Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1wx1a- -------------CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH-CCCCCCCCCEEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHHCCEEEEEEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHCCCHHHHCC-C----HHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHCCHHHHHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHCHHHHHHEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC-CCCHHHHCCCCC >P1;d4hdra- CCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH-CCCCCCCCEEEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHCCCEEEEEEEECCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEEEEECCCHHHHHHHHHHHHHCCCHHHHHCCC----CCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHCCCHHHHEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-C----------- >P1;d4hdrb- --CHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH-CCCCCCCCCEEEEEEEECCCCC------CC--CHHHHHHHHHC-CCCHHHHHHHHHCEEEEEEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCC-CCC----------HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHCHHHHHHEECCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCC >P1;d4kqia- --CHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCHHHCCCCCCCEEEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHHHCCEEEEEEEECCCCCCC--CCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC-CEEEEEEEEECCCCHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHHHHCHHHHHHEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC------- PSA >P1;d1wx1a- -------------3488125506710740117683492316001100002-3534050740000000000402728029753720352014007-5603016309806021100000057a0593840134303600520053500657104400500250053017590400000010110300000000001935173001-c----97327414700550282179-b173251001000000000000001025161000001000000000023227603400000010625005400630906002657225100000020043026006001-3411953a5a5f >P1;d4hdra- 483067038607604681274068408a429a9c7195227002200000-234809405000000000000064149386463026201401576813007308409031000000022707607a0253204600800164500749301600200040043128590400000010120400000000000a473470065a----5c85423260046017208064930010002000000000000000000230000000000000000013116202300000056114006200950717010659366000000030033026006304-8----------- >P1;d4hdrb- --329804950670498038603820350318684373406001200003-1544088060000000001449------86--80453054027-67150292088090411000000339187194045411361062228450054820440020005105402765040000010053046100000100277906-80a----------b6427407503840807484121000200000000000000000055000000100000000001420750330000002041300720084090702274916561000002004103501700462617954996ac >P1;d4kqia- --81831264038359703860494058061768549420800120000340923040871000000000303727014262640163023036-77050063088090501000000329519--a0460115510820073500649403800250062027219-b0200000010100200000000100a2705-0015188048a4195006005402750706483001000300000000000000000410000000201000000001301750330000002030600840074090701274824621000003004203501601483755a------- Translating the sequences -------------CCHHHHHHHHHHHHCCCCCCCCC*HHHHHHHHHHHHH-CCCCCCCC*EEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHH*C*EEEEEEEECCCCCCCCCC*EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC**EEEEEEECCCHHHHHHHHHHHHHCCC****CC-C----****HHHHHHHHHHHH**CC-CCCHHHHHHHHCCHHHHHHHHHHHHHHHCCC*EE*CCHHHHHHHHHHHHHCHHHHHHEE*CCCCCCC*HHHHHHH*CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH**-CCC********* ***HHHHHH*CCCCCHHHHHHHHHHHH**CCCCCCC*HHHHHHHHHHHHH-CCCCCCCC*EEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC*CCCHHHHHHHH*C*EEEEEEEECCCCCCCCCC*EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC**EEEEEEECCCHHHHHHHHHHHHHCCC*****C*C----******HHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCC*EECCCHHHHHHHHHHHHHC**HHHHEECCCCCCC**HHHHHHH*CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH*-C----------- --*HHHHHH*CCCCCHHHHHHHHHHHHCCCCCCCCC*HHHHHHHHHHHHH-CCCCCCCC*EEEEEEEECC***------CC--*HHHHHHHHHC-CCCHHHHHHHH*C*EEEEEEEECCCCCCCCCC*EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC**EEEEEEECCCHHHHHHHHHHHHHCCC**-*CC----------HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCC*EECCCHHHHHHHHHHHHHCHHHHHHEECCCCCCCC*HHHHHHH*CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH**CCC********* --*HHHHHH*CCCCCHHHHHHHHHHHHCCCCCCCCC*HHHHHHHHHH**H**CCCCCCC*EEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHH*C*EEEEEEEECCCCCCC--C*EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH*-C**EEEEEEECCC*HHHHHHHHHHHHCCC**-*CC*C********HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCC*EECCCHHHHHHHHHHHHHCHHHHHHEECCCCCCCC*HHHHHHH*CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH**CCC**------- 52733.tem _________________________________ --*HHHHHH*CCCCCHHHHHHHHHHHHCCCCCCCCC*HHHHHHHHHHHHH-CCCCCCCC*EEEEEEEECCHHHHHCCCCCCCCHHHHHHHHHHC-CCCHHHHHHHH*C*EEEEEEEECCCCCCCCCC*EECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC**EEEEEEECCCHHHHHHHHHHHHHCCC****CC*C----****HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHCCC*EECCCHHHHHHHHHHHHHCHHHHHHEECCCCCCCC*HHHHHHH*CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH**CCC********* Structural block scores 0 1 - 4.3 M 75.0 6.0 75.0 75.0 3 8 H 4.3 M 75.0 4.0 5.3 3.5 10 14 C 4.6 H 46.4 3.4 3.4 3.8 15 26 H 5.0 H 4.2 4.5 4.2 4.6 27 35 C 4.8 H 3.8 7.3 4.2 5.0 37 49 H 4.9 H 1.2 1.5 1.5 1.5 51 58 C 4.9 H 3.4 3.8 3.8 3.2 60 67 E 5.0 H 0.0 0.0 0.0 0.1 68 69 C 5.0 H 0.0 0.0 0.5 0.0 70 74 H 4.3 M 3.0 2.0 33.4 3.0 75 82 C 4.5 M 5.1 5.1 58.0 3.5 83 92 H 4.9 H 1.7 1.9 3.1 2.2 95 97 C 5.0 H 3.7 5.0 4.7 4.7 98 105 H 5.0 H 3.8 3.1 4.2 3.8 109 116 E 5.0 H 0.5 0.5 0.8 0.8 117 126 C 4.9 H 5.2 4.2 4.5 18.9 128 129 E 5.0 H 2.0 3.5 4.5 5.0 130 146 C 5.0 H 2.5 2.7 2.9 2.6 147 166 H 5.0 H 2.5 2.4 2.4 3.2 167 168 C 4.7 H 7.0 7.0 5.5 43.2 169 170 * 1.0 P 2.0 2.0 2.0 1.0 171 177 E 5.0 H 0.1 0.1 0.1 0.1 178 180 C 5.0 H 0.7 1.0 2.7 0.3 181 193 H 4.9 H 0.3 0.3 1.1 0.2 194 196 C 5.0 H 5.7 7.2 7.7 6.5 197 200 * 1.6 P 2.8 3.5 22.2 20.0 201 202 C 4.7 H 0.5 3.0 5.2 0.5 205 208 - 4.3 M 75.0 75.0 75.0 5.0 209 212 * 2.3 P 5.2 7.6 75.0 5.9 213 226 H 4.8 H 3.3 2.6 4.4 3.1 227 232 C 4.9 H 18.4 5.0 5.2 4.7 233 240 H 5.0 H 1.5 0.4 0.8 0.5 241 242 C 5.0 H 0.0 0.0 0.0 0.0 243 257 H 5.0 H 0.5 0.0 0.0 0.3 258 260 C 5.0 H 2.7 1.7 3.3 0.3 262 263 E 5.0 H 0.0 0.0 0.0 0.0 264 266 C 4.8 H 0.3 0.0 0.3 0.7 267 279 H 5.0 H 0.5 0.4 0.5 0.4 281 286 H 4.8 H 3.3 2.2 3.0 3.0 287 288 E 5.0 H 0.0 0.0 0.0 0.0 289 296 C 4.8 H 1.8 2.1 1.2 1.4 298 304 H 5.0 H 2.6 3.1 3.0 3.3 306 320 C 5.0 H 3.0 3.4 3.9 3.5 321 337 H 5.0 H 1.4 1.5 1.4 1.5 338 339 * 2.2 P 38.0 39.5 5.0 6.0 340 342 C 4.5 M 2.7 52.7 3.0 5.0 343 351 * 3.2 M 7.9 75.0 8.0 60.1 >>>>>>