AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i107_TRK_operon_mjan_reg_300.orf -o107_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 RMJ08949 251 M_jannaschii_chromosome #2 RMJ13850 17 M_jannaschii_chromosome #3 RMJ13412 101 M_jannaschii_chromosome #4 RMJ10489 300 M_jannaschii_chromosome #5 RMJ00447 140 M_jannaschii_chromosome #6 RMJ02262 46 M_jannaschii_chromosome #7 RMJ12766 32 M_jannaschii_chromosome Motif number 1 ATTCCTTATATTGAATTATAAAACTGTGAA 1 147 1 TTGAATTATA 0.775535 -105 AGGATTATTTTTTCATAATATTCATCACCA 1 205 0 TTTCATAATA 0.924603 -47 ACCAAAAAACTTTAATTATAGGATTATTTT 1 224 0 TTTAATTATA 0.906825 -28 CTTAAAAATTTTTAAAAATTTTATTTTACT 3 45 0 TTTAAAAATT 0.858699 -57 TTAGGAATTATTTATTTATTTAGAGGTTTT 4 31 0 TTTATTTATT 0.723847 -270 AATACTCTCATTTCTAAATTCCAAACTTAT 4 60 1 TTTCTAAATT 0.50619 -241 TGTTAATTGATTTATTGATTGTCTTGTTGT 4 90 0 TTTATTGATT 0.684858 -211 GATTTTCAATTTTGTTAATTGATTTATTGA 4 102 0 TTTGTTAATT 0.759938 -199 ACCCTAATAATGTAATGATAGAATAACGAT 4 137 1 TGTAATGATA 0.841396 -164 TTATAGTTTGTTTAATAATATTCTATCGTT 4 161 0 TTTAATAATA 0.966609 -140 TGTAGATAATTTTAATTATAGTTTGTTTAA 4 176 0 TTTAATTATA 0.906825 -125 ATAAACATTTTGTGATAATAAAGCTTTATT 4 215 1 TGTGATAATA 0.886493 -86 AATAATTAGTTGTAATAATAGGATAATTGA 4 248 0 TGTAATAATA 0.948551 -53 TTATCTTAGTTGTAATAATTAGTTGTAATA 4 261 0 TGTAATAATT 0.922717 -40 GATTAAAAACTGTCAAAATAGTATATAAAG 5 43 1 TGTCAAAATA 0.716624 -98 TGATGAAGTATTTAACAATTGTCATCAAAA 5 74 0 TTTAACAATT 0.73245 -67 GCTGGAGTTGATTAATATGGACAAAAC 6 8 1 TTGATTAATA 0.797491 -39 GGTTTTATTGGAAAATAAGGATGCATT 7 16 0 TTGGAAAATA 0.574734 -17 ********** Masking position 9 Map Score: 16.2198 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1310 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 2 TCACAGGAATAAATTTCTTATTGAACATAA 1 98 1 AAATTTCTTA 0.953429 -154 ATAGACATCATAATTCCTTATATTGAATTA 1 135 1 TAATTCCTTA 0.970259 -117 CAGTAAAATAAAATTTTTAAAAATTTTTAA 3 44 1 AAATTTTTAA 0.732331 -58 AGAATTTAGGAAATTCCTTAAAAATTTTTA 3 61 0 AAATTCCTTA 0.96488 -41 AGGAATTTCCTAAATTCTAAATATATGAAA 3 73 1 TAAATTCTAA 0.942633 -29 CACAAAAAATTTCATATATTTAGAAT 3 86 0 AAATTTCATA 0.722325 -16 GTTTTAAATTTAATTTCTAAGGGTT 4 6 0 TAATTTCTAA 0.976335 -295 AATAAATAAATAATTCCTAAATACTCTCAT 4 41 1 TAATTCCTAA 0.982258 -260 CTAAATACTCTCATTTCTAAATTCCAAACT 4 57 1 TCATTTCTAA 0.89589 -244 AACAAAATTGAAAATCCTAAAACCCTAATA 4 116 1 AAAATCCTAA 0.948877 -185 TCATCGTTAATTAATCCTAAGATAACATTT 5 101 1 TTAATCCTAA 0.756288 -40 ********** Masking position 3 Map Score: 13.7951 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 360 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TGGTTACTTCAAATCTCTATTAAAGTGGGGTTG 1 27 1 AAATCTATAA 0.905725 -225 TTGACACCAAAAAACTTTAATTATAGGATTATT 1 226 0 AAATTTAATA 0.972772 -26 AATTCCTTAAAAATTTTTAAAAATTTTATTTTA 3 47 0 AAATTTAAAA 0.95468 -55 CACAAAAAATTTCATATATTTAGAATTT 3 84 0 AAATTCATTA 0.888831 -18 ATTAAATTTAAAACCTCTAAATAAATAAATAAT 4 22 1 AAATCTAATA 0.932029 -279 GAGTCTGTAGATAATTTTAATTATAGTTTGTTT 4 178 0 ATATTTAATA 0.819481 -123 TATTATCACAAAATGTTTATATACGAGTCTGTA 4 202 0 AAATTTATTA 0.976988 -99 TTGTGATAATAAAGCTTTATTAAGTCAATTATC 4 224 1 AAATTTATAA 0.961586 -77 GTTTTTAATCCAATTTTTATCTACTTTACAAAG 5 20 0 CAATTTATTA 0.888831 -121 ATTGTCATCAAAACCTTTATATACTATTTTGAC 5 54 0 AAATTTATTA 0.976988 -87 AACGATGATGAAGTATTTAACAATTGTCATCAA 5 76 0 AAGTTTAAAA 0.79867 -65 *** ***** ** Masking position 9 Map Score: 12.6183 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 409 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 4 TTGGGTATACCACAGGACTTTCACAGGAAT 1 78 1 CACAGGACTT 0.995891 -174 ACAGGACTTTCACAGGAATAAATTTCTTAT 1 89 1 CACAGGAATA 0.960224 -163 GCCCTATTGGCACAGGACTTTCACAGTTTT 1 166 0 CACAGGACTT 0.995891 -86 TATTCATCACCATAGGGCTTCGCCCTATTG 1 187 0 CATAGGGCTT 0.972811 -65 ********** Masking position 4 Map Score: 4.07927 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 CCACTTTAATAGAGATTTGAAGTAACCAAT 1 25 0 AGAGATTTGA 0.882941 -227 CAGGACTTTCACAGTTTTATAATTCAATAT 1 154 0 ACAGTTTTAT 0.74384 -98 TCCTATAATTAAAGTTTTTTGGTGTCAAAC 1 231 1 AAAGTTTTTT 0.9151 -21 AAATTCCTTAAAAATTTTTAAAAATTTTAT 3 51 0 AAAATTTTTA 0.670214 -51 TTATTTATTTAGAGGTTTTAAATTTAATTT 4 20 0 AGAGGTTTTA 0.919398 -281 TTTAGAAATGAGAGTATTTAGGAATTATTT 4 48 0 AGAGTATTTA 0.871291 -253 TACTATTTTGACAGTTTTTAATCCAATTTT 5 36 0 ACAGTTTTTA 0.957318 -105 ATAGTATATAAAGGTTTTGATGACAATTGT 5 60 1 AAGGTTTTGA 0.826446 -81 AATAACCGAAAGAGTTTTGTCCATATTAAT 6 21 0 AGAGTTTTGT 0.956614 -26 ********** Masking position 7 Map Score: 3.1742 Number of sites scoring better than the average of aligned sites = 913 Number in coding regions = 784 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 GGGCATAACCCCATATTGGTTACTTCA 1 7 1 AACCCCTATT 0.960512 -245 TGCCAAAGGCAACCCCACTTTAATAGAGATT 1 38 0 AACCCCCTTT 0.992611 -214 TGCCTTTGGCAACCCCGCTCTTGGGTATACC 1 58 1 AACCCCCTCT 0.983744 -194 ATTATCCCTCTTTGTAAAGTAGA 5 3 1 TATCCCCTTT 0.954705 -138 GACAGTTTTTAATCCAATTTTTATCTACTTT 5 26 0 AATCCATTTT 0.817051 -115 GAACATAAAAATCCCCCAATAAATGTTATC 5 121 0 AATCCCCAAT 0.932964 -20 ****** **** Masking position 2 Map Score: 2.24986 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 91 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AGCATCATTATGTTCAATAAGAAATTTATT 1 105 0 TGTTCAATAA 0.87084 -147 ATAGGATTATTTTTTCATAATATTCATCAC 1 207 0 TTTTTCATAA 0.861614 -45 TAAAATAAAATTTTTAAAAATTTTTAAGGA 3 47 1 TTTTTAAAAA 0.478444 -55 AATTATAGTTTGTTTAATAATATTCTATCG 4 163 0 TGTTTAATAA 0.918572 -138 ATATAAACATTTTGTGATAATAAAGCTTTA 4 213 1 TTTGTGATAA 0.885147 -88 GTAATAATTAGTTGTAATAATAGGATAATT 4 250 0 GTTGTAATAA 0.935555 -51 TTTTATCTTAGTTGTAATAATTAGTTGTAA 4 263 0 GTTGTAATAA 0.935555 -38 GCATCCTTATTTTCCAATAAAACC 7 19 1 TTTCCAATAA 0.843157 -14 ********** Masking position 7 Map Score: 2.54839 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 405 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 ATTTATTCCTGTGAAAGTCCTGTGGTATAC 1 82 0 GTGAAAGTCC 0.99181 -170 TTATAAAACTGTGAAAGTCCTGTGCCAATA 1 162 1 GTGAAAGTCC 0.99181 -90 TTTAGAATTTAGGAAATTCCTTAAAAATTT 3 64 0 AGGAAATTCC 0.928198 -38 ATTAACAAAATTGAAAATCCTAAAACCCTA 4 113 1 TTGAAAATCC 0.966339 -188 GAACATAAAAATCCCCCAATAAAT 5 127 0 ATAAAAATCC 0.906544 -14 ********** Masking position 5 Map Score: 2.90121 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 34 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ********** No masking Map Score: -1.80235e-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 10 GTCTATAGCATCATTATGTTCAATAAGAAA 1 111 0 TCATTATGTT 0.941261 -141 ACATCATAATTCCTTATATTGAATTATAAA 1 139 1 TCCTTATATT 0.952704 -113 GATTATTTTTTCATAATATTCATCACCATA 1 203 0 TCATAATATT 0.864402 -49 TTTAATTATAGGATTATTTTTTCATAATAT 1 214 0 GGATTATTTT 0.815899 -38 CGTTATTCTATCATTACATTATTAGGGTTT 4 135 0 TCATTACATT 0.904289 -166 CCTATCACCAGCAGTATTTTTTATCTTAGT 4 281 0 GCAGTATTTT 0.876727 -20 AAATAAGGATGCATTATATT 7 1 0 GCATTATATT 0.972119 -32 ATATAATGCATCCTTATTTTCCAATAAAAC 7 12 1 TCCTTATTTT 0.939282 -21 ********** Masking position 6 Map Score: 5.03475 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 183 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 ********** No masking Map Score: -1.80235e-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 12 ********** No masking Map Score: -1.80235e-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 13 ********** No masking Map Score: -1.80235e-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