Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2gqfa2 -CCCCEECCHHHHHHHHHCCCEE-EEEEEECCCCEEE-EEEEECCCEEECHHHHHHCCCCCC--------CCCEEEECCCCC----CCCCCC--CCCCCC-CCHHHHCCCCC-CHHHHHHHCCCCCC-CCHHHCCHHHHHHHHHHHHCEEECCCEECCCCCCC-- >P1;d2i0za2 CCCCCEECCCHHHHCCCCCCCEEEEEEEEECCCEEEEEEEEEECCCEEECHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCHHHHCCCCCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHHEEEEECEECCHHHCCCC PSA >P1;d2gqfa2 -5300020496153056019240-3030307584525-540402860012500250044067--------a24030200044----a04406--12a257-40450046002-60041027493063-540480798606712640152603074209aa407-- >P1;d2i0za2 123020407260067630281207502010363540673304025700245003600330351176676b21501020219265760054017407844862046007a00475003200951907284506806694054007101504040330376960768 Translating the sequences -CCCCEECCHHHHHHHHHCCCEE-EEEEEECCC*EEE-EEEEECCCEEECHHHHHH******--------C**EEEECCCCC----******--*CCCCC-C*HHHHCCCCC-*HHHHHHH*CCCCC-CCHHHCCHHHHHHHHHHHH*EEE**CEECC***CC-- *CCCCEECC*HHHH****CCCEE*EEEEEECCCEEEE*EEEEECCCEEECHHHHHHHHHHHH********CEEEEEECCCCC****HHHHHH**HCCCCC*CHHHH*CCCCC*HHHHHHHHHCCCCC*CCHHHCCHHHHHHHHHHHHHEEEEECEECCHHHCC** 160996.tem _________________________________ -CCCCEECCHHHHHHHHHCCCEE-EEEEEECCCEEEE-EEEEECCCEEECHHHHHHHHHHHH--------CEEEEEECCCCC----HHHHHH--HCCCCC-CHHHHHCCCCC-HHHHHHHHHCCCCC-CCHHHCCHHHHHHHHHHHHHEEEEECEECCHHHCC-- Structural block scores 1 4 C 5.0 H 2.0 1.8 5 6 E 5.0 H 1.0 2.0 7 8 C 5.0 H 2.0 3.5 9 17 H 3.9 M 3.9 3.3 18 20 C 5.0 H 4.0 3.7 21 22 E 5.0 H 2.0 1.0 24 29 E 5.0 H 1.5 1.3 30 32 C 5.0 H 6.7 4.0 33 36 E 4.5 M 4.0 3.8 38 42 E 5.0 H 2.6 2.0 43 45 C 5.0 H 5.3 4.7 46 48 E 5.0 H 0.3 0.7 50 61 H 4.0 M 2.8 2.3 62 69 - 3.0 P 75.0 5.7 71 76 E 4.3 M 1.8 1.5 77 81 C 5.0 H 1.6 2.8 82 85 - 3.0 P 75.0 6.0 86 91 H 3.0 P 4.1 1.7 92 93 - 3.0 P 75.0 5.5 95 99 C 5.0 H 5.3 6.2 102 106 H 4.2 M 1.8 2.0 107 111 C 5.0 H 2.4 4.3 113 121 H 4.6 H 2.7 2.7 122 126 C 5.0 H 4.2 3.8 128 129 C 5.0 H 4.5 4.5 130 132 H 5.0 H 4.0 4.7 133 134 C 5.0 H 3.5 3.0 135 147 H 4.8 H 4.2 3.2 148 152 E 4.2 M 2.2 1.6 154 155 E 5.0 H 3.0 1.5 156 157 C 5.0 H 4.5 5.0 158 160 H 3.0 P 8.3 7.0 161 162 C 5.0 H 3.5 3.5 163 164 - 3.0 P 75.0 7.0 >>>>>>