Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1xq4a- CCCCCCEEEEEEEEECHHHCCHHHCCEEEEEEEEEEECCC----CCEEEEEEEEEEECCCCCEEEEEEECCCCCCCEECCCCEEEEEEEEEECCCCCE-EEEEEEEECC--CCEEEEEECCCCCC-CCC >P1;d1xvsa- CCCCCCEEEEEEEEECHHHCCHHHCCEEEEEEEEEEECCC----CCEEC-CEEEEEEECCCCEEEEEECCCCCCCCEECCCCEEEEEEEEEECCCEEE-EEEEC-CCCC--CCCCCEEECCCCEECCCC >P1;d5hdwa1 CEEECCEEEEEEEEECHHHCCCCCCCEEEEEEEEEEECCCCCHHHCEEEEEEEEEEEECCCCEEEEEEECCCCCCCEECCCCEEEEEEEEEECCCEEEEEEEEEEEECCCCCCEEEEEEEEEEEECCC- PSA >P1;d1xq4a- b776120607082611497044876612011204020404----4203032210221016964556667006a7315053852251446070415603-4120402056--97625070a42700-798 >P1;d1xvsa- ab87170506281700887045987511031401020319----32030-3250312048676545678004b6505073954230543250514403-30205-4248--67615160842801378b >P1;d5hdwa1 6344c402030526136a605996460202050303068907754002044220411146973764737005a6414031152241635150515403021302032165aa753506015160608a- Translating the sequences CCCCCCEEEEEEEEECHHHCCHHHCCEEEEEEEEEEECCC----CCEEEEEEEEEEE*CCCCEEEEEEECCCCCCCEECCCCEEEEEEEEEECCC**E-EEEEEEEECC--CCEEEEEECCCC**-CCC CCCCCCEEEEEEEEECHHHCCHHHCCEEEEEEEEEEECCC----CCEE*-*EEEEEEECCCCEEEEEE*CCCCCCCEECCCCEEEEEEEEEECCCEEE-EEEE*-**CC--CC***EEECCCCEECCCC C***CCEEEEEEEEECHHHCC***CCEEEEEEEEEEECCC*****CEEEEEEEEEEEECCCCEEEEEEECCCCCCCEECCCCEEEEEEEEEECCCEEE*EEEEEEEECC**CCEEEEEE****EECCC- 110069.tem _________________________________ CCCCCCEEEEEEEEECHHHCCHHHCCEEEEEEEEEEECCC----CCEEEEEEEEEEEECCCCEEEEEEECCCCCCCEECCCCEEEEEEEEEECCCEEE-EEEEEEEECC--CCEEEEEECCCCEECCCC Structural block scores 0 5 C 4.5 M 5.8 7.5 5.6 6 14 E 5.0 H 3.3 3.2 2.1 16 18 H 5.0 H 6.7 7.7 7.5 19 20 C 5.0 H 2.0 2.0 2.5 21 23 H 4.0 M 6.3 7.3 8.0 24 25 C 5.0 H 6.0 6.0 5.0 26 36 E 5.0 H 1.2 1.2 1.4 37 39 C 5.0 H 2.7 4.3 7.7 40 43 - 4.0 M 75.0 75.0 4.8 44 45 C 4.5 M 3.0 2.5 2.0 46 57 E 4.7 H 1.3 7.8 1.8 58 61 C 5.0 H 5.5 6.2 6.5 62 68 E 4.9 H 5.6 5.9 5.3 69 75 C 5.0 H 3.9 3.8 3.8 76 77 E 5.0 H 2.5 2.5 2.0 78 81 C 5.0 H 5.2 6.0 2.5 82 91 E 5.0 H 3.1 2.8 2.9 92 94 C 5.0 H 3.3 3.3 3.7 95 97 E 4.3 M 3.0 2.3 2.3 99 106 E 4.5 M 1.6 11.4 1.6 107 108 C 5.0 H 5.5 6.0 3.5 109 110 - 4.0 M 75.0 75.0 7.8 111 112 C 5.0 H 8.0 6.5 8.8 113 118 E 4.5 M 3.3 3.2 3.2 119 122 C 4.0 M 5.9 5.5 3.2 123 124 E 4.0 M 0.0 0.5 3.0 125 128 C 4.5 M 24.8 7.4 23.4 >>>>>>