AlignACE version 2.2 July 7, 1998 AlignACE -jHIS.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 YBR248C 416 bp YBR248C his7 1-1659 glutamine amidotransferase:cyclase #2 YCL030C 300 bp YCL030C his4 1-2400 histidinol dehydrogenase #3 YER055C 600 bp YER055C his1 1-894 ATP phosphoribosyltransferase #4 YFR025C 300 bp YFR025C his2 1-1008 Histidinolphosphatase #5 YIL116W 600 bp YIL116W his5 1-1158 histidinol-phosphate aminotransferase #6 YIL020C 300 bp YIL020C his6 1-786 phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase #7 YOR202W 300 bp YOR202W his3 1-663 imidazoleglycerol-phosphate dehydratase Motif number 1 CTTTGCCTTTAAAAATTGAGTTTCTAGTTA 1 102 0 AAAAATTGAG 0.82238 -315 TTCTGCAAAAAAAAATTGAGTCATATCGTA 1 180 1 AAAAATTGAG 0.82238 -237 GTGGAGAGAGAGAAAAATAATCCCAAAGCT 1 209 0 AGAAAAATAA 0.763342 -208 GGTGATCATGAAAAAATGAAAAATTCATGA 1 248 1 AAAAAATGAA 0.913049 -169 CAGGTTTTAAAAGAAAAGAGGCAGCTATTG 1 342 1 AAGAAAAGAG 0.78946 -75 TTACAAGTAAAGAAAAAGAGA 1 406 1 AGAAAAAGAG 0.96279 -11 TATTCAGAAAAAAAATTTTGTAAAC 2 286 0 AGAAAAAAAA 0.900718 -15 CCAAAAAGAAAAAAAAAAAGTAAGAATGCA 3 131 1 AAAAAAAAAG 0.960559 -470 ACTCCTTGTCAAAAAATTAATTAAAATATT 3 258 1 AAAAAATTAA 0.69862 -343 CCAACGATTGAAAAAAAAAGCTTCCAAGTG 3 399 1 AAAAAAAAAG 0.960559 -202 CTTTGAAAATAGAAAAGAAAGGATAGGTTT 3 561 1 AGAAAAGAAA 0.708924 -40 GATTTGACAAAAAAAATAAAAAAATTTAAA 4 138 0 AAAAAATAAA 0.867021 -163 TGCGGCAGAAAAAAAAAAAATTGATGAAGT 5 47 0 AAAAAAAAAA 0.932217 -554 ATAACTTTGCAAAAATAAAGGGTAAATGGT 5 88 1 AAAAATAAAG 0.858436 -513 GAGACTATTCAAAAAAGGAGTCAAGCATTG 5 237 1 AAAAAAGGAG 0.913269 -364 AACAGATCCAAGAAAAAAAAGCACTAACTA 5 380 0 AGAAAAAAAA 0.900718 -221 CAAGAGTAATAGAAAAAGAAAATTGCGGGA 7 86 0 AGAAAAAGAA 0.935945 -215 CGAGGCATAAAAAAATATAGAGTGTACTAG 7 123 0 AAAAATATAG 0.683136 -178 GCTAGGTGGAAAAAAAAAAATGAAAATCAT 7 156 0 AAAAAAAAAA 0.932217 -145 TCGCTAAGAAAAAAAAAGAGTCATCCGCTA 7 182 0 AAAAAAAGAG 0.975139 -119 AGAATATACTAAAAAATGAGCAGGCAAGAT 7 267 1 AAAAAATGAG 0.948967 -34 ********** Masking position 5 Map Score: 23.2891 Number of sites scoring better than the average of aligned sites = 14775 Number in coding regions = 2901 Number in noncoding regions = 11874 Number of orfs with sites within 600 bp upstream = 2695 Fraction of orfs with sites within 600 bp upstream = 0.432862 Motif number 2 GTGGATGTTATACTATCAGTTACTCTTCTGCAAAAAA 1 155 1 TACATTCTCT 0.949477 -262 TTATGTATGTTTCGATGTCTGACTCTTTTCTCATGAA 1 271 0 TTCATGCTCT 0.996286 -146 ATACTGCTACTTCAATAGCTGCCTCTTTTCTTTTAAA 1 347 0 TTCATGCTCT 0.996286 -70 GGTTGCCGGGTTACATCTCGTTCTCTTTACGTTCACA 3 186 0 TTAATTCTCT 0.921325 -415 AGGTCTCCGGTTCGATTCCGGACTCGTCCATTTAAAT 4 108 1 TTCATGCTCT 0.996286 -193 CATTAATTATTTCAATGCTTGACTCCTTTTTTGAATA 5 242 0 TTCATGCTCT 0.996286 -359 GTTGACTCACTTCAATTGATGTTTCTTACCCTGACAT 5 407 1 TTCATGTTCT 0.967699 -194 AAAACAGTTTTTCCATTGATTACTCTTAATTTGTTTC 5 527 1 TTCATTCTCT 0.990554 -74 *** ** * *** * Masking position 5 Map Score: 9.14291 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 114 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TTATACTATCAGTTACTCTTCTGCAAAAAA 1 162 1 AGTTACTCTT 0.836187 -255 TGTTTCGATGTCTGACTCTTTTCTCATGAA 1 271 0 TCTGACTCTT 0.876343 -146 TGACTCTAATAGTGACTCCGGTAAATTAGT 2 56 1 AGTGACTCCG 0.937362 -245 AAGAAAAGGATATGACTATGAACAGTAGTA 2 151 1 TATGACTATG 0.830515 -150 TAAACTATTGTATTACTATTACACAGCGCA 2 261 0 TATTACTATT 0.655395 -40 CTAGTGGTTATGTGACTATGTGAACGTAAA 3 168 1 TGTGACTATG 0.871302 -433 TTGATAACAGCGTGACTCTTCCCGGAAATT 3 317 1 CGTGACTCTT 0.940655 -284 AACTTTGGCATTTTACTCCTATTAACGGTT 3 526 1 TTTTACTCCT 0.785876 -75 AAACCTGTTTGATGACTACTTCATCAATTT 5 30 1 GATGACTACT 0.835435 -571 TATTTGATCATGTGACTACGATCCGGGTGA 5 209 1 TGTGACTACG 0.885101 -392 TATTTCAATGCTTGACTCCTTTTTTGAATA 5 242 0 CTTGACTCCT 0.855302 -359 GGAAAAAACAATTGACTCCTAACAATTAAC 5 290 0 ATTGACTCCT 0.876997 -311 TTTTTCCATTGATTACTCTTAATTTGTTTC 5 534 1 GATTACTCTT 0.816906 -67 AATTATTCCGTATGACTCTGCACACTAGAC 6 205 0 TATGACTCTG 0.948331 -96 GATACCTGGCAGTGACTCCTAGCGCTCACC 7 13 0 AGTGACTCCT 0.956053 -288 TTTCTTTTTCTATTACTCTTGGCCTCCTCT 7 95 1 TATTACTCTT 0.876902 -206 CCACCTAGCGGATGACTCTTTTTTTTTCTT 7 177 1 GATGACTCTT 0.943539 -124 ********** Masking position 5 Map Score: 10.5378 Number of sites scoring better than the average of aligned sites = 1395 Number in coding regions = 1125 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 4 GATCACCTAATTAGCCGTGGAGAGAGAGAAAAA 1 222 0 TTACGTGAGA 0.841059 -195 TTTTAATTATTTACAAGTAAAGAAAAAGAGA 1 396 1 TTAAGTAAGA 0.672959 -21 GTCATTCGATATAGAAGGTAAGAAAAGGATATG 2 132 1 ATAAGGAAGA 0.879596 -169 TCTTTTTGGCTTTTATTGTAAGACTGATATGCA 3 107 0 TTTATGAAGA 0.754131 -494 GAGAGGTTGTTTAGCATGCGAGGTATTAGACTC 3 229 1 TTACTGGAGG 0.875536 -372 AAATGAAAGAATTTCCGGGAAGAGTCACGCTGT 3 323 0 ATTCGGAAGA 0.939397 -278 GCGCGCTCCCTTAGCATGGGAGAGGTCTCCGGT 4 86 1 TTACTGGAGA 0.920872 -215 AAAATGTGTTTGAAAGGGAAAGATTGTACGGGA 4 235 0 TGAAGGAAGA 0.920555 -66 TATTAGTTACTGTCCAGGAAAGGTCTCAATATA 5 150 0 TGTCGGAAGG 0.936961 -451 AAGTATGTCATGTCAGGGTAAGAAACATCAATT 5 420 0 TGTAGGAAGA 0.887046 -181 TTCAAGTTATATAACGTGAGAGATAAAATATCA 5 452 0 ATACTGGAGA 0.816004 -149 TACTGCTGGTTTAGCAGGAAACAAATTAAGAGT 5 548 0 TTACGGAACA 0.834261 -53 ATATTGTGAATTTGCAGGCGAGGATTCTCAAAT 6 232 0 TTTCGGGAGG 0.952822 -69 GAAAAAGAAAATTGCGGGAAAGGACTGTGTTAT 7 72 0 ATTCGGAAGG 0.903574 -229 TACTAAAAAATGAGCAGGCAAGATAAACGAAGG 7 273 1 TGACGGAAGA 0.973176 -28 *** * ** **** Masking position 11 Map Score: 4.14022 Number of sites scoring better than the average of aligned sites = 2331 Number in coding regions = 1733 Number in noncoding regions = 598 Number of orfs with sites within 600 bp upstream = 497 Fraction of orfs with sites within 600 bp upstream = 0.0798265 Motif number 5 GTAGAGGAAAGAATGTACGTTACATATATCATTAAA 1 18 0 GAATGTACAA 0.957605 -399 TCCATATCTATTATATACACAGTATACTACTGTTCA 2 169 0 TTATATACAA 0.883533 -132 ATATTTTTATGTATGTACAACACACATCGGAGGTGA 2 214 0 GTATGTACAA 0.984504 -87 TTGAAGTTTTGTATATACCATAGAGATTATCTTTGA 3 21 0 GTATATACAA 0.985493 -580 TTTCAGGCGAGTATATTCTGCAAAAATATTTTATAA 3 450 0 GTATATTCAA 0.938351 -151 TGAACTGCAAGTATTTACCGTCTAAACTTTGGCATT 3 502 1 GTATTTACAA 0.924094 -99 GGGAAATGGAAAATGTACATATAATATCCAGTATCA 4 203 0 AAATGTACAA 0.892453 -98 TGTAATTTTAATATATACGGCACACACGTACTGCTG 5 573 0 ATATATACAA 0.961478 -28 CTTTTGGGTCATTTGTACTCTCAATATTGTTATAAC 6 49 1 ATTTGTACAA 0.839481 -252 AAGGCTGGGGGTATATACTAGAAAAAA 6 284 1 GTATATACAA 0.985493 -17 TCACATAATGAATTATACATTATATAAAGTAATGTG 7 221 1 AATTATACAA 0.66535 -80 TCATTTTTTAGTATATTCTTCGAAGAAATCACATTA 7 250 0 GTATATTCAA 0.938351 -51 ******** * * Masking position 14 Map Score: 4.71207 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 303 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 6 CCAAAGCTACGATATGACTCAATTTTTTTTTG 1 185 0 GATGACTCAA 0.99009 -232 CTAGGCAGTCGAACTGACTCTAATAGTGACTC 2 42 1 GATGACTCTA 0.985557 -259 GTAAGAAAAGGATATGACTATGAACAGTAGTA 2 149 1 GATGACTATG 0.909074 -152 ACACACATCGGAGGTGAATATAACGTTCCATA 2 199 0 GATGAATATA 0.826944 -102 TCCAACGGTAGAGGTGACTCACTTGGAAGCTT 3 416 0 GATGACTCAC 0.958919 -185 TAGATAGAGAGATTTGACAAAAAAAATAAAAA 4 146 0 GATGACAAAA 0.898117 -155 AATGGAATCTGAGATGACTAAACTACCAATTT 5 324 1 GATGACTAAA 0.984289 -277 AACATCAATTGAAGTGAGTCAACAGATCCAAG 5 398 0 GATGAGTCAA 0.968184 -203 TTTGAGCGATGAGATGAGTATACATTAACGAT 6 95 0 GATGAGTATA 0.928743 -206 CTGCACACTAGACATGGCTCAATCTTGGCAAT 6 186 0 GATGGCTCAA 0.954202 -115 ** ******** Masking position 5 Map Score: 6.24204 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 149 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 GTAGAGGAAAGAATGTACGTTACATATATCAT 1 22 0 GAATGTACTA 0.895333 -395 GTAGTATACTGTGTATATAATAGATATGGAAC 2 175 1 GTGTATATAA 0.868055 -126 ATATTTTTATGTATGTACAACACACATCGGAG 2 218 0 GTATGTACAA 0.970921 -83 AATCTCTATGGTATATACAAAACTTCAAAAAT 3 29 1 GTATATACAA 0.97584 -572 CGTGTGTGCCGTATATATTAAAATTACACT 5 581 1 GTATATATAA 0.888596 -20 GCGATGAGATGAGTATACATTAACGATGGCAG 6 90 0 GAGTATACTA 0.895369 -211 AAGGCTGGGGGTATATACTAGAAAAAA 6 284 1 GTATATACAA 0.975908 -17 AAAAAATATAGAGTGTACTAGAGGAGGCCAAG 7 112 0 GAGTGTACAA 0.95721 -189 TTTCTTCGAAGAATATACTAAAAAATGAGCAG 7 258 1 GAATATACAA 0.970481 -43 ******** * * Masking position 6 Map Score: 3.49637 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 271 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 CTAAACACAATTAAATAATACCGAATTGGCAGTGG 1 53 0 TAATATACCA 0.801644 -364 TTCTTTACTTGTAAATAATTAAAAAACCTAAACTG 1 385 0 GAATATTAAA 0.970675 -32 CATGGGTTTAGCAATTAATTAACTAATTTACCGGA 2 72 0 GAATATTAAA 0.970675 -229 CAATGACTTTGCAACTAATAAATTAACTAATAAAT 3 285 0 GAATATAAAA 0.965343 -316 CTCTACCGTTGGAACTTATAAAATATTTTTGCAGA 3 435 1 GAATATAAAA 0.965344 -166 AAAATAAAGGGTAAATGGTTAAAAATTGTTATCAT 5 99 1 GAATGTTAAA 0.861754 -502 TTCCTGGACAGTAACTAATACAGAAGCCATTGGTA 5 163 1 GAATATACAA 0.945788 -438 AGTCAAGCATTGAAATAATTAATGACTAATCCGAA 5 255 1 TAATATTAAA 0.891294 -346 GCGAGGATTCTCAAATTATTCCGTATGACTCTGCA 6 213 0 TAATATTCCA 0.827662 -88 CATTAGTCAGGGAAGTCATAACACAGTCCTTTCCC 7 55 1 GAATATAACA 0.963031 -246 AAAAAAAAATGAAAATCATTACCGAGGCATAAAAA 7 140 0 GAATATTACA 0.968707 -161 * ** * ***** * Masking position 4 Map Score: 4.42166 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 431 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 9 TAATACCGAATTGGCAGTGGTAGAGGAAAG 1 43 0 TTGGCAGTGG 0.974263 -374 GATCACCTAATTAGCCGTGGAGAGAGAGAA 1 225 0 TTAGCCGTGG 0.875533 -192 GCAGTTCTTCTAGGCAGTCGAACTGACTCT 2 33 1 TAGGCAGTCG 0.817048 -268 CGTGAGTCACTGTGCATGGGTTTAGCAATT 2 91 0 TGTGCATGGG 0.880279 -210 GAGAGGTTGTTTAGCATGCGAGGTATTAGA 3 229 1 TTAGCATGCG 0.95781 -372 GCGCGCTCCCTTAGCATGGGAGAGGTCTCC 4 86 1 TTAGCATGGG 0.964383 -215 CTAAAATGTGTTTGAAAGGGAAAGATTGTA 4 240 0 TTTGAAAGGG 0.702639 -61 GTTATGACCTTTGGAATGCGGCAGAAAAAA 5 63 0 TTGGAATGCG 0.878399 -538 TGGCTCAATCTTGGCAATGGACCCTGTGCT 6 174 0 TTGGCAATGG 0.927488 -127 ATATTGTGAATTTGCAGGCGAGGATTCTCA 6 235 0 TTTGCAGGCG 0.974397 -66 CTTTGCCTTCGTTTATCTTGC 7 290 0 TTTGCCTTCG 0.856427 -11 ********** Masking position 1 Map Score: 2.3437 Number of sites scoring better than the average of aligned sites = 1213 Number in coding regions = 990 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 10 ACACAATTAAATAATACCGAATTGGCAGTG 1 54 0 ATAATACCGA 0.915314 -363 AGAGAGAAAAATAATCCCAAAGCTACGATA 1 203 0 ATAATCCCAA 0.918006 -214 CAAAACTTCAAAAATGCCAAGACAATTTGC 3 46 1 AAAATGCCAA 0.984433 -555 GTCTCGCTTCGAAATGCCGAAATGAAAGAA 3 345 0 GAAATGCCGA 0.904867 -256 TAATAGGAGTAAAATGCCAAAGTTTAGACG 3 520 0 AAAATGCCAA 0.984433 -81 TGAGATGACTAAACTACCAATTTTCAATAG 5 333 1 AAACTACCAA 0.890504 -268 CGTGAGAGATAAAATATCAAGTATGTCATG 5 441 0 AAAATATCAA 0.773719 -160 TCATTATGTGATAATGCCAATCGCTAAGAA 7 202 0 ATAATGCCAA 0.97526 -99 ********** Masking position 3 Map Score: 2.09026 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 647 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 11 ********** No masking Map Score: 7.41397e-13 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 12 CGCTAAACACAATTAAATAATACCGAATTGGCA 1 57 0 AATTAATAAC 0.877883 -360 GCTATTTACTAATTAACTAGAAACTCAATTTTT 1 89 1 AATTAATAAA 0.971808 -328 AAAAATGAAAAATTCATGAGAAAAGAGTCAGAC 1 259 1 AATTCAGAAA 0.931141 -158 CTTTACTTGTAAATAATTAAAAAACCTAAACTG 1 385 0 AAATAATAAA 0.829072 -32 AATTATTTACAAGTAAAGAAAAAGAGA 1 400 1 AAGTAAGAAA 0.818267 -17 TGGGTTTAGCAATTAATTAACTAATTTACCGGA 2 72 0 AATTAATATA 0.814122 -229 CTTGTCAAAAAATTAATTAAAATATTTATTAGT 3 262 1 AATTAATAAT 0.829058 -339 GCAACTAATAAATTAACTAATAAATATTTTAAT 3 277 0 AATTAATAAA 0.971808 -324 GTTTCTAAAAAATTCAATAGAAAA 3 587 1 AATTCATAAA 0.955733 -14 TGATACGTACAATTCAGTAAAAATCCTCGAGGT 4 277 1 AATTCATAAA 0.955732 -24 GCATTGAAATAATTAATGACTAATCCGAAGTTA 5 261 1 AATTAAGAAA 0.955733 -340 ****** ** ** Masking position 6 Map Score: 4.45661 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 257 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 13 ********** No masking Map Score: 7.41397e-13 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 ********** No masking Map Score: 7.41397e-13 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: 7.41397e-13 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