Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2hjqa2 -------------CEEEEECCC-CEEEEC---------CEEEECCCEEECCHHHHHHHHCCCCEEEEECC-----------CC >P1;d2outa2 --------CCCCEEEEEECCCCC-CCCCCCCCCCCCEEEEEEEC-------CHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC >P1;d2q9qa2 CCHHHHHHHHCCCEEEEEECCCCCCEEEC------CEEECCCCCCCCEEEEHHHHHHHHHCCCEEEC---------------- >P1;d2q9qb2 ---------CCCCEEEEEECCCEEEEEECCCCCHHHCEEEEECCCCEEEEEHHHHHHHHHCCCEEC----------------- PSA >P1;d2hjqa2 -------------531020369-945a05---------a4405385327058911740783740615949-----------ba >P1;d2outa2 --------b99417030406365-73769020463451729349-------5703760564860905466a7a9a989ab89b >P1;d2q9qa2 57a86778653685330207176a3473b------b9510505476516013510541576940724---------------- >P1;d2q9qb2 ---------9656628050565359151415b6996165340775463511351037128760063----------------- Translating the sequences -------------*EEEEECCC-**EEEC---------*EEE*CCC*EE**HHHHHHHH*CCCEE*****-----------** --------**CC*EEEEE*CCC*-****C********EEEEE*C-------*HHHHHHH*CCC******************** **********CC*EEEEEECCC***EEEC------**EE****CCC*EE**HHHHHHHH*CCCEE**---------------- ---------*CC*EEEEEECCC***EEEC********EEEEE*CCC*EE**HHHHHHHH*CCCEE*----------------- 160059.tem _________________________________ --------**CC*EEEEEECCC***EEEC********EEEEE*CCC*EE**HHHHHHHH*CCCEE*****-----------** Structural block scores 0 7 - 4.3 M 75.0 75.0 7.3 75.0 8 9 * 2.9 P 75.0 10.2 5.5 42.0 10 11 C 4.3 M 75.0 6.5 4.5 5.5 13 18 E 4.8 H 1.8 2.3 2.2 3.5 19 21 C 5.0 H 6.0 5.0 5.0 5.3 22 24 * 1.9 P 29.3 29.0 6.5 5.7 25 27 E 4.3 M 5.2 5.3 4.7 2.3 29 36 * 3.2 M 75.0 3.0 58.8 6.1 37 41 E 4.3 M 18.7 4.4 2.2 3.6 43 45 C 4.5 M 5.3 53.0 5.7 5.3 47 48 E 4.3 M 4.5 75.0 3.5 4.0 49 50 * 2.3 P 2.5 75.0 0.5 1.0 51 58 H 4.9 H 4.6 4.1 3.0 2.8 60 62 C 5.0 H 4.7 6.0 6.3 4.3 63 64 E 4.3 M 3.0 4.5 3.5 3.0 65 69 * 2.8 P 5.6 4.2 46.2 60.6 70 80 - 4.3 M 75.0 9.4 75.0 75.0 81 82 * 3.5 M 11.0 10.2 75.0 75.0 >>>>>>