Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1a4ia2 -CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHH-----CCCCCEEEECCCCCCCCCCCHHHHHHCCCHHHCCCC--------------------------- >P1;d1edza2 --CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEEECC---CHHHHHHHHHHHHH-----CCCCCEEEECCCCCCCH--HHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCC-C >P1;d1luaa2 ---------------------------------CCCEEEEEECC-----CCCCHHHHHHHHHCCCCEEEEEC--CCCCCCHHHHHHHHHCCCCHHHHHHEEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEECCC---------------------- >P1;d1npya2 -----------------------------CCCCCCEEEEEECCCCC--C-HHHHHHHHHHHHHCCCEEEEEEC--CC--CHHHHHHHHHHH------CCCEEEECC-------CCCCCCHHHCC------EECHHHHCCCCCCEEEEEC-CEEEEECC >P1;d1nyta2 ----------------------------------CCCEEEEECCCC--CCCHHHHHHHHHHHHCCCCCEEEEE--CCCCCHHHHHHHHHHC------CCCEEEECC-------CCHHHHHHHCC------EECHHHHHHCCCCEEEECCCCCEEEECC >P1;d3ngxa1 ----CCCCCHHHHHHHHHHHHHHHHHC-----CCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCEEEEEEE-CCCCHHHHHHHHHHHHH-----CCCCCEEEECCCCCC--CCCHHHHHCCCCHHHCCCC--------------------------- >P1;d3tnla1 -------------------------CCCCCCCCCCEEEEEEECCCC--CCCHHHHHHHHHHHHCCCEEEEEEE--CCHHHHHHHHHHHHHC------CCCEEEECC-------CCCCCHHHHCC------EECHHHHHHCCCCEEEEEC-CEEEEECC >P1;d4b4ua1 C--CCCCCHHHHHHHHHHHHHHHHHHHHHHH-CCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHC-----CCCCCEEEECCCCC-C-CCCHHHHHHHCCHHHCCCC--------------------------- >P1;d4cjxa1 CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHH-----CCCCCEEEECCCCC-C-CCCHHHHHCCCCHHHCCCC--------------------------- >P1;d5dzsa1 ----------------------------------CEEEEEEECCCC--CCCHHHHHHHHHHHHCCCEEEEEEE--CCHHHHHHHHHHHHHH------CCCEEEECC-------CCCCHHHHHCC------EECHHHHHHCCCCEEEEEC-CEEEEECC >P1;d5o2aa1 -C-CCCCCHHHHHHHHHHHHH-CCHHHHHCCC-CCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCHHHHHHHHHHHHH-----CCCCCEEEECCCCC-C-CCCHHHHHHHCCHHHCCCC--------------------------- PSA >P1;d1a4ia2 -a8a9994a96555854764575156437767b4512200000074a4038607842830960526032330657053860374067027-----4a704000014502064b064860373037912569--------------------------- >P1;d1edza2 --bb8847a7767686598447805632675a850111000000c488166604721671481424041351a---6387047205702b-----4a703000002602579--507601410237103401164055158685622297777705-6 >P1;d1luaa2 ---------------------------------47532200006-----88249913774489713605130--8053a50283039005727b962710401000575620560151047406974509161609---------------------- >P1;d1npya2 -----------------------------b6797052101015938--a-8238543751857a552405145--2a--613620450387------814304059-------50367016203------423750576710330202b-44030317 >P1;d1nyta2 ----------------------------------a51300002807--a383165274527769692304336--056b504820471098------705102037-------30485037202------623860474430230633b866020235 >P1;d3ngxa1 ----97968877488738855871796-----a692211000077489016605223661991828062243-aa172970373054017-----48917000005604a--b161840174029701437--------------------------- >P1;d3tnla1 -------------------------b998456c9061100003915--b29227733761487a552106035--0179306720770285------905102038-------20375047304------722960795810230206b-85020426 >P1;d4b4ua1 b--a9995a9666875288448715752884-98312100010096a7057616641540360235045252658062970371067018-----48805000006500-a-507274026105a913568--------------------------- >P1;d4cjxa1 a989a987996757764864586179548759874201000001869504460764284067072521316167a083750271045018-----39205300014501-9-507594037404871427a--------------------------- >P1;d5dzsa1 ----------------------------------45620000280b--907329637651566a470507325--2459405702960287------615203038-------30383026203------620840895620330216a-86030316 >P1;d5o2aa1 -b-aa9a58956686647653-90994686a6-40201000002688505920653586086082613125266a062760171057008-----2c604000013701-b-b064850373058913578--------------------------- Translating the sequences -********************************CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE***CCHHHHHHHHHHHHH-----**CCCEEEECC*******CCHHHHHH*CC*******--------------------------- --*******************************CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEE**---CHHHHHHHHHHHHH-----**CCCEEEECC******--*HHHH***CC********************************-* ---------------------------------CCCEEEEEE*C-----****HHHHHHHHH*CC*EEEEE*--*CC***HHHHHHHHH***********EEEE*C*********HHHHHH*CC************---------------------- -----------------------------****CC*EEEEE**CCC--*-*HHHHHHHHHHH*CC*EEEEEE*--CC--*HHHHHHHHHH*------CCCEEEECC-------CC****HH*CC------*******************-******** ----------------------------------CC*EEEEE*CCC--***HHHHHHHHHHH*CC***EEEE*--CC***HHHHHHHHHH*------CCCEEEECC-------CCHHHHHH*CC------**************************** ----***********************-----*CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE-**CCHHHHHHHHHHHHH-----**CCCEEEECC****--*CCHHHHH**CC*******--------------------------- -------------------------********CC*EEEEEE*CCC--***HHHHHHHHHHH*CC*EEEEEE*--CCHHHHHHHHHHHHH*------CCCEEEECC-------CC***HHH*CC------*******************-******** *--****************************-*CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE***CCHHHHHHHHHHHH*-----**CCCEEEECC***-*-*CCHHHHHH*CC*******--------------------------- *********************************CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE***CCHHHHHHHHHHHHH-----**CCCEEEECC***-*-*CCHHHHH**CC*******--------------------------- ----------------------------------C*EEEEEE*CCC--***HHHHHHHHHHH*CC*EEEEEE*--CCHHHHHHHHHHHHH*------CCCEEEECC-------CC**HHHH*CC------*******************-******** -*-******************-**********-CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE***CCHHHHHHHHHHHHH-----**CCCEEEECC***-*-*CCHHHHHH*CC*******--------------------------- 53223-1.tem _________________________________ ---******************************CCCEEEEEE*CCC*****HHHHHHHHHHH*CC*EEEEEE***CCHHHHHHHHHHHHH*----**CCCEEEECC*****-*CCHHHHHH*CC*************************-******** Structural block scores 0 2 - 4.3 M 31.2 53.8 75.0 75.0 75.0 75.0 75.0 53.8 9.2 75.0 53.8 3 32 * 3.2 M 6.3 6.5 75.0 66.1 75.0 20.5 57.2 8.8 6.8 75.0 11.4 33 35 C 4.6 H 3.3 2.0 5.3 4.0 30.2 5.7 5.0 4.0 4.3 28.0 2.0 36 41 E 4.9 H 0.7 0.3 1.2 0.8 0.7 0.7 0.3 0.7 0.2 1.3 0.2 43 45 C 4.9 H 3.7 5.5 52.0 6.7 5.0 6.0 5.0 5.0 5.0 6.5 5.3 46 50 * 2.1 P 5.1 5.8 48.2 48.7 34.3 4.8 34.5 5.9 4.4 33.2 5.4 51 61 H 5.0 H 4.8 4.2 5.3 4.6 4.5 4.5 4.5 3.8 4.5 4.8 4.5 63 64 C 5.0 H 3.5 3.0 4.0 7.8 7.5 5.0 7.8 2.5 4.5 7.2 5.0 66 71 E 4.9 H 1.8 2.3 2.5 2.7 2.5 2.8 2.0 3.0 2.3 2.8 2.3 72 74 * 2.9 P 6.0 53.5 52.7 51.7 52.0 32.0 51.7 6.3 7.8 51.7 7.5 75 76 C 4.9 H 2.5 40.5 2.5 6.2 2.5 4.0 0.5 3.0 4.0 3.0 3.0 77 89 H 4.8 H 4.1 4.3 3.7 14.5 4.4 3.7 4.5 3.9 3.3 4.4 3.4 91 94 - 4.8 H 75.0 75.0 7.4 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 95 96 * 2.8 P 7.2 7.2 4.0 75.0 75.0 6.0 75.0 6.0 6.0 75.0 7.2 97 99 C 4.8 H 3.7 3.3 2.7 4.3 4.0 5.7 4.7 4.3 2.3 4.0 3.3 100 103 E 5.0 H 0.0 0.0 1.2 1.8 0.8 0.0 0.8 0.0 0.8 1.2 0.0 104 105 C 4.9 H 2.5 1.0 0.0 7.0 5.0 2.5 5.5 3.0 2.5 5.5 2.0 106 110 * 3.1 M 2.6 4.0 5.0 75.0 75.0 19.1 75.0 18.1 18.0 75.0 18.9 113 114 C 4.5 M 3.0 40.0 3.0 2.5 1.5 3.5 1.0 3.5 3.5 1.5 3.0 115 120 H 4.5 M 4.7 3.0 3.0 3.8 4.5 3.5 4.3 3.5 4.7 3.7 4.5 122 123 C 5.0 H 1.5 1.0 3.0 1.5 1.0 1.0 2.0 2.5 2.0 1.5 2.5 124 148 * 3.2 M 55.6 3.8 41.3 20.7 21.0 55.2 21.2 55.7 55.6 21.0 55.6 150 157 * 3.6 M 75.0 14.2 75.0 2.8 3.0 75.0 3.4 75.0 75.0 3.4 75.0 >>>>>>