Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fafa- CCCCCCHHHHHHHHHCCCCCC-----------------------CCCCCHHHHHHHHHHHHHHCCHHH------CCCHHHHHHHHHHHHHHHHHHH---------HHHHHCCCCCC---------------------------------------C >P1;d1fpoa1 ----------CHHHHHCCCCCCC-----------------------CCCHHHHHHHHHHHHHHCCHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHHC------HHHHHHHHHHCCC---------------------------------------- >P1;d1gh6a1 ------CHHHHHHHHHCCCCC-----------------------CCCCCHHHHHHHHHHCCCCCCCCC------CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCC----------CCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC >P1;d1iura1 -----CHHHHHHHHHHHCCCCC----------------------------HHHHHHHHHHHCCCCHHHCCC---C--HHHHHHHHHHHHHHHHHHHH--------HHHHC------CCCCCCCCCCC----------------------------- >P1;d1wjza1 CCCCCCCCC--CHHHHCCCCC-------------------------CCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC------HHHHHHHHHHC------------------------------------------ >P1;d2o37a- ------CCCCCHHHHHHCCCC-------------------------CCCHHHHHHHHHHHHHHHCCCCC---------CCCHHHHHHHHHHHHHHCC------HHHHHHHHHHCHHHHHCCCCCCCC----------------------------- >P1;d2qwob- ---CHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHCCHHHHC-----CC--CCHHHHHHHHHHHHHHHH--------HHHHC---------------------------------------------- >P1;d2yuaa1 C-CCCCCCCCCHHHHHHCCCC-------------------------CCCHHHHHHHHHHHHHHCCCCCCC------CCHHHHHHHHHHHHHHHHCCC------HHHHHHHHCCCCCCHHHHCCC-------------------------------- >P1;d3ag7a1 CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCC-CCCCCCHHHCCCHHHHHHHHHHHHHHHCHHHHHH---CCCCHHHHHHHHHHHHHHHHHHH--------HHCCC------CC-------------------------------------- >P1;d6rzya1 ----------CCHHHHHCCCC-------------------------CCCHHHHHHHHHHHHHHCCHHHH-CCC--CCHHHHHHHHHHHHHHHHHHCC------HHHHHHHHC-------------------------------------------- PSA >P1;d1fafa- 9a7918884246008207067-----------------------b22773a60591168128506475------b158652750661051038609---------63789b6b9aa---------------------------------------e >P1;d1fpoa1 ----------5a20830815155-----------------------80658403651552465157853-7b37a8647508663760470151033------584047128717b---------------------------------------- >P1;d1gh6a1 ------994084008009286-----------------------642840550181027308505298------4a35950440051026205b32666a789bc----------71822704809a5707701760476587788a98b8a9a8e >P1;d1iura1 -----66960562067026176----------------------------853653267146713299089---5--77608601830480385166--------74868------b88c98999ac----------------------------- >P1;d1wjza1 b1b578364--7007108083-------------------------91b383067207611672249517ba36aa449705842520530262007------97217602864------------------------------------------ >P1;d2o37a- ------91534500700a173-------------------------90769503513670276144948---------8055832640410260033------89428502760284038c57b946----------------------------- >P1;d2qwob- ---595476057029828460230013035000ba0880951a597075683047116601710429607-----a5--823610520270035017--------51697---------------------------------------------- >P1;d2yuaa1 b-b67a566382008007055-------------------------a0558604602671486345884a------c4a918943850440340025------663163247760688168388-------------------------------- >P1;d3ag7a1 983882255077018c25340230013037002bb0-a095156870684910450065035104664076---7a179633310630162057028--------41378------25-------------------------------------- >P1;d6rzya1 ----------a51092081a6-------------------------b1767305611582066135851-6b6--c34a507542640450262024------ba5188328-------------------------------------------- Translating the sequences ***********HHHH**CCCC-----------------------**CCCHHHHHHHHHHHHHHCC***------****HHHHHHHHHHHHHHHHH*---------HHHH*******---------------------------------------* ----------*HHHHH*CCCC**-----------------------CCCHHHHHHHHHHHHHHCC****-********HHHHHHHHHHHHHHHHH**------**HHHH*******---------------------------------------- ------*****HHHHH*CCCC-----------------------**CCCHHHHHHHHHH****CC***------*******HHHHHHHHHHHHHH**********----------***************************************** -----******HHHHH*CCCC*----------------------------HHHHHHHHHHH**CC******---*--*HHHHHHHHHHHHHHHHH**--------HHHH*------***********----------------------------- *********--*HHHH*CCCC-------------------------CCCHHHHHHHHHHHHH*CC*************HHHHHHHHHHHHHHHHH**------**HHHH*****------------------------------------------ ------*****HHHHH*CCCC-------------------------CCCHHHHHHHHHHHHHH*C****---------***HHHHHHHHHHHHHH**------**HHHH******************----------------------------- ---********HHHHH*CCC**************************CCCHHHHHHHHHHHHHHCC*****-----**--**HHHHHHHHHHHHHH**--------HHHH*---------------------------------------------- *-*********HHHHH*CCCC-------------------------CCCHHHHHHHHHHHHHHCC*****------**HHHHHHHHHHHHHHHH***------**HHHH***************-------------------------------- ***********HHH***CCC****************-*********CCCHHHHHHHHHHHHHH*C******---****HHHHHHHHHHHHHHHHH**--------HH***------**-------------------------------------- ----------**HHHH*CCCC-------------------------CCCHHHHHHHHHHHHHHCC****-***--***HHHHHHHHHHHHHHHHH**------**HHHH***-------------------------------------------- 46565.tem _________________________________ *-*********HHHHH*CCCC*----------------------**CCCHHHHHHHHHHHHHHCC******---****HHHHHHHHHHHHHHHHH**------**HHHH***************-------------------------------- Structural block scores 2 10 * 2.7 P 5.7 67.2 36.7 28.6 21.6 35.8 12.9 7.0 4.4 67.8 11 15 H 4.7 H 3.2 4.7 2.4 4.2 3.0 2.4 5.2 2.0 5.7 3.4 17 20 C 4.9 H 5.0 3.8 6.2 4.0 4.8 5.4 4.5 4.2 3.0 6.4 22 43 - 4.5 M 75.0 71.8 75.0 75.0 75.0 75.0 3.8 75.0 7.0 75.0 44 45 * 3.8 M 6.8 75.0 5.0 75.0 75.0 75.0 8.0 75.0 7.5 75.0 46 48 C 4.7 H 5.3 4.7 4.7 75.0 7.2 5.3 4.0 5.2 4.7 6.5 49 62 H 4.8 H 4.7 4.2 3.2 9.9 4.1 4.3 3.6 4.5 3.1 4.0 63 64 C 4.8 H 3.0 3.0 2.5 2.0 2.0 2.5 2.0 3.5 2.0 2.0 65 70 * 2.0 P 40.2 17.5 40.7 6.2 6.2 29.2 16.5 18.4 4.8 16.7 71 73 - 4.2 M 75.0 7.2 75.0 75.0 6.5 75.0 75.0 75.0 75.0 30.8 74 77 * 2.4 P 6.4 7.1 5.6 40.5 7.2 75.0 41.4 41.6 6.4 23.6 78 94 H 4.8 H 3.6 3.9 3.4 4.0 3.5 3.2 7.0 4.3 3.2 3.7 95 96 * 1.2 P 42.0 3.0 4.0 6.0 3.5 3.0 4.0 3.5 5.0 3.0 97 102 - 4.7 H 75.0 75.0 7.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 103 104 * 3.0 P 75.0 6.5 12.0 75.0 8.0 8.5 75.0 6.0 75.0 11.0 105 108 H 4.6 H 6.0 3.8 75.0 6.2 4.0 4.8 5.2 3.2 3.8 5.5 109 123 * 3.4 M 44.5 42.5 32.6 35.5 51.3 5.1 70.5 5.5 61.0 60.9 124 155 - 4.6 H 73.1 75.0 6.8 69.0 75.0 68.6 75.0 75.0 75.0 75.0 >>>>>>