AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nadC 87 quinolinate phosphoribosyltransferase #2 nadA 300 quinolinate synthetase, A protein #3 nadB 300 quinolinate synthetase, B protein Motif number 1 AGGCGCTTTTTTGCTATTCAGGCATCCTCAATTT 2 54 1 TTGCTCAGCA 0.995717 -247 TCGTCAGAGCTTACTGTGCAAGCAACTCTATGTC 2 109 1 TTACTCAGCA 0.989091 -192 TCGGTGTAATTTGTTTTATATGCTAAACAAGATA 2 216 0 TTGTTTAGCT 0.942439 -85 CTTACCATCTCGTTTTACAGGCTTAACGTTAAA 2 278 0 TCGTTCAGCT 0.974963 -23 GCATCTGTTTTTGTTTGTCATGCTGTAGACGGAT 3 19 1 TTGTTCAGCT 0.993226 -282 GGCCGTTGGGTTACTCTTCAGGCAGTTAAATGGG 3 111 0 TTACTCAGCA 0.989171 -190 TTTGTTACAGTTGCTAAACACGCTGACGCAGGGC 3 199 0 TTGCTCAGCT 0.997341 -102 TTTGTTTAATTTACTAAACATGGTTTGGTCAGCA 3 273 0 TTACTCAGGT 0.960422 -28 ***** ** *** Masking position 10 Map Score: 13.8347 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 132 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 GAATCATAAGGTAGAAACATGCTACTCTGAAC 1 44 0 GTAGAAAAGC 0.980923 -44 ACCCACCAATGTAAAAAAGCGCCCTAAAGGCG 2 27 1 GTAAAAAGGC 0.980924 -274 TGCCTGAATAGCAAAAAAGCGCCTTTAGGGCG 2 46 0 GCAAAAAGGC 0.923137 -255 GGTTTACAAAGTGAAATTGAGGATGCCTGAAT 2 69 0 GTGAAATGGG 0.928489 -232 CTCTATGTCGGTGGAATTAGGCGTAAAATGAC 2 134 1 GTGGAATAGC 0.976487 -167 GGAATTAGGCGTAAAATGACGCATCCTGCACA 2 146 1 GTAAAATAGC 0.969902 -155 GGAAAAGTCACTCGAATTACGCCTAATGTGCA 2 172 0 CTCGAATAGC 0.860843 -129 AAACAAGATAGTCGAATGGTGGGGAAAAGTCA 2 194 0 GTCGAATGGG 0.962277 -107 CATTATCTGTGTAGAAATGCCCATTTAACTGC 3 92 1 GTAGAAAGCC 0.93622 -209 ******* * ** Masking position 6 Map Score: 6.94446 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 667 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TATATGTGGTGCTAATACCCGGTTCAGAGTA 1 23 1 GCTAATACCG 0.915155 -65 CGTAATATTCGCTGTTATCGGTGTAATTTGT 2 236 0 GCTGTTACGG 0.989658 -65 CGAATATTACGCTAATGTCGGTTTTAACGTT 2 256 1 GCTAATGCGG 0.992866 -45 TGTTTGTCATGCTGTAGACGGATCATTATCT 3 30 1 GCTGTAGCGG 0.988678 -271 GAAGTTACTGGCTGGTGGAGGATTAGGTGGT 3 155 0 GCTGGTGAGG 0.987895 -146 TGCTAAACACGCTGACGCAGGGCGGCGAGAA 3 191 0 GCTGACGAGG 0.984266 -110 ******* *** Masking position 3 Map Score: 4.31922 Number of sites scoring better than the average of aligned sites = 1171 Number in coding regions = 1130 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 CGGGTATTAGCACCACATATAAGGAGATCCT 1 13 0 CACCACTATA 0.903304 -75 CTGACGATGTCATCAGGTTTACAAAGTGAAA 2 85 0 CATCAGTTTA 0.903824 -216 CTTACCATCTCGTTTTACAGGCTTAA 2 285 0 CATCTCTTTT 0.981944 -16 TCCGTAACGCATCTGTTTTTGTTTGTCATG 3 10 1 CATCTGTTTT 0.970951 -291 AGAATCTGAACATCGCATTATCTGTGTAGAA 3 77 1 CATCGCTTAT 0.899684 -224 CTTTTTATTTCACCACCTAATCCTCCACCAG 3 144 1 CACCACTAAT 0.903305 -157 CAGCCAGTAACTTCTCTTTTTCTCGCCGCCC 3 172 1 CTTCTCTTTT 0.90694 -129 TGCGGATAAACACCTGCTATTTTAATATTTG 3 229 0 CACCTGTATT 0.95332 -72 ****** **** Masking position 8 Map Score: 4.09709 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 551 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 TTGGTGGGTCGTGCAGGATGACTCG 2 6 0 GTGCAGGATG 0.997089 -295 ACAAAGTGAAATTGAGGATGCCTGAATAGC 2 66 0 ATTGAGGATG 0.955954 -235 TACGCCTAATGTGCAGGATGCGTCATTTTA 2 157 0 GTGCAGGATG 0.997089 -144 TTACTGGCTGGTGGAGGATTAGGTGGTGAA 3 152 0 GTGGAGGATT 0.988536 -149 ********** Masking position 5 Map Score: 4.74447 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 AGGATCTCCTTATATGTGGTGCTAATACCC 1 13 1 TATATGTGGT 0.816456 -75 AGCAACTCTATGTCGGTGGAATTAGGCGTA 2 129 1 TGTCGGTGGA 0.974015 -172 TATTCGCTGTTATCGGTGTAATTTGTTTTA 2 232 0 TATCGGTGTA 0.981992 -69 ATTACGCTAATGTCGGTTTTAACGTTAAGC 2 261 1 TGTCGGTTTT 0.938566 -40 TCCGTAACGCATCTGTTTTTGTTTGTCAT 3 10 1 CATCTGTTTT 0.810793 -291 AACATCGCATTATCTGTGTAGAAATGCCCA 3 85 1 TATCTGTGTA 0.971974 -216 ********** Masking position 7 Map Score: 1.36934 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 463 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ATTCGAGTGACTTTTCCCCACCATTCGACTAT 2 187 1 CTTTCCCACC 0.994823 -114 GTTAAATGGGCATTTCTACACAGATAATGCGA 3 89 0 CTTTCACACA 0.87177 -212 TAGAAATGCCCATTTAACTGCCTGAAGAGTAA 3 103 1 CTTTACTGCC 0.891427 -198 ACGGCCTTTTTATTTCACCACCTAATCCTCCA 3 139 1 TTTTCCCACC 0.993754 -162 TTTCACCACCTAATCCTCCACCAGCCAGTAAC 3 151 1 TATCCCCACC 0.910429 -150 AACTTCTCTTTTTCTCGCCGCCCTGCGTCAGC 3 180 1 TTCTCCCGCC 0.983367 -121 AAATAGCAGGTGTTTATCCGCACAACATGATG 3 238 1 TTTTACCGCA 0.934631 -63 * **** ***** Masking position 11 Map Score: 2.03172 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 1273 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 TCCAGATAGCTAACGAATCATAAGGTAGAA 1 60 0 TAACGAATCA 0.925556 -28 ATGCGTCATTTTACGCCTAATTCCACCGAC 2 140 0 TTACGCCTAA 0.888948 -161 AGGCGTAAAATGACGCATCCTGCACATTAG 2 152 1 TGACGCATCC 0.959435 -149 GTCACTCGAATTACGCCTAATGTGCAGGAT 2 168 0 TTACGCCTAA 0.888948 -133 TCCGTAACGCATCTGTTTTTGTTT 3 5 1 TAACGCATCT 0.962087 -296 ********** Masking position 3 Map Score: 0.541448 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 265 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 ********** No masking Map Score: 2.93755e-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 10 ********** No masking Map Score: 2.93755e-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: 2.93755e-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