Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1r71a- CCHHHHHHHHCCCCCHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHHHHHHHHC-CCCCCCHHHHHHHHHHHHC- >P1;d6sdka2 C-----------CCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC--CHHHHHHCC--CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC >P1;d7bm8a2 -----------CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC-------------------------CCCCCCCCCCC----------------- PSA >P1;d1r71a- 71772254067951745510610370285-9486860083073678208302202a0293027017723084130023014127844950371056-9929066a30780359076- >P1;d6sdka2 b-----------a72405206502531785a2847600863a47563027215018048801620158407--110510190--775b406600940375a1836504530793398 >P1;d7bm8a2 -----------bb651262066046337759472540088396758303401501817a421b7-------------------------d19056b8377----------------- Translating the sequences C**********CCCCHHHHHHHHHHHHH*-CCCHHHHHHHHCCCHHHHHHHHHH*CCCHHHHHHHHCCCCC***HHHHHH*****CHHHHHHHHHC-CCCCCCHHHHHHHHHHHHC- C-----------CCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC--*HHHHHH**--*CHHHHHHHHH*****CCCHHHHHHHHHHHHC* -----------CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH*CCCC******-------------------------******C*CCC----------------- 109709.tem _________________________________ C----------CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHCCCCC--*HHHHHH**--*CHHHHHHHHHC*CCCCCCHHHHHHHHHHHHC- Structural block scores 1 10 - 4.0 M 4.1 75.0 75.0 11 14 C 4.8 H 5.5 23.6 8.5 15 29 H 4.9 H 8.1 3.5 3.9 30 32 C 5.0 H 7.0 6.8 6.7 33 40 H 5.0 H 3.9 4.2 3.8 41 43 C 5.0 H 5.3 7.2 7.3 44 53 H 4.9 H 3.2 3.1 2.9 54 57 C 4.8 H 3.6 3.2 4.2 58 65 H 4.0 M 3.6 3.2 23.2 66 70 C 4.0 M 4.0 4.8 75.0 71 72 - 4.0 M 2.5 75.0 75.0 74 79 H 4.0 M 1.0 1.3 75.0 80 81 * 2.7 P 2.5 4.5 75.0 82 83 - 4.0 M 4.5 75.0 75.0 86 94 H 4.0 M 3.8 4.6 28.8 97 102 C 4.0 M 5.8 5.8 40.3 103 114 H 4.0 M 4.9 4.0 75.0 >>>>>>