Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bb8a- -----------------------CCCCCCCCCCCCCCCEECC----CCCEEEEEECCC---CCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC-------------------------------- >P1;d1gcca- --------------------------------CCCCCEEEEC----CCEEEEEEEECCCCCEEEEEEEECCHHHHHH---------HHHHHHHHHHCCCCCCCCCC-------------------------CC >P1;d1ub1a- CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEECCCC-----CEECCHHHHHHHHCCCCCCCCCCCCCCCIIIIICCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCC >P1;d1z1ba1 --------------------------------CCCCCEEEEC----CCEEEEE--CCC---CCCEEEEECCHHHHHH---------HHHHHHHHHHHC--C-------------------------------- >P1;d2ky8a- -------------------CCCCEEECCCCCCCCEEEEEECCCCCCCCCEEEEEECCCC-----CEECCHHHHHHHHCCCCCCC-----CCCCCCCCCC---------------------------------- >P1;d3vxva- ----------------------------CCCCCCEEEEEECCCCCCCCCEEEEEECCCC-----CEECCHHHHHHHHH---------------HHCCCCCCHHHCCCCCCCC--------------------- PSA >P1;d1bb8a- -----------------------b77407573418b705148----713022406038---6551403031045a2806bb4983700352266279836c-------------------------------- >P1;d1gcca- --------------------------------8a14304736----7732002160796d54744164287165004---------200710491597a090034a-------------------------9c >P1;d1ub1a- a99a899a998aaa776947884a3a28178a8021323364498a2975203020487-----4204548406412584b1c7150c9210301177848---979b879989889989aa97a9a79978b >P1;d1z1ba1 --------------------------------a21710554b----7450114--038---4283621665486026---------506731763878--b-------------------------------- >P1;d2ky8a- -------------------b8c637706004990412477599bbb497240204065a-----66064476038417e85809-----6042960649---------------------------------- >P1;d3vxva- ----------------------------b36b91742474489ca54776432330377-----54176aa6268248---------------952788679846998a979--------------------- Translating the sequences -----------------------*****CCCCCC****EECC----CCCEEEEEECCC---****EE**************************HH***CCC-------------------------------- --------------------------------CC***EEE*C----CC*EEEEEE*CCC******EE****HHHHHH---------*******HH**CCCC*****-------------------------** ****************************CCCCCC***EE*CC****CCC*EEEEECCCC-----*EE****HHHHHH********************CCCC---***************************** --------------------------------CC***EEE*C----CC*EEEE--CCC---****EE****HHHHHH---------*******HH**C--C-------------------------------- -------------------*********CCCCCC***EEECC****CCCEEEEEECCCC-----*EE****HHHHHH*******-----********CC---------------------------------- ----------------------------CCCCCC***EEECC****CCCEEEEEECCCC-----*EE****HHHHHH*---------------HH**CCCC***********--------------------- 54171.tem _________________________________ -----------------------*****CCCCCC***EEECC****CCCEEEEEECCCC--****EE****HHHHHH*******--*******HH**CCCC---**--------------------------- Structural block scores 0 22 - 4.4 M 75.0 75.0 8.4 75.0 63.6 75.0 23 27 * 3.4 M 5.9 75.0 6.8 75.0 4.6 75.0 28 33 C 4.5 M 4.5 53.1 5.8 52.1 3.7 7.0 34 36 * 1.0 P 8.8 2.7 2.0 3.0 2.3 4.3 37 39 E 4.7 H 2.0 3.7 2.7 3.3 6.0 5.0 40 41 C 4.5 M 6.0 4.5 5.0 7.8 7.0 6.0 42 45 * 3.4 M 75.0 75.0 7.9 75.0 10.9 9.2 46 48 C 4.7 H 3.7 5.7 6.0 5.3 6.7 6.0 49 54 E 4.8 H 2.3 1.8 2.0 26.0 2.0 3.5 55 58 C 4.7 H 21.5 5.5 4.8 21.5 5.4 4.2 59 60 - 4.5 M 75.0 9.2 75.0 75.0 75.0 75.0 61 64 * 2.8 P 4.2 4.8 57.2 4.2 57.8 57.5 65 66 E 5.0 H 2.0 3.5 1.0 4.0 3.0 2.5 67 70 * 1.0 P 1.8 5.2 5.2 4.5 5.2 8.5 71 76 H 4.5 M 4.9 2.7 2.8 4.3 3.7 4.7 77 83 * 3.3 M 7.1 75.0 7.0 75.0 7.4 65.4 84 85 - 4.1 M 5.0 75.0 3.0 75.0 75.0 75.0 86 92 * 2.2 P 2.6 2.0 3.9 4.1 33.9 75.0 93 94 H 4.1 M 4.0 5.0 0.5 4.5 7.5 7.0 95 96 * 1.0 P 8.0 7.0 4.0 7.5 3.0 4.5 97 100 C 4.5 M 7.4 6.6 6.8 42.4 40.8 7.2 101 103 - 4.1 M 75.0 1.0 75.0 75.0 75.0 7.0 104 105 * 3.4 M 75.0 7.2 8.0 75.0 75.0 7.5 106 132 - 4.4 M 75.0 70.2 8.9 75.0 75.0 60.3 >>>>>>