Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bx7a- CCCCCCC-CCCC---CEECCC---CCEECCCCCCCCCCCCCCCCCCCCCCCCCCCC---------C-- >P1;d1deca- CC----CCCCCCCCCCCCEECC-CCEECCC-CEECCCCCCCCEEC----------------------- >P1;d1e0fi- CCCCCCCCCCCCCCCCCCEECC-CCEECCCCCCC----------CCCCCCCCCCCCCCCCCCCCCCCC >P1;d1skza1 --CHHHH-CCCC---CCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCE-EEEECC---------CCC >P1;d2pw8i1 -------CCCCCCCCEECEECCCCCEECCCEEEECCCCCCCCEEEECCCEECCCCCCCCCCCCCCC-- PSA >P1;d1bx7a- ea50888-9169---01346a---71626838094707592463a54026825429---------3-- >P1;d1deca- a6----a1760a561b930405-8660435-60433acb571627----------------------- >P1;d1e0fi- 8846668270476a07630006-88406540407----------9a606693868798aa7988998c >P1;d1skza1 --30687-707b---b23203662824053072a590647231599023-528328---------867 >P1;d2pw8i1 -------688067550020205c982058a4304218bc79362395a07527ab399aa77a97d-- Translating the sequences CCC***C-CCCC---C****C---C*E*CCCCCCCCCCCCCC**CCCCC**CCCCC---------C-- CC----CCCCCCCCCCCCEECC-CCEECCC-C**CCCCCCCCE*C----------------------- CCC***CCCCCCCCCCCCEECC-CCEECCCCCCC----------CCCCC**CCCCC*********C** --C****-CCCC---CCC**CC*CC**CCCCCCCCCCCCC**E*CCCC*-****CC---------C** -------CCCCCCCC**CEECC*CCEECCC****CCCCCCCCE***CCC**CCCCC*********C-- 57262.tem _________________________________ CCC***CCCCCCCCCCCCEECC-CCEECCCCCCCCCCCCCCCE*CCCCC**CCCCC---------C-- Structural block scores 0 2 C 4.2 M 10.0 30.5 6.7 51.0 75.0 3 5 * 3.0 P 5.3 75.0 6.0 4.7 75.0 6 17 C 4.5 M 28.1 5.9 5.0 29.1 10.2 18 19 E 3.8 M 5.0 2.0 0.0 1.0 1.0 20 21 C 4.8 H 42.8 2.5 3.0 4.5 2.5 23 24 C 4.8 H 41.0 7.0 8.0 5.0 8.5 25 26 E 4.2 M 3.5 3.0 2.0 3.0 1.0 27 41 C 4.4 M 4.9 10.0 41.7 4.2 5.9 44 48 C 4.3 M 4.3 61.4 6.3 4.6 5.5 49 50 * 2.5 P 7.0 75.0 7.5 40.0 6.0 51 55 C 4.3 M 4.4 75.0 6.4 4.6 6.8 56 64 - 3.8 M 75.0 75.0 8.8 75.0 8.8 66 67 - 3.8 M 75.0 75.0 10.2 6.5 75.0 >>>>>>