Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1chua1 ------CCCCCCCHHHHHH--HHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC-------HHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCC-------------------CCCCCCCCC--------------------------------------------------------------------------------------------- >P1;d1jnra1 ----------CCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHCCEECHHHHHHHHHHHHHHHHHHC-CCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEECC--CCCCCCC-----------------CCCEEEEEEEE-CCCCEEEEEEEECCCCC------CCC----------------------------------------------------------------C >P1;d1kf6a1 ---------------CCC-CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCCCCCCCC-----------------CCCEEEEEEEC-C-CCCEEEEEEECCCC--------CCCCC-------------------------------------------------------------- >P1;d2bs2a1 ---------------CCC-CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCEECC-----------------CCCEEEEEECCCCCCCCCEEEEEECC--HHHCC----CCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHCCCCCCCCC >P1;d2wu2a3 ----------------CCCCCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCCC-----------------CCCCEEEEE---CCCC--EEEEECCC--C-CCCCCCCCCCCCCCC---------------------------------------------------------- >P1;d3sfda3 CCHHHHHHHHHHHCCCCC-EEHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHH-CEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCCCCCCCCCCCCCCCCCHHHCCCEEEEECCC-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC---------------------------------------------------------- PSA >P1;d1chua1 ------9828545893273--0560255058017610-28----5124840550274056037308850670575-------960550384066015504302425014c--b16065--46965a-------------------a2871828a--------------------------------------------------------------------------------------------- >P1;d1jnra1 ----------c5749387320062027307702342005843854034830540162066027408-613147-----9615640730274038103503302304001458914044--4584349-----------------71407051823-8a776181735738388------b59----------------------------------------------------------------b >P1;d1kf6a1 ---------------939-361260453288118500-4a----6233940560163066026137-505264979a91334650670376046003603212315002c--b14053bb1594329-----------------71336151534-b-746061725a3837--------9963a-------------------------------------------------------------- >P1;d2bs2a1 ---------------b49-350680175056029700-79----7122750650073017016307-7031958498907133125502740381035011014130126--a14064--5641104-----------------81015252615679333040725836--05823----9015347778794246166055057406624872787a4673312740376a47987797896ba7 >P1;d2wu2a3 ----------------5b0440560273067028610-49----6152a30670175048026307-903264769a906346527606850780034013022130126--b14075--5692339-----------------603151414---6a64--60446939--4-849a5838739968a---------------------------------------------------------- >P1;d3sfda3 b99988743680151847-250660264067129700-5a----6233940750063046119219-6020552879905305502602850381036021023140127--a13054--48823011614595ac2a64538702105241605-88707071615626593b77987639617767a---------------------------------------------------------- Translating the sequences ------*************--HHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHH****CCCCCC-------HHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCC-------------------CC*******--------------------------------------------------------------------------------------------- ----------*****CCC*CCHHHHHHHHHHHHHHHC*C*******CHHHHHHHHHHHHHHHHHHC-CCCCCC-----*HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC**CC**CC--CCCCCCC-----------------CCCEEEEEE**-CCCC**EEEEEECC***------*CC----------------------------------------------------------------* ---------------CCC-CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC**CCCCCCC-----------------CCCEEEEEE**-C-CC**EEEEEECC**--------CCCCC-------------------------------------------------------------- ---------------CCC-CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCC**CC-----------------CCCEEEEEE***CCCC**EEEEEECC--*****----CCCC************************************************************** ----------------CC*CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCCC-----------------CCC*EEEEE---CCCC--EEEEE*CC--*-******CCCCC****---------------------------------------------------------- ***************CCC-**HHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHH*-C**CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCCC*****************CCCEEEEE***-CCCC***EEEEECC**********CCCCC****---------------------------------------------------------- 46977.tem _________________________________ ----------*****CCC*CCHHHHHHHHHHHHHHHC-CC----CCCHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC--CCCCCCC-----------------CCCEEEEEE**-CCCC**EEEEEECC***-***--*CCCCC****---------------------------------------------------------- Structural block scores 0 9 - 4.3 M 47.7 75.0 75.0 75.0 75.0 7.5 10 14 * 3.4 M 6.2 7.5 75.0 75.0 75.0 3.0 15 17 C 4.4 M 4.0 6.0 7.0 8.2 30.5 6.3 19 20 C 4.2 M 75.0 1.0 4.5 4.0 4.0 3.5 21 35 H 5.0 H 3.4 3.0 3.6 3.7 3.5 3.7 38 39 C 4.8 H 5.0 6.5 7.2 8.0 6.5 7.8 40 43 - 4.5 M 75.0 5.0 75.0 75.0 75.0 75.0 44 46 C 4.7 H 2.7 2.3 3.7 3.3 4.0 3.7 47 64 H 5.0 H 3.5 3.2 3.4 2.9 3.6 3.4 67 78 C 4.5 M 27.9 33.8 5.6 5.2 5.5 4.4 79 103 H 4.9 H 12.0 3.0 3.2 2.7 3.5 2.8 104 109 C 5.0 H 4.1 1.5 3.4 2.2 2.2 2.5 110 111 - 4.5 M 75.0 6.5 75.0 75.0 75.0 75.0 112 117 C 4.8 H 4.9 3.7 4.1 4.2 4.8 3.9 118 119 - 4.5 M 75.0 75.0 11.5 75.0 75.0 75.0 120 126 C 4.8 H 16.5 5.3 4.7 3.0 5.3 3.7 127 143 - 4.5 M 75.0 75.0 75.0 75.0 75.0 5.9 144 146 C 4.8 H 29.2 4.0 3.7 3.0 3.0 1.0 147 152 E 4.4 M 5.7 3.5 3.5 3.5 2.7 3.0 153 154 * 2.3 P 42.8 2.5 3.5 3.0 75.0 2.5 156 159 C 4.5 M 75.0 8.1 24.4 5.5 6.6 5.8 160 161 * 2.7 P 75.0 3.5 3.0 1.5 75.0 3.5 162 167 E 4.4 M 75.0 5.2 5.2 4.3 4.8 4.3 168 169 C 4.5 M 75.0 5.5 5.5 4.5 6.0 4.0 170 172 * 3.2 M 75.0 6.3 28.3 50.0 51.3 5.7 174 176 * 3.4 M 75.0 75.0 75.0 4.3 7.0 7.7 177 178 - 4.1 M 75.0 75.0 75.0 75.0 7.8 7.5 180 184 C 4.3 M 75.0 47.8 7.5 18.0 6.0 5.2 185 188 * 3.4 M 75.0 75.0 75.0 5.2 8.4 7.6 189 246 - 4.5 M 75.0 73.9 75.0 5.6 75.0 75.0 >>>>>>