Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1aqta2 CCEEEEEEECCCEEEEEEEEEEEEECCCCEEEECCCCCCEEEEECCEEEEEEECCCEEEEEEECCEEEEEECCEEEEEECCEEEC >P1;d2hldh1 ----CEEE-CCCCCCC--CCCEEEEC--CEEEECCCCCCCC-CC-CC-CCCC--CC---CCCCCCEEEECCCCCCEEEECCC--- >P1;d2jdih2 ---CCCEECCCCEEEC----CCCCCCC-CCCCCCCCCCCEECEEECCCCCC---------------------------------- PSA >P1;d1aqta2 b2030303088660135503202040379624061c385371606555030146867325050311504047a603050760657 >P1;d2hldh1 ----0604-6677142--26303014--d552079a3a476-80-75-0626--9a---a480315613057a202060771--- >P1;d2jdih2 ---9340306a66169----9244290-76370644045688180870574---------------------------------- Translating the sequences *****EEE*CCCEEE******EEEECC*CEEEECCCCCCEE*EE*C********CC*******CCEEEE**CC**EEEECC**** ----CEEE-CCC***C--**CEEEEC--CEEEECCCCCC**-**-CC-CCC*--CC---****CCEEEE**CC**EEEECC*--- ---*C*EE*CCCEEEC----C****CC-C****CCCCCCEE*EE*CC*CCC---------------------------------- 51344.tem _________________________________ ---*CEEE*CCCEEEC--**CEEEECC-CEEEECCCCCCEE*EE*CC*CCC*--CC---****CCEEEE**CC**EEEECC*--- Structural block scores 0 2 - 4.0 M 4.5 75.0 75.0 5 7 E 4.7 H 2.0 3.3 2.3 9 11 C 5.0 H 7.3 6.3 7.5 12 14 E 4.0 M 2.3 4.0 4.3 16 17 - 4.0 M 5.0 75.0 75.0 18 19 * 2.7 P 1.5 4.0 75.0 21 24 E 4.0 M 1.5 1.0 3.0 25 26 C 4.5 M 1.5 39.5 4.5 29 32 E 4.0 M 3.0 3.0 4.0 33 38 C 5.0 H 5.9 7.3 3.8 39 40 E 4.0 M 5.0 6.5 7.0 42 43 E 4.0 M 3.0 4.0 4.5 45 46 C 4.5 M 5.0 6.0 7.5 48 50 C 4.0 M 1.0 2.7 5.3 52 53 - 4.0 M 5.0 75.0 75.0 54 55 C 4.0 M 7.0 9.8 75.0 56 58 - 4.0 M 4.0 75.0 75.0 59 62 * 2.7 P 2.5 5.6 75.0 63 64 C 4.0 M 2.0 2.0 75.0 65 68 E 4.0 M 2.5 3.8 75.0 69 70 * 2.7 P 2.0 2.5 75.0 71 72 C 4.0 M 8.8 8.8 75.0 73 74 * 2.7 P 3.0 1.0 75.0 75 78 E 4.0 M 2.0 2.0 75.0 79 80 C 4.0 M 6.5 7.0 75.0 82 84 - 4.0 M 6.0 75.0 75.0 >>>>>>