Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1lqba- -------------------------------CEEEEEEEEC-C-------EEE---EEEEECCCCHHHHHHHHHHHHC---------------CCHHHEEEEECC------------------EECCCCC-CCCCCCCCC-CCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHC >P1;d1t0ya- -----------------C------------CCEEEEEEEECC--CC----CCE---EEEEECCCCHHHHHHHHHHHHC---------------CCCCCEEEEEEC-CCC----------CEEEECCCCCC-CHHHHCCCC--------CEEEEEEECCCCCCC------------------ >P1;d1v2ya1 ---------------------------------CEEEEECC-------CCCCC---CEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHEEEECC------CCEECCC-----------CC-CCHHHCCC--------CCCEEEEEECC--------------------CCC >P1;d1we6a1 CCCHHH------CCCHHHHHHHCC-------CCEEEEECCCCCCCC----CCE-EEEECCCC-CCHHHHHHHHHHHCC---------------CCCCCCEEECC-C----------------CCCCC-CC-CCCCCCCCC--------CCEEEEECCC--------C-------------- >P1;d1wf9a1 ---------------------------------CEEEEEECC--------EEE-EEECCCC-CCCHHHHHHHHHHHCC---------------CCCCCCCCCCC-HHHHHCC--CHHHHHCCCCCCCCCC-CHHHCCCCC--------CCEEEECCCCCCCC---CC-------------- >P1;d1wfya1 ------------------------CCCCCCCCCEEEEEEECCC--C----EEE-EEEE--CCCCCHHHHHHHHHCCCC---------------CCCCCCEEECC-CCC--------------CCCCC-CC-CHHHHC-----------EEEEEEECCCCCCCCCCCC-------------- >P1;d1wgha1 ------------------------CCCCCCCCCEEEEEECC-------CCCEE---EEEECCCCCHHHHHHHHHHCCCCCCCCCC-------CCCCCCCEEEEC------------------CEEECCCC-CCCCC--CCC----CCCEEEEEEECCC--C----------CCCCCCCCCC >P1;d1wgya1 ------------------------------C-CCCCCEECCC-------CCEE---CCCCCCCCCCHHHHHHHHHHCC---------------CCHHHEEEEEEC-C------------CCCEEECCCCC-CCCCCCC--------CCCCEEEEEECC--CCCCCCCCCC----------C >P1;d1wxaa1 -------------------------------CCEEEEECCCCCC---CCCCCE---EEEECCCCCHHHHHHHHHHHHC----CCC--------CCCCCEEEEEEE-CCCCCCC--CCCCCCEEEECCCCC-CHHHHHHCCCCCCC--C-EEEEEEECC--C-------------------- >P1;d1x1ma1 C---CCCCCCEEEEECCCC----C-------CCCEEECCCCCCCCC----C--------CCCCCCHHHHHHHHHHHCC------------CCCCCCCCEEEEEC-C----------------EECCC-CC-CHHHHCCCC--------CCEEEEEECC--------C-------------- >P1;d2al6a3 ------------------------C-----CCCCEEEEECCCCCCCCHHHCEE---EEECCCCCCHHHHHHHHHHHCCCC--------------CHHHEEEEEEE-CCCC-----------CEEEECCCC-CHHHHHHHHHCCCCHHH-EEEEEEECC--C----------C--------- >P1;d2c5lc1 -------------------------------CEEEEEEE--CCC---CCCCEE---EEEEECCCCHHHHHHHHHHHCCCCHHHHH-------CCCHHHEEEEEEE-C------------CCEEEECCCCC-CHHHHHHCCC---C--C-EEEEEEECC--C-------------------- >P1;d2cr5a1 -----------------CCCCCCCCCCCCCCCEEEEEEECCC---C----CEE---EEEEECCCCHHHHHHHHHHH-C---------------CCCCCEEEEECC--------------CCEECCCCCCC-CHHHHCCCC--------CEEEEEEECC-----CCC--------------C >P1;d2dhza1 ------------------------------C-EECCCEECCC-------CCCC---CCCEECCCCHHHHHHHHHHHCC-------CCCCCCCCCC--CCEEEEEE-C------------CCCEEECCCCCCCHHHHCC---------CCEEEEEECCC--CCCCCCCCCCCCCCCCCCCCC >P1;d2m4na1 ------------------------------CCCCEEEEECCCCCCC---CCEE---EEECCCCCCHHHHHHHHHHHCC-------CCC------CCCCEEEEEEE-CCHHHHCCC-CCCCCCCCEECCCC-CCHHHHHHCCCCCCCCCCEEEEEEECC--C-------------------- >P1;d3kuza1 --------------------------------CEEEEEEECC--CCCCCCCCE---EEEECCCCCHHHHHHHHHHHHHHHH---CCCC-CC---CHHHCEEECCC------CEECCCCCCCCCCCCCCCC-CCCCC-CC--------CCCEEEEEC------------------------- >P1;d4e74a- ------------------------------CCEEEEEECCCC---------CE---EEEEECCCCHHHHC-CHHHHHCC-----CCCHHHC---CCCCEEEEEEC-CCCCEEEECCCCCCCC------CC-CHHHHCCC--------CCCEEEEEECC----------------------C >P1;d4x57b- ------------------------------CCEEEEEEECCCC-------CEE--EEEEEECCCCHHHHHHHHHHHCC---------CCCCCCCCHHHEEEEECC------------------EEECCCC-CHHHCC-CC-CCCCCCCCEEEEEEECCC---------------------- >P1;d6yooa1 ---CCHHHHHCC---HHHHHHHHHHHHHHCCCEEEEEEEECCCCCC----CCCCCCEEEEECCCCHHHHHHHHHHHCC---------CCC-----CCCCEEECCC------------------CCCCCCC-CHHHHHH---HHCCCCCCEEEEEECCCCCCC------------------- PSA >P1;d1lqba- -------------------------------7303010124-8-------511---625273823046005503a528---------------3319301013aa------------------85075b5-301606043-96065781240000063b97738152476a8898659964 >P1;d1t0ya- -----------------a------------956050203004--4a----925---6451419430640054009619---------------087a20400123-659----------84363126094-207503077--------a24020106587679------------------ >P1;d1v2ya1 ---------------------------------03030547-------a8450---4080987030630041037221755588a4898371a62182310108------c540365-----------a4-40551a08--------6736030535b--------------------a8a >P1;d1we6a1 a679a7------535298049738-------850303034279b57----c42-5240c604-49023007301a82a---------------162c5040307-9----------------87075-d3-100520007--------6230605569--------a-------------- >P1;d1wf9a1 ---------------------------------320404057--------823-4070516-7030460053045402---------------01384020025-6501708--68751851640655b3-60542b096--------633010008a845b---8b-------------- >P1;d1wfya1 ------------------------bb999a4d52305031667--9----542-7061--308440420065207857---------------252b4060243-b39--------------94172-85-404602-----------9620004219637a7b8ab-------------- >P1;d1wgha1 ------------------------a8aa2489300030127-------a8927---415032c1206600540268299923459-------4544b203011a------------------995167c3-30472--916----4272160405057--7----------a578aaaabb >P1;d1wgya1 ------------------------------6-9440403218-------9451---306085714044003300731b---------------443850000015-a------------85738118373-202868a--------360a41100447--6a960431a9----------e >P1;d1wxaa1 -------------------------------b435050306522---692753---308055a040550042006407----279--------492730100211-228a2b8--a95890938308673-2006154814ab63--8-010202733--9-------------------- >P1;d1x1ma1 9---b70905000201666----b-------293450705519688----7--------9017150430172005618------------81035296020306-9----------------63066-53-307617084--------8330405249--------a-------------- >P1;d2al6a3 ------------------------d-----a9744050205285b66575102---617097a23047005700672919--------------82a11002020-575a-----------544207464-20180286139535492-020003446--7----------7--------- >P1;d2c5lc1 -------------------------------b3070402--700---763560---506055a0201600530065058085067-------5572750101121-7------------a3945508482-3037025719---0--8-040003249--6-------------------- >P1;d2cr5a1 -----------------b64914b4067a3960030004037---9----734---64303292305201300231-8---------------14478240125a--------------668429158b3-205618059--------8240205347-----97b--------------a >P1;d2dhza1 ------------------------------9-535140012a-------4722---706164903097019404753b-------58b785ba59--91200003-0------------8382740848395008518---------9300000037b--32960710657baa043ac17 >P1;d2m4na1 ------------------------------b088415020051379---4530---8090529350350012005309-------43a------43920100201-221874797-758307476152a5-400670288595093512100002638--7-------------------- >P1;d3kuza1 --------------------------------4140603040--841bb3481---6070669020550164027205750---a560-30---7394010416e------5404453b60575a93550-10620-09--------852604035------------------------- >P1;d4e74a- ------------------------------88513020354b---------44---60602340205700-40173027-----9479881---32991201122-d7a554404272a538------60-20630906--------7613000474b----------------------a >P1;d4x57b- ------------------------------7943203040548-------521--05360225240450064027303---------e1a360844a1030316a------------------86075a4-204614-68-902799b3130605066a---------------------- >P1;d6yooa1 ---006037556---4760354047238727830000012058080----551a834120449240470183026509---------178-----7260300067------------------8406790-3016007---722390300000003369019------------------- Translating the sequences -------------------------------C**EEEEE*C-*-------**E---EE***CCCCHHHHHHHHHHH*C---------------*C****EEE***------------------***CCCC-C********-*******C*EEEEE*CC*********************** -----------------*------------*C**EEEEE*CC--**----C*E---EE***CCCCHHHHHHHHHHH*C---------------*C****EEE***-***----------*******CCCC-C*HH*****--------C*EEEEE*CC*****------------------ ---------------------------------*EEEEE*C-------**C**---*E***CCCCHHHHHHHHHHH***********************EEE**------*******-----------CC-C*HH****--------*C*EEEEE*CC--------------------*** ******------************-------C**EEEE**CC****----C*E-**EE***C-CCHHHHHHHHHHH*C---------------*C****EEE**-*----------------****C-CC-C********--------C*EEEEE*CC--------*-------------- ---------------------------------*EEEEE*CC--------**E-**E****-CCCHHHHHHHHHHH*C---------------*C*********-*******--************CCCC-C*HH*****--------C*EEEE**CC****---**-------------- ------------------------*******C**EEEEE*CC*--*----**E-**EE--*CCCCHHHHHHHHH***C---------------*C****EEE**-***--------------****C-CC-C*HH**-----------**EEEEE*CC*********-------------- ------------------------*******C**EEEEE*C-------**C*E---EE***CCCCHHHHHHHHHH**C*******-------**C****EEE**------------------****CCCC-C****--***----*****EEEEE*CC--*----------********** ------------------------------*-*****EE*CC-------*C*E---*****CCCC*HHHHHHHHHH*C---------------*C****EEE***-*------------*******CCCC-C******--------**C*EEEEE*CC--**********----------* -------------------------------C**EEEE**CC**---***C*E---EE***CCCCHHHHHHHHHHH*C----***--------*C****EEE***-*******--***********CCCC-C*HH**********--*-*EEEEE*CC--*-------------------- *---***************----*-------C**EEE***CC****----C--------**CCCCHHHHHHHHHHH*C------------****C****EEE**-*----------------****C-CC-C*HH*****--------C*EEEEE*CC--------*-------------- ------------------------*-----*C**EEEEE*CC********C*E---EE***CCCCHHHHHHHHHHH*C**--------------C****EEE***-****-----------*****CCCC-C*HH*************-*EEEEE*CC--*----------*--------- -------------------------------C**EEEEE--C**---***C*E---EE***CCCCHHHHHHHHHHH*C*******-------**C****EEE***-*------------*******CCCC-C*HH******---*--*-*EEEEE*CC--*-------------------- -----------------**************C**EEEEE*CC---*----C*E---EE***CCCCHHHHHHHHHHH-C---------------*C****EEE***--------------*******CCCC-C*HH*****--------C*EEEEE*CC-----***--------------* ------------------------------*-*****EE*CC-------*C**---*****CCCCHHHHHHHHHHH*C-------*********C--**EEE***-*------------*******CCCC*C*HH***---------*C*EEEEE*CC--********************* ------------------------------*C**EEEEE*CC****---*C*E---EE***CCCCHHHHHHHHHHH*C-------***------C****EEE***-*********-**********CCCC-C*HH*************C*EEEEE*CC--*-------------------- --------------------------------**EEEEE*CC--******C*E---EE***CCCCHHHHHHHHHHH*****---****-**---C****EEE***------***************CCCC-C****-**--------*C*EEEEE*------------------------- ------------------------------*C**EEEE**CC---------*E---EE***CCCCHHHH*-*HHHH*C*-----*******---C****EEE***-****************------CC-C*HH****--------*C*EEEEE*CC----------------------* ------------------------------*C**EEEEE*CC*-------C*E--*EE***CCCCHHHHHHHHHHH*C---------*******C****EEE***------------------***CCCC-C*HH**-**-*******C*EEEEE*CC*---------------------- ---*********---****************C**EEEEE*CC****----C*****EE***CCCCHHHHHHHHHHH*C---------***-----****EEE***------------------***CCCC-C*HH***---*******C*EEEEE*CC****------------------- 54236-4.tem _________________________________ ------------------------------*C**EEEEE*CC****--**C*E---EE***CCCCHHHHHHHHHHH*C*-----*--*-**-**C****EEE***-***--*----*--*******CCCC-C*HH*****-*******C*EEEEE*CC*-**---**-------------* Structural block scores 0 29 - 4.6 H 75.0 72.8 75.0 33.8 75.0 62.0 61.5 75.0 75.0 35.0 73.0 75.0 45.1 75.0 75.0 75.0 75.0 75.0 18.1 32 33 * 1.3 P 1.5 3.0 37.5 2.5 39.0 3.5 1.5 6.5 3.5 6.0 5.5 1.5 0.0 4.0 8.0 2.5 3.0 3.5 1.5 34 38 E 4.7 H 1.0 2.0 2.2 1.8 2.0 2.2 0.8 2.2 2.6 3.2 2.2 2.6 1.4 2.0 2.4 2.6 1.6 1.8 0.2 40 41 C 4.8 H 39.5 2.0 41.0 4.5 6.0 6.0 41.0 4.5 5.5 3.0 3.5 41.0 5.0 6.2 2.5 2.0 7.8 4.5 2.5 42 45 * 3.6 M 58.2 41.1 75.0 8.1 75.0 41.5 75.0 75.0 38.5 7.8 7.6 37.5 58.5 75.0 5.0 40.5 75.0 58.2 4.0 46 47 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 40.5 75.0 5.5 41.0 75.0 75.0 75.0 6.2 75.0 75.0 75.0 48 49 * 3.8 M 75.0 75.0 9.2 75.0 75.0 75.0 9.2 42.0 5.5 75.0 6.0 4.5 75.0 39.5 39.5 7.2 75.0 75.0 75.0 53 55 - 4.5 M 75.0 75.0 75.0 27.3 26.3 27.3 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 50.0 7.2 56 57 E 4.5 M 4.0 5.0 2.0 2.0 3.5 3.5 2.5 1.5 1.5 75.0 3.5 2.5 5.0 3.5 4.0 3.0 3.0 4.0 2.5 58 60 * 1.3 P 4.7 3.3 5.7 6.2 4.0 51.0 2.7 4.7 4.3 28.0 5.3 3.7 2.0 4.3 4.7 4.3 2.7 2.7 2.0 61 64 C 5.0 H 4.0 4.2 4.5 23.0 21.2 4.0 4.4 4.2 4.9 3.5 5.6 4.4 4.0 4.0 4.8 4.2 2.2 3.2 4.8 65 75 H 4.9 H 3.5 3.1 2.4 3.1 2.8 3.1 3.4 2.2 2.4 2.5 3.3 2.4 1.5 4.2 1.7 2.9 9.3 2.8 3.3 79 83 - 4.4 M 75.0 75.0 6.2 75.0 75.0 75.0 4.6 75.0 46.8 75.0 61.8 3.8 75.0 75.0 75.0 46.0 75.0 75.0 75.0 85 86 - 4.3 M 75.0 75.0 6.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.5 3.5 5.5 5.5 75.0 75.0 89 90 * 4.1 M 75.0 75.0 5.0 75.0 75.0 75.0 75.0 75.0 75.0 41.5 75.0 75.0 75.0 6.5 75.0 1.5 4.5 6.8 41.5 92 93 * 3.2 M 39.0 37.5 8.2 38.0 37.5 38.5 4.5 39.5 39.5 1.5 75.0 5.0 38.0 7.8 75.0 75.0 75.0 4.0 75.0 95 98 * 1.1 P 3.2 4.9 3.5 4.9 3.8 4.4 4.4 4.0 3.0 4.2 3.6 3.5 5.2 40.0 3.5 4.0 5.2 3.9 3.8 99 101 E 4.9 H 0.7 1.3 0.7 2.3 0.7 2.7 1.3 0.0 0.3 1.7 0.7 0.7 1.7 0.7 0.3 1.7 1.0 2.0 1.0 102 104 * 1.5 P 8.0 2.0 27.7 27.3 27.3 27.3 28.8 2.0 1.3 27.0 0.7 1.3 5.8 1.0 1.0 7.2 1.7 5.8 4.3 106 108 * 3.8 M 75.0 6.7 75.0 75.0 2.0 29.0 75.0 53.5 4.0 75.0 5.7 52.3 75.0 50.0 1.7 75.0 10.3 75.0 75.0 109 110 - 4.3 M 75.0 75.0 43.8 75.0 3.5 75.0 75.0 75.0 6.2 75.0 42.8 75.0 75.0 75.0 7.5 75.0 5.0 75.0 75.0 112 115 - 4.3 M 75.0 75.0 3.2 75.0 41.0 75.0 75.0 75.0 42.1 75.0 75.0 75.0 75.0 75.0 24.5 3.0 2.5 75.0 75.0 117 118 - 4.3 M 75.0 75.0 75.0 75.0 3.0 75.0 75.0 75.0 6.5 75.0 75.0 75.0 75.0 75.0 6.5 7.2 6.2 75.0 75.0 119 125 * 2.4 P 44.7 3.9 75.0 35.3 4.3 35.1 35.6 4.7 4.6 34.3 23.6 5.2 5.1 4.6 4.0 6.1 45.1 44.9 44.6 126 129 C 4.8 H 7.1 4.8 41.1 24.1 6.1 22.5 7.1 5.2 6.0 22.2 5.2 5.5 6.9 5.8 5.6 3.2 39.0 6.6 5.5 133 134 H 4.3 M 3.5 6.0 5.0 2.5 4.5 5.0 5.5 5.0 3.0 6.5 4.5 5.0 5.5 4.0 3.0 4.0 4.5 5.0 3.5 135 139 * 1.9 P 2.6 3.4 18.9 1.8 5.7 45.4 32.4 34.9 3.8 4.0 3.4 3.0 4.6 32.8 5.0 31.8 18.0 18.8 31.4 141 147 * 3.8 M 5.9 75.0 65.1 75.0 75.0 75.0 44.7 54.9 27.0 75.0 5.3 54.7 75.0 65.6 4.6 65.4 65.3 6.8 3.7 150 154 E 5.0 H 0.8 1.4 2.8 2.8 0.8 1.2 3.0 1.2 1.0 2.4 1.0 1.4 2.2 0.0 0.4 2.6 1.4 2.8 0.0 156 157 C 4.9 H 4.5 5.5 8.2 7.5 9.2 5.0 6.0 5.5 3.0 6.5 5.0 6.5 5.5 9.2 5.5 75.0 7.8 6.0 4.5 160 161 * 3.3 M 7.0 6.5 75.0 75.0 8.2 8.8 41.0 8.2 42.0 75.0 41.0 40.5 75.0 2.5 41.0 75.0 75.0 75.0 5.0 162 164 - 4.3 M 4.0 53.0 75.0 75.0 75.0 8.8 75.0 5.0 75.0 75.0 75.0 75.0 30.3 5.0 75.0 75.0 75.0 75.0 75.0 165 166 * 4.0 M 3.5 75.0 75.0 42.8 9.8 11.0 75.0 3.5 75.0 42.8 75.0 75.0 43.2 4.0 75.0 75.0 75.0 75.0 75.0 167 179 - 4.6 H 7.3 75.0 64.9 75.0 75.0 75.0 29.5 59.3 75.0 75.0 69.8 75.0 75.0 6.3 75.0 75.0 75.0 75.0 75.0 >>>>>>