AlignACE version 2.2 July 7, 1998 AlignACE -jTHI.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 Purged sequences: YFL058W 600 bp YFL058W THI5 1-1023 a thiamine regulated pyrimidine precursor biosynthesis enzyme YJR156C 600 bp YJR156C THI11 1-1023 Thiamine biosynthetic enzyme Input sequences: #1 YBR240C 600 bp YBR240C THI2 1-1353 Probable Zn-finger protein #2 YDL080C 479 bp YDL080C THI3 1-1830 positive regulatory factor with thiamin pyrophosphate-binding motif for thiamin metabolism #3 YGR144W 600 bp YGR144W THI4 1-981 component of the biosynthetic pathway producing the thiazole precursor of thiamine #4 YLR237W 300 bp YLR237W THI7 1-1797 thiamine transporter #5 YNL332W 600 bp YNL332W THI12 1-1023 A thiamine regulated gene, homologous to nmt1a in Schizosaccharomyces pombe. A proposed biosynthetic enzyme involved in pyrimidine biosynthesis pathway above the hydroxymethyl-pyrimidine precursor leading to the thiamine moiety. Three copies of this gene are present within the yeast genome, with a single copies on chromosome VI (THI5), chromsome X (THI11) and chromosome XIV (THI12), all appear to be functional. #6 YOR143C 374 bp YOR143C THI80 1-960 Thiamin pyrophosphokinase #7 YPL214C 422 bp YPL214C THI6 1-1623 TMP pyrophosphorylase, hydroxyethylthiazole kinase Motif number 1 TGCAGGTATAATATATACATATATATATATA 1 393 1 ATATATAATA 0.9875 -208 ATATATATATATATATATATATATATGTATA 1 406 0 ATATATAATA 0.9875 -195 ATATATATATATATATATATATATATATATG 1 417 1 ATATATAATA 0.9875 -184 ATATATATATATATATATGTACAATTTGTAT 1 429 1 ATATATAGTA 0.931327 -172 ATTTCACCACGTATATATATAGCCTATATAT 1 561 1 GTATATAATA 0.961477 -40 TCTAGTGCGGATATATATATAGGCTATATAT 1 575 0 ATATATAATA 0.9875 -26 AACTACCCAGATATATAAATATTGGAATAAA 3 485 1 ATATATAATA 0.9875 -116 TGTATCTCACATATATACCTAATAAAAAAAA 4 153 0 ATATATACTA 0.931327 -148 TTTAATTCTCATATATACAAACTGGCTGAAT 5 39 0 ATATATAAAA 0.893696 -562 AATCGTTCACGTATATACATATGTATGTTTA 5 124 1 GTATATAATA 0.961477 -477 TTGTAAACACATATATATATACGTAAACATA 5 147 0 ATATATAATA 0.9875 -454 CTACTACTTTATATATCAATAAATTCTGCAA 6 89 1 ATATATCATA 0.931327 -286 TCAATACTACATATATTTATAGCGGCAACGC 7 306 1 ATATATTATA 0.901481 -117 ******* *** Masking position 5 Map Score: 21.4816 Number of sites scoring better than the average of aligned sites = 3594 Number in coding regions = 203 Number in noncoding regions = 3391 Number of orfs with sites within 600 bp upstream = 427 Fraction of orfs with sites within 600 bp upstream = 0.0685834 Motif number 2 AATTAAATGAAGGAAAGAGGACGGTCGTTA 2 117 0 AGGAAAGAGG 0.964024 -363 GTAAAGTATGAAGAAAGGGAAATTTGTTCA 2 314 0 AAGAAAGGGA 0.832081 -166 ATAAAACGAAAAAAAAAAGGTTTGAAAGAA 2 425 1 AAAAAAAAGG 0.966609 -55 GTAAATTTGTAAAAAAAGGGTAAAAAACGG 3 96 0 AAAAAAAGGG 0.935955 -505 GGACGTCTACAGGAAAATGGGGTGGTAAAT 3 224 0 AGGAAAATGG 0.908531 -377 TGAAAACTTCAGAAAAAGGGCTTAAAGTAG 3 265 0 AGAAAAAGGG 0.940664 -336 TCTAGATGATAAGAAAGAGAACATAAAAGA 3 541 0 AAGAAAGAGA 0.907543 -60 GTAGTTGAAGAGAAAAGAGGAAGAGAATAG 4 73 1 AGAAAAGAGG 0.949954 -228 AATAGAAAAAAAAAAAAAGCGAAATTTTTA 4 98 1 AAAAAAAAGC 0.885595 -203 ATACCTAATAAAAAAAAAGAAATTACATTA 4 140 0 AAAAAAAAGA 0.920022 -161 GAAAACTTGAAAAAAAATGGCTGATGGGAA 6 222 1 AAAAAAATGG 0.866418 -153 CATCTATGATAAGAAAAAGACTAATAGGGC 7 116 1 AAGAAAAAGA 0.941993 -307 AGTTAATTATAGGAAAAAGCCCTATTAGTC 7 134 0 AGGAAAAAGC 0.922205 -289 AACCAGGAACAAAAAAAAGATAGATAAGGT 7 190 1 AAAAAAAAGA 0.920022 -233 TGCATATTATAGGAAAAAGGCAATCGTAAG 7 251 1 AGGAAAAAGG 0.97794 -172 ********** Masking position 5 Map Score: 16.4122 Number of sites scoring better than the average of aligned sites = 2997 Number in coding regions = 1443 Number in noncoding regions = 1554 Number of orfs with sites within 600 bp upstream = 1090 Fraction of orfs with sites within 600 bp upstream = 0.175072 Motif number 3 GGCTCAGGAAAATATGCAGATAGACGCTCG 1 124 0 AATATGCAGA 0.951103 -477 GCAGTCCTGCCGGATGCATTTATGCCGCTA 1 174 0 CGGATGCATT 0.895273 -427 CATTTTGGCACGGATGCATTCGCAGATTGG 1 264 0 CGGATGCATT 0.895273 -337 ACGCTTTTAAAGTGTGCAGAAATTGTTATA 1 522 0 AGTGTGCAGA 0.959103 -79 ACTATTACATAATATGCATTTGTCTTCTGC 2 51 1 AATATGCATT 0.781572 -429 GCTGTGTATCTGTGTGCAGAAGACAAATGC 2 66 0 TGTGTGCAGA 0.881107 -414 AGATACACAGCGTATGCAGTTAACCTAACG 2 85 1 CGTATGCAGT 0.966993 -395 CGTATGACTGCATATGCAGAACCTTGGCAA 2 199 1 CATATGCAGA 0.947891 -281 TATGCCGTAAAGTATGAAGAAAGGGAAATT 2 320 0 AGTATGAAGA 0.816751 -160 TAAGGCAAATAGTATGCATACCTTTTTCGG 4 43 1 AGTATGCATA 0.964145 -258 GCTTAATGCAAGGTTGCAGAATTTATTGAT 6 103 0 AGGTTGCAGA 0.863268 -272 GAAGGCTTGTTGGATGCAGAGTATGCGATT 7 66 1 TGGATGCAGA 0.940127 -357 TTTTTCCTATAATATGCATAAATTATGTTG 7 239 0 AATATGCATA 0.885443 -184 ********** Masking position 8 Map Score: 7.15374 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 727 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 4 CGCCACACGGATCTCATACAACAGCAATCCATTTGGTTT 1 17 0 ACACAACATC 0.615528 -584 AAAGAGTAAAATATAATAAAACGAAAAAAAAAAGGTTTG 2 410 1 AAAAAACAAA 0.971752 -70 AAAAGGTTTGAAAGAACATAACTACTAAAACGCACCGTC 2 439 1 AAATAACAAA 0.758989 -41 TTGTAAAAAAAGGGTAAAAAACGGTTAATCCTGAAGGGG 3 81 0 AGAAAACAAT 0.640183 -520 ATAATTATGCACGTTAAAAAACATACATAATTGATAGTA 3 344 1 AGAAAACATA 0.9079 -257 TCTAGAAATAATAAATCACAACCAAAAAAATCAACTAAC 3 565 1 AAACAACAAA 0.942642 -36 AAGAGAATAGAAAAAAAAAAAAAGCGAAATTTTTACATC 4 93 1 AAAAAAAAAA 0.64518 -208 ATATTATGTAGCACAACATGGAAACCATATTCAG 5 6 1 AGACAACAAA 0.908539 -595 TAAGACTGATAGGATGAAAAAGTTTTAACGTTTAATTCT 5 61 0 AGAAAAGAAC 0.597506 -540 ACACATATATATATACGTAAACATACATATGTATATACG 5 133 0 AATAAACATA 0.685175 -468 ATATACATGCATATTTGTAAACACATATATATATACGTA 5 153 0 AATAAACATA 0.685175 -448 TCATTGCATCATAGCCAAAAACCGATAAATGCATTAATG 5 305 0 AAAAAACAAA 0.971752 -296 TTGCGACGACAGCAAACAAAACATATAAAAACCTCGTAT 5 474 1 ACAAAACAAA 0.954115 -127 TATAAAATTGAAAAGGTAAAAGAACGAAAGAATGGACAA 5 536 0 AAAAAAGAAA 0.87841 -65 AATTTTATAAAAATACCACAACAACAATAAACACACTTC 5 566 1 AAACAACATA 0.886249 -35 CTCATAGTGCATATTTCAAAACAGCGAAAAATGCAAAAT 6 179 1 AAAAAACAAA 0.971752 -196 AAAATGCAAAATATGCGAAAACTTGAAAAAAAATGGCTG 6 206 1 AAAAAACAAA 0.971752 -169 GGTCACAAAGAACAATAAAAAGCTGAATATCACTGCT 6 348 1 ACAAAAGATA 0.674287 -27 GTCGAAAATCAACTTTGAAAACCAGGAACAAAAAAAAGA 7 171 1 ACAAAACAAC 0.876067 -252 * * ***** *** Masking position 10 Map Score: 5.98704 Number of sites scoring better than the average of aligned sites = 2977 Number in coding regions = 1698 Number in noncoding regions = 1279 Number of orfs with sites within 600 bp upstream = 910 Fraction of orfs with sites within 600 bp upstream = 0.146161 Motif number 5 TCAAGCTAAATGCCGTTTCATTTTGGCACGGAT 1 279 0 TCCTTTCATT 0.979869 -322 TTAAAAGCGTTTTCATTTCATTTCACCACGTAT 1 542 1 TTCTTTCATT 0.974232 -59 CTTTCCTTCATTTAATTTCACTTGCTGCTTTTC 2 130 1 TTATTTCATT 0.972143 -350 TACCAGATTCTTTACTATCAATTATGTATGTTT 3 362 0 TTATATCATT 0.830806 -239 AATTGATTTTTTGATTTTCAATTTATGAACTAC 3 458 1 TGATTTCATT 0.927326 -143 TCTATTGTAATGTAATTTCTTTTTTTTTATTAG 4 133 1 TTATTTCTTT 0.830806 -168 CGGGAAGCTTTACCATTTCATTTCCTATTCCAG 4 198 1 TCCTTTCATT 0.979869 -103 ATGCAATGAGTACAGTTCCAATTGAACGGCTCA 5 335 1 TCATTCCATT 0.903565 -266 TTCGTTCTTTTACCTTTTCAATTTTATAAAAAT 5 547 1 TCCTTTCATT 0.979869 -54 TTCCAAGTCCTGTAGTTTCACTTCGACCTGTTG 7 34 1 TTATTTCATT 0.972143 -389 * ** ***** ** Masking position 6 Map Score: 5.80947 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 465 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 6 TTATACCTGCAAGCAATTGCACGCGAGTAC 1 374 0 AAGCAATTGC 0.96133 -227 CTATTCACTAAAGCAATTGAGTGCCGATCC 3 174 0 AAGCAATTGA 0.940512 -427 GAAATGGATCATGAAATTGATTTTTTGATT 3 444 1 ATGAAATTGA 0.924324 -157 ATTGATATAATGCAATTGGCTCTACAGTC 4 282 0 ATGCAATTGG 0.975745 -19 TTTTAGGGGGACGAGATTGGCGCGTTAGTG 5 243 1 ACGAGATTGG 0.867857 -358 TATTCAGATTATGAAAATGGTGCTGTTATA 5 421 1 ATGAAAATGG 0.875195 -180 CTGTCGTCGCAAGAGATTGATGTTGCTTAT 5 456 0 AAGAGATTGA 0.875912 -145 CACTGATATGAAATTGCGTGCATCGTT 6 8 1 ATGAAATTGC 0.95051 -367 ACCTTGCATTAAGCAAATGCAGCACAATCC 6 119 1 AAGCAAATGC 0.873587 -256 GATGCAGAGTATGCGATTGGCCTAATATAA 7 78 1 ATGCGATTGG 0.966266 -345 ********** Masking position 6 Map Score: 3.986 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 741 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 AAAGAGAACATAAAAGATATTTCCCGACTACTT 3 525 0 TAAAATTTTC 0.908081 -76 TACAGTCCTTTAAATGATGTTGCGATGAATCTC 4 256 0 TAAAATTTGC 0.977374 -45 CTCGTCCCCCTAAAAAATTAAGCCGACTCATCG 5 225 0 TAAAATAAGC 0.925478 -376 GTGACAACATTAATGCATTTATCGGTTTTTGGC 5 298 1 TAATATTATC 0.852999 -303 CACGTATGTATAATAAATATAGCATGGTAGTGC 6 45 1 TAATATTAGC 0.962077 -330 AAGGCGTTTATAAAAGATTTAGCTTCTTAAGTA 6 274 1 TAAAATTAGC 0.985775 -101 ATAATATGCATAAATTATGTTGCCCTAAAAGAG 7 228 0 TAAAATTTGC 0.977374 -195 CTGTTTGATTTAAATAATTTAGCTTCAGAGTGA 7 395 0 TAAAATTAGC 0.985775 -28 **** ** **** Masking position 7 Map Score: 3.19127 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 111 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TTGTATATTCCTTTTCTCGGCAGTCCTGCC 1 193 0 CTTTTCTCGG 0.987706 -408 AGTGGGTGCACCTTTCTCGGTCGGAATTAT 1 464 1 CCTTTCTCGG 0.987455 -137 TCACTTGCTGCTTTTCTAGGCAGCGGTCGC 2 147 1 CTTTTCTAGG 0.980636 -333 TACTTTAAGCCCTTTTTCTGAAGTTTTCAT 3 266 1 CCTTTTTCTG 0.847189 -335 AGTATGCATACCTTTTTCGGGTAGTTGAAG 4 53 1 CCTTTTTCGG 0.98025 -248 CATGTATATTCTTTTCGAGGAAGATTATTA 5 183 1 CTTTTCGAGG 0.930808 -418 AGTCGGCTTAATTTTTTAGGGGGACGAGAT 5 230 1 ATTTTTTAGG 0.780988 -371 GTTTATTTCACTCTTTTAGGGCAACATAAT 7 218 1 CTCTTTTAGG 0.894533 -205 ********** Masking position 5 Map Score: 3.11751 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 210 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 9 TACTCGCGTGCAATTGCTTGCAGGTATAATAT 1 375 1 CAATTGTGCA 0.833025 -226 AGAACCTTGGCAACTGTAAGAACTCCTATGTT 2 216 1 CAACTGAGAA 0.962525 -264 GTGCTTTTAGCAACTGTTTGCAATAAAGAAAC 2 245 0 CAACTGTGCA 0.980728 -235 TTGAACTTGGTAACTGATAGAATACCAGATTC 3 385 0 TAACTGTGAA 0.920798 -216 CTTTTCTCTTCAACTACCCGAAAAAGGTATGC 4 58 0 CAACTACGAA 0.970968 -243 TCATATATACAAACTGGCTGAATATGGTTTCC 5 30 0 AAACTGCGAA 0.919325 -571 ACGAATTATTCAACTAGCAGAAGGCTTGAAAT 5 383 1 CAACTACGAA 0.970968 -218 GAAATAAAGGCAACTATTAGAAGGAATTTAGG 6 147 0 CAACTATGAA 0.971527 -228 AACAAGCCTTCAACAGGTCGAAGTGAAACTAC 7 45 0 CAACAGTGAA 0.942568 -378 ****** * *** Masking position 3 Map Score: 2.37369 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 389 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 GCGTCTATCTGCATATTTTCCTGAGCCCAA 1 127 1 GCATATTTTC 0.943519 -474 ATATATATATGTATATATTATACCTGCAAG 1 391 0 GTATATATTA 0.729328 -210 GAAGACAAATGCATATTATGTAATAGTAAT 2 48 0 GCATATTATG 0.906664 -432 TCGCCTAATAGCATATAATAATCTTCCTCG 5 198 0 GCATATAATA 0.745019 -403 TGAATAATTCGTATATTTCATAGTTCATGA 5 365 0 GTATATTTCA 0.910384 -236 GATTGATGTTGCTTATTTTGCTATAACAGC 5 442 0 GCTTATTTTG 0.858178 -159 TAAAGTAGTAGTATATTTCCCCGCACTACC 6 70 0 GTATATTTCC 0.851802 -305 TCCTCATAGTGCATATTTCAAAACAGCGAA 6 177 1 GCATATTTCA 0.965095 -198 TCAAGTTTTCGCATATTTTGCATTTTTCGC 6 202 0 GCATATTTTG 0.960609 -173 GATAGATAAGGTTTATTTCACTCTTTTAGG 7 208 1 GTTTATTTCA 0.71596 -215 CATAATTTATGCATATTATAGGAAAAAGGC 7 242 1 GCATATTATA 0.921733 -181 ********** Masking position 5 Map Score: 2.1266 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 663 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 11 ATACTTTCTCTTTATGAGCATTCCTCAACAGG 3 143 1 TTTATGACAT 0.981283 -458 GATCGGACATTTTATGAAAACTTCAGAAAAAG 3 277 0 TTTATGAAAT 0.854108 -324 CGTAAATTTTTTTACGAGCACTAATAGAAATG 3 418 1 TTTACGACAT 0.932997 -183 AAAAATCAATTTCATGATCCATTTCTATTAGT 3 437 0 TTCATGACCT 0.966776 -164 TATTTCATAGTTCATGAGCCGTTCAATTGGAA 5 350 0 TTCATGACCT 0.966776 -251 TATTATCATCTTCATGAACAATATTCTTGTCC 5 510 1 TTCATGACAT 0.980911 -91 TTTATTGTTCTTTGTGACCAATTGTGATCTAC 6 335 0 TTTGTGACAT 0.932996 -40 AATATCAGTTTTTATAAGCAATA 7 2 0 TTTATAACAT 0.854108 -421 ******* ** * Masking position 7 Map Score: 0.945263 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 136 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: 1.26075e-11 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 13 ********** No masking Map Score: 1.26075e-11 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 14 CTATTTTGGCCCCGGCAGTACAAGCGGTAG 1 66 0 CCCGGCAGTA 0.988694 -535 TATTCCTTTTCTCGGCAGTCCTGCCGGATG 1 188 0 CTCGGCAGTC 0.966108 -413 TATAGCTCTAACCCGTAGTATTAGTTCCCC 1 496 0 ACCCGTAGTA 0.878331 -105 CTATATATATATCCGCACTAGAACCAA 1 584 1 ATCCGCACTA 0.953522 -17 CAGAATTATTCCCCGCCGTAAATTTGTAAA 3 113 0 CCCCGCCGTA 0.972483 -488 CTCAACAGGGATCGGCACTCAATTGCTTTA 3 166 1 ATCGGCACTC 0.913122 -435 TAGTATATTTCCCCGCACTACCATGCTATA 6 62 0 CCCCGCACTA 0.988702 -313 ********** Masking position 9 Map Score: 0.292262 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 140 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 ********** No masking Map Score: 1.26075e-11 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