001065-44040220366------85526a2143014020267205b72696144105510880807403650670178046744----------- >P1;d3ceia2 -----7914a--5058004601a4394037302820460aa2030100013a5-74030241768730377------8201013020377105982694156106721a90717401320330367337017545653476ac >P1;d3qvna2 8c-d11606982700620573185176017302850290ab302000022466b230703317777708-39-----3234003020377105a725953661074208617085027418---------------------- >P1;d4h3ea2 ---c25a04a---05830585184287027500730270a9203010002298-a405123177a740786------a1530020203671059817941441066219615066016317714------------------- >P1;d6s0da2 -----b9058--602600560084296028500640281ab30202000-5a7-74041321676770---9-----c134010020376105a8269414610631088080840165068049------------------ Translating the sequences --**CCCCCH--HHHHHHHHH*CCHHHHHHHHHHHHH*CC--*EEEEEE*CCC-C*EEEEEE*CC------******CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH************-------- ----CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE*C---C*EEEEEEECCCC**********CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH*------------------- ****CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE*CCC-C*EEEEEEECCCC*****-----CC*EEEEEECCHHHCHHHHCCCHHHHHHHHH**CCHHHHHH**----------------------- ----CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE*CCC-C*EEEEEEECC------******CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH*********----------- -----CCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE*CCC-C*EEEEEEECCCC****------CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH******************** **-*CCCCC***HHHHHHHHH*CCHHHHHHHHHHHHH*CCCCEEEEEEE*CCC*C*EEEEEEECCCC**-**-----C*EEEEEEECCHHH*HHHHCCCHHHHHHHHHH*CCHHHHHHH**---------------------- ---*CCCCC*---HHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE****-C**EEEEEECCCC****------CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH*------------------- -----CCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE-CCC-C**EEEEEECCCC*---*-----CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH**------------------ 54719.tem _________________________________ ---*CCCCCH--HHHHHHHHHHCCHHHHHHHHHHHHH*CCCCEEEEEEE*CCC-C*EEEEEEECCCC**********CCEEEEEEECCHHHCHHHHCCCHHHHHHHHHH*CCHHHHHHHHHHH*********----------- Structural block scores 0 2 - 4.3 M 54.2 75.0 10.3 75.0 75.0 31.8 75.0 75.0 4 8 C 4.9 H 5.6 6.1 3.8 5.7 19.2 2.8 4.3 20.1 10 11 - 4.7 H 75.0 75.0 75.0 75.0 75.0 5.0 75.0 75.0 12 21 H 4.9 H 3.0 2.8 3.2 3.0 2.9 3.1 11.0 2.5 22 23 C 5.0 H 4.5 6.5 7.0 4.5 7.2 6.5 6.0 6.0 24 36 H 5.0 H 4.0 3.8 3.3 3.2 3.5 3.2 3.3 3.4 38 41 C 4.8 H 40.2 6.2 5.9 5.6 5.8 6.2 5.4 6.5 42 48 E 5.0 H 0.4 0.4 0.9 0.3 0.6 0.6 0.6 0.6 50 52 C 4.5 M 3.0 53.8 5.0 3.7 6.2 5.3 6.3 7.5 56 62 E 4.9 H 0.9 1.4 2.4 1.6 2.4 3.0 2.7 2.4 63 66 C 4.8 H 39.8 4.5 4.8 40.5 6.0 7.0 7.1 6.8 67 76 * 3.3 M 33.8 4.8 40.5 33.6 46.7 47.0 47.1 60.9 77 78 C 4.8 H 2.0 2.5 6.5 1.5 5.0 2.5 5.8 6.8 79 85 E 5.0 H 1.7 0.7 1.6 2.0 1.0 1.7 1.7 1.4 86 87 C 5.0 H 1.0 1.5 1.5 1.0 1.5 1.5 1.5 1.5 88 90 H 5.0 H 5.3 5.0 5.3 5.0 5.0 5.0 4.7 4.7 92 95 H 5.0 H 6.4 6.1 6.1 6.4 6.0 6.1 5.8 6.4 96 98 C 5.0 H 7.0 7.5 6.3 7.0 6.3 6.3 6.7 6.3 99 108 H 5.0 H 3.0 3.3 3.3 2.9 4.0 3.7 3.4 3.0 110 111 C 5.0 H 2.5 3.0 3.0 4.0 3.5 4.0 3.0 4.0 112 122 H 4.8 H 3.5 4.0 22.6 3.5 2.2 16.8 3.5 3.5 123 131 * 3.7 M 5.1 67.2 75.0 4.6 4.1 75.0 67.1 59.8 132 142 - 4.6 H 56.8 75.0 75.0 75.0 6.2 75.0 75.0 75.0 >>>>>>