Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1o4ua2 -------------------CCHHHHHHHHHHHHHCC--C----CCCHHH--CCCEEEEEEEEC----------CCEEECCCHHHHHH-HHHHCC----------------------------------------CEEEECC--CCCCEEECC------EEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- >P1;d1qpoa2 ------------CCCHHHHHHHHHHHHHHHHHHHCCCCC----HHHHHHCCCCCEEEEEEECC----------C-CEECCCHHHHHH-HHHHHHC--------------------------------------CCCEEEEEECCCCCEECCC------CEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- >P1;d1vlpa1 -----------CCCCCCCCCCCC-CCCC-CHHHHHHCC--------------CCEEEEECCCCCCCCCCCCH-HH----HHHHHHHH-HHH-CCCCHHHHHHHHHHCC------CCCCCCCCCCCCCCCCCHHHH-EEEECCC---------CCCCCCCCEEEEEEE-HHHHCCCHHHHHHHHHHHHHHHCC-- >P1;d1x1oa1 -----------------CCCCHHHHHHHHHHHHHCCC-C----HHHHHHCCCCCEEEEEEECC----------C-CEECCCHHHHHH-HHHHHCC--------------------------------------CCEEEECC--CCCCEECCC------CEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- >P1;d1ybea2 ----CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC--------------CCCCCEECCCCCCCCCCCCCCHH----HHHHHHHH-HCC-CCCCHHHHHHHHHCCCC-CCCCCCCHHHHHHC--CCCCCC----CCCC----------------CCCCCCEECCC-HHHHHHHHHHHHHHHHHHHHHHHC-- >P1;d1yira2 ----CCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHCC--------------CCEEEEECCCCCCCCC-HHH-HH----HHHHHHHH-HHH-CCCCHHHHHHHHC-CC------CCCHHHHHHHH-HCCCCH-HH-EEEEEEC--------------CEEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHCCC >P1;d2b7na1 -------------------CCCHHHHHHHHHHHHCCC-C-----CHHHHCCCCCEEEEEEECC----------C-CEECCCHHHHHH-HHHHCC------------------------------------------CEEEEECCCCCEECCC------CEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- >P1;d2i1oa1 ----CCCCCCCCHHHHHCCCCCCCHHHHHHHHHHH--------------HHHHCEEEEEEECC-------CCCCCCEECCCHHHHHH-HHC----------------------------------------CCC--CEEEE-CCCCCEECCCCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHHHHHC------ >P1;d2im5a1 --------------CCCCCCCCCHHHHHHHHHHHHHCC--------------CCEEEEECCCCCCCCCCHHH-HH----HHHHHHHH-HHH-CCCCHHHHHHHHHHCC------CCCHHHHHHHH-HCCCCH-HH-EEEEECC-------------CCCEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHCCC- >P1;d3os4a1 ---------CCCCCCCCCCCCCCHHHHC-CHHHHHHCC--------------CCEEEEECCCCCCCCC-HHH-HH----HHHHHHH--CCC-CCCCHHHHHHHHC-CC------CCCHHHHHHHH-HCCCCH-HH-EEEEEEC--------------CEEEEEEEEE-HHHHC-CHHHHHHHHHHHHHHHHCCC >P1;d3paja1 CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCHHH-CCCCCEEEEEEECC----------C-CEECCCHHHHHH-HHHHCCC--------------------------------------CCEEEECC--CCCCEECCC------CEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- >P1;d4hl7a1 ------CCCCCCCCCCCCCCCCCHHHHC--CHHHHHCC--------------CCEEEEEEEE------CCCC-HH----HHHHHHHH-HHH-CCCCHHHHHHHHHHCC------CCCCCCCCHH--HCCCCHHHH-EE-CCC----------------CCEEEEEEE-HHHHCCHHHHC-CHHHHHHHHHHCCC >P1;d4kfna1 --------------CCCHHHCCCHHHHHHHHCCCC-------------CCC---CCEEEECCCC--CCCC-----EEECCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH---HCCCCCEEEEE-CCCCCEEECC------CCCEEEEECCHHHCCHHHHCHHHHHC-CHHHHHHHC >P1;d4mzya1 ---------CCC--CCCCCCCCCHHHHHHHHHHHH-------------CCCCCCEEEEEECCCCCHHHCC-----CEECCCHHHHHH-HHHCCCCC----HHHHHHHHHCCC---CCHHHHHHHH------CCCCCCEEEE-CCCCCEECCC------CCCEEEEEE----HHHHHHHHHHHHHHHHHHHC--- >P1;d5huoa1 --------------CCCCHHHHHHHHHHHHHHHCCCC-C----HHHHHHCC-CCEEEEEEECC----------C-CEECCCHHHHHH-HHHHHC---------------------------------------CCEEECCCCCCCCCEECCC------CEEEEEEEEHHHHHHHHHHHHHHHHHHHC------- PSA >P1;d1o4ua2 -------------------4a418602740894245--3----8a0455--586645450518----------87626040062045-008517----------------------------------------0707060--848561864------93003051311514006700571078308------- >P1;d1qpoa2 ------------c27b95375155306740674458764----981477166a4565431338----------9-694041030010-0025109--------------------------------------7b31622822848480558------3400203032310420460037208842a------- >P1;d1vlpa1 -----------484306302606-6004-007025664--------------94724461539688510470-29----00840072-018-1407ba1176057525------804a9012055aa03030870-0707143---------bb4785307040552-324010041006500750165117-- >P1;d1x1oa1 -----------------698724730544078527b4-3----88056715695716521428----------9-485040050044-0030017--------------------------------------60605332--846480979------3400303213210310561027107842a------- >P1;d1ybea2 ----a975985422006302505350044015015653--------------85634241639797910840627----50360063-037-15069924760494509-98772038800820--704029----1604----------------b2308020584-213000031005401840652545-- >P1;d1yira2 ----ba7--81784004402406570035016014674--------------a462548172698360-491-17----50581183-029-1504a92246067-28------60496007201-605035-82-071135a--------------8602040623-2030000120076007203335466a >P1;d2b7na1 -------------------3915560673188529b6-2-----844771a946522440609----------9-675041173041-00821a------------------------------------------0713702639571659------5400203153110320560027106a419------- >P1;d2i1oa1 ----7599b7449812560440666067518829b--------------7298573444132a-------774b5625031164057-009----------------------------------------b38--07160-27374436025a97742400303242040021331059217930b8------ >P1;d2im5a1 --------------008401605550034026226664--------------94742351719875817770-05----50262057-039-1307692146057615------60288007302-905042-81-0805149-------------77202030633-2220000320056006503663495- >P1;d3os4a1 ---------ab73401840261676114-017002754--------------956326317297b350-070-09----2044007--219-13078a2286037-27------50776007205-814152-81-080437a--------------7705050553-30102-0520056006501744476a >P1;d3paja1 aaa7755766778689446740362036204850a8426283398058-267a5645641318----------8-696040351041-0071086--------------------------------------60908030--838580757------43002051103104004500241067229------- >P1;d4hl7a1 ------6895129500540240696006--18125755--------------a472535363------40c0-29----40682076-027-2507781076078535------a05aa00106--804040871-08-82a----------------760020562-31302004300-60182044343659 >P1;d4kfna1 --------------940002205470022166279-------------b26---5154512287--9988-----6030600770455206641038910650465067528782014a30430176---37050005062-2627641631------55001010406602000300530057-067206731 >P1;d4mzya1 ---------b38--a51501605580054036136-------------6a51956243423279127b5b-----405030285056-00890604----a21124046528---0466007304------9081705150-2747550436------440030212----10000003200571088315--- >P1;d5huoa1 --------------b6565a512a7047207942954-3----7a02775a-65735521417----------9-796041040032-004144---------------------------------------a081633691838490757------3200102012300300550026217942a------- Translating the sequences -------------------CC**HHHHHHHHHHH**--*----******--*CCEEEEE***C----------********HHHHHH-HHH*CC----------------------------------------**EEE**--*********------**EEEEEEE*HHHHHHHHHHHHHHHHHH*------- ------------***********HHHHHHHHHHH**C**----*********CCEEEEE**CC----------*-******HHHHHH-HHH***C--------------------------------------***EEE*************------C*EEEEEEE*HHHHHHHHHHHHHHHHHH*------- -----------********CC**-****-*HHHH**C*--------------CCEEEEE**CC*********-**----**HHHHHH-HHH-CCC*************------*********************-EEE****---------******C*EEEEEEE-HHHH***HHHHHHHHHHH******-- -----------------**CC**HHHHHHHHHHH**C-*----*********CCEEEEE**CC----------*-******HHHHHH-HHH**CC--------------------------------------***EEE**--*********------C*EEEEEEE*HHHHHHHHHHHHHHHHHH*------- ----***************CC**HHHHHHHHHHH**C*--------------CC***EE**CC************----**HHHHHH-H**-CCC**************-**************--******----****----------------**C***EE***-HHHHHHHHHHHHHHHHHH******-- ----***--**********CC**HHHHHHHHHHH**C*--------------CCEEEEE**CC*****-***-**----**HHHHHH-HHH-CCC**********-**------***********-******-**-EEE****--------------***EEEEEEE-HHHHHHHHHHHHHHHHHH******** -------------------CC**HHHHHHHHHHH**C-*-----********CCEEEEE**CC----------*-******HHHHHH-HHH*CC------------------------------------------*EE*************------C*EEEEEEE*HHHHHHHHHHHHHHHHHH*------- ----***************CC***HHHHHHHHHH*--------------****CEEEEE**CC-------***********HHHHHH-HH*----------------------------------------***--*EE**-****************C*EEEEEEE*HHHHHHHHHHHHHHHHHH**------ --------------*****CC**HHHHHHHHHHH**C*--------------CCEEEEE**CC*********-**----**HHHHHH-HHH-CCC*************------***********-******-**-EEE****-------------**C*EEEEEEE-HHHHHHHHHHHHHHHHHH*******- ---------**********CC**HHHH*-*HHHH**C*--------------CCEEEEE**CC*****-***-**----**HHHHH--***-CCC**********-**------***********-******-**-EEE****--------------***EEEEEEE-HHHH*-*HHHHHHHHHHH******** ***********************HHHHHHHHHHH**C***********-***CCEEEEE**CC----------*-******HHHHHH-HHH*CCC--------------------------------------***EEE**--*********------C*EEEEEEE*HHHHHHHHHHHHHHHHHH*------- ------*************CC**HHHH*--*HHH**C*--------------CCEEEEE***------****-**----**HHHHHH-HHH-CCC*************------**********--*********-EE-***----------------C*EEEEEEE-HHHH**HHHH*-*HHHHH******** --------------******C**HHHHHHHH****-------------***---**EEE**CC*--****-----******HHHHHH*H***CCC********************************---******EEE**-**********------C**EEEEE**HHH**HHHH*HHHHH*-********* ---------***--*****CC**HHHHHHHHHHH*-------------****CCEEEEE**CC*******-----******HHHHHH-HHH*CCC*----************---**********------******EE**-**********------C**EEEEEE----HHHHHHHHHHHHHHH*****--- --------------*********HHHHHHHHHH***C-*----********-CCEEEEE**CC----------*-******HHHHHH-HHH**C---------------------------------------***EE**************------C*EEEEEEE*HHHHHHHHHHHHHHHHHH*------- 54675.tem _________________________________ ------*--**********CC**HHHHHHHHHHH**C**----*********CCEEEEE**CC*********-********HHHHHH-HHH*CCC*************------***********-**********EEE*************-----*C*EEEEEEE*HHHHHHHHHHHHHHHHHH*******- Structural block scores 0 5 - 4.6 H 75.0 75.0 75.0 75.0 53.2 53.7 75.0 52.0 75.0 75.0 8.4 75.0 75.0 75.0 75.0 7 8 - 4.2 M 75.0 75.0 75.0 75.0 7.0 75.0 75.0 10.2 75.0 75.0 6.5 8.5 75.0 75.0 75.0 9 18 * 2.7 P 75.0 27.5 17.8 61.5 3.0 3.6 75.0 4.6 38.7 4.9 6.5 3.1 38.8 19.4 40.9 19 20 C 4.3 M 7.2 6.0 4.0 7.5 3.5 3.0 6.0 4.0 3.5 4.0 5.5 3.0 2.0 3.5 7.8 21 22 * 1.0 P 2.5 3.0 3.0 3.0 2.5 3.0 3.0 3.0 2.5 3.5 1.5 3.0 2.5 2.5 1.5 23 33 H 4.7 H 4.5 4.2 15.4 4.1 2.1 2.5 4.6 5.3 2.6 9.3 3.3 16.6 3.4 3.2 4.8 34 35 * 1.6 P 4.5 6.5 5.5 9.2 5.5 5.0 10.2 43.2 6.0 4.5 9.2 6.0 42.0 40.5 7.0 37 38 * 3.5 M 39.0 5.0 39.5 39.0 39.0 39.5 38.5 75.0 39.5 39.5 4.0 40.0 75.0 75.0 39.0 39 42 - 4.8 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 4.0 75.0 75.0 75.0 75.0 43 51 * 3.6 M 20.8 5.4 75.0 5.1 75.0 75.0 13.9 52.0 75.0 75.0 13.3 75.0 52.2 44.2 13.8 52 53 C 4.8 H 7.0 7.2 6.5 7.0 6.5 7.2 5.0 6.5 6.5 7.0 7.8 7.2 75.0 7.0 5.5 54 58 E 4.8 H 4.8 4.6 4.6 4.2 3.8 5.0 3.4 4.4 4.2 4.0 5.0 4.4 4.0 3.8 4.4 59 60 * 1.0 P 2.5 2.0 3.0 2.5 3.5 4.0 3.0 2.0 4.0 4.0 2.0 4.5 1.5 2.5 2.5 61 62 C 4.7 H 4.5 5.5 6.0 5.0 6.0 4.0 4.5 6.2 5.0 5.5 4.5 39.0 5.0 4.5 4.0 63 71 * 3.6 M 75.0 75.0 4.3 75.0 5.0 12.8 75.0 59.9 5.6 12.1 75.0 43.5 37.9 21.9 75.0 73 80 * 2.4 P 4.1 13.5 38.9 13.1 39.2 39.1 13.4 4.2 38.8 38.9 13.5 39.4 20.6 20.2 13.9 81 86 H 5.0 H 2.8 0.7 3.5 2.2 3.0 4.3 2.7 3.8 3.7 15.0 2.3 4.8 3.8 4.3 1.5 88 90 H 4.5 M 2.7 0.7 3.0 1.0 3.3 3.7 2.7 3.0 4.0 4.0 2.3 3.0 2.7 2.7 1.3 92 94 C 4.5 M 27.7 3.3 1.7 2.7 2.0 2.0 28.8 75.0 1.3 1.3 4.7 2.3 1.7 2.0 27.7 95 107 * 3.4 M 75.0 75.0 5.2 75.0 5.0 10.4 75.0 75.0 4.5 10.6 75.0 4.9 4.1 25.3 75.0 108 113 - 4.6 H 75.0 75.0 75.0 75.0 19.2 75.0 75.0 75.0 75.0 75.0 75.0 75.0 6.2 28.5 75.0 114 124 * 3.4 M 75.0 75.0 4.0 75.0 9.6 3.2 75.0 75.0 3.3 3.5 75.0 10.8 2.6 9.5 75.0 126 135 * 3.3 M 60.7 54.6 10.7 53.7 32.2 17.9 75.0 54.8 17.9 18.0 54.0 10.7 24.6 40.0 54.4 136 138 E 4.5 M 2.3 3.0 2.3 2.7 2.3 2.7 2.7 2.7 2.7 2.7 2.7 27.7 1.7 2.0 3.3 139 151 * 2.7 P 15.8 4.9 53.1 16.2 69.5 53.4 4.8 9.2 53.4 53.8 15.7 59.3 9.3 9.5 5.4 152 156 - 4.5 M 75.0 75.0 8.4 75.0 62.3 75.0 75.0 7.7 61.4 75.0 75.0 75.0 75.0 75.0 75.0 160 166 E 4.8 H 1.7 1.1 3.3 1.3 3.9 2.4 1.6 1.7 2.4 3.3 1.3 2.1 0.9 1.1 0.6 168 185 H 4.8 H 3.1 3.0 2.1 2.8 1.8 1.7 2.8 2.8 1.8 6.1 2.3 6.0 6.2 13.6 2.7 186 192 * 3.1 M 65.4 65.8 13.7 65.8 14.6 4.3 65.6 56.4 5.1 4.7 65.6 4.1 4.4 25.0 65.8 >>>>>>