Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3aa0a- CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHH---CCCEECCCCCCCCEECCHHHEEECCEEEECCCCEEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCEEEEEEEEEEEEEEHHHCEEEEEEEEEEEEEEC------CEEEEEEEEEEEEEECCC----CCEEEEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCCCCCHHHHCC >P1;d3aa7b- ---CHHHHHHHHHHHCCCCHHHHHHHHHHHHHH----------CHHHHHHHHHHCCCCCEEEEECCCCEEEEECHHHEEC-CEEECCCCCCEEC------CCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEEEEEEC-CCCCCEEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEEEEEECCCEEEEEEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHC----------------- PSA >P1;d3aa0a- a577945054005601601021087216704980a56b1059408701350015---1010050aa39220000710428c42010012300050416635076358364566057104100830470057317902000002349a530000000025243974302011010302045------73050702041150525a----97833726471956170873750063016103820670866277667766467868786a4387988467a8588 >P1;d3aa7b- ---6a9628804540873533515710660187----------279049502841322053350773553001133034b-b020001125056------82ba09--406a50181057007402811684187310000034398000000001357-649775542100001040525a748403030300001123145bb5a5643033254444562714ba24113004600380057077206850567467677a7b----------------- Translating the sequences ***HHHHHHHHHHHHHCCC***HHHHHHHHHHH**********CHHHHHHHHHH---CC*EE**CCCC**EE*CHHHEEE*CEEEECCCCEEEE******EEEEEE**CCC***HHHHHHHHHHHHHHHHHH*CCCEEEEEEEEECCEEEEEEEEEEEE*EHHHCEEEEEEEEEEEEEE*------*EEEEEEEEEEEEEE**C----**EEEEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*HHHHHC***************** ---*HHHHHHHHHHH*CCCHHHHHHHHHHHHHH----------CHHHHHHHHHH***CCEEEEECCCCEEEEECHHHEE*-CEEE*CCCC*EE*------******--CCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEEEEEE*-****CEEEEEEEEEEEEEEE******EEEEEEEEEEEEEEEEEC****EEEEEEEEEEEEEEEECCC***HHHHHHHHHHHHHHHHHHHHHHHHH*HHHHHHHHHC----------------- 90096.tem _________________________________ ---HHHHHHHHHHHHHCCCHHHHHHHHHHHHHH----------CHHHHHHHHHH---CCEEEEECCCCEEEEECHHHEEE-CEEEECCCCEEEE------EEEEEE--CCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEEEEEEE-EHHHCEEEEEEEEEEEEEEE------EEEEEEEEEEEEEEEEEC----EEEEEEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------- Structural block scores 0 2 - 3.0 P 7.5 75.0 3 15 H 4.7 H 3.5 5.4 16 18 C 5.0 H 2.3 5.0 19 32 H 4.6 H 3.9 3.8 33 42 - 3.0 P 5.2 75.0 44 53 H 5.0 H 3.0 4.8 54 56 - 3.0 P 75.0 2.0 57 58 C 5.0 H 0.5 1.0 59 63 E 3.8 M 1.2 3.2 64 67 C 5.0 H 8.2 5.5 68 72 E 3.8 M 0.8 1.8 74 76 H 5.0 H 2.7 2.0 77 79 E 4.3 M 4.7 6.2 82 85 E 4.5 M 0.8 0.5 86 89 C 5.0 H 1.5 1.0 90 93 E 4.0 M 1.2 4.0 94 99 - 3.0 P 3.3 75.0 100 105 E 3.0 P 4.3 6.8 106 107 - 3.0 P 5.5 75.0 108 110 C 5.0 H 5.0 3.3 111 132 H 4.6 H 3.1 3.6 133 135 C 5.0 H 5.3 6.0 136 144 E 5.0 H 1.2 1.2 145 146 C 5.0 H 9.8 8.5 147 158 E 4.8 H 1.2 1.3 161 163 H 3.0 P 6.3 6.7 165 179 E 4.9 H 1.5 1.9 180 185 - 3.0 P 75.0 6.4 186 202 E 4.6 H 2.8 1.5 204 207 - 3.0 P 75.0 8.0 208 223 E 4.8 H 5.3 3.9 224 226 C 5.0 H 5.0 5.5 227 264 H 4.7 H 4.7 4.3 266 282 - 3.0 P 7.1 75.0 >>>>>>