AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i093_Galactoside_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 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #2 mglB 279 galactose-binding transport protein; receptor for galactose taxis #3 galS 141 mgl repressor, galactose operon inducer #4 folE 257 GTP cyclohydrolase I #5 HI0821 207 galactose operon repressor (galR) #6 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #7 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 TCACAGTATCTTAACAATGTGATAGCTATGAT 2 34 1 TTAACATGTA 0.800114 -246 TTGCACCGTTTTAACGTTGTAACCCGTATGTA 2 65 1 TTAACTTGTA 0.84055 -215 CAAAAGTGATTATTCACTGTTACATACGGGTT 2 85 0 TATTCCTGTA 0.785181 -195 AAAACGGCTTTAATTGTTGTTATGACGCTGTT 2 124 0 TAATTTTGTA 0.943233 -156 TCATACCGTTTATTCAATGTGCTGTGAGTAAC 4 47 1 TATTCATGTC 0.761275 -211 TTCACAGCGATAATTATTGTAATTGCCGCTGC 4 128 0 TAATTTTGTA 0.94323 -130 ATTTACAGCCTGATTATTGTGCGTGAGGCGGC 4 175 0 TGATTTTGTC 0.786297 -83 CTCCTGTTTTTTATCAATGTAAACGATTACAT 5 16 1 TTATCATGTA 0.95844 -192 AATTTAGTATAAATTAATGTAATCGTTTACAT 5 32 0 AAATTATGTA 0.686495 -176 AATTTATACTAAATTATTGTAAATAAACCGTG 5 49 1 AAATTTTGTA 0.74252 -159 AAATAAACCGTGATCTTTGTCACAAAATAAGA 5 69 1 TGATCTTGTA 0.961616 -139 AACTTTTTCCTTGTTATAATCTATAA 5 192 0 TTTTCTTGTA 0.939918 -16 TATGAATTTGTGATCCATGTCACAAA 6 5 0 TGATCATGTA 0.95006 -86 AAATTCATAATTTTTTATGTAATCATTTTCAT 6 28 1 TTTTTATGTA 0.866635 -63 TTCCCATCAATTTTTGTTGTAATCTAAGGGGA 7 12 1 TTTTTTTGTA 0.895375 -54 ***** **** * Masking position 8 Map Score: 13.7137 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 220 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 CTATCACATTGTTAAGATACTGTGAAATCACT 2 27 0 GTTAAAACTG 0.985938 -253 GGGTTACAACGTTAAAACGGTGCAATCATAGC 2 58 0 GTTAAAGGTG 0.967977 -222 TTTAATTGTTGTTATGACGCTGTTACCTCGGC 2 116 0 GTTATAGCTG 0.968089 -164 GGGCAGTAGAGTTAATGAAGTGTTACTGAACG 2 206 0 GTTAAGAGTG 0.895421 -74 GATCACATTCGTTAACAAAACGGCTGTAACCG 3 18 1 GTTAAAAACG 0.917232 -124 TTCACTACCTGTTATGAGATTGCAGTAAATGA 3 119 0 GTTATAATTG 0.925527 -23 ATCAGCAGATGTTAAAACATCGTTATGCAAAT 4 91 0 GTTAAAATCG 0.951318 -167 TGGGGGCAAAGTTATTAAGCTGATTTACAGCC 4 197 0 GTTATAGCTG 0.968089 -61 CTAAATTATTGTAAATAAACCGTGATCTTTGT 5 57 1 GTAAAAACCG 0.901154 -151 ***** * **** Masking position 4 Map Score: 6.90082 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 135 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 CCGCTTTCAATCTGTGAGTGA 2 2 1 CGCTTTCAAT 0.894626 -278 ACCGTTTTAACGTTGTAACCCGTATGTAAC 2 69 1 CGTTGTAACC 0.763879 -211 GTTGTTATGACGCTGTTACCTCGGCAAAAG 2 111 0 CGCTGTTACC 0.910172 -169 TCCAGAAAACGGCTTTAATTGTTGTTATGA 2 131 0 GGCTTTAATT 0.656729 -149 TTAACAAAACGGCTGTAACCGTTTCCATTG 3 29 1 GGCTGTAACC 0.961863 -113 CCGTTTCCATTGCTGTGACTCGATTCACGA 3 47 1 TGCTGTGACT 0.961722 -95 GTTATGAGATTGCAGTAAATGACTGCTTGC 3 111 0 TGCAGTAAAT 0.716694 -31 TTATTCAATGTGCTGTGAGTAACTTTCACT 4 56 1 TGCTGTGAGT 0.877084 -202 CAATAATTATCGCTGTGAATACTGGATTAT 4 141 1 CGCTGTGAAT 0.980363 -117 ACAATAATCAGGCTGTAAATCAGCTTAATA 4 187 1 GGCTGTAAAT 0.969047 -71 TGAAAGTAACCGCTTTCAATTTATCGTAAA 5 138 1 CGCTTTCAAT 0.894626 -70 ********** Masking position 8 Map Score: 6.66844 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 897 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 AGTCTATTACTGCGCCCTTATTGTATGGCCAACA 1 25 1 TGCCCTTTTT 0.947359 -36 TAACAACAATTAAAGCCGTTTTCTGGAGCGTTAC 2 134 1 TAGCCGTTTT 0.975911 -146 GGTATCTCCGGTTTTTCTTATGCAGG 2 264 0 TATCCGGTTT 0.971559 -16 TGGAAACGGTTACAGCCGTTTTGTTAACGAATGT 3 22 0 TAGCCGTTTT 0.97596 -120 GCGTGGCTCCTTGTTGTGTTGTTTGCA 4 4 1 TGTCCTTTTT 0.980087 -254 TAAGCTGATTTACAGCCTGATTATTGTGCGTGAG 4 180 0 TAGCCTGTTT 0.975954 -78 TTTGACTCCTGTTTTTTATCAATGTA 5 3 1 TGTCCTGTTT 0.975959 -205 AAATTTTGCTTATTTTCTTATTTTGTGACAAAGA 5 82 0 TATTCTTTTT 0.831159 -126 AACTTTTTCCTTGTTATAATCTATAAA 5 191 0 TTTCCTTTTT 0.925307 -17 ** ***** ** * Masking position 11 Map Score: 7.78396 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 184 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 CGTTCTTCCATGCCCGGTAACGCTCCAGAAAAC 2 151 0 TGCGGTAAGC 0.960011 -129 GAAGTGTTACTGAACGCCGAAGCTCACTTTTTA 2 189 0 TGAGCCGAGC 0.938132 -91 TTGAGATAAATGCTCGGCGGGGCAGTAGAGTTA 2 224 0 TGCGGCGGGC 0.998493 -56 GTTTTTCTTATGCAGGGTAGTGCTTGAGATAAA 2 247 0 TGCGGTAGGC 0.990563 -33 AGTAAATGACTGCTTGCTGGCGGCTATTTTGTC 3 95 0 TGCGCTGGGG 0.983162 -47 CATCTGCTGATGAAAGGCAGCGGCAATTACAAT 4 112 1 TGAGGCAGGG 0.978272 -146 GATTATTGTGCGTGAGGCGGCGCACATAATCCA 4 163 0 CGTGGCGGGC 0.983654 -95 TTTGCCCCCACGCAGGGCGGAGGCGTCACACCT 4 219 1 CGCGGCGGGG 0.995827 -39 *** ***** ** Masking position 6 Map Score: 9.48395 Number of sites scoring better than the average of aligned sites = 1213 Number in coding regions = 1174 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 TGCAGGGTAGTGCTTGAGATAAATGCTCGGC 2 239 0 TGCTTGGATA 0.861681 -41 AGCACTACCCTGCATAAGAAAAACCGGAGAT 2 256 1 TGCATAGAAA 0.974533 -24 CTGTATTCAGTGCTGACAAAATAGCCGCCAG 3 81 1 TGCTGAAAAA 0.957027 -61 ATAAACGGTATGATGAAGAAATTGCAAACAA 4 29 0 TGATGAGAAA 0.915779 -229 TTTTAACATCTGCTGATGAAAGGCAGCGGCA 4 106 1 TGCTGAGAAA 0.989834 -152 GCGTCACACCTGCAGGAGAAATCATAA 4 241 1 TGCAGGGAAA 0.971728 -17 ATTTAGTTCATACTTATGAAAGTAACCGCTT 5 122 1 TACTTAGAAA 0.933516 -86 TGAAAATGATTACATAAAAAATTATGAATTT 6 28 0 TACATAAAAA 0.666881 -63 ****** **** Masking position 9 Map Score: 5.13989 Number of sites scoring better than the average of aligned sites = 950 Number in coding regions = 875 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 GACTGATTGGGCGCAGTCTATTACTGC 1 8 1 TGGGCGCAGT 0.966786 -53 CCATACAATAAGGGCGCAGTAATAGACTGC 1 23 0 AGGGCGCAGT 0.972587 -38 CAACGTTAAAACGGTGCAATCATAGCTATC 2 54 0 ACGGTGCAAT 0.836797 -226 TAAATGCTCGGCGGGGCAGTAGAGTTAATG 2 221 0 GCGGGGCAGT 0.987772 -59 TGTGCGTGAGGCGGCGCACATAATCCAGTA 4 160 0 GCGGCGCACA 0.896701 -98 CCGCCCTGCGTGGGGGCAAAGTTATTAAGC 4 209 0 TGGGGGCAAA 0.899434 -49 GTTGTAATCTAAGGGGAAGTGGATCTTCCC 7 27 1 AAGGGGAAGT 0.908779 -39 CCTCTTTAAAAAGGGGAAGATCCACTTCCC 7 40 0 AAGGGGAAGA 0.861306 -26 ********** Masking position 8 Map Score: 4.04137 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 1001 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 ATTGTTGTTATGACGCTGTTACCTCGGCAA 2 114 0 TGACGCTGTT 0.920114 -166 TAACAACAATTAAAGCCGTTTTCTGGAGCG 2 134 1 TAAAGCCGTT 0.983202 -146 TGGAAACGGTTACAGCCGTTTTGTTAACGA 3 26 0 TACAGCCGTT 0.952859 -116 CGTATTTGCATAACGATGTTTTAACATCTG 4 88 1 TAACGATGTT 0.914156 -170 ACGATAAATTGAAAGCGGTTACTTTCATAA 5 135 0 GAAAGCGGTT 0.954617 -73 TTCCCCTTTTTAAAGAGGTTGGAT 7 52 1 TAAAGAGGTT 0.952083 -14 ********** Masking position 9 Map Score: 1.67216 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 247 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ********** No masking Map Score: 3.33488e-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 TACTGTGAAATCACTCACAGATTGAAAGCGG 2 10 0 TACTCACAAT 0.950332 -270 AAGTATGAACTAAATCATAAAAAATTTTGCTT 5 105 0 TAATCATAAA 0.872902 -103 ATCTTATATTTTGATCATAAATAATTTACGAT 5 160 0 TGATCATAAT 0.977666 -48 TTATAATCTATAAATCTTATATTTTGATCATA 5 173 0 TAATCTTAAT 0.872902 -35 TTTGTGACATGGATCACAAATTCATAATTTT 6 10 1 TGATCACAAT 0.973184 -81 TTTTGCAAATTTGCTCATAGATTAATTACGAT 6 60 1 TGCTCATAAT 0.973184 -31 * ******* ** Masking position 5 Map Score: 0.307858 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 20 Number in noncoding regions = 23 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: 3.33488e-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: 3.33488e-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: 3.33488e-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