AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i069_Serine_Metabolism_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 pabB 73 p-aminobenzoate synthetase, component I #2 sdaA 183 L-serine deaminase #3 sdaC 300 probable serine transporter #4 HI0288 34 L-serine deaminase (sdaA) #5 HI0289 222 serine transporter (sdaC) #6 HI0291 74 H. influenzae predicted coding region HI0291 #7 HI0292 76 mercuric ion scavenger protein (merP) Motif number 1 CAGTCCTGACTCTACTGGCTATGTGCCGGGTAG 1 51 0 TACTCTCATG 0.979028 -23 GATAATACTCCTGACAAGGTGACTGGACT 2 165 0 TACTCTCAGG 0.995124 -19 TTAAACGACATCTGACTTCTTCCGGGGCGCGCAA 3 8 0 TTCTCTCGGG 0.972863 -293 AGCGTTGGGATAATCTATCTTCCAAGTAGATTATTGT 3 95 1 TATACTCAGT 0.893194 -206 TACACACAAGTTATGTATCTATCAGTGATCTTGATCT 3 137 0 TATACTCGTG 0.943786 -164 ATTTTTACGGTCAGGCACCTTCCCGGGCTGAACTGGC 3 236 1 TACACTCGGG 0.996894 -65 CATTCATCAATAAAACAACTAACAAGGAGTAAAA 6 51 1 TACACTCAGG 0.996955 -24 TAACCATCAATAAAACAACTAACAAGGAGTAAAA 7 53 1 TACACTCAGG 0.996955 -24 * * ** ** * *** Masking position 10 Map Score: 10.5689 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 77 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 TTAAATTCTCTTTTACTTTTGATTTACAGAGTAA 3 61 1 TTTTATTGTT 0.978343 -240 TTTCATTTATTTTTATACGCAATC 5 1 1 TTTCATTTTT 0.95041 -222 AATTGACAAATTTAAGTAATTTATGCTTTGGAGC 5 194 1 TTTAATTTAT 0.71997 -29 AAAAATTTCAATTCAGATTGGTGGGATGG 6 6 1 TTTCATAGTT 0.844906 -69 TTGTTAGTTGTTTTATTGATGAATGCGATTGGCA 6 42 0 TTTTATTGAT 0.942957 -33 TTTTACTCCTTGTTAGTTGTTTTA 6 61 0 TTTTATTTTT 0.96608 -14 TTGTTAGTTGTTTTATTGATGGTTAAACTATAAA 7 44 0 TTTTATTGTT 0.978343 -33 TTTTACTCCTTGTTAGTTGTTTTA 7 63 0 TTTTATTTTT 0.96608 -14 ***** * ** ** Masking position 5 Map Score: 5.99466 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 82 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 ACTCCTGCTAAATTGTTGGCGCTAATTATTT 1 16 1 AATTGTGGCG 0.981107 -58 GTAAAAGAGAATTTAAGGGCAATATTTGCCC 3 46 0 ATTTAAGGCA 0.975512 -255 CGCCGTAATAATTTGAGGGCGGAAAGATACA 3 170 0 ATTTGAGGCG 0.981107 -131 CTAAAAGCTGAATTATTTGCATTCCTCCAGG 3 272 1 AATTATTGCA 0.860387 -29 ATTCGTTAAAAATTAAAGGCGA 4 2 0 AATTAAGGCG 0.984286 -33 GAGATTCTCTATTTATTGGCATAACATAATA 5 130 1 ATTTATGGCA 0.975512 -93 ****** **** Masking position 4 Map Score: 4.39123 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 194 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TACAAAACACTACTTGAGACAATCATCGCAATATTAGTTAAA 2 30 1 TGCATTCGCT 0.989543 -154 TCACATGAATTAAACTAATCAAAAACCGCGATTTAACTAATA 2 61 0 TACAACCGCT 0.992307 -123 TTCATGTGAATAGTTAAGCCAGTCGCCGCGTTCCCTCTTACA 2 94 1 TGCATCCGCT 0.997125 -90 TCAGATGTCGTTTAATGGGCAAATATTGCCCTTAAATTCTCT 3 30 1 TGCAATTGCT 0.904088 -271 CTATCGGCGATGGCTTAATCATTTACCGCCGTAATAATTTGA 3 185 0 TACATCCGCT 0.994081 -116 CCGATTTTTTTGTCGCTGAAAATTACCGCACTTTTTATAAAA 5 50 1 TGAATCCGCT 0.978258 -173 AATTTGTCAATTTGTAGAGCAAAATCCGCTCCAACTAAATTT 5 164 0 TACAACCGCC 0.975423 -59 * * ** * **** * Masking position 11 Map Score: 3.53469 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 239 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GCGATGATTGTCTCAAGTAGTGTTTTGTAGATGT 2 25 0 TCCAATAGTT 0.973455 -159 GAGACAATCATCGCAATATTAGTTAAATCGCGGT 2 45 1 TCCAAATGTT 0.973442 -139 GTGATCTTGATCTCAAATACAATAATCTACTTGG 3 116 0 TCCAATAATA 0.785084 -185 GGAAAGATACACACAAGTTATGTATCTATCAGTG 3 147 0 ACCAATTGTA 0.96571 -154 AAATTTCTCAAAATTCGTTAAAAATTAAA 4 16 0 TCCAAATGTT 0.973333 -19 TTTAACTTGATCACAATTTTAGAATTTGCTCTTT 5 96 1 TCCAATTGAA 0.930721 -127 ATAACATAATACTCAAATTTAGTTGGAGCGGATT 5 150 1 ACCAATTGTT 0.973296 -73 ** *** ** *** Masking position 6 Map Score: 2.59176 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 37 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TGTGTGTATCTTTCCGCCCTCAAATTATTA 3 166 1 TTTCCGCCCT 0.992188 -135 GCTTAATCATTTACCGCCGTAATAATTTGA 3 185 0 TTACCGCCGT 0.991852 -116 TCGCTGAAAATTACCGCACTTTTTATAAAA 5 62 1 TTACCGCACT 0.987969 -161 ********** Masking position 2 Map Score: 0.595297 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 58 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TGCTAAATTGTTGGCGCTAATTATTTCATG 1 21 1 TTGGCGCTAA 0.742876 -53 ACCGATTTTTTTGTCGCTGAAAATTACCGC 5 49 1 TTGTCGCTGA 0.967831 -174 TCAAATTTAGTTGGAGCGGATTTTGCTCTA 5 162 1 TTGGAGCGGA 0.983999 -61 AATTTATGCTTTGGAGCAAACT 5 211 1 TTGGAGCAAA 0.946786 -12 ********** Masking position 2 Map Score: 0.541739 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 160 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AAAACCGCGATTTAACTAATATTGCGATGA 2 52 0 TTTAACTAAT 0.964083 -132 TTCACATGAATTAAACTAATCAAAAACCGC 2 74 0 TTAAACTAAT 0.95464 -110 CGGCGACTGGCTTAACTATTCACATGAATT 2 92 0 CTTAACTATT 0.818922 -92 TATTTGCCCATTAAACGACATCTGACTTCT 3 25 0 TTAAACGACA 0.735263 -276 GCCTTTAATTTTTAACGAATTTTGAGAAAT 4 13 1 TTTAACGAAT 0.948565 -22 AATTGACAAATTTAAGTAATTTATGCTTTG 5 194 1 TTTAAGTAAT 0.839924 -29 TTATTGATGGTTAAACTATAAACCTTTACA 7 36 0 TTAAACTATA 0.830788 -41 ********** Masking position 5 Map Score: 0.972666 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 68 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 ********** No masking Map Score: -4.02005e-14 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: -4.02005e-14 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: -4.02005e-14 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