Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1c8za- CCCCCCCCCHHHHHHCCCCCCCCEEEEEEECCCCCCCCEEEEECCCCCCEEEEEEECC---CCCCEEEECCHHHHCCCCCCCEEEEECCCCCEEEEECCCCCHHHCCCCHHHCCCCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCEEEEEECCCEEECCCCEEEEEECCEEEECCCCEEEEECCCCCCCEEEEEEEEECCEEEEEECCCCCHHHHHHHHHHHHHCCCCCC >P1;d2q4ma- C---CCCCC----HHHCCC--CCC-CCEECC----CCCEEEECC---CCCEEEEEECCCCCCCCEEEEECC----C--CCEEEEEEC----CEEEEEECCCCC------------HHHEEEEEEC---------CCEEEEECCCC--------------------------CCCCCEEEEC---CCC----------------CCCCEEEEHHHC-CEEEE-EECCCCCEEEEECCCCCHHHHHHHHHHHHHHHC--- PSA >P1;d1c8za- d65a1708726600432055b3306030422579b731030303379a432000034b---85521000153a406c287200305148710300001634319708a924848702200000106889778225500000010497671540304687330221286857920250213708438a46240071888527141210000449659520010023674303010210000000000000013042289 >P1;d2q4ma- d---25003----771116--741-400439----805010124---979220403116b86743000135----8--663000033----950100644327------------7921001035---------92040023829--------------------------8570102036---307----------------815110220567-74103-466952600210438101000100100001254--- Translating the sequences C***CCCCC****HH*CCC**CCE*EEEEEC****CCCEEEEEC***CCEEEEEEECC---CCC*EEEECC****C**CC**EEEEE****CEEEEE*CCCCH***************EEEEEEC*********CC*EEEEECCC**************************CCEEEEEE*C***ECC****************CCEEEEE****C*CEEEE*EEEECCEEEEEECCCCCHHHHHHHHHHHHH**C*** C---CCCCC----HHHCCC--CC*-**EE*C----CCCEEEE*C---CC*EEEEEECC***CCCEEEEECC----C--CCEEEEEE*----CEEEEEECCCC*------------HHHEEEEEEC---------CCEEEEE*CCC--------------------------CC***EEEEC---*CC----------------CC**EEEEHHHC-CEEEE-EE**CC*EEEEECCCCCHHHHHHHHHHHHHHHC--- 54518.tem _________________________________ C---CCCCC----HHHCCC--CCE-EEEEEC----CCCEEEEEC---CCEEEEEEECC---CCCEEEEECC----C--CCEEEEEEE----CEEEEEECCCCH------------HHHEEEEEEC---------CCEEEEEECCC--------------------------CCEEEEEEEC---ECC----------------CCEEEEEEHHHC-CEEEE-EEEECCEEEEEECCCCCHHHHHHHHHHHHHHHC--- Structural block scores 1 3 - 3.0 P 7.2 75.0 4 8 C 5.0 H 4.6 2.0 9 12 - 3.0 P 3.5 75.0 13 15 H 4.3 M 2.3 5.0 16 18 C 5.0 H 2.3 2.7 19 20 - 3.0 P 8.2 75.0 21 22 C 5.0 H 3.0 5.5 25 29 E 3.8 M 1.8 2.2 31 34 - 3.0 P 8.1 75.0 35 37 C 5.0 H 3.7 4.3 38 42 E 4.6 H 1.2 0.8 44 46 - 3.0 P 6.3 75.0 47 48 C 5.0 H 7.2 8.0 49 55 E 4.7 H 1.1 2.9 56 57 C 5.0 H 7.8 1.0 58 60 - 3.0 P 75.0 8.5 61 63 C 5.0 H 6.0 5.7 64 68 E 4.6 H 0.6 0.8 69 70 C 5.0 H 3.0 4.0 71 74 - 3.0 P 4.4 75.0 76 77 - 3.0 P 7.2 75.0 78 79 C 5.0 H 7.5 6.0 80 86 E 4.1 M 1.6 1.3 87 90 - 3.0 P 5.0 75.0 92 97 E 4.7 H 0.7 2.0 98 101 C 5.0 H 4.0 3.2 103 114 - 3.0 P 6.4 75.0 115 117 H 3.0 P 1.3 6.0 118 123 E 5.0 H 0.2 0.8 125 133 - 3.0 P 6.3 75.0 134 135 C 5.0 H 5.0 5.5 136 141 E 4.3 M 0.0 1.5 142 144 C 5.0 H 1.7 6.3 145 170 - 3.0 P 4.4 75.0 171 172 C 5.0 H 5.5 6.5 173 179 E 3.9 M 1.9 1.9 181 183 - 3.0 P 4.0 75.0 185 186 C 5.0 H 9.2 3.5 187 202 - 3.0 P 4.2 75.0 203 204 C 5.0 H 1.5 4.5 205 210 E 4.0 M 0.8 1.8 211 213 H 3.0 P 6.3 3.7 217 220 E 5.0 H 0.8 2.0 222 225 E 4.0 M 2.8 6.2 226 227 C 5.0 H 5.5 3.5 228 233 E 4.7 H 1.2 1.5 234 238 C 5.0 H 0.6 3.2 239 253 H 4.7 H 0.5 0.7 255 257 - 3.0 P 6.3 75.0 >>>>>>