Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1yqea1 ----------CEEEEEECCCHHHHHHHHHHCCCCCCEEEEEC--CEEEEECCCCEEEEECCCHHHCCCHHHHHCC--CCCCCEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCEEEEEEEECHHHHCCHHHHHHHHHHHHHHHHC--CCC-CCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECHHHHHHCCHHHHHHHHHHH--CCCEEEECCCCCCHHHHHHHHHHHHHHCCEEEE-HHHHHHHCCCC >P1;d2gfqa1 CHHHHHHHCCCCCEEEECCCCCC-CC-CHHHHHCCCEEEEEEECCEEEEEECCEEEEEECCC-CCCCCHHHHHHHHHCCCCCCEEEEEEEECCCCCCEEEEECCEECCCC-CCCCCCEECCCCCCC-CHHHHC-CCCCCC--CCEEEECCCCCCCCCCCCCEEEEEEEECHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECHHHCC-CCCC-CCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHCCEEEEE----------- PSA >P1;d1yqea1 ----------310000029030020006202812b0745537--5030021a30100007350160250064037--21a060000012152a444400000000000708600654200200120001001104822a406507000000240002093300000000458015274003000300140052--a55-8041000001861043014002603000000006600850728000500730--707200003910699047206400870906106-08503753729 >P1;d2gfqa1 88a8188407b700011640500-10-8004542b0680a2703a050222a5000022493-26215105306730217020001012162a8a230000000010790-810665100100000-000041-372172--b1500000021000205020000000065921547300100030014004404a74a81400000028230640163026850000000046204-1749-0250082021905000002930567026305800a54a151153----------- Translating the sequences ----------CEEEEEECCCHHH*HH*HHH***CCCEEEEE*--CEEEEE*CC*EEEEECCC*HHCCCHHHHH**--CCCCCEEEEEEEEECCCCCCEEEEECC**CCCC*CCCCCC**CCCCHHH*HHHHHH*HHHHHH**CCEEEECCCCCCCCCCCCCEEEEEEEECHHHHCCHHHHHHHHHHHHHHHH*--**C-CCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECHHHHH*CCHH*HHHHHHHH--CCCEEEE*CCCCCHHHHHHHHHHHHHHCCEEEE-*********** **********C**EEEECCC***-**-*HHHHHCCCEEEEEE**CEEEEEECCEEEEEECCC-**CCCHHHHHHH**CCCCC*EEEEEEEECCCCCCEEEEECCEECCCC-CCCCCCEECCCC***-*HHHH*-******--CCEEEECCCCCCCCCCCCCEEEEEEEECHHHHCCHHHHHHHHHHHHHHHHH**HHC*CCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECHHH**-CC**-**********CCCEEEEECCCCCHHHHHHHHHHHHHHCCEEEE*----------- 142535.tem _________________________________ ----------CEEEEEECCCHHH-HH-HHHHHHCCCEEEEEE--CEEEEEECCEEEEEECCC-HHCCCHHHHHHH--CCCCCEEEEEEEEECCCCCCEEEEECCEECCCC-CCCCCCEECCCCHHH-HHHHHH-HHHHHH--CCEEEECCCCCCCCCCCCCEEEEEEEECHHHHCCHHHHHHHHHHHHHHHHH--HHC-CCEEEEEECCCCCCHHHHHHHHHCCEEEEEEECHHHHH-CCHH-HHHHHHHH--CCCEEEEECCCCCHHHHHHHHHHHHHHCCEEEE------------ Structural block scores 0 9 - 3.0 P 75.0 6.2 11 16 E 4.3 M 0.2 1.5 17 19 C 5.0 H 3.7 3.3 20 22 H 3.0 P 1.0 1.7 24 25 H 3.0 P 0.0 0.5 27 32 H 3.7 M 3.2 3.5 33 35 C 5.0 H 4.5 4.5 36 41 E 4.7 H 5.2 5.6 42 43 - 3.0 P 75.0 1.5 45 50 E 4.7 H 1.0 1.8 51 52 C 5.0 H 6.8 7.8 53 58 E 4.7 H 0.2 0.7 59 61 C 5.0 H 5.0 5.3 63 64 H 3.0 P 3.5 4.0 65 67 C 5.0 H 2.3 2.7 68 74 H 4.4 M 2.9 3.1 75 76 - 3.0 P 75.0 1.5 77 81 C 5.0 H 3.9 2.4 82 90 E 4.8 H 1.0 1.2 91 96 C 5.0 H 4.8 6.0 97 101 E 5.0 H 0.0 0.0 102 103 C 5.0 H 0.0 0.0 104 105 E 3.0 P 0.0 0.5 106 109 C 5.0 H 1.8 4.0 111 116 C 5.0 H 3.5 4.3 117 118 E 3.0 P 1.0 0.5 119 122 C 5.0 H 0.5 0.2 123 125 H 3.0 P 1.0 0.0 127 132 H 4.3 M 0.5 0.8 134 139 H 3.0 P 5.1 3.7 140 141 - 3.0 P 3.0 75.0 142 143 C 5.0 H 2.5 6.2 144 147 E 5.0 H 1.8 1.2 148 160 C 5.0 H 1.8 0.9 161 168 E 5.0 H 0.0 0.0 170 173 H 5.0 H 3.5 4.2 174 175 C 5.0 H 3.5 4.5 176 192 H 4.9 H 1.7 1.6 193 194 - 3.0 P 75.0 2.0 195 196 H 3.0 P 7.8 8.8 199 200 C 5.0 H 4.0 4.5 201 206 E 5.0 H 0.8 0.7 207 212 C 5.0 H 2.7 2.5 213 221 H 5.0 H 2.2 3.1 222 223 C 5.0 H 1.5 6.5 224 230 E 5.0 H 0.0 0.0 232 236 H 4.2 M 4.0 3.2 238 239 C 5.0 H 3.5 4.0 240 241 H 3.0 P 5.0 6.5 243 250 H 3.0 P 1.9 2.1 251 252 - 3.0 P 75.0 1.5 253 255 C 5.0 H 4.7 4.7 256 260 E 4.6 H 0.4 0.0 261 265 C 5.0 H 3.8 3.8 266 279 H 5.0 H 4.0 4.0 280 281 C 5.0 H 4.5 5.8 282 285 E 5.0 H 3.2 3.0 286 297 - 3.0 P 10.3 69.0 >>>>>>