Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2ppva- CCEEEEECHHHHHHHHHHHCC-CCC-CEEEEECCC-CCCHHHHHHHHCCCCCCHHHHHHHHHCCCCCCHHHHHHC--CCCC--CC----------CHHHCCHHHHHHHCCCCCC-CHHHHHHHHHHHCCCCCEEEECCCCCCEEEEECCCCEECCCCCCCC--------EEEEEC-CCCCC-CHHHHHHHHCCEEEECCCCIIIIIHHHHCCCHHHHHHHCCCCEEEECCCCC--------CCCCCC--CCHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCEEECCCCCEEECHHHHHCCHHHHHHHCCCCCC >P1;d3c3da1 ---CEEECCCHHHHHHHHHCCCCCHHHCEEEECCCCCEEEC-------CEEECHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEECC-CCCCEEEEEECC-CCCHHHHHCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHCCEEEECCCCCCCCCHHHHHCCCCHHHHC--CEEEEECCEECCEECCCHHHCCCCCCCCCCCCHHHHHC-----CCCCEEEEEHHHCCCHHHHHH-------HCCEEEEE-CCCC---------CHHHHHHHHHHHHHHC----- PSA >P1;d2ppva- 550000006940160042037-250-600000000-334b10120097900000200400000075958506603--5529--7a----------657010200350281992b-40340065219609052401000642040001a7742711670307--------503066-8b080-b50271037040000003200010000000301700250a02000002213--------55005b--120350030026207780041000074a0850593b2405170b4c053255a700435a75808123920060150155256b889 >P1;d3c3da1 ---00000644004000000414526701000000113415-------b110041000000001820147515206b082961565759872624003611600440062259934005006502742907050000-349030303066-841127045956060607104144178071075056108727300001010000000004149474048--14000000017a6047410540413a392500006204-----600410000552747776058-------29080730-2047---------7574235005404921----- Translating the sequences ***EEEECHHHHHHHHHHHCC-CC*-*EEEEECCC-C***H*******C***CHHHHHHHHHCCCCCCHHHHHHC--CCC*--*C----------CHHH**HHHHHHH****CC-CHHHHHHHHHHH*CCCCEEEEC*CCCCEEEEE*CC*EEC*****CC--------EEEEEC-CCCCC-*HHHHHHHHCCEEEECCCC*****HHHH*CCHHHHHHH**C*EEEECC**C--------*CCCCC--CCHHHHHHHHH*****CCCCEEE*****CCC**************CCEEE***CCEE*********CHHHHH**HHHHHHHC***** ---*EEEC**HHHHHHHHHCC*CCH*H*EEEECCC*CEEE*-------CEEECHHHHHHHHHCCCCCC******C**CCCH**HC**********C*HHHHHHHHHHHHHHHCC*CHHHHHHHHHHHHCCCCEEE*C-CCCCEEEEEECC-**CHHHHHCC********EEEEEC*CCCCC*HHHHHHHHHCCEEEECCCCCCCCCHHHHHCC**HHHH*--CEEEEECCEEC********HCCCCC**CC***HHHHH*-----CCCCEEEEEHHHCCCHHHHHH-------HCCEEEEE-CC**---------CHHHHHHHHHHHHHHC----- 142338.tem _________________________________ ---EEEECHHHHHHHHHHHCC-CCH-HEEEEECCC-CEEEH-------CEEECHHHHHHHHHCCCCCCHHHHHHC--CCCH--HC----------CHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHCCCCEEEEC-CCCCEEEEEECC-EECHHHHHCC--------EEEEEC-CCCCC-HHHHHHHHHCCEEEECCCCCCCCCHHHHHCCHHHHHHH--CEEEEECCEEC--------HCCCCC--CCHHHHHHHHH-----CCCCEEEEEHHHCCCHHHHHH-------HCCEEEEE-CCEE---------CHHHHHHHHHHHHHHC----- Structural block scores 0 2 - 3.0 P 3.3 75.0 3 6 E 4.5 M 0.0 0.0 8 18 H 4.6 H 2.9 1.6 19 20 C 5.0 H 5.0 2.0 22 23 C 5.0 H 3.5 4.5 27 31 E 4.6 H 0.0 0.2 32 34 C 5.0 H 0.0 0.0 37 39 E 3.0 P 6.2 2.7 41 47 - 3.0 P 2.7 75.0 49 51 E 3.0 P 0.0 0.7 53 61 H 5.0 H 0.7 0.6 62 67 C 5.0 H 4.3 2.0 68 73 H 3.0 P 4.2 4.0 75 76 - 3.0 P 75.0 8.8 77 79 C 5.0 H 4.0 3.3 81 82 - 3.0 P 75.0 3.5 85 94 - 3.0 P 75.0 5.5 96 111 H 4.1 M 3.2 2.5 112 113 C 5.0 H 6.8 9.0 116 127 H 4.8 H 3.0 2.6 128 131 C 5.0 H 4.0 4.0 132 135 E 4.5 M 1.2 1.2 138 141 C 5.0 H 3.0 4.0 142 147 E 4.7 H 2.6 1.5 148 149 C 5.0 H 7.0 6.0 151 152 E 3.0 P 4.5 6.0 154 158 H 3.0 P 3.4 2.8 159 160 C 5.0 H 3.5 7.0 161 168 - 3.0 P 75.0 3.8 169 173 E 5.0 H 2.8 2.0 176 180 C 5.0 H 5.5 4.6 182 190 H 4.8 H 4.1 4.3 191 192 C 5.0 H 2.0 4.5 193 196 E 5.0 H 0.0 0.8 197 205 C 3.9 M 0.7 0.2 206 210 H 4.6 H 0.0 0.8 211 212 C 5.0 H 1.5 2.5 213 219 H 4.1 M 2.1 5.1 220 221 - 3.0 P 5.2 75.0 223 227 E 4.6 H 0.4 0.8 228 229 C 5.0 H 1.0 0.0 230 231 E 3.0 P 1.5 0.5 233 240 - 3.0 P 75.0 4.1 242 246 C 5.0 H 4.3 2.4 247 248 - 3.0 P 75.0 6.8 249 250 C 5.0 H 1.5 5.5 251 259 H 4.1 M 1.4 1.9 260 264 - 3.0 P 4.4 75.0 265 268 C 5.0 H 3.0 2.5 269 273 E 4.2 M 0.2 0.2 274 276 H 3.0 P 7.2 4.0 277 279 C 5.0 H 4.3 6.0 280 285 H 3.0 P 5.1 5.5 286 292 - 3.0 P 4.1 75.0 294 295 C 5.0 H 6.2 4.5 296 300 E 4.2 M 4.0 3.6 302 303 C 5.0 H 3.5 1.0 304 305 E 3.0 P 2.0 5.5 306 314 - 3.0 P 5.3 75.0 316 329 H 4.7 H 2.8 3.6 331 335 - 3.0 P 8.5 75.0 >>>>>>