Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1f7ca- ---------------------CCCC----HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCC------CCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCCCC-C---------------------------CHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHHCCCC------CCHHH--HHHHHHHHHHHHHHCHHHHHHCCC------------------------------------------------------------------------------------------------ >P1;d1pbwa- ---------------CCCHHHHCCCC---CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCHHHHHCCCCCCCC-CHHH---CCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCC------------------------HHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHHHCCC------CCCHH--HHHHHHHHHHHHHHCCC------------------------------------------------------------------------------------------------------- >P1;d1tx4a- --------CCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-CCC-CCCHH--HCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCHHH-CC-------------------------HHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHHCCCC----CHHHHHH--CHHHHHHHHHHHHHCHHHHC---------------------------------------------------------------------------------------------------- >P1;d1wera- CCHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCC----------CHHHHHHHHHHHHHHHCCCHHHCCCC----CCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHC----CCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCC >P1;d2osaa- ------------CCCCCCHHHHHHHHC--CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH-CCC------------------------HHHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHHCCC-CCC-CHHHHHH--HHHHHHHHHHHHHHCHHHHC---------------------------------------------------------------------------------------------------- >P1;d2ovja1 ---------------CCCHHHHCC--CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCC-CCC-CC--CCCCCCC-CCCCC---CCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH-CC-------------------------CCHHHHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH-CCCC-CCHHHHHHHHHHHHCCCCCCCCCHHHHCC--C--CHHHHHHHHHHCCHHHHH---HHHCC------------------------------------------------------------------------------------------C >P1;d3byia1 CCCCCCCCCCCCCCCCCCCC-CHHHHC--CCCCHHHHHHHHHHHHHCCCCCCCCC-CCCHHHHHHHHHHHHCC---CCCCCCCCC-CHHHHHHHHHHHHHHCCCCCCCHHHC-CHHHHHC-C-C------------------------HHHHHHHHHHHHH----HCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHHHCCCCCC-C--CHHH--HHHHHHHHHHHHHHCCCCCC---------------------------------------------------------------------------------------------------- >P1;d3iuga1 -----------CCCCCCCHHHHHHHHC--CCCCHHHHHHHHHHHHHCC-CCCCCCCCCCHHHHC-CHHHHH-CCC-CCCCC--CCCCHHHHHHHHHHHC-CCCCCCCCCCCHHHHHHHHC-CCC------------------------HHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHCCHHHHCCCHHHHHHHHHHHHCCC-------------------CHHHHHHHHCHHHHCC--------------------------------------------------------------------------------------------------- >P1;d3msxb- -----------CCCCCCCHHHHCH---HHC-CCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH-CCC-CCCCC--CC-CHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-CCC------------------------HHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHCCHHHHCCCHHHHHHHHHHHHCCCC-CCCCHHHHHH--HHHHHHHHHHHHHHHHHHHC---------------------------------------------------------------------------------------------------- >P1;d5c5sa1 C-------CCCCCCCCCCHHHHCC--C--CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHC-CCCCCHH--HC-CHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCC------------------------HHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHHCCC-CC--CCCCHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHCC------------------------------------------------------------------------------------------C >P1;d5irca1 ---------CCCCCCCCCHHHHCCC----CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCC---CCCCCC-CCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC-C-C------------------------HHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHCCHHHHCCCHHHHHHCCHHHHHCCCCC---CHHHHH--CCHHHHHHHHHHHHC-CCCCC-C------------------------------------------------------------------------------------------------- >P1;d5my3a1 -------------CCCCCHHHHCCC----CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH-C-C------------------------CCCC-CHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHHHCCCCCC-----CCC---CCHHHHHHHHHHHHHHHHHCC-CC------------------------------------------------------------------------------------------------ >P1;d6v6fb- -----CCCC-CCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCC----------CHHHHHHHHH-CCCCCCC--CCCCCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCC-CHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC----CCC-HHHHHHHHHHHCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHHCCHHHHHHHHHHHCCCC--------------CCCCCCCCCCHHHC-CCCCCC--------CCCCCCC-CCCCCCC----- PSA >P1;d1f7ca- ---------------------3716----a301300620150025302766000467079940570076038896058------9151400000012005406400036911a5010055-8---------------------------944275004002----605660250034004002500934960504274007100400024b------87687--337302400210063176006682------------------------------------------------------------------------------------------------ >P1;d1pbwa- ---------------15202710639---67004003500600152036346002661b19-4870461018b7515-7047---271320000022003204600018802660383278176------------------------8740051028105--49914610120021006002501513960606133004200310031a------907a9--23550140013005618------------------------------------------------------------------------------------------------------- >P1;d1tx4a- --------858611051405401743897431040034007103640272720076907853165026201-546-90606--52c5210001001000540440000390271036039-29-------------------------9962243057207----504710220053005004401732a406062640072003000218----7985288--0381023004100431a600---------------------------------------------------------------------------------------------------- >P1;d1wera- 1729307401700048502001002700aa73860030005003103----------41130023006420652a51660069----6300010041005430580026003600470083----a4101016a5199b463860272038107400630080283026101200130072049326a--3a403040005000410004005604819019972694052005000300220061630a99364046016006813840450036008269422989775a700910330081037337405830878193380055017107504645b6a9 >P1;d2osaa- ------------50063303600764a--38101002100720271005370005580999416503720382-18806056b50950100010012006204500005a0063015005-286------------------------7961271054006----604910320033004003501634a60504072005100510032-65a-8a74463--05520440021004217600---------------------------------------------------------------------------------------------------- >P1;d2ovja1 ---------------144077208--a95220060054006102730185830035807-832-81--5049675-40a07---2b4010002101400550720000360035006004-4a-------------------------7a80272039007----5054001000020020015008-1760-07465007200400022267907794470--5--402500220060569102---4215a------------------------------------------------------------------------------------------8 >P1;d3byia1 95866449a24221034304-00952a--24007003301800263018474006-90868205602541043---b07066b50-60100010002005304200004911-5018005-4-8------------------------5953273035007----603510330044002003503854b-06051740072003000203a4b-9--7575--1472025001000532900a---------------------------------------------------------------------------------------------------- >P1;d3iuga1 -----------a600422037009719--5800300320080037301-350004570799516-029301-666-50904--9354220001001400-30440000590286048017-197------------------------7943475057104----805720230024004003402843960606266005200630037-------------------3800200053086007--------------------------------------------------------------------------------------------------- >P1;d3msxb- -----------c70053403810a---a19-0183033006105630071830076908873265037502-685-90807--82-6120003001200440560003191086015027-498------------------------5861063047008----604600220055006002402652b706050540052004000204-ba26893497--23950150020004208501---------------------------------------------------------------------------------------------------- >P1;d5c5sa1 b-------c997320427187118--b--471050043005100660182720075926a6316402640396-0780707--71-5220003001300530340000491056006003-476------------------------7851183037117----805900320071005000300233950604043007100400034-46--6786587--17820150031005131633666487768------------------------------------------------------------------------------------------b >P1;d5irca1 ---------972b004250660078----931050042006202750373710075a0788515400540285---905088-4a08120002002200640380002681082028017-4-6------------------------6871152036106----604841220032003001400634a60605054004200210030848---78a254--807323400300063-43007-a------------------------------------------------------------------------------------------------- >P1;d5my3a1 -------------106450652194----6400500420050015501519300558079851470375037783274051bc87840120010023005204620018a1185036017-2-7------------------------6962-64038108----806601130010001002302735950-06552006100310005137-----68a---386010300210060085006-85------------------------------------------------------------------------------------------------ >P1;d6v6fb- -----5871-60038ce043032011057942840040003202349----------3143004200-320691a--270049----9400020041007310790036101410571295417951001004961688164-50373038007600620250398016302500300240027326----970-06000000041001400440463900b9503850420050003001100257416-948204402a107710720370054006a9--------------d29a2722104914-71ba68--------9599357-0793836----- Translating the sequences ---------------------****----****HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH**C*C*CC------C*CHHHHHHHHHHHHH*CCCCCCCHHHHHHH*****-C---------------------------*HHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC*------*****--**HHHHHHHHHHHH*HHHH*****------------------------------------------------------------------------------------------------ ---------------CCCHHHH****---CCCCHHHHHHHHHHHHH*CCCCCCCCCCCC**-**HHHHH***C*C*C-C***---*CHHHHHHHHHHHHH*CCCCCCCHHHHHHHHHHH**C*C------------------------HHHHHHHHHHHH*--**CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC*------*****--**HHHHHHHHHHHH***------------------------------------------------------------------------------------------------------- --------*****CCCCCHHHH*******CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH*-C*C-CCC**--*C*C*HHHHHHHHHHHH*CCCCCCCHHHHHHHH*HH*-C*-------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC*----*******--**HHHHHHHHHHHH*HHHH*---------------------------------------------------------------------------------------------------- *************CCCCCHHHH*******CC**HHHHHHHHHHHH*C----------C*HHHHHHHHHHH****C****CC**----**HHHHHHHHHHH**C*****HHHHHHHHHHH**----***********************HHHHHHHHHHHH******CCHHHHHHHHHHHHHHHHH**C--**C**HHHHHHHH***********************HHHHHHHHHHHH*HHHH***************************************************************************************************** ------------*CCCCCHHHH*****--CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH***-***CCCC***C*CHHHHHHHHHHHHH*CCCCCCC***HHHHHHHH*-C*C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC-***-*******--**HHHHHHHHHHHH*HHHH*---------------------------------------------------------------------------------------------------- ---------------CCCHHHH**--***CCCCHHHHHHHHHHHHHCCCCCCCCCCCCC-***-**--****C*C-CCCCC---C*CHHHHHHHHHHHHH*CCCCCCC***HHHHHHHH*-C*-------------------------**HHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*-****-CCHHHHHHHHHHHH*CC************--*--*HHHHHHHHHH**HHH**---*****------------------------------------------------------------------------------------------* *************CCCCC**-******--CCCCHHHHHHHHHHHHHCCCCCCCCC-CCCHHHHHHHHHHH**C---CCCCC***C-CHHHHHHHHHHHHH*CCCCCCCHHH*-*HHHHH*-C-C------------------------HHHHHHHHHHHH*----*CCHHHHHHHHHHHHHHHHHH*C**-*CCCHHHHHHHHHHHH*CC****-*--****--**HHHHHHHHHHHH******---------------------------------------------------------------------------------------------------- -----------**CCCCCHHHH*****--CCCCHHHHHHHHHHHHHCC-CCCCCCCCCCHHHH*-*HHHH*-C*C-CCCCC--*C*CHHHHHHHHHHH*-*CCCCCCC***HHHHHHHH*-C*C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC-------------------*HHHHHHHH*HHHH**--------------------------------------------------------------------------------------------------- -----------**CCCCCHHHH**---**C-CCHHHHHHHHHHHHH***CCCCCCCCCCHHHHHHHHHHH*-C*C-CCCCC--*C-CHHHHHHHHHHHHH*CCCCCCCHHHHHHHHHHH*-C*C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC*-**********--**HHHHHHHHHHHH*HHHH*---------------------------------------------------------------------------------------------------- *-------*****CCCCCHHHH**--*--CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH**C-C*CCC**--*C-CHHHHHHHHHHHHH*CCCCCCC***HHHHHHHH*-C*C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC-**--*******--**HHHHHHHHHHHH*HHHH**********------------------------------------------------------------------------------------------* ---------****CCCCCHHHH***----CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH**C---CCCCC*-*C*CHHHHHHHHHHHHH*CCCCCCCHHHHHHHHHHH*-C-C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHH**HHHH*CC***---******--**HHHHHHHHHHHH*-*****-*------------------------------------------------------------------------------------------------- -------------CCCCCHHHH***----CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH*********CC******HHHHHHHHHHHHH*CCCCCCCHHHHHHHHHHH*-C-C------------------------****-*HHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****-CCHHHHHHHHHHHH*CC***-----***---**HHHHHHHHHHHH*HHHH**-**------------------------------------------------------------------------------------------------ -----****-***CCCCCHHHH***********HHHHHHHHHHHH*C----------C*HHHHHHHH-****C*C--CCCC**----**HHHHHHHHHHH********HHHHHHHHHHH**C*C******************-*****HHHHHHHHHHHH*****CCCHHHHHHHHHHHHHHH****----*CC-HHHHHHHHHHH********************HHHHHHHHHHHH*HHHH*******-******************************--------------**************-******--------*******-*******----- 48350.tem _________________________________ --------*****CCCCCHHHH*******CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH**C*C*CCCCC***C*CHHHHHHHHHHHHH*CCCCCCCHHHHHHHHHHH*-C*C------------------------HHHHHHHHHHHH*----CCCHHHHHHHHHHHHHHHHHH*C****CCCHHHHHHHHHHHH*CC****-*******--**HHHHHHHHHHHH*HHHH**-**------------------------------------------------------------------------------------------------ Structural block scores 0 7 - 4.5 M 75.0 75.0 75.0 4.1 75.0 75.0 6.4 75.0 75.0 67.1 75.0 75.0 49.4 8 12 * 3.3 M 75.0 75.0 5.6 1.6 61.0 75.0 4.1 48.3 48.9 8.1 20.9 75.0 16.4 13 17 C 4.7 H 75.0 31.6 2.2 3.4 2.4 31.8 2.2 1.6 2.4 3.0 2.2 3.2 7.6 18 21 H 4.6 H 57.0 2.5 2.2 0.8 2.2 4.0 19.8 2.5 3.0 4.2 3.0 3.2 2.5 22 28 * 2.6 P 44.9 34.7 5.6 2.8 25.4 26.1 25.2 25.1 35.3 45.8 45.0 44.9 2.3 29 32 C 4.5 M 3.6 3.2 2.0 7.1 3.0 1.0 1.5 3.2 21.2 3.0 3.2 2.5 5.8 33 45 H 5.0 H 2.1 2.0 2.5 1.4 1.8 2.6 2.5 2.2 2.9 2.3 2.5 2.1 1.7 46 58 C 4.6 H 3.5 3.7 3.8 58.3 3.2 3.7 9.4 8.2 3.8 3.8 3.9 3.4 58.7 59 69 H 4.6 H 4.3 10.5 3.5 1.9 4.2 29.7 3.5 10.8 4.2 3.9 3.6 4.5 8.5 70 71 * 1.6 P 5.5 4.5 38.0 3.0 5.5 6.5 2.0 38.0 38.5 6.0 5.0 5.0 3.0 76 80 C 4.3 M 47.6 18.2 4.2 2.6 3.8 4.3 4.9 3.6 4.8 4.4 4.4 3.4 16.8 81 83 * 3.3 M 75.0 52.3 51.7 30.0 7.5 75.0 7.5 53.0 52.7 52.3 29.0 10.7 29.3 87 99 H 4.9 H 1.0 1.0 0.8 1.5 0.8 1.1 0.7 6.5 1.0 1.2 1.2 1.1 2.1 101 107 C 4.6 H 1.9 1.6 1.1 2.6 1.3 1.3 0.9 1.1 2.0 1.0 1.9 1.9 2.9 108 118 H 4.6 H 3.5 4.2 3.1 2.4 2.8 2.1 9.5 3.9 3.0 2.8 3.3 4.0 2.5 124 147 - 4.6 H 75.0 75.0 75.0 7.6 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.8 148 159 H 4.8 H 9.2 3.0 4.1 2.7 3.5 4.0 3.5 4.3 3.3 3.8 3.3 10.0 2.7 161 164 - 4.5 M 75.0 40.8 75.0 4.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 4.2 165 167 C 4.9 H 3.7 4.7 3.0 1.7 3.3 3.3 3.0 4.3 3.3 4.3 3.3 4.7 3.0 168 185 H 5.0 H 2.1 1.5 1.9 2.3 1.9 0.8 1.8 1.8 1.9 1.7 1.7 1.1 2.2 188 191 * 1.6 P 4.8 4.5 4.1 40.9 5.1 3.5 22.6 4.5 5.1 4.2 5.1 4.8 58.5 192 194 C 4.7 H 3.0 4.0 4.0 2.3 3.0 27.3 3.7 4.0 3.7 3.3 3.7 27.0 27.3 195 206 H 4.9 H 2.1 1.4 2.0 1.2 1.8 2.3 2.0 2.5 1.7 1.6 1.5 1.9 0.9 208 209 C 4.6 H 3.0 2.0 1.5 2.0 2.5 2.0 1.0 5.0 1.0 3.5 1.5 2.5 2.5 210 213 * 2.8 P 59.1 58.9 58.2 2.8 24.1 6.0 7.2 75.0 25.2 40.0 23.8 21.5 2.0 215 221 * 2.0 P 26.6 26.5 6.7 4.6 6.1 5.4 26.1 75.0 6.6 6.7 15.9 46.4 4.8 222 223 - 4.6 H 75.0 75.0 75.0 8.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.0 224 225 * 1.6 P 3.0 2.5 1.5 4.0 2.5 40.0 2.5 75.0 2.5 4.0 4.0 5.5 1.5 226 237 H 4.9 H 2.1 2.0 1.9 2.3 1.8 8.0 1.8 20.2 2.2 2.1 2.3 1.6 2.2 239 242 H 4.4 M 3.5 39.8 4.4 1.0 3.5 5.2 2.8 3.5 3.2 3.2 20.5 3.2 0.5 243 244 * 2.1 P 3.0 75.0 37.5 3.0 37.5 1.0 42.8 3.5 38.0 4.5 3.5 3.0 1.0 246 247 * 3.7 M 5.0 75.0 75.0 4.5 75.0 75.0 75.0 75.0 75.0 5.0 42.8 6.5 5.5 248 343 - 4.6 H 75.0 75.0 75.0 4.2 75.0 70.6 75.0 75.0 75.0 70.8 75.0 75.0 26.7 >>>>>>