Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1fcda3 -----------------------------------------------------------------------CCCCCEEEEEEEEEEC--CEEEEEEEEEEECCCCCCEEECCCCCEECCCCCCHHHHHHHHHHHHHH--HHHHHHHCC------------------------------------C >P1;d1feca3 -----CCCCCEEECCC--CCEEEEECCHHHHHHHCC---EEEEEEEEE------------CCHHHHHH----------------CCCCCC-EEEEEEEE--CC-----CCCEEEEEEECC-CHHHHHHHHHHHHHCCC---CHHHHHCCCCCC----CCCHHHHHCC-CCCC--EEEECCEEECC >P1;d1h6va3 -----CCCCCEEECCC--CCEEEEECCHHHHHHHHCHHH-EEEEEEEE------------CCHHHHCC----------------CCCCCC-EEEEEEEE--HHH----CCCEEEEEEECC-CHHHHHHHHHHHHHCCC---CHHHHHHCCCCC----CCHHHHHHHC-CCCHHHCCCCCCCCCCC >P1;d1m6ia3 ------CCCEEEEECCCCCEEEEEECCCC--------CCCEEEEEECCCCCCHHHHHHHHCCCCHHHHCCC------------CCCC--CCEEEEEEEE--C-------CEEEEEEEE---CCCCCHHHHHHHHHHCCCCCCCCCHHHHC----------------------------------- >P1;d1mo9a3 -----CCCCCEEEECC--CEEEEEECCHHHHHHCC---CCEEEEEECC-CCCCCCCCCCCCCCCCHHHHHC------------CCCHHHH-CEEEEEEE--CC-----CCCEEEEEEEEC-CCHHHHHHHHHHHHCCC---CHHHHHCCCCCC----CCCCCHHHHH-HHHCCCCCCCCC----- >P1;d1nhpa3 -----CCCCCEEEEECC-EEEEEEECCHHHHHHH---CCCCEEEEEE-------------EECCCCCCC------------------CCCEEEEEEEEC--CC-----CCCEEEEEEEECCCCCCHHHHHHHHHHCCC---CHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCC--------- >P1;d1ojta3 -----CCCCCEEECCC--CCEEEEECCHHHHHHH---CCCEEEEEEE----------HHH-CHHHHHC-------------------CCCCCEEEEEEE--CC-----CCCEEEEEEECC-CHHHHHHHHHHHHHCCC---CHHHHHCCCCCC----CCCCCHHHHHHHHHHCCCC--CCCCCCC >P1;d1q1ra3 CCCCC-CCCEEEEEEC-CEEEEEEECCC---------CCCEEEEEEECC----------------------------------------CCEEEEEEEE--C-------CEEEEEEEE---CCHHHHHHHHHHHHCCCCCC-HHHHCCCC---CCHH----HHHHHHHHHHHHC----------- >P1;d1v59a3 -----CCCCCEEECCC--CEEEEEECCHHHHCC----CCCEEEEEEE----------HHH-CHHHHHC-------------------CCCCCEEEEEEE--C------CCCEEEEEEEEC-CHHHHHHHHHHHHHCCC---CHHHHHCCCCCC----CCCCHHHHHHHHHHHCCCC--CC----- >P1;d1xdia2 -----CCCCEEEECCC--CEEEEEECCHHHHHCC---CCCEEEEEEE----------CCC-CHHHHHC-------------------CCCCCEEEEEEE--CC-----CCCEEEEEEEEC-CHHHHHHHHHHHHHHCC---CHHHHHCCCCCC----CCCHHHHHHHHHHHCC------------ >P1;d2gqwa3 CCCCCCCCCEEEEEEC-CEEEEEEECC----------CCCEEEEECCCC-------------------------------------C--CCCEEEEEEE--C-------CEEEEEEEE---CCHHHHHHHHHHHHCCCCCC--CCCCCCC---CCCC---------------------------- >P1;d3dk9a3 -----CCCCCEEECCC--CCEEEEECCHHHHHHHHCHHH-EEEEEEEE------------CCHHHHHC----------------CC-CCC-EEEEEEEE--CC-----CCEEEEEEEECC-CHHHHHHHHHHHHHCCC---CHHHHHCCCCCC----CCCHHHHHCC-C---------------- PSA >P1;d1fcda3 -----------------------------------------------------------------------b994745629154568--75031542424239abb656446b329606ba05a6217510660654--789448969------------------------------------e >P1;d1feca3 -----b9370716869--414020245174007438---400004333------------22a71695----------------726825-03020001--46-----633000010317-60192078017307761---51460286a397----7524220260-5812--0114758437a >P1;d1h6va3 -----b946261675a--224020024296047635782-01010321------------206913a4----------------755336-02010000--374----833010010302-8038108b208306841---108605868187----5423320170-8413476771586999a >P1;d1m6ia3 ------6380734277683040105535a--------91624123727b6120620475293650561058------------734b--7521030115--a-------630200203---0005402200301643762a408610760----------------------------------- >P1;d1mo9a3 -----a886253556a--22203062519605849---3701102003-86a77583650008804a3086------------ab42440-14010001--17-----625010020302-90485067106415740---20450083a2a5----4121002200-4631c6ab0753----- >P1;d1nhpa3 -----d91b383756a7-4340202148841765---a491421413-------------431039718------------------835503030001--29-----622010030304161293084028017675---30650053b27363671245110020024017428--------- >P1;d1ojta3 -----74093705789--3250402133960987---8480540404----------062-1840675-------------------804503020000--19-----773000030304-60081074037103632---51550086a177----521510002002113460a--51852a7 >P1;d1q1ra3 a9aba-805476476a-a281310084a---------746441200769----------------------------------------6541010105--b-------850000301---41681072034014660305-09402449---3607----6005805776989----------- >P1;d1v59a3 -----aa264506766--223040143286076----a491530504----------063-0540675-------------------a32713020002--2------834010010400-40080073036016752---20461077a186----4313200200022016907--76----- >P1;d1xdia2 -----a6472717669--5140500133940769---7280222515----------047-2440655-------------------916902020004--69-----712000020104-60171074015006683---10561087a289----2304310030045035------------ >P1;d2gqwa3 c98c98746466376c-946222017a----------81554141a56a-------------------------------------a--a161020004--8-------750100100---128a2060027305502628--9505588---3a06---------------------------- >P1;d3dk9a3 -----ab262516739--11303013639603a626884-05115353------------40870693----------------a7-526-05030000--5a-----634000020304-8039108a107305731---20860696a287----5413130150-a---------------- Translating the sequences -----------------------------------------------------------------------****************--C**EEEEEEE**C*************EE**C*C*HHHHHHHHHHHH**--***HHHH*C------------------------------------* -----CCCC*EEE**C--**EEEEECC*********---*EEEEEE**------------********----------------*****C-*EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHHCCC***----*****HHH**-****--*********** -----CCCC*EEE**C--**EEEEECC************-EEEEEE**------------********----------------*****C-*EEEEEEE--***----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHH*CC***----*****HHH**-***************** ------CCC*EEE**C****EEEEECC**--------***EEEEEE*************************------------****--C**EEEEEEE--C-------C*EEEEEEE---C****HHHHHHHHH*CC***C***HH**C----------------------------------- -----CCCC*EEE**C--**EEEEECC********---**EEEEEE**-**********************------------*******-*EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHHCCC***----*****HHH**-************----- -----CCCC*EEE**C*-**EEEEECC*******---****EEEEE*-------------*********------------------**C**EEEEEE*--C*-----*C*EEEEEEE*C*C***HHHHHHHHHHCCC---CHHHHHCCC************HHH***********--------- -----CCCC*EEE**C--**EEEEECC*******---***EEEEEE*----------***-*******-------------------**C**EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHHCCC***----*****HHH***********--******* *****-CCC*EEE**C-***EEEEECC*---------***EEEEEE***----------------------------------------C**EEEEEEE--C-------C*EEEEEEE---C*HHHHHHHHHHHHCCC***-HHHH*CCC---****----*HHH*********----------- -----CCCC*EEE**C--**EEEEECC******----***EEEEEE*----------***-*******-------------------**C**EEEEEEE--C------*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHHCCC***----*****HHH***********--**----- -----CCCC*EEE**C--**EEEEECC*******---***EEEEEE*----------***-*******-------------------**C**EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHH*CC---CHHHHHCCC***----*****HHH********------------ *****CCCC*EEE**C-***EEEEECC----------***EEEEE****-------------------------------------*--C**EEEEEEE--C-------C*EEEEEEE---C*HHHHHHHHHHHHCCC***--****CCC---****---------------------------- -----CCCC*EEE**C--**EEEEECC************-EEEEEE**------------********----------------**-**C-*EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC---CHHHHHCCC***----*****HHH**-*---------------- 55424.tem _________________________________ -----CCCC*EEE**C--**EEEEECC********--***EEEEEE**---------***********----------------*****C**EEEEEEE--C*-----*C*EEEEEEE*C-C*HHHHHHHHHHHHCCC-**CHHHHHCCC***----*****HHH***********--**----* Structural block scores 0 4 - 4.6 H 75.0 75.0 75.0 75.0 75.0 75.0 75.0 10.4 75.0 75.0 10.2 75.0 5 8 C 4.7 H 75.0 7.6 7.6 23.0 8.1 8.8 5.0 22.0 7.2 6.9 6.2 7.5 10 12 E 4.8 H 75.0 4.7 4.3 4.7 4.3 6.0 4.0 5.7 3.7 5.0 5.0 4.0 13 14 * 1.5 P 75.0 7.0 6.0 4.5 5.5 5.5 7.5 6.5 6.5 6.0 6.5 5.0 16 17 - 4.4 M 75.0 75.0 75.0 7.0 75.0 41.0 75.0 42.8 75.0 75.0 42.0 75.0 18 19 * 1.5 P 75.0 2.5 2.0 1.5 2.0 3.5 2.5 5.0 2.0 3.0 5.0 1.0 20 24 E 4.8 H 75.0 1.6 1.2 2.0 2.2 1.6 2.2 1.0 1.6 1.8 1.4 1.4 25 26 C 4.8 H 75.0 4.5 3.0 4.0 3.5 2.5 2.0 6.0 3.5 2.0 8.8 4.5 27 34 * 2.8 P 75.0 3.2 4.6 58.2 5.2 14.2 14.6 66.9 22.4 14.1 75.0 4.9 35 36 - 4.4 M 75.0 41.5 6.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 7.0 37 39 * 2.2 P 75.0 51.3 28.3 5.3 28.3 7.8 6.7 5.7 7.8 5.7 4.7 29.0 40 45 E 4.7 H 75.0 1.2 0.8 3.2 0.7 2.2 2.2 1.8 2.3 2.0 4.2 2.5 46 47 * 2.3 P 75.0 3.0 1.5 4.5 1.5 39.0 39.5 6.5 39.5 40.0 5.5 4.0 48 56 - 4.6 H 75.0 75.0 75.0 3.6 14.4 75.0 75.0 67.7 75.0 75.0 67.8 75.0 57 67 * 2.8 P 75.0 24.3 23.7 4.5 4.0 23.0 10.4 75.0 10.1 10.2 75.0 23.8 68 83 - 4.7 H 18.8 75.0 75.0 57.5 57.8 70.8 75.0 75.0 75.0 75.0 75.0 75.0 84 88 * 3.1 M 33.8 5.0 4.6 33.7 5.1 47.2 46.6 75.0 47.7 47.0 62.1 19.9 90 91 * 1.9 P 2.5 37.5 37.5 3.5 38.0 2.5 2.5 4.5 4.0 4.5 3.5 37.5 92 98 E 5.0 H 3.0 0.9 0.4 1.6 0.9 1.0 0.7 1.1 1.0 1.1 1.0 1.1 99 100 - 4.8 H 3.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 103 107 - 4.8 H 8.9 75.0 60.8 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 75.0 111 117 E 4.9 H 5.4 0.6 0.7 1.0 0.9 1.0 0.9 0.6 0.9 0.4 0.3 0.7 123 134 H 4.9 H 4.2 3.8 4.2 1.9 3.9 3.7 2.8 3.0 2.8 2.7 3.6 4.0 135 137 C 4.6 H 28.0 4.7 4.3 4.7 3.7 6.0 3.7 4.0 4.7 5.7 2.3 3.7 139 140 * 4.0 M 7.5 75.0 75.0 6.2 75.0 75.0 75.0 2.5 75.0 75.0 5.0 75.0 142 146 H 4.6 H 6.2 2.6 3.8 3.0 1.8 2.2 2.2 3.0 2.2 2.4 18.8 4.0 147 149 C 4.7 H 53.0 8.2 7.3 4.3 7.2 6.5 8.2 5.7 8.2 8.5 7.0 8.5 150 152 * 2.7 P 75.0 6.3 5.3 75.0 5.8 4.0 5.0 75.0 5.0 6.3 75.0 5.7 153 156 - 4.3 M 75.0 75.0 75.0 75.0 75.0 5.5 75.0 4.0 75.0 75.0 4.9 75.0 157 161 * 2.6 P 75.0 4.0 3.4 75.0 1.6 2.6 2.8 61.2 2.6 2.4 75.0 2.8 162 164 H 4.5 M 75.0 1.3 1.0 75.0 1.3 0.3 0.0 1.7 0.7 0.3 75.0 1.3 165 175 * 2.9 P 75.0 22.5 11.1 75.0 11.8 2.7 2.7 19.0 2.5 22.3 75.0 56.0 176 177 - 4.3 M 75.0 2.5 4.0 75.0 3.5 75.0 75.0 75.0 75.0 75.0 75.0 75.0 178 179 * 3.7 M 75.0 6.0 6.5 75.0 4.0 75.0 3.0 75.0 6.5 75.0 75.0 75.0 180 183 - 4.3 M 75.0 5.5 8.2 75.0 75.0 75.0 6.4 75.0 75.0 75.0 75.0 75.0 >>>>>>