Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1t3ta4 --CCCCCEEECCEEEC--CCHHHHHHHHHHH-------CCCC---EEECC-----------------------------CCCCEEEEEEEEEEEEECCCCCCEEEEEEEEEEEEEEEEC--HHHHHH-----CHHHHHHHHHHHHHHHHHCCCCCCEE---EEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH-HHHHHHCCCEEEEEEEECEEEEEEC----CEEEEEECCCCEEEEEEEEEE-CHHHCCCCC >P1;d1t3ta5 -----CCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC-CCHHHHCCCCCCCCCCEEECCEECCCCEE-------------CCCCEEEECCC----------------CCCCEEEEEEEEC--HHHHHC-----CHHHHHHHHHHHHHHHHCCC--CCCCHHHCEEEEEEECCCCC------------------CCHHHHHHHHHHHHHCCHHHHHCCEEEEEEEECCCEEEEECCC----CEEEEECCCEEEEEEEEEECCHHHCCC-- >P1;d1vk3a1 CHHHHHHCCC-CCCC----CHHHHHHHHCCCHHHHCCCCHHHHHCCCCCC-----------------------------CCCCCEEECCC------------------CCEEEEEEEEC--HHHHHH-----CHHHHHHHHHHHHHHHHHC---CCEE---EEEEEEEECC--------------------------CCHHHHHHHH-HHHHHHCCCEEEEEECCC------HHHCC---------CCEEEEEEEEEE-C-CCCC--C >P1;d1vk3a2 -----CCCCCC--CCCCCCCCC-------------C-CCCCCCCCCCCC---CCCCCH---HH------------------CCCCCC--------------------CCCEEECCCCCC--HHHHCC-----CHHHHHHHHHHHHHHHHHHC--CCEE---EEEEEEEECCCCC------------------CC-HHHHHC--CHHH-HHHHHHCCCEEEEEEECCCCC-------------CCCCCCEEEEE-EEEE-CHHHC---- >P1;d2v9ya1 --------------------------------------------------------------------------------------------CCCCCCCC--CCC---CEEEEEEEECCCCHHHHHH--HHCCCCCHHHHHHHHHHHHHHCC--CCEE---EEEEEEEEEC--CCC-------------------HHHHHHHHHHHH-HHHHHHCCEEEEEEEEECC--------CCCCC------CCEEEEEEEEEEEEHHHCC--- >P1;d2yyda1 -------------------------------------------------------------------CHHHHCCCCCCHHHHHCCCCCCCCCEEEE-C----------CEEEEEEEEEEC---CCCC-----CHHHHHHHHHHHHHHHHHHC--CCEE---EEEEEEEEECCCCCC-------------------HHHHHHHHHHHH-HHHHHCCCEEEEEEEEECC-------------------CCEEEEEEEEEC--HHHCC--- >P1;d2z1ea1 -----------------------------------------------------------------------------------------CCEEEEEC-----------CEEEEEEEEEEC---C-CCEECCEE---HHHHHHHHHHHHHHCC--CCEE---EEEEEEEEEEC-CCC-------------------HHHH-CCHHHHH-HHHHHCCCCEEEEEEEEEC------------C------CCCEEEEEEEEEEE---CC--- >P1;d3c9ua1 ----------------------------------------------------------CCHHHHC-HHHHHHHHHHH---HCCCCC-CCCCEEEEE-C----------CEEEEEEEEEEE---CCCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCEE---EEEEEEEEECC-CCC-------------------HHHHHHHHHHHH-HHHHHHCCEEEEEEEEECC-------------------CCEEEEEEEEEEC--------- >P1;d3qtya1 --------------------------------------------------CCCCCCCCCCCCCCC-HHHHHCCHHHHCCCCCCEEECCCCCCEEECCHHHHHHCC---CEEEEEEEECCCCHHHHHC---CCCCCCHHHHHHHHHHHHHH-C--CCEE---EEEEEEEEEC--CCC-------------------CC-CCHHHHCC--HHHHHCCCEEEEEEEEC-C--------CCCCC------CCEE-EEEEEEEEEHHHCC--- >P1;d3u0oa1 -------------------------------------------------------------------CCCCCCCCCCCCCCC-----CCCCEEEECCC----------CEEEEEEEEEEC---CCCC-----CHHHHHHHHHHHHHHHHHHC--CC-C---CEEEEEEEECCC--C-------------------HHHHHHHHHHHH-HHHHHCCCCEEEEEEEECC-------------------CCEEEEEEEEEE-EHHH-C--- >P1;d5cm7a1 ----------------------------------------------------------------C-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC----------CCEEEEEEEEEE---CCCCCCCCCCHHHHHHHHHHHHHHHHHCC--CCEE---EEEEEEEEECC---C-------------------HHHHHHHHHHHH-HHHHHHCCEEEEEEEEECC-------------------CCEEEEEEEEEEC--------- PSA >P1;d1t3ta4 --8685a465a98748--3124456347456-------6578---22013-----------------------------606030440855225434a958764737240130434443--374005-----60550016000300720460057070---510320000002347b763770661934871240340054036005-440894705367355625044492a----977355133603020015010-44a30655b >P1;d1t3ta5 -----b7655a4aa7a77a48a95467766768844-64485047872987932222501678550-------------70713042447----------------a365060606044--163066-----41130044007302820750--50a73750401031200483------------------701720296055005762049340524728652941764669b----986381320203020403041056083-- >P1;d1vk3a1 9954760583-b580----789246638845585453856884686966b-----------------------------b2ca5344669------------------75031555443--394039-----6347001600030174068---2090---5205011127--------------------------7294046006-431982a16455244654------99349---------913020302042-2-a469--a >P1;d1vk3a2 -----5a292b--a53a1955b-------------9-8686599a642a---b10362---c7------------------504057--------------------878050607223--011032-----22020112002112730671--9061---4106132300218------------------85-462420--2027-301681a0636828542532b-------------b9453120302-4060-30680---- >P1;d2v9ya1 --------------------------------------------------------------------------------------------aa273973--809---62450666240c9605700--85880780053004501750774--1071---0204040000--608-------------------a81383056005-600b729053273732543--------b6167------830504050200036a667--- >P1;d2yyda1 -------------------------------------------------------------------7048126dc747776b7b5987a872566-9----------a51205155323---0436-----52250015005400660582--9060---430402001278407-------------------782273025005-4308719071583856737-------------------002000401030--4a385--- >P1;d2z1ea1 -----------------------------------------------------------------------------------------b176577c-----------b64305075417---4-90539b20---0034004501730572--7071---52031403106-b07-------------------5831-5049305-6007527062574646528------------4------92604020204030---b4--- >P1;d3c9ua1 ----------------------------------------------------------6787638-78434665388---692963-865043588-9----------b45204153305---17640639560260045002400620543--9080---3505030510a-807-------------------a61374044007-600772907148277593a-------------------7000205020328--------- >P1;d3qtya1 --------------------------------------------------bc9a9a87b7a857c-9515643530570249105a0ab542071459517872a---52453537231aa606812---77515702321064008504-8--4061---0105241001--735-------------------68-33315400--50047490001127544-6--------c9299------9204-20301000268858--- >P1;d3u0oa1 -------------------------------------------------------------------a889869a785544a-----85305052498----------940307053535---354b-----62440044007500610550--80-0---450413101369--5-------------------665165024004-50066190606c0866519-------------------623000502050-4387-3--- >P1;d5cm7a1 ----------------------------------------------------------------a-598038600433928a0443296a80718538----------b38415244403---02740779262450035003200750776--9092---30040503154---7-------------------7a1054004000-500565a010032815829-------------------5130302000139--------- Translating the sequences --**************--*************-------****---*****-----------------------------**C****************************EEEEEEEE*--******-----CHHHHHHHHHHHHHHHHH*C**CCEE---EEEEEEEEECC*C*C*******************HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*C*******----*********CCEEEEEEEEEE-****CC*** -----*******************************-*****************************-------------**C*******C----------------**C*EEEEEEEE*--*****C-----CHHHHHHHHHHHHHHHH**C--CC******EEEEEEE*CC*C------------------***HHHHHHHHHHHH**HHHH*CC*EEEEEEE*CC********----*******CCEEEEEEEEEE*****CC*-- **********-****----*******************************-----------------------------**C*******C------------------C*EEEEEEEE*--******-----CHHHHHHHHHHHHHHHHH*---CCEE---EEEEEEEE*C--------------------------**HHHHHHHH-HHHHH*CC*EEEEEE**C------*****---------CCEEEEEEEEEE-*-**CC--* -----******--*********-------------*-************---******---**------------------C*****--------------------*C*EEE******--*****C-----CHHHHHHHHHHHHHHHHH*C--CCEE---EEEEEEEE*CC*C------------------**-HHHHH*--*HHH-HHHHH*CC*EEEEEEE*CC**-------------****CCEEEEE-EEEE-****C---- --------------------------------------------------------------------------------------------********--***---C*EEEEEEE**********--***C***HHHHHHHHHHHHHH*C--CCEE---EEEEEEEEEC--C*C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC--------*****------CCEEEEEEEEEE*****CC--- -------------------------------------------------------------------**********************C******-*----------C*EEEEEEEE**---***C-----CHHHHHHHHHHHHHHHHH*C--CCEE---EEEEEEEEECC*C*C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC-------------------CCEEEEEEEEE*--***CC--- -----------------------------------------------------------------------------------------C*******-----------C*EEEEEEEE**---*-*C******---HHHHHHHHHHHHHH*C--CCEE---EEEEEEEEE*C-C*C-------------------HHHH-**HHHHH-HHHHH*CC*EEEEEEE**C------------*------CC*EEEEEEEEE**---CC--- ----------------------------------------------------------*******-***********---*C****-**C******-*----------C*EEEEEEEE**---***C*****CHHHHHHHHHHHHHHHHH*C--CCEE---EEEEEEEEECC-C*C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC-------------------CCEEEEEEEEEE*--------- --------------------------------------------------***************-***************C*******C***************---C*EEEEEEE*********C---**C***HHHHHHHHHHHHHH-C--CCEE---EEEEEEEEEC--C*C-------------------**-**HHHH**--HHHHH*CC*EEEEEEE*-C--------*****------CCEE-EEEEEEE*****CC--- -------------------------------------------------------------------**************C-----**C********----------C*EEEEEEEE**---***C-----CHHHHHHHHHHHHHHHHH*C--CC-*---*EEEEEEEECC*--C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC-------------------CCEEEEEEEEEE-****-C--- ----------------------------------------------------------------*-***************C*******C********----------C*EEEEEEEE**---***C*****CHHHHHHHHHHHHHHHHH*C--CCEE---EEEEEEEEECC---C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC-------------------CCEEEEEEEEEE*--------- 55326.tem _________________________________ -----*****---**----***----------------****---****------------**-*--**************C*******C********----------C*EEEEEEEE**-*****C--***CHHHHHHHHHHHHHHHHH*C--CCEE---EEEEEEEEECC*C*C-------------------HHHHHHHHHHHH-HHHHH*CC*EEEEEEE*CC------------*------CCEEEEEEEEEE*****CC--- Structural block scores 0 4 - 4.6 H 34.4 75.0 6.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 5 9 * 3.9 M 6.1 6.9 4.4 5.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 10 12 - 4.2 M 9.2 8.3 30.5 53.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 13 14 * 3.9 M 5.5 8.8 4.0 7.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 15 18 - 4.3 M 40.2 8.8 75.0 5.9 75.0 75.0 75.0 75.0 75.0 75.0 75.0 19 21 * 3.9 M 2.3 7.5 8.0 7.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 22 37 - 4.3 M 35.6 10.5 5.2 66.7 75.0 75.0 75.0 75.0 75.0 75.0 75.0 38 41 * 3.9 M 6.5 5.2 6.8 6.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 42 44 - 4.2 M 75.0 3.7 6.0 9.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 45 48 * 3.9 M 1.2 6.5 6.8 5.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 49 60 - 4.3 M 69.0 3.9 69.7 39.5 75.0 75.0 75.0 58.0 15.2 75.0 75.0 61 62 * 3.9 M 75.0 7.5 75.0 9.8 75.0 75.0 75.0 6.5 6.5 75.0 75.0 65 66 - 4.5 M 75.0 37.5 75.0 75.0 75.0 75.0 75.0 41.0 42.0 75.0 40.0 67 80 * 3.5 M 64.7 64.8 65.2 75.0 75.0 6.1 75.0 20.4 3.6 7.3 4.5 82 88 * 2.5 P 2.7 2.6 5.5 23.7 75.0 8.4 75.0 15.6 5.5 55.4 4.0 90 97 * 2.7 P 4.4 75.0 75.0 75.0 24.0 14.8 15.1 14.0 4.0 4.1 5.0 98 107 - 4.3 M 5.8 61.4 75.0 68.3 40.2 75.0 75.0 75.0 26.6 75.0 75.0 110 117 E 4.8 H 2.9 2.8 3.4 2.8 4.1 2.8 3.5 2.9 4.0 2.9 4.0 118 119 * 1.9 P 39.0 39.5 39.0 39.0 6.2 2.5 4.0 2.5 5.8 4.0 1.5 121 125 * 2.0 P 2.8 3.2 3.8 1.0 3.6 31.4 47.6 32.8 4.2 32.4 31.8 127 128 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 4.0 3.0 75.0 75.0 3.5 129 131 * 3.7 M 75.0 75.0 75.0 75.0 7.0 75.0 7.5 5.7 29.7 75.0 6.0 133 149 H 4.9 H 1.9 2.5 2.5 1.8 3.1 2.4 15.1 2.1 2.8 2.5 2.5 152 153 - 4.8 H 2.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 154 155 C 5.0 H 3.5 2.5 1.0 4.5 0.5 4.5 3.5 4.5 2.0 4.0 4.5 156 157 E 4.5 M 3.5 8.8 4.5 3.5 4.0 3.0 4.0 4.0 3.5 37.5 5.5 158 160 - 4.8 H 75.0 5.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 161 169 E 4.9 H 1.2 1.2 1.9 2.2 1.1 1.6 2.1 2.4 1.4 2.1 1.8 170 171 C 4.7 H 0.0 2.0 41.0 1.0 37.5 4.5 3.0 5.2 38.0 4.5 4.5 176 194 - 4.7 H 4.9 63.6 75.0 67.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 195 206 H 4.7 H 2.5 3.4 15.7 14.9 4.1 3.4 9.8 3.9 15.2 3.2 2.6 208 212 H 5.0 H 5.0 4.2 5.0 3.6 4.9 4.4 3.6 4.0 3.2 3.4 3.2 214 215 C 5.0 H 3.5 2.0 5.8 5.2 4.5 4.5 3.5 4.5 4.5 4.5 5.2 217 223 E 5.0 H 5.0 4.9 4.3 5.1 3.9 5.1 4.9 4.9 2.9 5.5 2.7 225 226 C 4.6 H 2.5 6.5 39.5 4.0 3.5 5.0 5.0 6.8 40.5 5.0 5.5 227 238 - 4.3 M 29.1 29.2 46.6 63.6 52.0 75.0 75.0 75.0 52.7 75.0 75.0 240 245 - 4.3 M 3.3 4.8 75.0 29.9 75.0 75.0 75.0 75.0 75.0 75.0 75.0 246 247 C 5.0 H 3.0 1.0 5.0 2.0 5.5 0.0 5.5 3.5 5.5 4.0 3.0 248 257 E 4.9 H 1.2 1.4 1.6 9.2 1.6 1.0 1.8 1.4 8.5 1.5 1.2 258 262 * 2.6 P 19.3 3.2 33.3 18.4 5.1 33.5 45.6 61.6 4.8 19.4 61.8 263 264 C 4.5 M 3.0 4.0 7.5 37.5 6.5 6.5 7.8 75.0 6.5 39.0 75.0 265 267 - 4.6 H 7.2 51.0 53.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>