AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_mjan_reg_100.orf -o005_mjan_100.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 RMJ11224 154 M_jannaschii_chromosome #4 RMJ15032 300 M_jannaschii_chromosome #5 RMJ02393 89 M_jannaschii_chromosome #6 RMJ01985 153 M_jannaschii_chromosome #7 RMJ04712 278 M_jannaschii_chromosome Motif number 1 ATGGTTGTTAATAATTGATGAAATGGTGAATAG 1 13 0 ATAATTTAAA 0.769241 -120 ATTAACAACCATAAATTATAAAATGCATAATGT 1 34 1 ATAAATTAAA 0.853747 -99 TATTTCACCAAAATACCTATAAACTATCACATA 1 109 0 AAATACAAAA 0.558369 -24 TTTACCTACCATTAACTTTAAAAACCTTAACTG 2 21 1 ATTAACTAAA 0.744589 -164 TAATCTGAATAATAATAGTTAAATATATAAATA 2 134 1 AATAATTAAA 0.967578 -51 TTAAATATATAAATATTGTAAAATATTATTGTG 2 152 1 AAATATTAAA 0.868081 -33 AAGACGTTCCTAAAATAAAGAAAGAAGTTGAGA 3 62 1 TAAAATAAAA 0.63037 -93 TTTTATTTTCAATATCTTTTAAAACTATCTCAA 3 89 0 AATATCTAAA 0.851748 -66 CAAATTAATAAAAAATATATAAAATTATT 4 7 0 AAAAATAAAA 0.919967 -294 ATCATGCCAAAATAATATATAAATCTTACGATT 4 78 1 AATAATAAAA 0.944651 -223 TTTGAGTAATAATATTTTTTAAAAAATCGTAAG 4 102 0 AATATTTAAA 0.944651 -199 TTACTCAAATATTAATTTTTAAACAAATAATGA 4 126 1 ATTAATTAAA 0.895701 -175 TTTTTAAACAAATAATGATAAAAGATATTTTAA 4 141 1 AATAATTAAA 0.96758 -160 GAAAACTTTAAAATATTTTAAAATATCTTTTAT 4 158 0 AAATATTAAA 0.868081 -143 TTTTCCTAACAATATTAAAGAAAACTTTAAAAT 4 177 0 AATATTAAAA 0.906919 -124 TTATATCACATTTAATATTTAAAGTTTAACAGC 4 250 0 TTTAATTAAA 0.524728 -51 CAATCATCAAAATTTCTGTTAAAAG 4 286 1 AATTTCTAAA 0.652451 -15 AAACACAAATAAAAATGCTAAAAATATTAGAGA 5 40 1 AAAAATTAAA 0.952691 -50 AATATTAGAGAAAATTGAACAAAAGCTTTAAAT 5 62 1 AAAATTAAAA 0.86775 -28 TAAAAATAGATAAATTCCCATAGC 6 2 1 AAAAATAAAA 0.919966 -152 AAAAATAAAAAGTATTAAATAAAAATATTAACC 6 96 0 AGTATTAAAA 0.6553 -58 ATACAAAACTAATAAAAATAAAAAGTATTAAAT 6 109 0 AATAAATAAA 0.65852 -45 ATTAGCAAATTATTATCTTGAAAGACACACAAT 7 160 1 TATTATTAAA 0.591788 -119 GATTTATAAAAATTTTGGAGAAAATATTGTGTG 7 185 0 AATTTTAAAA 0.760989 -94 GGTTTGATAGAGTATTTATAAAAAAGATTTATA 7 210 0 AGTATTTAAA 0.769082 -69 ****** * *** Masking position 11 Map Score: 27.74 Number of sites scoring better than the average of aligned sites = 2806 Number in coding regions = 2000 Number in noncoding regions = 806 Number of orfs with sites within 600 bp upstream = 557 Fraction of orfs with sites within 600 bp upstream = 0.0894635 Motif number 2 ACCATTTCATCAATTATTAACAACCATAAA 1 19 1 CAATTATTAA 0.650409 -114 TAACAACCATAAATTATAAAATGCATAATG 1 36 1 AAATTATAAA 0.623112 -97 AAATTGCATAACTATATTTATGTTACTTAA 2 79 0 ACTATATTTA 0.417142 -106 AAGCTCATCCTCAATATTAAGATAATCTGA 2 112 1 TCAATATTAA 0.58273 -73 ATAATATTTTACAATATTTATATATTTAAC 2 151 0 ACAATATTTA 0.808005 -34 TAAATATTGTAAAATATTATTGTGGTGGAT 2 161 1 AAAATATTAT 0.868254 -24 AATCAATCCCAAAATATTTATGAA 3 5 0 AAAATATTTA 0.645684 -150 AAAGATATTGAAAATAAAAAATAGGTGATT 3 103 1 AAAATAAAAA 0.546286 -52 AAATTAATAAAAAATATATAAAATTATT 4 9 0 AAAATATATA 0.586759 -292 TAACCTACACAAATTAATAAAAAATATATA 4 19 0 AAATTAATAA 0.742461 -282 CTGCATAAGTAATATAATATACATAATAAC 4 45 0 AATATAATAT 0.440526 -256 ATATCATGCCAAAATAATATATAAATCTTA 4 76 1 AAAATAATAT 0.818321 -225 GATTTTTTAAAAAATATTATTACTCAAATA 4 107 1 AAAATATTAT 0.868254 -194 TATTATTACTCAAATATTAATTTTTAAACA 4 121 1 CAAATATTAA 0.848933 -180 ATAATGATAAAAGATATTTTAAAATATTTT 4 152 1 AAGATATTTT 0.380868 -149 AAGATATTTTAAAATATTTTAAAGTTTTCT 4 162 1 AAAATATTTT 0.494417 -139 TATTTTCCTAACAATATTAAAGAAAACTTT 4 182 0 ACAATATTAA 0.933396 -119 TGTTAAACTTTAAATATTAAATGTGATATA 4 252 1 TAAATATTAA 0.772692 -49 AAAAATGCTAAAAATATTAGAGAAAATTGA 5 50 1 AAAATATTAG 0.801636 -40 GTATTAAATAAAAATATTAACCATCTTTAA 6 88 0 AAAATATTAA 0.962734 -66 ATAAAAATAAAAAGTATTAAATAAAAATAT 6 101 0 AAAGTATTAA 0.788909 -53 TATTAATACAAAACTAATAAAAATAAAAAG 6 117 0 AAACTAATAA 0.470929 -37 ATCACATCTTAATTTATTAATACAAAACTA 6 131 0 AATTTATTAA 0.632928 -23 ATTCAATCATAAAATTTTATTTCTGTGAAA 7 85 1 AAAATTTTAT 0.681235 -194 GTAAATTAGCAAATTATTATCTTGAAAGAC 7 156 1 AAATTATTAT 0.861469 -123 TGAAAGACACACAATATTTTCTCCAAAATT 7 178 1 ACAATATTTT 0.612997 -101 ATTTTCTCCAAAATTTTTATAAATCTTTTT 7 193 1 AAATTTTTAT 0.412075 -86 ********** Masking position 5 Map Score: 22.8106 Number of sites scoring better than the average of aligned sites = 2469 Number in coding regions = 1756 Number in noncoding regions = 713 Number of orfs with sites within 600 bp upstream = 538 Fraction of orfs with sites within 600 bp upstream = 0.0864118 Motif number 3 TCAATTATTAACAACCATAAATTATAAAATGC 1 28 1 AAACATAAAT 0.900227 -105 TATGATTGGGATAATCATCTATCTACTGCTTT 1 73 0 AAACATCTAT 0.935239 -60 GATGATTATCCCAATCATATATATATGTGATA 1 86 1 CAACATATAT 0.790732 -47 ATACCTATAAACTATCACATATATATATGATT 1 98 0 ATACACATAT 0.827548 -35 ATTATCACCATTTACCTACCAT 2 1 1 ATACACCATT 0.356081 -184 CTTAAAGTTAAGTAACATAAATATAGTTATGC 2 72 1 ATACATAAAT 0.795585 -113 CCATATCCATATAATCACCTATTTTTTATTTT 3 113 0 AAACACCTAT 0.908542 -42 CACAAATTAATAAAAAATATATAAAATTATT 4 10 0 TAAAATATAT 0.601175 -291 ATATCATGCCAAAATAATATATAAATCTTACG 4 76 1 AAAAATATAT 0.601175 -225 TGATTGATATTATATCACATTTAATATTTAAA 4 260 0 TTACACATTT 0.526061 -41 TGATATAATATCAATCATCAAAATTTCTGTTA 4 275 1 TAACATCAAA 0.722915 -26 ATGAGATAAAAGAAACACAAATAAAAATGCTA 5 28 1 AAACACAAAT 0.861239 -62 AATAAAAATATTAACCATCTTTAAGAGTTTAG 6 80 0 TAACATCTTT 0.769606 -74 TACAGCTTTTTATACCATATAAGGAATTTTGA 7 37 1 TTACATATAA 0.693153 -242 GCATCTTTATTCAATCATAAAATTTTATTTCT 7 77 1 TAACATAAAA 0.74501 -202 TTATCCCTATTAAAGCATATATATGAGGTTTG 7 237 0 TAACATATAT 0.941767 -42 GGGATAATTATGAAGCATCTAATATCA 7 262 1 TAACATCTAA 0.823831 -17 * ** ******* Masking position 7 Map Score: 9.28562 Number of sites scoring better than the average of aligned sites = 1172 Number in coding regions = 1010 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 4 TAAATTATAAAATGCATAATGTCCTCTAAAAG 1 45 1 ATGCATAAGT 0.940602 -88 AGCTTTTAAAATTGCATAACTATATTTATGTT 2 85 0 ATGCATAATA 0.987249 -100 GGCATGATATACTGCATAAGTAATATAATATA 4 54 0 ATGCATAATA 0.987249 -247 GCAATTGGGAAATGCAGAAGTATTTTATATAG 6 34 0 ATGCAGAATA 0.965883 -120 GCATTTCCCAATTGCATAACTACCAGCCTCTA 6 51 1 ATGCATAATA 0.987249 -103 AAATTTTATGATTGAATAAAGATGCCTTTGGC 7 70 0 ATGAATAAGA 0.908512 -209 * ******* ** Masking position 6 Map Score: 5.3745 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ATATATATGATTGGGATAATCATCTATCTA 1 80 0 TTGGGATAAT 0.953899 -53 TAACTGATTATTAGGAAAAGGATACTTAAA 2 48 1 TTAGGAAAAG 0.890074 -137 ATCCTCAATATTAAGATAATCTGAATAATA 2 118 1 TTAAGATAAT 0.890191 -67 AAGAAAGAAGTTGAGATAGTTTTAAAAGAT 3 79 1 TTGAGATAGT 0.782727 -76 TTTAATATTGTTAGGAAAATAGAGCCAAAT 4 191 1 TTAGGAAAAT 0.928201 -110 CAGTTACGTATTAAGAAATGTGAATGTTTA 4 221 0 TTAAGAAATG 0.626478 -80 CTAAAAATATTAGAGAAAATTGAACAAAAG 5 57 1 TAGAGAAAAT 0.852725 -33 AGTTATGCAATTGGGAAATGCAGAAGTATT 6 42 0 TTGGGAAATG 0.81064 -112 TGTGTGTCTTTCAAGATAATAATTTGCTAA 7 161 0 TCAAGATAAT 0.682861 -118 ATAAAAATTTTGGAGAAAATATTGTGTGTC 7 183 0 TGGAGAAAAT 0.829542 -96 TATGCTTTAATAGGGATAATTATGAAGCAT 7 250 1 TAGGGATAAT 0.867351 -29 ********** Masking position 6 Map Score: 5.75799 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 521 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 ATTATTAACAACCATAAATTATAAAATGCATA 1 31 1 ACATAAATAT 0.615943 -102 CCATTTACCTACCATTAACTTTAAAAACCTTA 2 18 1 ACATTAATTT 0.930079 -167 TATGTTACTTAACTTTAAGTATCCTTTTCCTA 2 59 0 ACTTTAATAT 0.951731 -126 CAATATTTATATATTTAACTATTATTATTCAG 2 138 0 AATTTAATAT 0.553004 -47 TAGGAACGTCTTCTTTAACTATCTTCCAAAGA 3 42 0 TCTTTAATAT 0.895258 -113 TAATATTTCCTTTAATTTTTCCATATCCA 3 136 0 TCTTTAATTT 0.930342 -19 TTATTACTCAAATATTAATTTTTAAACAAATA 4 123 1 ATATTAATTT 0.401633 -178 TTTTAAAGTTTTCTTTAATATTGTTAGGAAAA 4 178 1 TCTTTAAATT 0.796301 -123 ACTGCTGTTAAACTTTAAATATTAAATGTGAT 4 247 1 ACTTTAATAT 0.904127 -54 CTCATTCAATACCTCTAATTTT 5 1 0 ACTCTAATTT 0.902707 -89 TTGTTCAATTTTCTCTAATATTTTTAGCATTT 5 52 0 TCTCTAAATT 0.531956 -38 ATTGAACAAAAGCTTTAAATTTTAA 5 75 1 ACTTTAATTT 0.96762 -15 AATATTAACCATCTTTAAGAGTTTAGAGGCTG 6 74 0 ACTTTAAAGT 0.685608 -80 TCTTTATTCAATCATAAAATTTTATTTCTGTG 7 80 1 ACATAAATTT 0.714583 -199 * ****** *** Masking position 7 Map Score: 11.317 Number of sites scoring better than the average of aligned sites = 1037 Number in coding regions = 911 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 ********** No masking Map Score: -1.57497e-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 8 ********** No masking Map Score: -1.57497e-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 9 ********** No masking Map Score: -1.57497e-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