Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1dk0a- CCEEEECHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCHHH-CCEEECCCCEEEEEEEECCCCCCEEEEEEEEEEECCCCCCCCCEEEEEEEEEEEEEEECCC---CCCCEEEEEEEEEECCCEEEC-----HHHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHC-------- >P1;d4jera- CCEEEECHHHCCCCHHHHHHHHHHHHCCHHHCC---HHHCCCCEEECCCCEEEEEEEECCCCCCEEEEEEEEEEECCC--CCCCEEEEEEEEEEEECEEECCCCHHHCEEEC-CCEEEECCCEEECCCCCCHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHC----CCCCCCCHHHC-CCEEECCCCCCC PSA >P1;d1dk0a- b060816a811931056008501850650625cb538b81-325027795536200030364850000023804204889344002170640300421550a---a651707852040330b1608-----49415903015004300307082029105a208839140803066038307-------- >P1;d4jera- b05030249137310350074007404204805---787146041174b550610003003a4400000417041157--814001230530200260334ba57a412506-3100037070429198a75880375500300320041606201700582----90707310570-a30733895a74 Translating the sequences CCEEEECHHHCCCCHHHHHHHHHHHHCC***CC****HHH-CCEEECCCCEEEEEEEECCCCCCEEEEEEEEEEECCC**CCCCEEEEEEEEEEEEEEE*CC---**C*EEE*EEEEEECCCEEEC-----HHHHHHCHHHHHHHHHHCCCCHHHHHHHHHH****CCCCCCCHHHH*HH**-------- CCEEEECHHHCCCCHHHHHHHHHHHHCCHHHCC---HHH**CCEEECCCCEEEEEEEECCCCCCEEEEEEEEEEECCC--CCCCEEEEEEEEEEEE*EEECC***HHCEEE*-**EEEECCCEEEC*****HHHH**CHHHHHHHHHHCCCCHHHHHHHHH*----CCCCCCCHHH*-**EE******** 54621.tem _________________________________ CCEEEECHHHCCCCHHHHHHHHHHHHCCHHHCC---HHHH-CCEEECCCCEEEEEEEECCCCCCEEEEEEEEEEECCC--CCCCEEEEEEEEEEEEEEEECC---HHCEEEE-EEEEEECCCEEEC-----HHHHHHCHHHHHHHHHHCCCCHHHHHHHHHH----CCCCCCCHHHH-HHEE-------- Structural block scores 0 1 C 5.0 H 5.8 5.8 2 5 E 5.0 H 3.8 2.0 7 9 H 5.0 H 6.5 4.7 10 13 C 5.0 H 3.5 3.5 14 25 H 5.0 H 3.2 2.5 26 27 C 5.0 H 5.5 3.0 28 30 H 3.0 P 2.7 4.0 31 32 C 5.0 H 8.8 2.5 33 35 - 3.0 P 6.5 75.0 36 39 H 4.0 M 7.1 5.8 41 42 C 5.0 H 2.5 3.0 43 45 E 5.0 H 2.3 2.0 46 49 C 5.0 H 7.0 6.9 50 57 E 5.0 H 2.4 1.9 58 63 C 5.0 H 4.3 3.6 64 74 E 5.0 H 1.7 1.5 75 77 C 5.0 H 4.0 4.3 78 79 - 3.0 P 8.5 75.0 80 83 C 5.0 H 2.8 3.2 84 99 E 4.8 H 2.5 1.9 100 101 C 5.0 H 5.2 7.8 102 104 - 3.0 P 75.0 7.5 105 106 H 3.0 P 8.2 7.2 108 111 E 4.0 M 3.8 3.2 113 118 E 4.3 M 2.3 1.2 119 121 C 5.0 H 4.8 4.7 122 124 E 5.0 H 2.3 2.0 126 130 - 3.0 P 75.0 7.1 131 136 H 4.3 M 5.3 5.2 138 147 H 5.0 H 1.6 1.3 148 151 C 5.0 H 2.5 2.8 152 161 H 4.8 H 4.0 3.1 162 165 - 3.0 P 4.8 75.0 166 172 C 5.0 H 3.6 3.9 173 176 H 4.5 M 3.0 3.0 178 179 H 3.0 P 5.5 6.8 180 181 E 3.0 P 3.5 3.5 182 189 - 3.0 P 75.0 6.2 >>>>>>