Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1b67a- --------------CCCCHHHHHHHHHHCCC-------CCCC--CHHHHC-CHHHHHHHHHHHHCCCC--CCCC-------------------------------------------------------------CCCHHHHHHHHHHC----------------------------- >P1;d1bh9a- ----------------CCHHHHHHHHHH------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--------------------------------------------------------------------------------------------------------------- >P1;d1bh9b- CCHHHHHHHHHHHHCCCCHHHHHHHHHHHH-C-C-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCC---------------------------------------------------------------------------------- >P1;d1f1ea- ----------------CCHHHHHHHHHCCCC--------CCCHHHHHHHHHHCCCC-CCCCC-HHHHHHCCC----CCCCCCCHH-------HHCCCCCC----CCCCCCHHHHHHH-CCCCC-CCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHCCHHHCC-- >P1;d1h3ob1 ---------------CCCHHHHHHHHHHHC-CCC-----CCCHHHHC-CHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCC------------------------------------------------------------------------------------- >P1;d1jfia- --------------CCCCHHHHHHHHCCCCCC-C-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCHHHHHCCCC------------------------------------------------------------------------------------------- >P1;d1jfib- ------------CCCCCCHHHHHHHHHHHCC-CC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--------------------------- >P1;d1q9ca- CCCCCCCCCCHHHHCCCCHHHHHHHHHHHCCC-C-----CCCHHHHHHHHHHHHHHHC-CCCCCCC-----------CCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCC >P1;d1r4va- -----------CCCCCCCHHHHHHHHHHHHC-------CCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCC-CCHHHCCCC-------HHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCC-CCHHHHHHHC--CCCCCCCCCCHHHHHHHCCC---- >P1;d1tafb- ----------CCCCCCCCHHHHHHHHHHCC-C-C-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHC------------------------------------------------------------------------------------------ >P1;d2byka1 ----------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCHHHCCCCCCC---------------------------------------------------------------------------- >P1;d2bykb1 ------------C------CHHHHHHHHHCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHCCCC-------CCHHHHHHHHHHHHHHHCC------------------------------------------------------------ >P1;d4csrb- ------------CHHHCCHHHHHHHHCCCCCC-C-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHCCHHHHHHCCCCCC----------------------------------------------------------------------------- >P1;d5y27b1 --------CCCCCCCCCCHHHHHHHHCCCCCC-C-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHCHHHHHHCCCCCC----------------------------------------------------------------------------- >P1;d6w4la1 ---------------CCCHHHHHHHHHHHC-CCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHCCCC------------------------------------------------------------ PSA >P1;d1b67a- --------------994647402662697a3-------b909--559830-6437487526750740a--5b49-------------------------------------------------------------938a0465056439----------------------------- >P1;d1bh9a- ----------------735870386169------89588809795057318635876666567778a--------------------------------------------------------------------------------------------------------------- >P1;d1bh9b- 769766677487567647797148712575-b-9-----7178a505752983375583048104400864a38591574047203830585750b---------------------------------------------------------------------------------- >P1;d1f1ea- ----------------06670025003300c--------30476026201a20340-63102-03830683c----250520502-------9711980b----16350a5a40380-06290-8067700530000013013004200510566b27041007601775594092-- >P1;d1h3ob1 ---------------838477035605874-795-----62779606-4287367458605730582089483a-733860344111665869------------------------------------------------------------------------------------- >P1;d1jfia- --------------972649604772396993-b-----a18a8305740674366467157605730875----a35850375178------------------------------------------------------------------------------------------- >P1;d1jfib- ------------9b93473950476186656-b5-----a179a52585056328457516820671079495a-93366041500751922a51884686277675855767566769878857aa466756667656777765756878--------------------------- >P1;d1q9ca- 8916023b812640442016004700672067-0-----8337700420041006105-0094606-----------52840253066503820176017504732740237802510450184a09560020001002200320063006304938564043800550892a31739 >P1;d1r4va- -----------69a14800530161044517-------030457104300701480024008604430675a2b4-025800307-------9904731741472a47016303a30809150a9129b058304100000-1004304710--c5660757145147406872---- >P1;d1tafb- ----------82aaa447185027708769-5-a-----a2889506660254037547266404731795949-9358803560577------------------------------------------------------------------------------------------ >P1;d2byka1 ----------------------------------a987c777b957776655656376626930364217a78c262657030300463a807715b71589---------------------------------------------------------------------------- >P1;d2bykb1 ------------b------a62475088747a94-----91899535553775784786177206800975928-82527051500262947-------9526746772667566697------------------------------------------------------------ >P1;d4csrb- ------------8287365a714872487aa2-6-----906b8207860554574774266203610686928-82487030200352970671597166----------------------------------------------------------------------------- >P1;d5y27b1 --------b67897083639613681575a94-a-----8167950285037527377425640452057592a-93576021300463b708713b7191----------------------------------------------------------------------------- >P1;d6w4la1 ---------------872476156713867-7a6-----828a951764377425477624510461089586a-8466914540165227a---8717733779657677a7868a8------------------------------------------------------------ Translating the sequences --------------**CCHHHHHHHHH**C*-------*CCC--*HHHH*-*HHHHHHHHHHHH****--CCCC-------------------------------------------------------------**************----------------------------- ----------------CCHHHHHHHHH*------*****CCCHHHHHHHHHHHHHHHHHHHHHHHH*--------------------------------------------------------------------------------------------------------------- ****************CCHHHHHHHHH***-*-*-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC**CCHHHHHHH***********---------------------------------------------------------------------------------- ----------------CCHHHHHHHHH**C*--------CCCHHHHHHHHHH****-*****-HHHHHH*CC----CC*****HH-------********----*************-*****-****************************************************-- ---------------*CCHHHHHHHHH**C-***-----CCCHHHH*-*HHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH********------------------------------------------------------------------------------------- --------------**CCHHHHHHHH***C**-*-----CCC**HHHHHHHHHHHHHHHHHHHHHHHHH*C----*CCHHHHH****------------------------------------------------------------------------------------------- ------------****CCHHHHHHHHH**C*-**-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH******************************************************************--------------------------- ****************CCHHHHHHHHH**C**-*-----CCCHHHHHHHHHHHHHHH*-*******-----------C**HHHHH********************************************************************************************* -----------*****CCHHHHHHHHH****-------*CCCHHHHHHHHHHHHHHHHH****HHHHHH*CCCC*-CCHHH****-------*************************************************-**********--********************---- ----------******CCHHHHHHHHH**C-*-*-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH***------------------------------------------------------------------------------------------ ----------------------------------*****CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC**CCHHHHHHH*****************---------------------------------------------------------------------------- ------------*------*HHHHHHH**C****-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH*******-------*******************------------------------------------------------------------ ------------****CCHHHHHHHH***C**-*-----CCC*HHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH****************----------------------------------------------------------------------------- --------********CCHHHHHHHH***C**-*-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH****************----------------------------------------------------------------------------- ---------------*CCHHHHHHHHH**C-***-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH*******---***********************------------------------------------------------------------ 47113.tem _________________________________ -----------*****CCHHHHHHHHH**C**-*-----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH*CCCC-*CCHHHHHHH*********************************-----------------******-*******----------------------------- Structural block scores 0 10 - 4.5 M 75.0 75.0 6.6 75.0 75.0 75.0 75.0 4.7 75.0 68.9 75.0 75.0 75.0 56.8 75.0 11 15 * 3.2 M 48.6 75.0 6.2 75.0 61.6 48.2 21.5 3.6 6.1 7.5 75.0 62.3 20.0 6.4 61.6 16 17 C 4.7 H 5.0 5.0 5.5 3.0 5.5 4.0 5.5 1.0 4.0 5.5 75.0 75.0 4.5 4.5 4.5 18 26 H 4.7 H 4.1 4.9 5.1 2.6 4.1 4.7 4.8 2.7 2.2 4.2 75.0 13.1 5.4 4.7 4.4 27 28 * 1.5 P 8.0 42.0 6.0 1.5 7.5 7.5 6.0 4.5 4.5 6.5 75.0 7.5 7.5 6.0 7.0 30 31 * 3.0 P 39.0 75.0 43.2 43.8 41.0 6.0 40.5 6.5 41.0 40.0 75.0 8.8 6.2 6.5 41.0 34 38 - 4.5 M 62.3 7.6 75.0 75.0 75.0 75.0 75.0 75.0 60.0 75.0 9.4 75.0 75.0 75.0 75.0 39 41 C 5.0 H 6.0 5.7 5.0 2.3 5.0 6.5 6.2 4.7 2.3 6.8 7.0 6.0 5.0 5.0 6.0 42 68 H 4.7 H 15.4 11.1 4.5 8.4 7.4 4.8 4.7 13.4 2.9 4.3 5.3 5.3 4.5 4.2 4.6 70 73 C 4.6 H 7.4 75.0 6.4 41.4 6.4 57.5 7.1 75.0 7.2 6.8 9.5 6.0 6.2 6.6 7.4 76 77 C 4.7 H 75.0 75.0 3.0 3.5 3.0 4.0 3.0 40.0 1.0 4.0 4.0 3.5 3.0 4.0 5.0 78 84 H 4.4 M 75.0 75.0 3.4 2.0 3.7 4.1 3.1 3.4 3.3 4.3 2.6 2.9 2.9 2.7 4.1 85 117 * 3.4 M 75.0 75.0 51.7 30.4 58.1 70.9 5.6 3.4 19.4 68.8 39.2 20.2 40.9 41.1 12.5 118 134 - 4.2 M 75.0 75.0 75.0 7.5 75.0 75.0 7.0 3.2 4.6 75.0 75.0 75.0 75.0 75.0 75.0 135 140 * 4.0 M 5.8 75.0 75.0 0.7 75.0 75.0 6.3 0.8 0.2 75.0 75.0 75.0 75.0 75.0 75.0 142 148 * 4.0 M 4.6 75.0 75.0 1.3 75.0 75.0 6.3 2.0 1.7 75.0 75.0 75.0 75.0 75.0 75.0 149 177 - 4.5 M 75.0 75.0 75.0 9.0 75.0 75.0 70.3 4.3 19.2 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>