Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1na6a1 CHHHHHHHHHHHCCEEEEEEECCHHHHCCCCCCCCCCHHHHHHHCHHHCCCCCCCCEEEEEEEECCCCCCCEEEEEEEECHHHCCCCCCEEEEECCCCCCHHHCHHHCCCEEEEEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHCCCCCCCCEEEEHHHHCCCCCCCCCC >P1;d1yela1 ---------CCCCCCEEEEEECCHHHHC---CCEECCHHHHCCCCCC--------CCCEEEEECCCC--CEEEEEEEEC--C------CCEEECCCHHHHHHHHCCCCCCEEEEEEC------CCCEEEEEEECCCCC---------------------------------- >P1;d5os9a- -----------CCCEEEEEEECCHHHHCC--CCEEECHHHHHHHCCCCC---CCCCCEEEEEECCCC--CEE-EEEEEECCC------CEEEEECHHHHHC-CCCCCCCCEEEEEEC---CCCCCCCEEEEEECCC-C---------------------------------- PSA >P1;d1na6a1 a807801850176602000010638005365800702381048003604247654023503050203b2945404010202343b894430402506781000448237100000053389991075020000559921750193068067b33112505700a5a658479 >P1;d1yela1 ---------9256573355060639406---7103036900861548--------51750303159a--6405040418--7------6503039004601632b055a24020207------4564150406449ac---------------------------------- >P1;d5os9a- -----------6945500316057501a7--810302572056106065---93b904529040675--660-040013996------8100026103701-619084700010116---b28cb0802041663a-c---------------------------------- Translating the sequences ************CCEEEEEEECCHHHHCC**CC**CCHHHHHHHC***C***CCCC*EEEEEE*CCC**C*EEEEEEEEC********CEEEEECC****HHHC***CCCEEEEEE****CCCCCCEEEEEE*CC************************************* ---------**CCC*EEEEEECCHHHHC---CCEECCHHHH***CCC--------CC*EEEEECCCC--CEEEEEEEE*--C------C*EEE*CCHHHHHHH*CCCCCCEEEEEEC------CCCEEEEEEECCC*C---------------------------------- -----------CCCEEEEEEECCHHHHCC--CCEE*CHHHHHHHCCC*C---CCCCCEEEEEECCCC--CEE-EEEEEEC*C------CEEEEEC*HHHH*-*CCCCCCCEEEEEEC---CCCCCC*EEEEEECCC-C---------------------------------- 101936.tem _________________________________ ---------**CCCEEEEEEECCHHHHCC--CCEECCHHHHHHHCCC*C---CCCCCEEEEEECCCC--CEEEEEEEEEC*C------CEEEEECCHHHHHHHCCCCCCCEEEEEEC---CCCCCCEEEEEEECCC*C---------------------------------- Structural block scores 0 8 - 4.0 M 5.3 75.0 75.0 9 10 * 2.7 P 0.5 5.5 75.0 11 13 C 4.7 H 6.3 5.3 6.3 14 20 E 4.9 H 0.4 4.1 2.9 21 22 C 5.0 H 3.0 3.0 2.5 23 26 H 5.0 H 2.8 4.0 3.2 27 28 C 4.5 M 4.0 40.5 8.8 29 30 - 4.0 M 5.5 75.0 75.0 31 32 C 5.0 H 4.0 4.0 4.5 33 34 E 4.0 M 3.5 1.5 1.5 35 36 C 4.5 M 1.0 1.5 1.0 37 43 H 4.6 H 3.4 4.3 3.7 44 46 C 4.3 M 3.0 5.7 2.0 49 51 - 4.0 M 4.3 75.0 75.0 52 56 C 4.2 M 3.4 46.2 6.5 57 62 E 4.8 H 2.7 3.0 4.0 63 66 C 4.8 H 1.2 6.4 4.5 67 68 - 4.0 M 6.8 75.0 75.0 70 78 E 4.7 H 2.2 2.9 9.9 82 87 - 4.0 M 6.6 75.0 75.0 89 93 E 4.6 H 1.8 2.2 0.6 94 95 C 4.5 M 2.5 4.5 3.5 96 102 H 4.0 M 3.1 2.9 13.1 103 109 C 4.4 M 4.1 5.1 4.1 110 115 E 5.0 H 0.0 1.3 0.5 117 119 - 4.0 M 4.7 75.0 75.0 120 125 C 4.5 M 5.8 40.0 7.6 126 132 E 4.7 H 1.0 2.9 3.0 133 135 C 4.7 H 6.3 5.7 6.5 138 171 - 4.0 M 4.6 75.0 75.0 >>>>>>