Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1d06a- -------------CCH-HHHHHHHHHHHCCCHHHHHCCCCCEEEEEEC---CCCEEEECHHHHHHHCCC-HHHHCCCCH--HHHCCC---------CHHHHHHHHHHH-HHHHCCCCCCCCCEEEEEECCCCCEEEEEEEEEEEEECC---EEEEEEEEEECC---------- >P1;d1ll8a1 ---------------------------------------CCEEEEEECC--CCCCCEECHHHHHHCCCC-CCCCCCCC--HHHHCCCCC----------CHHHHCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEECCEECCCCCC---CCEEEEEEEECCC--------- >P1;d1nwza- -------------CCCCCCCCCCHHHHCCCCCHHHHCCCCCEEEEEEC---CCCEEEECHHHHHHHCCC-HHHHCCCCII-IIICHH---------HCCCCCHHHHHH-HHHHCC---CEEEEEEEECC-CCCCEEEEEEEEECCC-----CCEEEEEEEEC----------- >P1;d1oj5a- --------------------------------------CCEEEEEECC---CCCEEEEECHHHHCCCCCCHHHHHHHHCCCCCCCC------------CCCHHHHHCCCC------CCCEECCCEEEECCCCCEEEEEEEECCCC------CCCEEEEEEEEC---------- >P1;d1v9ya- -----------------------------CCHHHHHHCCCCEEEEECC---CCCEEEECHHHHHHHCCC-HHHCCCCCH--HHHCCH---------HHCCCHHHHHHH-HHC-----------CEEEECCCCCEEEEEEEEEEEEECC---EEEEEEEEEC------------ >P1;d2gj3a- --------------------------CCHHHHHHHHHHCCCEEEEECC----CCEEEECHHHHHHHCCC-CCHHHHCC--HHHHCC---------CCCCHHHHHHHHH-HHH----CCCCEEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEECCCCC------- >P1;d3f1pb- -----------------------------------CCCCCEEEEEECC---CCCEEEECCCHHHHHCCC-HHHCCCCCH--HHHCCC---------CCHHHHHHHHHH-HCC---CCCCCEEEEEEEECCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEECC--------CC >P1;d3nhqa1 ------------------CCCCCCCHHHCCCCCCCCCCCCEEEEEECC---CCCEEEECCCHHHHHCCC-CC--CCCCCC-HHHH--H-----------HHHHHHHHH-HHCCCCC-CC-CEEEECCC-----CCCEEEEEEEEC-------CEEEEEEEECC-CCC------ >P1;d3zq5a1 ------------CCCCCCCHHHHHHHHCCCHHHCCCCCCCCEEEEEECC--CCEEEEECCCHHHHHCCC-C-CCCCCCH--HHHC--EECCCCCCC--CCCCHHHHH-----------HCCCEEEEEEECCCEEEEEEEEEEECC------CCCEEEEEEECCCCCC------ >P1;d4cqha1 CCCCCHHHCCCCCC---------CCHHHCCCCCCCCCCCCCEEEEEECC--CCCEEEECCCHHHHHCCC-HHHHCCCCH--HHHC----C----------CCHHHHHH-HC-CCCC-C--CCEEEECCCC-CC--EEEEEEEEEC-------CEEEEEEEEE----------- >P1;d4e04a1 -----------------------CCHHHCCCCCCCCCCCCCEEEEECC---CCCEEEECCCHHHHHCCC-HHHHCCCCH--HHHC--C-H----------HHHHHHHH-HHHCCCC-CCEEEEEEECCCC-CCCCEEEEEEEEEC-------CEEEEEEECCCCC-C------ >P1;d4hoia1 ----------------------------------------CCEEEEECCCCCCCEEEECHHHHHHHCCC-HHHHCCCCCCCHHHCC---------CCCCHHHHHHHHH-HHH----CCCCEEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEECCCCC------- >P1;d4hqaa- ---------------------------------------CCCEEEEECCCCCCCEEEECHHHHHHHCCC-HHHHCCCCCCCHHHCC---------CCCCHHHHHHHHH-HHH----CCCCEEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEEEEE-C------- >P1;d4kuka1 -----------------------------CCCCCCCCCCCCEEEEECCCCCCCCEEEECHHHHHHHCCC-HHHHCCCC--HHHHCC---------CCCCHHHHHHHHH-HHH----HCC-CEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEEC----------- >P1;d4wn5a1 -----------------------------------C--CCCEEEEECC---CCCEEEECCCHHHHHCCC-HHHHCCCCH--HHHCCC---------CCHHHHHHHHHH-HHH----HCEEECCCEEEECCCCCEEEEEEEEEEECCCCHHH-CEEEEEEEEEE--------C- >P1;d5f68a- ----------------------------------------CEEEEECC---CCCEEEECCCHHHHHCCC-HHHHCCCCH--HHCCCC---------CCHHHHHHHHHH-HHH---CCCCEECCCEEEECCCCCEEEEEEEEEEEECCCCCCEEEEEEEEEEC----------- >P1;d5svva- -------------------------------------CCCCEEEEEECCCCCCCEEEECHHHHHHHCCC-HHHHCCCC--HHHHHCCCCCCCCCCCCCCHHHHHHHHH-HHH----HCCCEEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEEE----------- >P1;d5viqa1 ------------------------CCCCCCCCCCCCCCCCCEEEEECCC--CCCEEEECCCHHHHHCCC---CCCCCCH--HHHC----H----------HHHHHHHH-HHCCCCC-CCCEEEEEEE-CC--CCEEEEEEEECCC------CCCEEEEEEECCC--------- >P1;d6bafa1 -----------------------CCHHHCCCCCCCCCCCCCEEEEECCC--CCCEEEECCCHHHHHCCC-HHHHCCCCH--HHHC--C-H----------HHHHHHHH-HHCCCCC-CCCCCEEEEEECC-CCEEEEEEEEEEEC-------CEEEEEEEECCCC-C------ >P1;d6gg9a1 -------------------------CCCHHHHHHHHHHCCCEEEEEEEECCEEEEEEECHHHHHHHCCC-HHHHCC-C--HHHHHC---------C--CCCCHHHHC--CCC----CCCCEEEEEEEECCCCCEEEEEEEEEEEEEC-CCCEEEEEEEEEECCCCC---CCCC >P1;d6qqha- --------------------------------------CCCCEEEECCCCCCCCEEEECHHHHHHHCCC-HHHHCCCC--HHHHCC---------CCCCHHHHHHHHH-HHH----HCCCEEEEEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEECCCCCHHHHCCC >P1;d6ywha1 ---------------------------------------CCEEEEEEC-CCCCCEEEECHHHHHHHCCC-HHHHCCCC--HHHHCC---------CCCCHHHHHHHHH-HHH----CCCCEE-EEEEECCCCCEEEEEEEEEEEECC-CCCEEEEEEEEEECCC--------- PSA >P1;d1d06a- -------------a59-7665575668884747651482820000022---804030004104720814-284047511--310116---------633741585184-1374754621b66551302248764040524151467cb---622112306239---------- >P1;d1ll8a1 ---------------------------------------a503000028--604036039501810513-49505543--003000639----------600920049562648a7a4050375160305855744010416445579---54010000643ab--------- >P1;d1nwza- -------------73909013970165039076950460500002031---804042005200800926-2980395200-841132---------053770434067-128659---15331414044-8196350200012157-----c6100000464----------- >P1;d1oj5a- --------------------------------------8110403134---817247361650583b5b9362007402104863e------------860107402407------65816066060619875402020502474------922030301082---------- >P1;d1v9ya- -----------------------------e8a7364284940002013---724051004201910516-384048561--520116---------953753578178-616-----------463002583743605276644757c---4301113067------------ >P1;d2gj3a- --------------------------7987566574252940003045----16041005202810609-6a404a34--383031---------a606871285149-406----654516660204056854050514130433b-7771441213061239a4------- >P1;d3f1pb- -----------------------------------aa74530404044---703045027503700506-2a4047530--150016---------713760440076-026---394761502020305a963320403030429694a9833020302318--------77 >P1;d3nhqa1 ------------------9956a95489458865c8388620101047---61204602b317820814-06--664506-7920--4-----------460170066-0192c89-29-55241628-----862020304377-------9303040431a-9b7------ >P1;d3zq5a1 ------------b9b7aa5965867787569877983986202010605--712037018306b20836-3-5047430--9500--60851794a--9606a9517-----------812504011516aa453403040523a------836010406208895b------ >P1;d4cqha1 a6150667a05818---------a4793408655883887202000309--504037029402710957-186046440--5610----5----------91165059-40-45c1-c--662350751a-a7--5030303078-------9302050555----------- >P1;d4e04a1 -----------------------79a77858875d8388720200039---814046019203820626-2a7049530--5600--5-a----------80374048-31879ba-5805806020609-76848080503478-------b302040544987-9------ >P1;d4hoia1 ----------------------------------------91302030469711045029401910618-4840395101051014---------9606891356055-005----645642150100259654030404010455b-986033030406325884------- >P1;d4hqaa- ---------------------------------------87220203064b611045027001800717-4940375302062023---------8605a80363046-008----a26736040001258830010302030445b-9651430302072375-6------- >P1;d4kuka1 -----------------------------ba79275209920000111859720023019401930718-5a303851--251023---------8807791355155-226----636-242403013588531505141311429-87714200000534----------- >P1;d4wn5a1 -----------------------------------e--6a51404044---604055019106620606-285048231--371029---------913880472185-036----73815095021316a5b213130504449e768a4-30020215346--------8- >P1;d5f68a- ----------------------------------------70403031---80504501a604a20615-484036340--36003a---------814950572056-037---27741405305020488732403030404449868806303060415----------- >P1;d5svva- -------------------------------------92700402120758611046018101630606-3a406742--251012513a399427805692155077-028----506505340100348145040403020542b-99813302020506----------- >P1;d5viqa1 ------------------------797a868866c82888302000048--62504701b403a1051c---7068120--5702----6----------70184046-2157983-b073418050-0a--7433030404329------aa1020506536a--------- >P1;d6bafa1 -----------------------b9a98858876b82977102000438--70403502a204910314-397047250--1700--1-4----------91395027-3043660-6721607000419-06236040505378-------c402040453987-9------ >P1;d6gg9a1 -------------------------a5879565663583b302031166bb411023007102a10725-4a4027-1--343016---------b--352017717--019----775616140402358865030211150554a-a4744113040432337b---9a9b >P1;d6qqha- --------------------------------------8961203110559721035018201810416-39304742--351024---------8607871165164-137----5376241001020477851202130415449-8771330204064644557761a77 >P1;d6ywha1 ---------------------------------------930302152-9b623056039102810316-5a404842--361024---------8806a71335077-028----516516-20101348765050514150545b-868161031504355b--------- Translating the sequences -------------***-*********************CCCEEEEE*C---CCCEEEEC**HHHHHCCC-HHHHCCCC*--HHHC**---------****HHHHHHHH-HH******CC***EEEEEECCCCCEEEEEEEEEEE****---**EEEEEEEEC*---------- ---------------------------------------CCEEEEE*C*--CCC**EEC**HHHH*CCC-****CCCC--*HHHC****----------*HHHH*************CC*****EEE*CCCCC*EEEE**EE******---**EEEEEEEEC**--------- -------------*************************CCCEEEEE*C---CCCEEEEC**HHHHHCCC-HHHHCCCC**-***C**---------******HHHHHH-HH****---C***EEEEE*C-CCC*EEEEEEEEE***-----**EEEEEEEEC----------- --------------------------------------CC*EEEEE*C---CCCEEEE***HHH**CCC*HHHH**********C*------------***HHHHH****------*CC*****EEEECCCCCEEEEEEEE****------***EEEEEEE**---------- -----------------------------*********CCCEEEEE*C---CCCEEEEC**HHHHHCCC-HHH*CCCC*--HHHC**---------*****HHHHHHH-HH*-----------*EEEECCCCCEEEEEEEEEEE****---**EEEEEEE*------------ --------------------------************CCCEEEEE*C----CCEEEEC**HHHHHCCC-**HH**CC--*HHHC*---------*****HHHHHHHH-HH*----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC****------- -----------------------------------***CC*EEEEE*C---CCCEEEEC**HHHHHCCC-HHH*CCCC*--HHHC**---------****HHHHHHHH-H**---**CC***EEEEEECCCCCEEEEEEEEEEE*********EEEEEEEEC*--------** ------------------********************CC*EEEEE*C---CCCEEEEC**HHHHHCCC-**--CCCC**-HHH*--*-----------*HHHHHHHH-HH*****-CC-**EEE***-----***EEEEEEEE*-------*EEEEEEEEC*-***------ ------------**************************CCCEEEEE*C*--CC*EEEEC**HHHHHCCC-*-**CCCC*--HHHC--*********--****HHHHH-----------****EEEEEE*CCC*EEEEEEEEEE**------***EEEEEEEC*****------ **************---------***************CCCEEEEE*C*--CCCEEEEC**HHHHHCCC-HHHHCCCC*--HHHC----*----------**HHHHHH-H*-****-C--**EEEE**CC-CC--EEEEEEEEE*-------*EEEEEEEE*----------- -----------------------***************CCCEEEEE*C---CCCEEEEC**HHHHHCCC-HHHHCCCC*--HHHC--*-*----------HHHHHHHH-HH*****-CC***EEEE**CC-CC**EEEEEEEEE*-------*EEEEEEE*C***-*------ ----------------------------------------C*EEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC***HHHC*---------*****HHHHHHHH-HH*----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC****------- ---------------------------------------CC*EEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC***HHHC*---------*****HHHHHHHH-HH*----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEE***-*------- -----------------------------*********CCCEEEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC--*HHHC*---------*****HHHHHHHH-HH*----*CC-**EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC----------- -----------------------------------*--CCCEEEEE*C---CCCEEEEC**HHHHHCCC-HHHHCCCC*--HHHC**---------****HHHHHHHH-HH*----*C******EEEECCCCCEEEEEEEEEEE*******-*EEEEEEEE**--------*- ----------------------------------------CEEEEE*C---CCCEEEEC**HHHHHCCC-HHHHCCCC*--HH*C**---------****HHHHHHHH-HH*---**CC*****EEEECCCCCEEEEEEEEEEE*********EEEEEEEEC----------- -------------------------------------*CCCEEEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC--*HHH****************HHHHHHHH-HH*----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEE*----------- ------------------------**************CCCEEEEE*C*--CCCEEEEC**HHHHHCCC---**CCCC*--HHHC----*----------HHHHHHHH-HH*****-CC***EEEEE-CC--C*EEEEEEEE***------***EEEEEEEC**--------- -----------------------***************CCCEEEEE*C*--CCCEEEEC**HHHHHCCC-HHHHCCCC*--HHHC--*-*----------HHHHHHHH-HH*****-CC***EEEEEECC-CCEEEEEEEEEEE*-------*EEEEEEEEC***-*------ -------------------------*************CCCEEEEE********EEEEC**HHHHHCCC-HHHHCC-C--*HHH**---------*--****HHHH*--***----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC****---**** --------------------------------------CCC*EEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC--*HHHC*---------*****HHHHHHHH-HH*----*CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC*********** ---------------------------------------CCEEEEE*C-**CCCEEEEC**HHHHHCCC-HHHHCCCC--*HHHC*---------*****HHHHHHHH-HH*----*CC***-EEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC**--------- 55785.tem _________________________________ -----------------------***************CCCEEEEE*C***CCCEEEEC**HHHHHCCC-HHHHCCCC*-*HHHC**--------*****HHHHHHHH-HH******CC***EEEEEECCCCCEEEEEEEEEEE***-*****EEEEEEEEC****------- Structural block scores 0 22 - 4.7 H 48.3 75.0 44.5 75.0 75.0 75.0 75.0 60.4 43.2 32.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 23 37 * 3.4 M 5.8 75.0 4.1 75.0 34.2 19.7 61.9 6.8 7.1 5.9 7.6 75.0 75.0 33.6 71.0 75.0 70.6 12.1 8.0 15.6 75.0 75.0 38 40 C 4.6 H 4.0 30.2 1.7 3.3 5.7 5.0 4.0 5.3 5.3 5.7 5.7 53.0 30.0 6.7 7.2 52.3 3.0 6.3 5.0 5.8 7.7 29.0 41 45 E 4.9 H 0.0 0.6 0.4 1.6 0.4 0.6 1.6 0.4 0.6 0.4 0.4 1.2 1.2 0.2 1.8 1.4 1.4 0.4 0.4 1.2 1.4 1.2 48 50 * 3.9 M 75.0 52.7 75.0 75.0 75.0 75.0 75.0 75.0 51.7 53.0 75.0 6.3 7.2 7.3 75.0 75.0 6.7 52.7 52.7 9.7 6.3 31.8 51 53 C 4.8 H 4.0 3.3 4.0 5.3 4.3 27.3 3.3 3.0 3.3 3.0 4.3 3.0 2.7 3.0 3.3 4.3 2.7 4.3 3.7 2.0 3.3 3.7 54 57 E 5.0 H 0.8 2.2 1.5 4.0 1.5 1.2 2.2 2.5 2.5 2.5 2.5 2.2 2.2 1.2 2.5 2.2 2.5 2.8 2.0 1.2 2.0 2.8 59 60 * 1.0 P 2.5 7.0 3.5 3.5 3.0 3.5 6.0 7.2 5.5 6.5 5.5 6.5 3.5 6.5 5.0 8.2 4.5 7.8 6.2 4.0 5.0 5.0 61 65 H 4.9 H 2.6 2.0 1.6 4.2 2.2 2.2 2.0 3.6 3.9 2.0 2.6 2.2 1.8 2.6 2.8 3.3 2.0 2.9 2.8 2.7 2.0 2.2 66 68 C 5.0 H 4.3 3.0 5.7 9.3 4.0 5.0 3.7 4.3 5.7 7.0 4.7 5.0 5.0 5.3 4.0 4.0 4.0 6.2 2.7 4.7 3.7 3.3 70 73 H 4.4 M 3.5 4.5 4.8 2.8 3.8 5.1 4.1 39.0 20.8 3.8 4.9 4.0 4.2 4.6 3.8 4.0 4.4 39.2 4.8 4.6 3.8 4.9 74 77 C 4.8 H 4.2 4.2 4.8 2.8 5.8 5.4 4.8 5.2 4.5 4.5 5.2 4.5 4.5 4.2 4.2 4.0 4.8 4.2 4.5 21.2 4.2 4.5 81 83 H 4.7 H 1.3 1.0 4.3 6.0 2.3 3.7 2.0 6.0 4.7 4.0 3.7 2.0 2.7 2.0 3.7 3.0 2.0 4.0 2.7 2.3 2.0 2.3 85 86 * 3.1 M 3.5 3.0 2.5 44.8 3.5 38.0 3.5 75.0 75.0 75.0 75.0 39.5 39.0 39.0 5.5 6.8 3.5 75.0 75.0 40.5 39.5 39.5 87 94 - 4.6 H 75.0 57.8 75.0 75.0 75.0 75.0 75.0 66.1 5.0 66.2 58.2 75.0 75.0 75.0 75.0 75.0 5.2 66.4 56.9 75.0 75.0 75.0 95 99 * 2.8 P 18.8 61.2 18.0 47.8 19.8 6.1 18.6 60.8 35.1 75.0 75.0 5.8 5.9 6.0 19.2 19.4 5.2 75.0 75.0 33.9 5.8 6.5 100 107 H 4.7 H 4.5 3.0 3.9 2.2 5.5 4.6 3.4 3.2 14.2 4.5 4.2 4.2 3.8 4.2 4.4 3.8 4.5 3.8 4.5 12.5 3.9 4.1 109 110 H 4.4 M 2.0 4.0 1.5 41.0 3.5 2.0 1.0 0.5 75.0 2.0 2.0 0.0 0.0 2.0 1.5 1.5 1.0 1.5 1.5 0.5 2.0 1.0 111 116 * 3.3 M 5.5 7.7 29.7 63.5 63.5 52.0 40.5 19.2 75.0 28.8 20.2 51.8 53.1 52.0 52.2 40.2 52.2 17.8 15.7 52.7 52.0 52.2 117 118 C 4.7 H 1.5 2.0 38.0 6.5 75.0 4.5 5.5 5.5 41.5 43.8 6.5 4.5 4.0 4.5 5.5 5.5 3.0 5.8 6.5 6.0 5.0 3.5 119 121 * 1.5 P 7.8 2.7 3.7 2.3 75.0 4.0 4.0 28.3 2.7 29.0 4.3 4.0 5.3 27.0 2.0 1.7 3.3 4.7 3.0 4.3 4.0 4.0 122 127 E 4.6 H 2.7 3.7 2.3 4.0 14.7 3.0 1.2 3.8 1.8 3.7 2.3 1.2 0.8 1.7 3.3 2.5 1.3 14.8 1.8 1.8 0.7 13.2 128 132 C 4.7 H 5.4 4.6 19.4 6.0 5.0 4.8 6.1 75.0 6.4 20.8 19.4 5.4 5.2 5.8 6.8 5.4 4.0 33.5 18.2 6.0 5.2 5.6 133 143 E 4.8 H 2.7 3.2 1.8 2.4 4.3 2.5 2.0 3.2 2.6 15.5 4.3 1.8 1.2 2.3 2.5 2.1 2.1 2.4 3.2 2.1 2.2 2.8 144 146 * 2.1 P 8.5 5.7 29.0 51.3 6.3 5.8 5.7 52.3 53.5 52.7 52.7 7.2 6.8 5.0 10.2 5.7 5.8 53.0 52.7 6.5 5.7 6.8 148 152 * 2.7 P 46.6 46.8 48.7 47.2 46.4 5.2 6.9 61.8 47.2 61.8 62.3 5.2 5.0 5.4 20.1 5.6 6.0 49.2 62.5 5.9 5.2 5.8 153 160 E 4.9 H 2.1 1.4 1.4 1.1 2.4 2.2 1.6 2.1 2.4 2.5 2.2 2.4 2.1 1.2 1.6 2.1 1.5 2.4 2.4 2.0 2.4 2.1 162 165 * 3.4 M 58.5 43.0 75.0 56.8 75.0 6.6 58.2 26.5 7.5 75.0 24.8 6.2 23.2 75.0 57.8 75.0 75.0 41.6 24.8 6.1 4.5 41.6 166 172 - 4.7 H 75.0 75.0 75.0 75.0 75.0 75.0 55.6 65.3 65.9 75.0 65.6 75.0 75.0 75.0 65.4 75.0 75.0 75.0 65.6 37.9 6.5 75.0 >>>>>>