AlignACE version 2.2 July 7, 1998 AlignACE -jSTB.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 YDR169C 600 bp YDR169C STB3 1-1542 Binds Sin3p in two-hybrid assay #2 YHR178W 600 bp YHR178W STB5 1-2232 Zinc finger (6-Cys) #3 YKL072W 506 bp YKL072W STB6 1-2301 Binds Sin3p in two-hybrid assay #4 YMR019W 403 bp YMR019W STB4 1-2850 Binds Sin3p in two-hybrid assay #5 YMR053C 404 bp YMR053C STB2 1-2553 Binds Sin3p in two-hybrid assay and is part of large protein complex with Sin3p and Stb1p #6 YNL309W 300 bp YNL309W STB1 1-1380 Binds Sin3p in two-hybrid assay and is present in a large protein complex with Sin3p and Stb2p Motif number 1 TCAGTGTCTTTTATAATCGATTTGTCTTGGATATGGAT 1 280 0 TTTATTTTTT 0.94396 -321 TAATGTCTTTTTATTCAAAATTTCAATTTATTAGAAAA 1 554 0 TTTTATTTTT 0.898112 -47 TCTTGTTTTTTTTTTGCACTTTTGCTTTTATTCGGGTT 2 45 0 TTTTCTTTTT 0.982752 -556 AGATTGAAGCCTTTTTTTTGTTTCAATTCCTGATGTTC 2 228 0 CTTTTTTTTT 0.947872 -373 GAGTGTAGTTTTCTTCCCGTTTTCCGTTGAGATTGAAG 2 257 0 TTTTCTTTTT 0.982752 -344 TTTCGGAAGCTTATTTTTCTTTTAGTATTTCCGCTCGC 2 457 0 TTTTTTTTAT 0.851517 -144 GTCCTTCTTTTACACCTTTGTATTAATTTTTTAG 2 577 0 CTTTCTTTTT 0.942984 -24 TGTTTTTAAATTTTTCTGAATTTTGCTTCAGTGCCACT 3 303 0 TTTTTTTTTT 0.984288 -204 GAAATTCTTCTTTTTTTTCTTTTATATTTATATGTTTT 3 335 0 TTTTTTTTTT 0.984288 -172 TTTTGCACGCTTGTTATTACTTTCACTTTTCGTAGCAG 3 377 0 TTTTTTTTTT 0.984288 -130 CATATTTGGTTTGTTTCAGCTTTAATTTTTTTTATTTT 4 45 0 TTTTCTTTTT 0.982752 -359 TCAGCCGGGTATCTTTTTTCTTTGTTTTGAGAGGCTGA 4 374 0 ATTTTTTTTT 0.869563 -30 GCTTACAGTTTTGTACTCGCTTTTGCTTTTGCTTGCAA 5 112 0 TTTATTTTTT 0.94396 -293 AGCACACTCTTTTTATTTCGTTTTGCTTACAGTTTTGT 5 136 0 TTTATTTTTT 0.94396 -269 GAGGTGTCCTTTTTTGCCATTTTTGTTTATGTAGTCAA 5 249 0 TTTTCTTTTT 0.982752 -156 ** ** * *** ** Masking position 11 Map Score: 19.1898 Number of sites scoring better than the average of aligned sites = 4476 Number in coding regions = 946 Number in noncoding regions = 3530 Number of orfs with sites within 600 bp upstream = 1307 Fraction of orfs with sites within 600 bp upstream = 0.209926 Motif number 2 CTCAGTTCGCCCTTTTTTGCGATAAATTTA 1 356 0 CCTTTTTTGC 0.967795 -245 TACTCTTTTTCCTTCTTTTCAGCGGAAATT 1 473 0 CCTTCTTTTC 0.983607 -128 ACGCCAAGCTCCTGCTTTGTGCTTTTCTAA 1 532 1 CCTGCTTTGT 0.814981 -69 GAAATAATGTCTTTTTATTCAAAATTTCAA 1 566 0 CTTTTTATTC 0.895375 -35 TTGCACTTTTGCTTTTATTCGGGTTGAAAT 2 40 0 GCTTTTATTC 0.880269 -561 CTAAGCGCTTCTTGTTTTTTTTTTGCACTT 2 62 0 CTTGTTTTTT 0.591003 -539 TTCCTTGCAACCTTCTATTTTGATGAACAT 2 204 1 CCTTCTATTT 0.933274 -397 GAGATTGAAGCCTTTTTTTTGTTTCAATTC 2 237 0 CCTTTTTTTT 0.941561 -364 TTCCGCTCGCCCTATTTTTCCCGTGGTATC 2 437 0 CCTATTTTTC 0.926628 -164 ATTTCGGAAGCTTATTTTTCTTTTAGTATT 2 466 0 CTTATTTTTC 0.743362 -135 GTCCTTCTTTTACACCTTTGTA 2 589 0 CCTTCTTTTA 0.798061 -12 CGTATATCCACCTTCTATGCATTATTATCT 3 254 0 CCTTCTATGC 0.963082 -253 CGAAATTCTTCTTTTTTTTCTTTTATATTT 3 344 0 CTTTTTTTTC 0.920933 -163 GTAGCACACTCTTTTTATTTCGTTTTGCTT 5 146 0 CTTTTTATTT 0.730828 -259 AAAAGAGTGTGCTACTATTCTATTATTGTC 5 161 1 GCTACTATTC 0.683561 -244 ATAGAGGTGTCCTTTTTTGCCATTTTTGTT 5 260 0 CCTTTTTTGC 0.967795 -145 GCTTCTATTTCCTGTTATGCGGGTAGCGGG 5 310 0 CCTGTTATGC 0.896203 -95 GATCATTATAGCTTCTATTTCCTGTTATGC 5 320 0 GCTTCTATTT 0.733749 -85 CCCAAATGAACCTTCTTATCGTCCTTTTTC 6 19 1 CCTTCTTATC 0.811063 -282 ********** Masking position 6 Map Score: 14.2209 Number of sites scoring better than the average of aligned sites = 5467 Number in coding regions = 3210 Number in noncoding regions = 2257 Number of orfs with sites within 600 bp upstream = 1602 Fraction of orfs with sites within 600 bp upstream = 0.257308 Motif number 3 AAGGAAGGCGCCTCTACCCTCTCAGCGCGCA 1 134 0 CCTCACCCTC 0.984137 -467 CGGTGTACAAACGCCAAGCTCCTGCTTTGTG 1 522 1 ACGCAAGCTC 0.939337 -79 ATTCATGGCGCCATCACCCGCAGGGAATATA 2 395 1 CCATACCCGC 0.957678 -206 ATTTTTTAGCCCTGTACGCTCGGATATTATA 2 555 0 CCTGACGCTC 0.92264 -46 ATAGAAATTACCGCAAAGCGCAAAGAGTTAT 3 442 1 CCGCAAGCGC 0.982888 -65 AAAAGAGTCACCGTCAGCCTCTCAAAACAAA 4 361 1 CCGTAGCCTC 0.948462 -43 AAAATAAGCCCCGCTACCCGCATAACAGGAA 5 301 1 CCGCACCCGC 0.995874 -104 CGTGTGCCGTACTCTACCCGCAGCAGCGTTG 6 78 0 ACTCACCCGC 0.976859 -223 GTTGTAGCGTACGCGAGGCGCCCAACATCTG 6 108 1 ACGCAGGCGC 0.970292 -193 CTTGAAGCCAACATGACGCTCTTTCACCTTT 6 252 1 ACATACGCTC 0.858268 -49 **** ****** Masking position 6 Map Score: 5.52482 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 147 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 CTTTTGCACGTTATTATGGGAATATCATTGCC 1 70 0 TTATATGGAA 0.798017 -531 CCACGCTATAATATAAAGATACAGGTACGGTA 1 243 1 ATATAAGTAC 0.880782 -358 AAAACAAGATATATTATGTGAAATTAAGTAGA 2 335 0 ATATATGGAA 0.965635 -266 CCCGCAGGGAATATAACGACAAGGCCGATACC 2 411 1 ATATACGCAA 0.941131 -190 GACAAGGCCGATACCACGGGAAAAATAGGGCG 2 428 1 ATACACGGAA 0.945474 -173 TCAGTTACTTATATAAAGTTAACCACTTGTTA 3 59 1 ATATAAGTAA 0.945002 -448 TCTTGCAAGAATATGAAGGTAATTTCACTTTA 4 168 1 ATATAAGTAA 0.944998 -236 CAAAAATCAAATATTACGTGAATACGTGAGAT 4 277 0 ATATACGGAA 0.988118 -127 TGCAACTGGAATATCAAGAGACTGAACATGAT 6 193 0 ATATAAGGAC 0.957515 -108 CATAATTTTGATATCACGCGAAA 6 288 1 ATATACGGAA 0.988116 -13 **** *** *** Masking position 6 Map Score: 4.83607 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 180 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 GCAGCCAATTCATGCAAATGACTGTAGTAT 1 17 0 CATGCAAATG 0.91347 -584 CCCATAATAACGTGCAAAAGTCCCTACGGT 1 82 1 CGTGCAAAAG 0.986824 -519 ACCCTCTCAGCGCGCACGTGCGGAGTGATC 1 120 0 CGCGCACGTG 0.902632 -481 GTTTCCAATCGGAGCACGTGAATTTGTAAC 1 412 1 GGAGCACGTG 0.837932 -189 CTCCATTGTTGATGCAAAAGTTGTAAATTT 2 156 1 GATGCAAAAG 0.934367 -445 TTAATACAAAGGTGTAAAAGAAGGAC 2 585 1 GGTGTAAAAG 0.822294 -16 TATGATCTTCGGTGCAAGATTTAGTGCCCT 3 153 1 GGTGCAAGAT 0.871773 -354 TAATAACAAGCGTGCAAAAGTTCATAATAT 3 396 1 CGTGCAAAAG 0.986824 -111 CCTTCATATTCTTGCAAGAGGAACTTATAT 4 157 0 CTTGCAAGAG 0.912836 -247 TTCACTTTATCGCGCAAGTGCATATTTCTG 4 191 1 CGCGCAAGTG 0.967106 -213 ATATTATTTGCAAGCAAAAGCAAAAGCGAG 5 105 1 CAAGCAAAAG 0.804035 -300 AAGCAGCACCGGTGCAACTGGAATATCAAG 6 207 0 GGTGCAACTG 0.9269 -94 TGAGAGGAAAGGTGAAAGAGCGTCATGTTG 6 260 0 GGTGAAAGAG 0.881041 -41 ********** Masking position 6 Map Score: 6.86014 Number of sites scoring better than the average of aligned sites = 1181 Number in coding regions = 912 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 6 CAGAAGCACGTTAAATTTATCGCAAAAAAG 1 345 1 TTAAATTTAT 0.872677 -256 TATTCAAAATTTCAATTTATTAGAAAAGCA 1 551 0 TTCAATTTAT 0.709958 -50 TAAGCGCTTCTTGTTTTTTTTTTGCACTTT 2 61 0 TTGTTTTTTT 0.728374 -540 TTTCGGAAGCTTATTTTTCTTTTAGTATTT 2 465 0 TTATTTTTCT 0.790884 -136 CACCTTTGTATTAATTTTTTAGCCCTGTAC 2 569 0 TTAATTTTTT 0.942842 -32 TAACAAGTGGTTAACTTTATATAAGTAACT 3 61 0 TTAACTTTAT 0.720862 -446 TTATATGTTTTTAAATTTTTCTGAATTTTG 3 316 0 TTAAATTTTT 0.922892 -191 TTTTTTTCTTTTATATTTATATGTTTTTAA 3 332 0 TTATATTTAT 0.859049 -175 CTCGAAATTCTTCTTTTTTTTCTTTTATAT 3 346 0 TTCTTTTTTT 0.831506 -161 GTTTTAGTTAATTTTTTTGCTATATAG 4 8 1 TTAATTTTTT 0.942842 -396 TGTTTCAGCTTTAATTTTTTTTATTTTGAA 4 42 0 TTAATTTTTT 0.942842 -362 CAAGAGGAACTTATATTTTTGAGAAGAACT 4 143 0 TTATATTTTT 0.911841 -261 GTAGCGGGGCTTATTTTTGTTTCTCAAAAT 5 288 0 TTATTTTTGT 0.790884 -117 ********** Masking position 6 Map Score: 4.42385 Number of sites scoring better than the average of aligned sites = 2323 Number in coding regions = 892 Number in noncoding regions = 1431 Number of orfs with sites within 600 bp upstream = 859 Fraction of orfs with sites within 600 bp upstream = 0.13797 Motif number 7 TATACAATACTACAGTCATTTGC 1 4 1 ACAATACTAC 0.887139 -597 CGGAGTGATCAGCCTACTACCGTAGGGACT 1 100 0 AGCCTACTAC 0.9524 -501 ACACGATTAAAGACCGTTACTAAATTTCCG 1 451 1 AGACCGTTAC 0.851906 -150 ACATTATTTCAGACTACCACTAATA 1 586 1 AGACTACCAC 0.9524 -15 TGAATCATTTAGAACACTACTAATGCTGGT 2 98 1 AGAACACTAC 0.982863 -503 GAAAACGGGAAGAAAACTACACTCGATTAT 2 271 1 AGAAAACTAC 0.935213 -330 AAGAATTTCGAGACTGCTACGAAAAGTGAA 3 364 1 AGACTGCTAC 0.977095 -143 TCCGAGGACTAGAACACTACTGCAAAGTAA 6 163 0 AGAACACTAC 0.982863 -138 ********** Masking position 9 Map Score: 2.15869 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 306 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 8 TAAGGTAAGGAAGGCGCCTCTACCCTCTCAG 1 140 0 AAGCGCCTCT 0.986673 -461 CGATAAATTTAACGTGCTTCTGATCAGGATT 1 336 0 AAGTGCTTCT 0.930961 -265 TCAACAGTGCTAAGCGCTTCTTGTTTTTTTT 2 70 0 TAGCGCTTCT 0.985873 -531 AACAATGGAGTAAGCCACTCTTCATTCTTGA 2 135 0 TAGCCACTCT 0.895852 -466 CCATGAATTAAATGCGACGCTATATAATAAG 2 372 0 AAGCGACGCT 0.84622 -229 CTCAAAAATATAAGTTCCTCTTGCAAGAATA 4 150 1 TAGTTCCTCT 0.886272 -254 CTGAGTTTACTATGTGCTTCGTCTGAAACCT 4 218 1 TAGTGCTTCG 0.927566 -186 GAAACAAAAATAAGCCCCGCTACCCGCATAA 5 295 1 TAGCCCCGCT 0.955384 -110 TATTTATTAATAGGTGCTTCTTCCAGGGTCT 5 381 0 TAGTGCTTCT 0.967513 -24 TGCCAGATGTTGGGCGCCTCGCGTACGCTAC 6 111 0 TGGCGCCTCG 0.936159 -190 ** ******** Masking position 10 Map Score: 2.56893 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 417 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 9 AAATAAGTCATCTCTCGAAATTGCCCCACC 3 213 0 TCTCTCGAAA 0.929618 -294 TATGCTAGTTCTTCTCAAAAATATAAGTTC 4 137 1 CTTCTCAAAA 0.973199 -267 TCGTCTGAAACCTCTCATTATCTACTTAAT 4 236 1 CCTCTCATTA 0.934275 -168 TCACCGTCAGCCTCTCAAAACAAAGAAAAA 4 368 1 CCTCTCAAAA 0.990783 -36 CTTATTTTTGTTTCTCAAAATAGAGGTGTC 5 279 0 TTTCTCAAAA 0.924477 -126 TTTCACCTTTCCTCTCATAATTTTGATATC 6 273 1 CCTCTCATAA 0.982941 -28 ********** Masking position 5 Map Score: 1.6415 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 295 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 AGAGGCGCCTTCCTTACCTTAGTAACCGAA 1 150 1 TCCTTACCTT 0.823262 -451 GACCGTTACTAAATTTCCGCTGAAAAGAAG 1 462 1 AAATTTCCGC 0.932627 -139 ATCGTCGTACACATTACCACAAGTACCATT 2 12 0 ACATTACCAC 0.914022 -589 CAAGGTTCGGTTATTTCCTCTACGTAACAA 2 521 1 TTATTTCCTC 0.750469 -80 AGATCATATAACCTTTCCGCATAAACAGAG 3 131 0 ACCTTTCCGC 0.967818 -376 TTGGACATAGAAATTACCGCAAAGCGCAAA 3 436 1 AAATTACCGC 0.932627 -71 CGATAAAGTGAAATTACCTTCATATTCTTG 4 173 0 AAATTACCTT 0.825639 -231 CGTGCATGATACATTTCCTTGTTCAAATTA 4 332 1 ACATTTCCTT 0.935268 -72 AGGGTCTAGTTCATTACCTCCCCTAAATAT 5 358 0 TCATTACCTC 0.958655 -47 ACGCTCTTTCACCTTTCCTCTCATAATTTT 6 267 1 ACCTTTCCTC 0.973304 -34 ********** Masking position 5 Map Score: 2.62561 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 775 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 11 TTATTATGGGAATATCATTGCCAACGCAAC 1 62 0 AATATCATTG 0.955487 -539 CAGGTACGGTAATACCATCCATATCCAAGA 1 264 1 AATACCATCC 0.929186 -337 AAAAGAGTATAGTATCATCTGAATCATTCG 1 494 1 AGTATCATCT 0.892784 -107 CATTACCACAAGTACCATTG 2 1 0 AGTACCATTG 0.922566 -600 TGGCATATATAGTATAATCGAGTGTAGTTT 2 284 0 AGTATAATCG 0.857361 -317 GCTTGCAAATAATATCCTCGTGACCTCGAG 5 90 0 AATATCCTCG 0.935838 -315 ACCTCCCCTAAATATCATTCTCAGATCATT 5 343 0 AATATCATTC 0.900573 -62 GTTGCATACCAATATCATCGCACATAATGA 6 52 0 AATATCATCG 0.982115 -249 ********** Masking position 4 Map Score: 0.566448 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 570 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 12 ATTGCAAACGGTGCCTGGCAATCCTGATCAG 1 317 1 GTCCTGGCAA 0.935756 -284 TATTTAATGCGTTCCTTGCAACCTTCTATTT 2 193 1 GTCCTTGCAA 0.986544 -408 CGACAATGAAGTTCTTGGCAAGGTTCGGTTA 2 503 1 GTCTTGGCAA 0.986544 -98 ATCTGGCAAAGTACCTGGTAATTGGTATTTT 6 134 1 GTCCTGGTAA 0.970088 -167 ** ******** Masking position 6 Map Score: 0.225637 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 AAAATCTCAGTTCGCCCTTTTTTGCGATAA 1 361 0 TTCGCCCTTT 0.964573 -240 TTGTTTTTTTTTTGCACTTTTGCTTTTATT 2 51 0 TTTGCACTTT 0.865831 -550 CAAGAAGCGCTTAGCACTGTTGAATCATTT 2 78 1 TTAGCACTGT 0.979697 -523 TATTAATTTTTTAGCCCTGTACGCTCGGAT 2 561 0 TTAGCCCTGT 0.986779 -40 ACTATTATTGTTAGCTCTGTTTATGCGGAA 3 117 1 TTAGCTCTGT 0.979697 -390 GTACTACTATTTCTCTCTGTCATACGTGCA 4 308 1 TTCTCTCTGT 0.88961 -96 ********** Masking position 8 Map Score: 0.427055 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 178 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 ********** No masking Map Score: -3.84871e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -3.84871e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0