AlignACE version 2.2 July 7, 1998 AlignACE -jRRN.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YBL025W 442 bp YBL025W RRN10 1-438 Upstream activation factor subunit #2 YBL014C 307 bp YBL014C RRN6 1-2685 member of yeast Pol I core factor (CF) also composed of Rrn11p, Rrn7p and TATA-binding protein #3 YJL025W 363 bp YJL025W RRN7 1-1545 member of yeast Pol I core factor (CF) also composed of Rrn11p, Rrn6p and TATA-binding protein #4 YKL125W 497 bp YKL125W RRN3 1-1884 DNA-independent RNA Polymerase I transcription factor #5 YLR141W 300 bp YLR141W RRN5 1-1092 transcription factor, member of UAF (upstream activation factor) along with Rrn9p and Rrn10p #6 YML043C 600 bp YML043C RRN11 1-1524 Component of rDNA transcription factor CF, which also contains Rrn6p and Rrn7p, which is required for rDNA transcription by RNA polymerase I #7 YMR270C 441 bp YMR270C RRN9 1-1098 Upstream activation factor subunit Motif number 1 TGATGAGGAATTCTTTTTTTTTGCCCCATTTT 1 234 1 TTTTTTTTTT 0.988909 -209 TTATGAGGTTTTGTTTTGTTTTACTAAATGCG 1 281 1 TTTTTTTTTT 0.988909 -162 TTAAAAACATTTACTTTTTTATTGGAGTGTTG 1 347 0 TTCTTTTTAT 0.772896 -96 CTAGGTCCCCTTCCTTTTTTTTCTTACCTCTC 2 52 1 TTCTTTTTTT 0.9814 -256 CAGGTACAGCTTTTTTTGCTTTTTTCTTAATG 2 127 1 TTTTTTCTTT 0.960053 -181 CATATAAACTTTTTTTTATATTGAATCTAATA 3 107 1 TTTTTTTATT 0.845711 -257 TTTTTAAGCTTTTCTTACTTTTCCGATGCCCT 3 194 0 TTCTTATTTT 0.764349 -170 TTTTTTTTTTTTCAATTTTTTTAAGCTTTTCT 3 211 0 TTAATTTTTT 0.620794 -153 TTTTTATTTTTTATTTTTTTTTTTTTTTTTTT 3 231 0 TTTTTTTTTT 0.988909 -133 ATTGTATAGGTTTTTTTATTTTTTATTTTTTA 3 250 0 TTTTTTTTTT 0.988909 -114 CACCTTTTTTTTTTTTTATTTTCTGCCGCCCC 4 269 0 TTTTTTTTTT 0.988909 -229 GATACATAACTTTTTTTTTTTTTTTCAGTTCA 5 173 1 TTTTTTTTTT 0.988909 -128 TCTATACTTTTTTTTTTGTTTTTCACCTCGCC 5 223 0 TTTTTTTTTT 0.988909 -78 AGTAATTATGTTACTTTATTCTAGCGAGAGTT 6 199 1 TTCTTTTTCT 0.834548 -402 CTAGCGAGAGTTGATTTTTTTTGTTATGTTAT 6 219 1 TTATTTTTTT 0.935038 -382 TTTTTTTTTTTTTTTTTTTTTTCATTTTTCAA 6 356 0 TTTTTTTTTT 0.988909 -245 TTTTCTTTTTTTATTTTTTTTTTTTTTTTTTT 6 369 0 TTTTTTTTTT 0.988909 -232 TATGATCCATTTCTTTTCTTTTTTTATTTTTT 6 382 0 TTTTTTTTTT 0.988909 -219 AATTTCTTTCTTCTTTTTCTTTAAAACACTTT 6 532 0 TTTTTTCTTT 0.960053 -69 TAAATTTTTCTTGTATTCTTTTTTAATCAGTA 7 63 1 TTTATTTTTT 0.910245 -379 TTAAGGTTTCTTACTTTTCTTTTTGTCATGCT 7 166 1 TTCTTTCTTT 0.934304 -276 GAAAGGCCTTTTTGTTTATTTTGTAGAAGAAA 7 247 0 TTGTTTTTTT 0.923652 -195 ** **** **** Masking position 6 Map Score: 44.6375 Number of sites scoring better than the average of aligned sites = 7431 Number in coding regions = 994 Number in noncoding regions = 6437 Number of orfs with sites within 600 bp upstream = 1689 Fraction of orfs with sites within 600 bp upstream = 0.271282 Motif number 2 AAAAAACTAATGAGAAAAAATGCCATGAGG 1 27 0 TGAGAAAAAA 0.792967 -416 TAAAATGGGGCAAAAAAAAAGAATTCCTCA 1 237 0 CAAAAAAAAA 0.863935 -206 AAAAGAGAGGTAAGAAAAAAAAGGAAGGGG 2 58 0 TAAGAAAAAA 0.901831 -250 AAGCGTCCATTAAGAAAAAAGCAAAAAAAG 2 136 0 TAAGAAAAAA 0.901831 -172 TTCTTAATCGAGAGAATAAAAATTATCGTA 2 203 0 AGAGAATAAA 0.752549 -105 AGAGACTGCGTAAAAAGAAATATATAGAGA 3 18 0 TAAAAAGAAA 0.931776 -346 TTAGATTCAATATAAAAAAAAGTTTATATG 3 107 0 TATAAAAAAA 0.52633 -257 AAAAAAATTGAAAAAAAAAAAAAAAAAAAT 3 221 1 AAAAAAAAAA 0.962162 -143 AAAAAAAAAAAAAAAATAAAAAATAAAAAA 3 234 1 AAAAAATAAA 0.899022 -130 AATAAAAAATAAAAAATAAAAAAACCTATA 3 248 1 AAAAAATAAA 0.899022 -116 ATACTTTATATAAAAAGAAAGGTTTTCTTT 4 48 1 TAAAAAGAAA 0.931776 -450 AGTAAGTAACGGAAAAGAAAACCTTTCTTT 4 61 0 GGAAAAGAAA 0.824466 -437 GGCAGAAAATAAAAAAAAAAAAAGGTGTTG 4 274 1 AAAAAAAAAA 0.962162 -224 TACATTGTCTGGTAAAGAAATAACTTTTGT 4 458 1 GGTAAAGAAA 0.31762 -40 CCCTTCATGGGAAGAAGAAAC 5 2 0 GAAGAAGAAA 0.902245 -299 AACTGAAAAAAAAAAAAAAAGTTATGTATC 5 173 0 AAAAAAAAAA 0.962162 -128 CAGTTCACTGAAATAAGAAAAGGCGGGCGA 5 198 1 AAATAAGAAA 0.713281 -103 GGTGAAAAACAAAAAAAAAAGTATAGAGAA 5 228 1 AAAAAAAAAA 0.962162 -73 TTGAAAAATGAAAAAAAAAAAAAAAAAAAA 6 356 1 AAAAAAAAAA 0.962162 -245 AAAAAAAAAAAAAAAAAAAAAATAAAAAAA 6 366 1 AAAAAAAAAA 0.962162 -235 AAAAAAAATAAAAAAAGAAAAGAAATGGAT 6 380 1 AAAAAAGAAA 0.968724 -221 TTTTAAAGAAAAAGAAGAAAGAAATTGAAG 6 538 1 AAAGAAGAAA 0.962087 -63 TTTGTATAGGAAAGAATAAATTTTTCTTGT 7 47 1 AAAGAATAAA 0.879434 -395 TGAAGCATGACAAAAAGAAAAGTAAGAAAC 7 171 0 CAAAAAGAAA 0.885504 -271 AAATGTCTAGAGAGAAAAAACCGCCGACAC 7 346 0 AGAGAAAAAA 0.896759 -96 ********** Masking position 5 Map Score: 33.3202 Number of sites scoring better than the average of aligned sites = 16974 Number in coding regions = 3580 Number in noncoding regions = 13394 Number of orfs with sites within 600 bp upstream = 2912 Fraction of orfs with sites within 600 bp upstream = 0.467716 Motif number 3 CAAGTGGTCATCCAAAATTTTTTTGGCCAGAG 1 186 1 TCAAATTTTT 0.785793 -257 CTGTGGGCATACGATAATTTTTATTCTCTCGA 2 194 1 ACATATTTTT 0.883441 -114 TATCTCTCTATATATTTCTTTTTACGCAGTCT 3 14 1 TAATTCTTTT 0.842605 -350 CACTGAATCATATAAACTTTTTTTTATATTGA 3 99 1 TAAAATTTTT 0.751134 -265 GAGAAAATTTTCAACACCTTTTTTTTTTTTTA 4 283 0 TCACACTTTT 0.923175 -215 GATGCTCATCAAAATATCTTTTATACAAGGAG 4 312 0 AAATACTTTT 0.921211 -186 GTCTGGTAAAGAAATAACTTTTGTGCAAGACA 4 464 1 GAATACTTTT 0.856077 -34 ACATTAAAGATACATAACTTTTTTTTTTTTTT 5 165 1 TAATACTTTT 0.966135 -136 CTTCTGTTTCTCTATACTTTTTTTTTTGTTTT 5 233 0 TCATATTTTT 0.942439 -68 TTTATTATGATCCATTTCTTTTCTTTTTTTAT 6 387 0 TCATTCTTTT 0.866781 -214 TGGCAATGAAAATATAACTTTTTTAGATGTTA 6 457 0 AAATACTTTT 0.92958 -144 CTTTTTCTTTAAAACACTTTTTTATTGAAGAA 6 520 0 AAACATTTTT 0.682515 -81 TCAGTATACGTAAATAGCTTTTTATTGTTGGA 7 89 1 TAATACTTTT 0.96613 -353 TCTACTACTTTCCATAATTTTTCACTAAAATA 7 213 1 TCATATTTTT 0.942439 -229 ** *** ***** Masking position 4 Map Score: 7.07396 Number of sites scoring better than the average of aligned sites = 1405 Number in coding regions = 849 Number in noncoding regions = 556 Number of orfs with sites within 600 bp upstream = 434 Fraction of orfs with sites within 600 bp upstream = 0.0697077 Motif number 4 TCATTAACGTAAAAAGAGAGGTAAGAAAAAAAAGG 2 64 0 AAAGAGTAAG 0.976056 -244 ACCTGCTATTATGGAGAGGAGTAAGCGCTTTTCTC 2 97 0 AGAGAGTAAG 0.977858 -211 TGGCAAGTTGAAGTAAAGAGAGAAGGCGTTCTATG 2 275 1 AGAAAGGAAG 0.931856 -33 GAAAGCCCACATAAAGAGATTGAAGAGACTGCGTA 3 36 0 AAAGAGGAAG 0.993126 -328 TACATAATATATACGGAGCTTGAAGGCACTGGAGA 5 119 0 AAGGAGGAAG 0.967876 -182 AAAAAAAAGTATAGAGAAACAGAAGTGGAAGAAGA 5 240 1 AAAGAAGAAG 0.984039 -61 TGTTAACGAGATGAAGAATTGGTAGCACGCTCTTC 6 53 1 AGAGAAGTAG 0.903835 -548 TAAGTGGCTAAGGGAGAGTCCGAAGAGCGTGCTAC 6 74 0 AGAGAGGAAG 0.993652 -527 AAGAAAAAGAAGAAAGAAATTGAAGCACGAATAAA 6 543 1 AAAGAAGAAG 0.984039 -58 GAAGCATGACAAAAAGAAAAGTAAGAAACCTTAAA 7 165 0 AAAGAATAAG 0.94564 -277 * * **** **** Masking position 7 Map Score: 8.8677 Number of sites scoring better than the average of aligned sites = 1317 Number in coding regions = 1141 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 5 CCTAAAATGATACTCGTGTAAAAAACTAATGAG 1 43 0 TCTCGTAAAA 0.956532 -400 TGCAGATCAACACTCCAATAAAAAAGTAAATGT 1 340 1 CCTCCTAAAA 0.944964 -103 TAGCGTGATATACTTCTTTAAAAACATTTACTT 1 363 0 TCTTCTAAAA 0.987011 -80 GAAAATTTTCTCCTTGTATAAAAGATATTTTGA 4 303 1 TCTTGTAAAA 0.953096 -195 TTGCAGTAGCTTCTCCTTTTAAAAATATAAAGG 4 350 1 TCTCCTTAAA 0.920538 -148 AACAAACTGGTTCTCCGTTAAAAATTGTGCTAT 6 24 0 TCTCCTAAAA 0.987985 -577 TACTTGAGCATTCTTCAATAAAAAAGTGTTTTA 6 510 1 TCTTCTAAAA 0.986997 -91 TTCTTTCTTCTTTTTCTTTAAAACACTTTTTTA 6 528 0 TTTTCTAAAA 0.9288 -73 CTTTCCATAATTTTTCACTAAAATATTTTTCTT 7 220 1 TTTTCTAAAA 0.923986 -222 TAAAATATTTTTCTTCTACAAAATAAACAAAAA 7 238 1 TCTTCCAAAA 0.940632 -204 * **** ***** Masking position 4 Map Score: 7.89782 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 199 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 CGTAAAAAGAGAGGTAAGAAAAAAAAGGAA 2 62 0 GAGGTAAGAA 0.837884 -246 TTAAGAAACCGAGATGAGCTTTCATATTAG 2 226 1 GAGATGAGCT 0.845315 -82 ATATAAATAAGAGGTGCGAAAGCCCACATA 3 58 0 GAGGTGCGAA 0.925182 -306 GGAAGGGTAAGAGAGGAAATCCTTTATCTA 4 224 0 GAGAGGAAAT 0.756834 -274 AAAAAAAAAGGTGTTGAAAATTTTCTCCTT 4 288 1 GTGTTGAAAA 0.754063 -210 AAAGGCGGGCGAGGTGAAAAACAAAAAAAA 5 216 1 GAGGTGAAAA 0.978263 -85 GTTTGTTAACGAGATGAAGAATTGGTAGCA 6 50 1 GAGATGAAGA 0.868127 -551 CTCTGAAACAGCGTTGAGAAGAGGTGAAAA 6 137 1 GCGTTGAGAA 0.930486 -464 GCGTTGAGAAGAGGTGAAAAAGTTGGACCG 6 147 1 GAGGTGAAAA 0.978263 -454 TCTATTACCCGCGTTGAAAAATGAAAAAAA 6 343 1 GCGTTGAAAA 0.893197 -258 GAGATGAGATGAGATGAGATGTTTATTATG 6 410 0 GAGATGAGAT 0.966687 -191 TATATCATCTGAGATGAGATGAGATGAGAT 6 420 0 GAGATGAGAT 0.966687 -181 ********** Masking position 3 Map Score: 5.03077 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 781 Number in noncoding regions = 425 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 7 TTTAGGTTAACGTTCGAAATATAGTGCTTATGA 1 403 0 CGTTCGATAA 0.984735 -40 TTCCGATGCCCTTTCCACTTTAATCAATATACG 3 173 0 CTTTCCATTA 0.944657 -191 AAAGACACATCGTTCCAGGTTTATATTCATATA 3 293 0 CGTTCCATTA 0.98427 -71 GTATTGCCCACGTTCGAAATATAAATCCTAGAA 4 132 0 CGTTCGATAA 0.984735 -366 TTTTAATCAGCGTTCGACTTTAAATTAACCCAA 4 386 1 CGTTCGATTA 0.993301 -112 ACAATGTATCCGTTCGTGGTTAAGGTAAGAATT 4 433 0 CGTTCGTTTA 0.984734 -65 ACAAAAAGGCCTTTCGTGTTTGAAGATTACTCA 7 264 1 CTTTCGTTTA 0.94623 -178 ******* ** * Masking position 13 Map Score: 3.62432 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 27 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AGATTATATGTATATGTATATATGTAGGCCA 1 82 1 TATATTATAT 0.954123 -361 CAGGGTAACCCATATTTATATCAAATGGAAG 2 166 0 CATATTATAT 0.970329 -142 ACCTCTTATTTATATATATATATATACACTG 3 73 1 TATATTATAT 0.954123 -291 GGCTGAATTTCATACGTATATTGATTAAAGT 3 159 1 CATACTATAT 0.964428 -205 ACAATACATACATATGTATATGAATATAAAC 3 277 1 CATATTATAT 0.970329 -87 TTTTAATCAGTATACGTAAATAGCTTTTTAT 7 83 1 TATACTAAAT 0.809657 -359 ***** ***** No masking Map Score: -0.0633324 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 99 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 9 TGGCCTACATATATACATATACATATAATCT 1 82 0 ATATAATATA 0.955953 -361 CTTCCATTTGATATAAATATGGGTTACCCTG 2 166 1 ATATAATATG 0.971532 -142 CAGTGTATATATATATATATAAATAAGAGGT 3 73 0 ATATAATATA 0.955953 -291 ACTTTAATCAATATACGTATGAAATTCAGCC 3 159 0 ATATAGTATG 0.965862 -205 GTTTATATTCATATACATATGTATGTATTGT 3 277 0 ATATAATATG 0.971532 -87 ATAAAAAGCTATTTACGTATACTGATTAAAA 7 83 0 ATTTAGTATA 0.81614 -359 ***** ***** No masking Map Score: -0.0633324 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 99 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 10 AGATTATATGTATATGTATATATGTAGGCCA 1 82 1 TATATTATAT 0.955953 -361 CAGGGTAACCCATATTTATATCAAATGGAAG 2 166 0 CATATTATAT 0.971532 -142 ACCTCTTATTTATATATATATATATACACTG 3 73 1 TATATTATAT 0.955953 -291 GGCTGAATTTCATACGTATATTGATTAAAGT 3 159 1 CATACTATAT 0.965862 -205 ACAATACATACATATGTATATGAATATAAAC 3 277 1 CATATTATAT 0.971532 -87 TTTTAATCAGTATACGTAAATAGCTTTTTAT 7 83 1 TATACTAAAT 0.81614 -359 ***** ***** No masking Map Score: -0.0633324 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 99 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028