Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1grja2 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCHHH--CEEECCCHHHHHHCCCCCCCEEC------CCCEEEEEEECC >P1;d1w26a3 ---------CCHHHHHCCHHHHHH-----------CCEECCC-----CCCCCCCCCEEECEEEECC-----------------CCCCCCCCCCCEEECCC----CCCCCHHHHCCCCCCCCEEEEEEECCC------------------------------------------------CCCCC---CCCCCEEEEEEECCEECCEECCC---------------------------------------------------- >P1;d2f23a2 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC-CCCCCCCCEEEEECCCCCCEEEEEEECHHHCCCCCCCEEEECCCHHHHHHCCCCCCCEEEEEECCEEEEEEEEEEEC- >P1;d2f4ea- ----------------CCCCCCCCCCEEEEC--CEEEEEEECCCC---CCCCCCCEEEEEEEEEECCCCCEEEECCC-------------CCCCEEEECCCCC-HHHHHHHHHHCCCCCCCEEEEEE-CHHHCCCCCCCCC-------------------------------------------CCCCCCCCCEEEEEEEEEECCCCCC----------------------------------------------------- >P1;d2y78a1 --------------------C---CCEE-CCCC-CEEEEEECCCC---CCCCCCCEEEEEEEEEEC-CCCEEEECCC-------------CCCCEEEECCCC--CCCHHHHHHCCCCCCCCEEEEEE-CHHHCCCCCCCC--------------------------------------------C-CCCCCCCEEEEEEEEEC----------------------------------------------------------- >P1;d3b7xa- ---------CCHHHHHCC------CCEECCCCCCEEEEEEECCEE---EECCCCCEEEEEEEEECCCCCCCCEEC---------------------CCCC----CCCHHHHHHHHCCEECCEEEEEE-CHHHCCCCCCCCC---------------------------------------------CCCCCCCEEEEEEEEEEE---------------------------------------------------------- >P1;d3ey6a1 ------------------------CCEECCCCCCEEEEEEECCC-CCCCCCCCCCEEEEEEEEEEC-CCCEEEE----------------EEE-EEEECCCC--CCCHHHHCCHHHCCCCCEEEEEE-CHHHCCHHHCCCC---------------------------------------------CCCCCCCEEEEEEEEEEECCC------------------------------------------------------- >P1;d3ni6a- --------------------CCCCCEEECCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHH-------------HCCCEEEECCCC--CCCHHHHHHHHCCCCCCEEEEEE-CHHHCCCCCCCC--------------------------------------------C-CCCCCCCEEEEEEEEEEEC--------------------------------------------------------- >P1;d3pr9a- -------------------------------------------------CCCCCCEEEEEEEEEEC--CEEEEECCHHHHHHCCCCCCCCCCCCEEEECCC--CCCCHHHHHHHHHCCCCCEEEEEE-CHHHCCC-CCCHHHEEEEEHHHHHHCCCCCCCCCEEEECCEEEEEEEEECCEEEEECCCCCCCCCEEEEEEEEEEEC--------------------------------------------------------- >P1;d4dipa1 ----------------------CCCCC----CCCCEEEEEECCC-CCCCCCCCCCEEEEEEEEEECCCCCEEEECCCCC------------CCCEEEECCC--CCCCHHHHHHCCCCCCCCEEEEEE-CHHHCCC-CCC----------------------------------------------CCCCCCCCEEEEEEEEEEECCC------------------------------------------------------- >P1;d4jysa- ------------------------CCCCEECCCCCEEEEEECC---CCCCCCCCCEEEEEEEEEECCCCCEEEECCCCC-------------CCCEEECCCCCCCCCHHHHHHCCCCCCCCEEEEEE-CHHHCCC-C-------------------------------------------------CCC-CCCEEEEEEEEEEECCCCCCHHHHHHHHCCC----------------------------------------C >P1;d5gpga1 --------------------------------CCEEEEEEECCCC--CCCCCCCCEEEEEEEEECC-CCCEEEECCC-------------CCCCEEEECCCC--CCCHHHHHHHHHCCCCCEEEEEE-CHHHCCCCCCCHH-------------------------------------------H-CCCCCCCEEEEEEEEEEC---------------------------------------------------------- >P1;d5xb0a- CCCCCHHHHHHHHHHHHHHHHCCCCCEEC--HHHCEEEEEECCCC---CCCCCCCEEEEEEEEECCC-CCEEEECC----------------CCEEEEHH----HCCHHHHHHHHHCCCCCEEEEEE-CHHHCCCCCCCCC---------------------------------------------CCCCCCCEEEEEEEEEEEC--------------------------------------------------------- PSA >P1;d1grja2 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------8848250465020102337676554140057c515888--32012727306203834394408------244220260416 >P1;d1w26a3 ---------88a867796677548-----------a072552-----7060553020202250429-----------------98717808096561276----b42771364039160757753705048------------------------------------------------92919---8032670605040450132622b---------------------------------------------------- >P1;d2f23a2 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------7a-b650657110502027677823020045a73669483130125470064037334744140603897440403304f- >P1;d2f4ea- ----------------c79132b9a277149--40201226708a---440287020502000003b7561030029-------------6973350306827-93120003004104260300020-22420148a03a4-------------------------------------------a17055515000002053076458d----------------------------------------------------- >P1;d2y78a1 --------------------a---8555-2b46-041343670b6---630658360201020215-8884040056-------------5c7335060148--71170013004503370304040-32910357802a--------------------------------------------c-60558130102030372----------------------------------------------------------- >P1;d3b7xa- ---------956165416------a0721096510005235809a---94067814050622030462a820554---------------------510b----61160023002204480104000-32a0025990569---------------------------------------------504661201030204417---------------------------------------------------------- >P1;d3ey6a1 ------------------------a3641385640404337706-9c2860858130103020217-8866034----------------467-3514015a--92250023002203360102030-3160022680496---------------------------------------------705472202030303607919------------------------------------------------------- >P1;d3ni6a- --------------------b8a3a64512b6400102134705b69821067512000102040494684040039-------------5a7345050448--41170012005303450203040-41700369a05b--------------------------------------------a-506271201030103417a--------------------------------------------------------- >P1;d3pr9a- -------------------------------------------------80964330301100318--a802300648204849336694a0643406004--851150015103607563436260-4254016-734795265263840573a3806764605299660605429a570301105910346030203035158--------------------------------------------------------- >P1;d4dipa1 ----------------------8aa88----a47073443863b-819460766030101120214766640400544b------------6714401046--654160014006600480202020-2260026-a08----------------------------------------------c604671202010303405908------------------------------------------------------- >P1;d4jysa- ------------------------a683752b43042123690---7b8507621202020203028666505204a5a-------------81250502434871050004004603460202020-2360045-b-------------------------------------------------825-91401030204513359e5996757645787----------------------------------------a >P1;d5gpga1 --------------------------------7519153387056--7630763340202120229-8744053257-------------c28243140048--62150003002500480404020-426103599057b-------------------------------------------6-605671301040304416---------------------------------------------------------- >P1;d5xb0a- ca6675a62587187217a0585990641--765001334461a4---7506690302050304129-76316509----------------82532604----61160032003501280402000-10820446a04ca---------------------------------------------907111001050203314a--------------------------------------------------------- Translating the sequences -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*****CCCCCC*EEEEE****EE***************--***********************------************ ---------***************-----------**EE**C-----*CCCCCCC*EEE*EEEE*C-----------------*********CCEEE*CC----CCC**HHHH***CCCCCEEEEEE*C**------------------------------------------------*****---CCCCC*EEEEEE**EE*******---------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------**-**CCCCCC*EEEE******E*********************************************************- ----------------***************--**EEEEEECC**---CCCCCCCEEEEEEEEE*C**CCEEEE***-------------**CCEEEECC***-***HHHHHH***CCCCCEEEEEE-CHHHCCC*CCC**-------------------------------------------**CCCCCCCEEEEEEEEEE******----------------------------------------------------- --------------------*---****-****-*EEEEEECC**---CCCCCCCEEEEEEEEE*C-*CCEEEE***-------------**CCEEEECC**--CCCHHHHHH***CCCCCEEEEEE-CHHHCCC*CCC*--------------------------------------------*-CCCCCCCEEEEEEEEE*----------------------------------------------------------- ---------*********------***********EEEEEECC**---**CCCCCEEEEEEEEE*C**CC**EE*---------------------**CC----CCCHHHHHH***C**CCEEEEEE-CHHHCCC*CCC**---------------------------------------------CCCCCCCEEEEEEEEEEE---------------------------------------------------------- ------------------------***********EEEEEECC*-***CCCCCCCEEEEEEEEE*C-*CCEEEE----------------***-EEEECC**--CCCHHHH*****CCCCCEEEEEE-CHHHCC***CC**---------------------------------------------CCCCCCCEEEEEEEEEEE***------------------------------------------------------- --------------------***************EEEEEECC*****CCCCCCCEEEEEEEEE*C**CCEEEE***-------------**CCEEEECC**--CCCHHHHHH***CCCCCEEEEEE-CHHHCCC*CCC*--------------------------------------------*-CCCCCCCEEEEEEEEEEE*--------------------------------------------------------- -------------------------------------------------CCCCCCEEEEEEEEE*C--C*EEEE******************CCEEEECC*--*CCCHHHHHH***CCCCCEEEEEE-CHHHCCC-CCC***********************************************CCCCCCCEEEEEEEEEEE*--------------------------------------------------------- ----------------------*****----****EEEEEECC*-***CCCCCCCEEEEEEEEE*C**CCEEEE*****------------*CCEEEECC*--*CCCHHHHHH***CCCCCEEEEEE-CHHHCCC-CCC----------------------------------------------*CCCCCCCEEEEEEEEEEE***------------------------------------------------------- ------------------------***********EEEEEECC---**CCCCCCCEEEEEEEEE*C**CCEEEE*****-------------CC*EEECC****CCCHHHHHH***CCCCCEEEEEE-CHHHCCC-C-------------------------------------------------CCC-CCCEEEEEEEEEEE*****************----------------------------------------* --------------------------------***EEEEEECC**--*CCCCCCCEEEEEEEEE*C-*CCEEEE***-------------**CCEEEECC**--CCCHHHHHH***CCCCCEEEEEE-CHHHCCC*CCC**-------------------------------------------*-CCCCCCCEEEEEEEEEE*---------------------------------------------------------- *****************************--****EEEEEECC**---CCCCCCCEEEEEEEEE*C*-CCEEEE**----------------CCEEEE**----*CCHHHHHH***CCCCCEEEEEE-CHHHCCC*CCC**---------------------------------------------CCCCCCCEEEEEEEEEEE*--------------------------------------------------------- 54534-1.tem _________________________________ --------------------*-*************EEEEEECC**--*CCCCCCCEEEEEEEEE*C**CCEEEE***-------------**CCEEEECC**--CCCHHHHHH***CCCCCEEEEEE-CHHHCCC*CCC**-------------------------------------------**CCCCCCCEEEEEEEEEEE*****----------------------------------------------------- Structural block scores 0 19 - 4.5 M 75.0 37.9 75.0 61.5 75.0 43.4 75.0 75.0 75.0 75.0 75.0 75.0 6.1 22 34 * 3.2 M 75.0 64.4 75.0 16.5 26.7 14.7 15.4 4.9 75.0 28.2 16.2 58.7 15.5 35 40 E 4.4 M 75.0 4.9 75.0 2.2 3.5 2.5 3.5 1.8 75.0 4.8 3.0 4.8 2.5 41 42 C 4.5 M 75.0 38.5 75.0 3.5 3.5 4.0 3.5 3.5 75.0 4.5 4.5 3.5 3.5 43 44 * 3.2 M 75.0 75.0 75.0 9.2 8.8 9.8 40.5 8.2 75.0 43.2 75.0 5.5 7.2 45 46 - 4.2 M 75.0 75.0 75.0 75.0 75.0 75.0 10.8 7.5 75.0 4.5 41.0 75.0 75.0 48 54 C 4.6 H 75.0 2.7 75.0 3.6 4.4 5.0 5.1 3.1 15.0 4.1 4.1 4.0 4.7 55 63 E 4.6 H 75.0 1.9 75.0 1.0 1.4 2.4 1.2 1.0 1.2 1.1 1.2 1.4 1.9 66 67 * 3.2 M 75.0 75.0 75.0 9.2 41.5 4.0 41.5 6.5 75.0 6.5 7.0 41.5 42.0 68 69 C 4.5 M 75.0 75.0 75.0 5.5 8.0 9.2 7.0 7.0 9.2 6.0 6.0 5.5 6.5 70 73 E 4.5 M 75.0 75.0 75.0 1.0 2.0 3.0 3.2 2.0 1.2 2.0 3.0 3.0 3.8 74 76 * 2.9 P 75.0 75.0 75.0 3.7 3.7 51.3 75.0 4.0 3.3 3.0 4.8 4.7 28.0 77 89 - 4.6 H 75.0 37.7 75.0 75.0 75.0 75.0 75.0 75.0 5.1 64.7 64.7 75.0 75.0 90 91 * 3.0 P 75.0 4.0 75.0 7.5 8.8 75.0 5.0 7.8 5.2 40.5 75.0 7.2 75.0 92 93 C 4.4 M 75.0 7.5 75.0 5.0 5.0 75.0 41.0 5.0 5.0 4.0 4.5 5.0 5.0 94 97 E 4.4 M 75.0 3.5 75.0 2.8 3.5 39.0 3.2 3.5 3.2 2.2 3.0 3.0 4.0 98 99 C 4.5 M 75.0 6.5 75.0 3.0 0.5 5.8 0.5 2.0 0.0 2.0 1.0 0.0 2.0 100 101 * 3.2 M 75.0 75.0 75.0 5.0 6.0 75.0 7.8 6.0 39.5 40.5 3.5 6.0 75.0 102 103 - 4.5 M 75.0 75.0 75.0 41.0 75.0 75.0 75.0 75.0 41.5 40.5 6.0 75.0 75.0 104 106 C 4.4 M 75.0 5.8 75.0 4.3 3.0 2.7 4.3 2.0 2.3 3.3 2.7 3.0 2.7 107 112 H 4.5 M 75.0 4.7 75.0 0.8 1.8 1.8 1.7 1.7 2.0 1.8 1.5 1.3 1.8 113 115 * 1.8 P 75.0 4.0 75.0 1.7 3.0 1.3 1.3 2.7 3.0 4.0 3.3 2.3 2.7 116 120 C 4.6 H 75.0 3.8 75.0 2.4 2.6 3.2 2.4 2.4 4.2 2.4 2.6 2.4 2.2 121 126 E 4.6 H 75.0 4.8 75.0 0.8 1.8 0.8 1.0 1.5 3.5 1.0 1.0 1.7 1.0 129 131 H 4.5 M 75.0 29.0 75.0 2.7 4.0 4.2 2.3 2.7 3.7 2.7 3.0 3.0 3.3 132 134 C 4.5 M 75.0 75.0 75.0 1.7 2.7 2.3 1.3 3.0 2.3 2.7 3.0 2.7 2.7 136 138 C 4.4 M 75.0 75.0 75.0 4.5 3.3 4.7 4.0 5.2 4.7 6.2 53.8 4.7 4.8 139 140 * 3.2 M 75.0 75.0 75.0 7.2 42.8 7.5 7.5 43.2 8.0 75.0 75.0 9.2 11.5 141 183 - 4.7 H 70.2 67.0 71.9 75.0 75.0 75.0 75.0 75.0 4.6 75.0 75.0 75.0 75.0 184 185 * 3.5 M 5.0 75.0 8.8 5.8 43.8 75.0 75.0 42.8 0.5 43.8 75.0 40.5 75.0 186 192 C 4.9 H 3.1 14.4 3.6 4.0 4.0 3.4 3.9 3.3 4.0 3.7 14.9 4.0 2.7 193 203 E 4.7 H 3.6 2.3 4.0 1.5 8.5 2.0 2.2 1.8 2.0 1.6 1.7 2.1 1.7 204 208 * 3.2 M 2.8 3.0 1.4 7.3 75.0 75.0 33.8 62.1 61.6 33.4 7.3 75.0 62.1 209 261 - 4.6 H 14.6 73.8 5.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 58.3 75.0 75.0 >>>>>>