AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_mjan_reg_300.orf -o005_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ13879 132 M_jannaschii_chromosome #2 RMJ07763 184 M_jannaschii_chromosome #3 RMJ04742 25 M_jannaschii_chromosome #4 RMJ11224 154 M_jannaschii_chromosome #5 RMJ15032 300 M_jannaschii_chromosome #6 RMJ02393 89 M_jannaschii_chromosome #7 RMJ05936 121 M_jannaschii_chromosome #8 RMJ11131 18 M_jannaschii_chromosome #9 RMJ10096 125 M_jannaschii_chromosome #10 RMJ16684 112 M_jannaschii_chromosome #11 RMJ01985 153 M_jannaschii_chromosome #12 RMJ04712 278 M_jannaschii_chromosome Motif number 1 TTAAGTAACATAAATATAGTTATGCAATTT 2 79 1 TAAATATAGT 0.829206 -106 GGATGAGCTTTTAAAATTGCATAACTATAT 2 92 0 TTAAAATTGC 0.66938 -93 GTTAAATATATAAATATTGTAAAATATTAT 2 151 1 TAAATATTGT 0.934201 -34 ATCCACCACAATAATATTTTACAATATTTA 2 161 0 ATAATATTTT 0.825436 -24 TTCATAAATATTTTGGGATTGATT 4 5 1 TAAATATTTT 0.875467 -150 AATAATTTTATATATTTTTTATTAATTT 5 9 1 TATATATTTT 0.798339 -292 AATCGTAAGATTTATATATTATTTTGGCAT 5 81 0 TTTATATATT 0.695456 -220 TATTTGAGTAATAATATTTTTTAAAAAATC 5 107 0 ATAATATTTT 0.825436 -194 TGTTTAAAAATTAATATTTGAGTAATAATA 5 121 0 TTAATATTTG 0.750444 -180 AAGATATTTTAAAATATTTTAAAGTTTTCT 5 162 1 AAAATATTTT 0.49325 -139 AAAGTTTTCTTTAATATTGTTAGGAAAATA 5 182 1 TTAATATTGT 0.956745 -119 GCTGTTAAACTTTAAATATTAAATGTGATA 5 250 1 TTTAAATATT 0.565975 -51 ATAAAAATGCTAAAAATATTAGAGAAAATT 6 48 1 TAAAAATATT 0.812586 -42 GAACAAAAGCTTTAAATTTTAA 6 78 1 TTTAAATTTT 0.799617 -12 ATTTTAATGCTAAAAATTTTTTGGTGAAAT 7 13 0 TAAAAATTTT 0.928805 -109 ATTTTTAGCATTAAAATTTTATTCTATACT 7 26 1 TTAAAATTTT 0.951742 -96 AAAGGAATCATTAATATAGTTTTTTGTTAA 7 65 1 TTAATATAGT 0.878583 -57 TCATTTGAGATAAATATTGTTTAGGGAGCA 7 100 1 TAAATATTGT 0.934201 -22 ATTTTTCGTTTTAAAATTTCTCTAAAATTT 9 81 1 TTAAAATTTC 0.759618 -45 GAACGATAAAATAATATATTACATAGATAA 10 48 1 ATAATATATT 0.767475 -65 TTAAAGATGGTTAATATTTTTATTTAATAC 11 88 1 TTAATATTTT 0.97015 -66 ATATTTTTATTTAATACTTTTTATTTTTAT 11 101 1 TTAATACTTT 0.734075 -53 TTATTCAATCATAAAATTTTATTTCTGTGA 12 83 1 ATAAAATTTT 0.864365 -196 AATTTTGGAGAAAATATTGTGTGTCTTTCA 12 178 0 AAAATATTGT 0.703593 -101 AAAAGATTTATAAAAATTTTGGAGAAAATA 12 192 0 TAAAAATTTT 0.928805 -87 ********** Masking position 6 Map Score: 32.2176 Number of sites scoring better than the average of aligned sites = 1496 Number in coding regions = 1023 Number in noncoding regions = 473 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 2 CTATTCACCATTTCATCAATTATTAACAACCATA 1 13 1 TTTCATTATT 0.785247 -120 ACATTATGCATTTTATAATTTATGGTTGTTAATA 1 33 0 TTTTATTATG 0.935103 -100 AAACTATCACATATATATATGATTGGGATAATCA 1 88 0 ATATATTATT 0.632274 -45 ATATGTGATAGTTTATAGGTATTTTGGTGAAATA 1 108 1 GTTTATTTTT 0.700619 -25 CAGTTAAGGTTTTTAAAGTTAATGGTAGGTAAAT 2 20 0 TTTTAATATG 0.851909 -165 TTTACAATATTTATATATTTAACTATTATTATTC 2 140 0 TTATATTACT 0.615906 -45 TTGGGATTGATTATATCCTTCTTTGGAAGATAGT 4 23 1 TTATATTTTT 0.902838 -132 TTTCAATATCTTTTAAAACTATCTCAACTTCTTT 4 82 0 TTTTAATTCT 0.70425 -73 AAATAGGTGATTATATGGATATGGAAAAATTAAA 4 121 1 TTATATTTGG 0.600461 -34 AATAATTTTATATATTTTTTATTAATTTG 5 6 1 TTTTATTTTT 0.958805 -295 ATTATGTATATTATATTACTTATGCAGTATATCA 5 48 1 TTATATTATG 0.85191 -253 AAATCGTAAGATTTATATATTATTTTGGCATGAT 5 78 0 ATTTATTATT 0.811668 -223 TTAAAATATCTTTTATCATTATTTGTTTAAAAAT 5 140 0 TTTTATTTTT 0.958803 -161 TTTTAAAATATTTTAAAGTTTTCTTTAATATTGT 5 168 1 TTTTAATTCT 0.70425 -133 TTTTTAGCATTTTTATTTGTGTTTCTTTTATCTC 6 30 0 TTTTATTTTT 0.958805 -60 TTAAAATTTAAAGCTTTTGTTCAATTTTC 6 71 0 ATTTAATTTG 0.70141 -19 GAAATTTTGCTTTTAATCTTAATTATATTATTTA 9 43 0 TTTTAATATT 0.862205 -83 AAAAGCAAAATTTCAACTATTTTTCGTTTTAAAA 9 63 1 TTTCAATTTT 0.68432 -63 TAATATATTATTTTATCGTTCATGAGCATCACAA 10 35 0 TTTTATTATG 0.935103 -78 AAATAATATATTACATAGATAATGCAGTATCAAT 10 56 1 TTACATTATG 0.573022 -57 AGCTATGGGAATTTATCTATTTTTA 11 2 0 ATTTATTTTT 0.864866 -152 CAGAAGTATTTTATATAGCTATGGGAATTTATCT 11 18 0 TTATATTTGG 0.600461 -136 TAATATTTTTATTTAATACTTTTTATTTTTATTA 11 99 1 ATTTAATTTT 0.718722 -55 TACTTTTTATTTTTATTAGTTTTGTATTAATAAA 11 115 1 TTTTATTTTG 0.955351 -39 TCTCCAAAATTTTTATAAATCTTTTTTATAAATA 12 197 1 TTTTATTTTT 0.958805 -82 ****** * *** Masking position 10 Map Score: 26.7506 Number of sites scoring better than the average of aligned sites = 2203 Number in coding regions = 1586 Number in noncoding regions = 617 Number of orfs with sites within 600 bp upstream = 470 Fraction of orfs with sites within 600 bp upstream = 0.0754899 Motif number 3 TATCTACTGCTTTTAGAGGACATTATGCATTTTATAATT 1 47 0 TTTAAAATTA 0.971832 -86 AATATATAAATATTGTAAAATATTATTGTGGTGGATATT 2 155 1 TTTGAAATTT 0.453808 -30 GGTTTCACACTATATACTATATTTC 3 5 0 TTCAAAATAA 0.864573 -21 GTTGAGATAGTTTTAAAAGATATTGAAAATAAAAAATAG 4 88 1 TTTAAAATTA 0.971347 -67 CTACACAAATTAATAAAAAATATATAAAATTATT 5 6 0 TATAAAATAA 0.892758 -295 ACTGCATAAGTAATATAATATACATAATAACCTACACAA 5 37 0 TATAAAACAA 0.761189 -264 TATATATTATTTTGGCATGATATACTGCATAAGTAATAT 5 60 0 TTGGAAATAA 0.564304 -241 TCTTACGATTTTTTAAAAAATATTATTACTCAAATATTA 5 101 1 TTTAAAATTC 0.767344 -200 AAACAAATAATGATAAAAGATATTTTAAAATATTTTAAA 5 146 1 TATAAAATTA 0.917816 -155 TTCCTAACAATATTAAAGAAAACTTTAAAATATTTTAAA 5 169 0 TTTAAAACTA 0.907467 -132 TGATGATTGATATTATATCACATTTAATATTTAAAGTTT 5 256 0 TTTAAAATTA 0.735661 -45 AAATTAGAGGTATTGAATGAGATAAAAGAAACACAAATA 6 12 1 TTTGAAATAA 0.920555 -78 ATGCTAAAAATATTAGAGAAAATTGAACAAAAGCTTTAA 6 54 1 TTTAAAATTA 0.971829 -36 ACAATATTTATCTCAAATGAGATAATTAACAAAAAACTA 7 81 0 TTCAAAATAA 0.864538 -41 ATAGAACAACTACTAAATAATATAATTAAGATTAAAAGC 9 30 1 TCTAAAATAA 0.804159 -96 AGAAATCAAATTTTAGAGAAATTTTAAAACGAAAAATAG 9 79 0 TTTAAATTTA 0.679449 -47 AACGATAAAATAATATATTACATAGATAATGCAGTATCA 10 49 1 TATAAAATAA 0.915837 -64 AAATAAAAAGTATTAAATAAAAATATTAACCATCTTTAA 11 88 0 TTTAAAAATA 0.711682 -66 CTTTACAGCTTTTTATACCATATAAGGAATTTTGATGCC 12 34 1 TTTAAAATAA 0.971829 -245 CAAATTATTATCTTGAAAGACACACAATATTTTCTCCAA 12 165 1 TTTGAAACAA 0.785363 -114 GATAGAGTATTTATAAAAAAGATTTATAAAAATTTTGGA 12 199 0 TATAAAATTA 0.909613 -80 TAATTATCCCTATTAAAGCATATATATGAGGTTTGATAG 12 233 0 TTTAAAATAA 0.969635 -46 * *** * * *** * Masking position 1 Map Score: 28.8066 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 497 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 CCATAAATTATAAAATGCATAATGTCCTCTAAA 1 42 1 TAAAGATAAT 0.894006 -91 CATATATATATGATTGGGATAATCATCTATCTA 1 80 0 TGATGATAAT 0.229847 -53 TACTTAAAGTTAAGTAACATAAATATAGTTATG 2 70 1 TAAGAATAAA 0.795425 -115 AATATTAAGATAATCTGAATAATAATAGTTAAA 2 124 1 TAATGATAAT 0.617275 -61 ATAATAATAGTTAAATATATAAATATTGTAAAA 2 142 1 TTAAAATAAA 0.607373 -43 AAGACGTTCCTAAAATAAAGAAAGAAGTTGAGA 4 62 1 TAAAAAGAAA 0.777058 -93 ATGGAAAAATTAAAGGAAATATTA 4 141 1 TAAAAATATT 0.896744 -14 CACAAATTAATAAAAAATATATAAAATTATT 5 9 0 TAAAAATATA 0.824986 -292 ATATACTGCATAAGTAATATAATATACATAATA 5 47 0 TAAGAATAAT 0.877503 -254 TACGATTTTTTAAAAAATATTATTACTCAAATA 5 104 1 TAAAAATTAT 0.720868 -197 ATATTAATTTTTAAACAAATAATGATAAAAGAT 5 134 1 TTAAAATAAT 0.740262 -167 CAAATAATGATAAAAGATATTTTAAAATATTTT 5 149 1 TAAAAATTTT 0.484906 -152 TTAGAGGTATTGAATGAGATAAAAGAAACACAA 6 15 1 TGAAAATAAA 0.705262 -75 CTTTAAAAGCTAAAGTATAGAATAAAATTTTAA 7 36 0 TAAAAAGAAT 0.865256 -86 ATATTTATCTCAAATGAGATAATTAACAAAAAA 7 84 0 CAAAAATAAT 0.694893 -38 ACAAATAAGGGAGATATT 8 6 1 TAAGAATATT 0.72309 -13 TAAATGACAGAATAGATAAATAG 9 1 1 TAAAAAGAAT 0.865256 -125 GAACAACTACTAAATAATATAATTAAGATTAAA 9 33 1 TAAAAATAAT 0.959715 -93 AGAGAAATTTTAAAACGAAAAATAGTTGAAATT 9 71 0 TAAAGAAAAT 0.363949 -55 CATGAACGATAAAATAATATATTACATAGATAA 10 45 1 AAAAAATATT 0.496912 -68 TAAAAATAGATAAATTCCCATAGC 11 2 1 AAAAAATAAA 0.59527 -152 AATACAAAACTAATAAAAATAAAAAGTATTAAA 11 110 0 TAATAATAAA 0.712042 -44 TTATCCCTATTAAAGCATATATATGAGGTTTGA 12 236 0 TAAAAATATA 0.824986 -43 **** * ***** Masking position 9 Map Score: 16.166 Number of sites scoring better than the average of aligned sites = 1600 Number in coding regions = 1233 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 5 TAAAAGCTCATCCTCAATATTAAGATAATCT 2 109 1 TCCTCATATT 0.816804 -76 TTTAAAGTTTTCTTTAATATTGTTAGGAAAA 5 179 1 TCTTTATATT 0.571216 -122 ATAATATCAATCATCAAAATTTCTGTTAAAA 5 279 1 TCATCAAATT 0.926238 -22 AATATTTTTAGCATTTTTATTTGTGTTTCTT 6 37 0 GCATTTTATT 0.860338 -53 AAAATTTTTAGCATTAAAATTTTATTCTATA 7 23 1 GCATTAAATT 0.942366 -99 TCGTTCATGAGCATCACAATTGGTTTTTTGA 10 23 0 GCATCAAATT 0.980655 -90 ATTAAAGTTAGCTTTATTATTGATACTGCAT 10 77 0 GCTTTATATT 0.843212 -36 ATAACTACCAGCCTCTAAACTCTTAAAGATG 11 66 1 GCCTCTAACT 0.68811 -88 GGTATCACATCTTAATTTATTAATACA 11 137 0 ACATCTAATT 0.720479 -17 GATGCCTTTGGCATCAAAATTCCTTATATGG 12 51 0 GCATCAAATT 0.980655 -228 GATGCCAAAGGCATCTTTATTCAATCATAAA 12 67 1 GCATCTTATT 0.950246 -212 GATATTAGATGCTTCATAATTATCCCTATTA 12 257 0 GCTTCAAATT 0.958253 -22 ****** **** Masking position 9 Map Score: 10.0283 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 213 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 GTTGTTAATAATTGATGAAATGGTGAATAG 1 13 0 ATTGATGAAA 0.710921 -120 ATCTACTGCTTTTAGAGGACATTATGCATT 1 55 0 TTTAGAGGAC 0.789985 -78 TTATAGGTATTTTGGTGAAATAT 1 120 1 TTTGGTGAAA 0.888157 -13 ATATGGAAAAATTAAAGGAAATATTA 4 139 1 ATTAAAGGAA 0.860639 -16 TCCTAACAATATTAAAGAAAACTTTAAAAT 5 177 0 ATTAAAGAAA 0.868477 -124 AAAATTAGAGGTATTGAATGAGA 6 4 1 ATTAGAGGTA 0.681097 -86 TGCTAAAAATATTAGAGAAAATTGAACAAA 6 55 1 ATTAGAGAAA 0.947295 -35 CTAAAAATTTTTTGGTGAAATTT 7 4 0 TTTGGTGAAA 0.888157 -118 TACTTTAGCTTTTAAAGGAATCATTAATAT 7 52 1 TTTAAAGGAA 0.880072 -70 GAAATCAAATTTTAGAGAAATTTTAAAACG 9 87 0 TTTAGAGAAA 0.95526 -39 TTATAAAAATTTTGGAGAAAATATTGTGTG 12 185 0 TTTGGAGAAA 0.952308 -94 ********** Masking position 3 Map Score: 10.2831 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 422 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 TTTCATCAATTATTAACAACCATAAATTAT 1 23 1 TATTAACAAC 0.718409 -110 CTTAACTGATTATTAGGAAAAGGATACTTA 2 46 1 TATTAGGAAA 0.947539 -139 TCATCCTCAATATTAAGATAATCTGAATAA 2 116 1 TATTAAGATA 0.717751 -69 ACGTTCCTAAAATAAAGAAAGAAGTTGAGA 4 65 1 AATAAAGAAA 0.648783 -90 AACCTACACAAATTAATAAAAAATATATAA 5 18 0 AATTAATAAA 0.784843 -283 TCTTTAATATTGTTAGGAAAATAGAGCCAA 5 189 1 TGTTAGGAAA 0.756135 -112 AGCAGTTACGTATTAAGAAATGTGAATGTT 5 223 0 TATTAAGAAA 0.956437 -78 CAAATGAGATAATTAACAAAAAACTATATT 7 77 0 AATTAACAAA 0.915221 -45 GTAGTTATGCAATTGGGAAATGCAGAAGTA 11 44 0 AATTGGGAAA 0.819724 -110 ATTAGTTTTGTATTAATAAATTAAGATGTG 11 129 1 TATTAATAAA 0.833934 -25 GGGAAAACCCTATTGACAAAGGACTTTACA 12 11 1 TATTGACAAA 0.837413 -268 CGGAGGTGTAAATTAGCAAATTATTATCTT 12 149 1 AATTAGCAAA 0.898795 -130 ********** Masking position 8 Map Score: 6.76032 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 396 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 CATAATGTCCTCTAAAAGCAGTAGATAGAT 1 59 1 TCTAAAAGCA 0.903145 -74 GTTATGCAATTTTAAAAGCTCATCCTCAAT 2 97 1 TTTAAAAGCT 0.956302 -88 TTGAGATAGTTTTAAAAGATATTGAAAATA 4 89 1 TTTAAAAGAT 0.895335 -66 ATATTTAAAGTTTAACAGCAGTTACGTATT 5 239 0 TTTAACAGCA 0.97176 -62 CTTTTAACAGAAATTTTGATGA 5 289 0 TTTAACAGAA 0.9308 -12 TAATGATTCCTTTAAAAGCTAAAGTATAGA 7 48 0 TTTAAAAGCT 0.956302 -74 TATAATTAAGATTAAAAGCAAAATTTCAAC 9 50 1 ATTAAAAGCA 0.862853 -76 ATCACAGGACTTTCACAGAAATAAAATTTT 12 95 0 TTTCACAGAA 0.781308 -184 ********** Masking position 5 Map Score: 6.55305 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 117 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 TTATGGTTGTTAATAATTGATGAAATGGTG 1 18 0 TAATAATTGA 0.778075 -115 ATTATGCATTTTATAATTTATGGTTGTTAA 1 35 0 TTATAATTTA 0.702878 -98 ATGATTGGGATAATCATCTATCTACTGCTT 1 74 0 TAATCATCTA 0.894993 -59 CTTTTCCTAATAATCAGTTAAGGTTTTTAA 2 38 0 TAATCAGTTA 0.813888 -147 TCCACCACAATAATATTTTACAATATTTAT 2 160 0 TAATATTTTA 0.691063 -25 CATATCCATATAATCACCTATTTTTTATTT 4 114 0 TAATCACCTA 0.893096 -41 ATAATATACATAATAACCTACACAAATTAA 5 32 0 TAATAACCTA 0.921449 -269 TTTAATAACTTAATAACTTAT 10 102 1 TAATAACTTA 0.942092 -11 AGTTTTGTATTAATAAATTAAGATGTGATA 11 132 1 TAATAAATTA 0.786853 -22 TCTTTCAAGATAATAATTTGCTAATTTACA 12 155 0 TAATAATTTG 0.778077 -124 ********** Masking position 4 Map Score: 2.55638 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 134 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 10 ********** No masking Map Score: -7.64954e-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 11 ********** No masking Map Score: -7.64954e-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 ********** No masking Map Score: -7.64954e-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