AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i097_Phosphate_Transport_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pitB 291 low-affinity phosphate transport #2 gsp 156 glutathionylspermidine synthetase/amidase #3 HI1603 207 conserved hypothetical protein #4 HI1604 24 phosphate permease, putative Motif number 1 CAGGTATTCCACTGGTTAATATATTCACATAT 1 109 0 AGGTTAATAT 0.979683 -183 CACTCTTTTTATCGTTAAAAAATGATATTTCA 1 201 1 AGTTAAAAAA 0.873005 -91 CGGCATGGGCAAAGTGAAATATCATTTTTTAA 1 215 0 AGTGAAATAT 0.870765 -77 GGCTGGCGCAAAGGGTTAAAAAATTCACATTC 2 21 0 AGGTTAAAAA 0.979684 -136 AGAAAATTTGAAAGGTAAAAAA 3 1 0 AGGTAAAAAA 0.967803 -207 TAAGTAAGCAACTGGGTAATATTTCCTAGTGT 3 74 0 AGGGTAATAT 0.979281 -134 ATCAACAAAAATCGGGTAATATGCGCACGAAT 3 155 1 AGGGTAATAT 0.979281 -53 CTCCAAATTAAGGGGTTAAAAATTCGTGCGCA 3 176 0 AGGTTAAAAA 0.979684 -32 * ********* Masking position 8 Map Score: 9.25719 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 234 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 TAGCAACCCCGTACTGATTATGAAGAATAA 1 20 1 GTACTGATTA 0.976273 -272 ATTAATCCCCGTACTGATTATTCTTCATAA 1 37 0 GTACTGATTA 0.976273 -255 AATATTGAATATTTTGATTAATCCCCGTAC 1 53 0 ATTTTGATTA 0.83626 -239 GAATACCTGTGTTTTGATTATTTCTAAAGG 1 132 1 GTTTTGATTA 0.975232 -160 GCCGTTAAAGTCACTGATAATGCGTCCGTT 1 243 1 TCACTGATAA 0.666688 -49 TAATTGTTGTGCTCTGATTACCTGCTCAGC 2 100 0 GCTCTGATTA 0.961208 -57 TGCTTAGGTTGTATTGTTAAAGGTAAAGTG 2 137 1 GTATTGTTAA 0.879414 -20 TATTACCCGATTTTTGTTGATAGTTAAAAT 3 146 0 TTTTTGTTGA 0.760703 -62 TATTTCCTATGTTTTGTTGA 4 1 0 GTTTTGTTGA 0.932879 -24 ********** Masking position 5 Map Score: 7.49015 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 562 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 TAATATATTCACATATGAAATGAATAAATAT 1 94 0 ACATAGAAAT 0.970567 -198 AATAATCAAAACACAGGTATTCCACTGGTTA 1 123 0 ACACAGTATT 0.960121 -169 ATTGTCTGATACACAAGAAATAACACTCTTT 1 178 1 ACACAGAAAT 0.989857 -114 GGTAATCAGAGCACAACAATTACGCCAACTG 2 108 1 GCACACAATT 0.948851 -49 CGGGTAATATGCGCACGAATTTTTAACCCCT 3 167 1 GCGCAGAATT 0.967302 -41 TCAACAAAACATAGGAAATAAACT 4 9 1 ACATAGAAAT 0.970567 -16 ***** ***** Masking position 5 Map Score: 3.73743 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 85 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ATATATAAATATTGAATATTTTGATTAATCC 1 59 0 ATTGAATTTT 0.82071 -233 TGAATAAATATTGGAATATATAAATATTGAA 1 74 0 TTGGAATTAT 0.896281 -218 TCATTTCATATGTGAATATATTAACCAGTGG 1 102 1 TGTGAATTAT 0.933286 -190 TTCAAAACCTTTAGAAATAATCAAAACACAG 1 138 0 TTAGAAAAAT 0.760754 -154 TTCTAAAGGTTTTGAATGAATGCTTATTGTC 1 153 1 TTTGAATAAT 0.935916 -139 ATTACGCCATTTTGAATTTACGAACGGACGC 1 264 0 TTTGAATTAC 0.871547 -28 CTGTACAGAATGTGAATTTTTTAACCCTTTG 2 14 1 TGTGAATTTT 0.933287 -143 TTTTTTACCTTTCAAATTTTCTCGCTTTTA 3 10 1 TTTCAAATTT 0.855957 -198 ACCTTTTTTCTTACAAATTTTTTTGAAAAAT 3 117 1 TTACAAATTT 0.652515 -91 TACAAATTTTTTTGAAAAATTTTAACTATCA 3 128 1 TTTGAAAATT 0.909605 -80 ******* *** Masking position 6 Map Score: 3.23418 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 301 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 TTAACGGCATGGGCAAAGTGAAATATCATT 1 221 0 GGGCAAAGTG 0.995659 -71 GCAGCGGCTGGCGCAAAGGGTTAAAAAATT 2 28 0 GCGCAAAGGG 0.986098 -129 GTATTGTTAAAGGTAAAGTG 2 147 1 AGGTAAAGTG 0.966001 -10 CGCTTTTAAAGCGAAAAGTGTATTGAGTTA 3 33 1 GCGAAAAGTG 0.982972 -175 AACAAAAATCGGGTAATATGCGCACGAATT 3 158 1 GGGTAATATG 0.896221 -50 ********** Masking position 5 Map Score: 3.02026 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 283 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ATGTTGTAGCAACCCCGTACTGATTATGAA 1 14 1 AACCCCGTAC 0.996164 -278 ATTTTGATTAATCCCCGTACTGATTATTCT 1 43 0 ATCCCCGTAC 0.99036 -249 TGAATTTTTTAACCCTTTGCGCCAGCCGCT 2 26 1 AACCCTTTGC 0.961219 -131 ACGAATTTTTAACCCCTTAATTTGGAGTAA 3 181 1 AACCCCTTAA 0.976881 -27 ********** Masking position 8 Map Score: 2.54755 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 34 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TAAATTCAAAATGGCGTAATCTAATAT 1 275 1 ATGGCGTAAT 0.978008 -17 ATCGCAGCGGCTGGCGCAAAGGGTTAAAAA 2 31 0 CTGGCGCAAA 0.956157 -126 ACCTAAGCAGTTGGCGTAATTGTTGTGCTC 2 116 0 TTGGCGTAAT 0.985325 -41 ACCCCTTAATTTGGAGTAAATCACTT 3 192 1 TTGGAGTAAA 0.961777 -16 ********** Masking position 8 Map Score: 1.6841 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 235 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AACCCTTTGCGCCAGCCGCTGCGATGAGGT 2 36 1 GCCAGCCGCT 0.995592 -121 CAACAATTACGCCAACTGCTTAGGTTGTAT 2 121 1 GCCAACTGCT 0.988489 -36 GGAAATATTACCCAGTTGCTTACTTAGTCG 3 80 1 CCCAGTTGCT 0.981903 -128 ********** Masking position 4 Map Score: 0.00177326 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 255 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 4.35863e-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: 4.35863e-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: 4.35863e-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