AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i093_Galactoside_Transport_ecoli_hinf_reg_100.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 HI0821 207 galactose operon repressor (galR) #4 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #5 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 TACATACGGGTTACAACGTTAAAACGGTGCAA 2 65 0 TTACAAGTTA 0.860146 -215 AACAGCGTCATAACAACAATTAAAGCCGTTTT 2 124 1 TAACAAAATA 0.933654 -156 ATGTAATCGTTTACATTGATAAAAAACAGGAG 3 16 0 TTACATGATA 0.963951 -192 ATGTAAACGATTACATTAATTTATACTAAATT 3 32 1 TTACATAATT 0.923985 -176 CACGGTTTATTTACAATAATTTAGTATAAATT 3 49 0 TTACAAAATT 0.963312 -159 TCTTATTTTGTGACAAAGATCACGGTTTATTT 3 69 0 TGACAAGATA 0.956859 -139 CATAAATAATTTACGATAAATTGAAAGCGGTT 3 145 0 TTACGAAAAT 0.793399 -63 TTATAGATTATAACAAGGAAAAAGTT 3 192 1 TAACAAGAAA 0.869086 -16 TTTGTGACATGGATCACAAATTCATA 4 5 1 TGACATGATA 0.911259 -86 ATGAAAATGATTACATAAAAAATTATGAATTT 4 28 0 TTACATAAAA 0.923985 -63 ATGAGCAAATTTGCAAAAATGAAAATGATTAC 4 46 0 TTGCAAAATA 0.899453 -45 CATAGATTAATTACGATAATTTATTT 4 75 1 TTACGAAATT 0.892418 -16 TCCCCTTAGATTACAACAAAAATTGATGGGAA 5 12 0 TTACAAAAAA 0.963312 -54 ****** *** * Masking position 1 Map Score: 14.3728 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 206 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 ATAATTTTACCTTGTTGGCCATACA 1 46 0 TTTACCTTGT 0.949884 -15 TCACAGTATCTTAACAATGTGATAGCTATG 2 34 1 TTAACAATGT 0.891693 -246 TTGCACCGTTTTAACGTTGTAACCCGTATG 2 65 1 TTAACGTTGT 0.928625 -215 CTCCTGTTTTTTATCAATGTAAACGATTAC 3 16 1 TTATCAATGT 0.947868 -192 AAATAAACCGTGATCTTTGTCACAAAATAA 3 69 1 TGATCTTTGT 0.888743 -139 AACTTTTTCCTTGTTATAATCTAT 3 194 0 TTTTCCTTGT 0.976667 -14 TATGAATTTGTGATCCATGTCACAAA 4 7 0 TGATCCATGT 0.924776 -84 AAATTCATAATTTTTTATGTAATCATTTTC 4 28 1 TTTTTTATGT 0.686877 -63 TATGTAATCATTTTCATTTTTGCAAATTTG 4 43 1 TTTTCATTTT 0.699315 -48 TTCCCATCAATTTTTGTTGTAATCTAAGGG 5 12 1 TTTTTGTTGT 0.832432 -54 ********** Masking position 8 Map Score: 7.04631 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 659 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 CCGCTTTCAATCTGTGAGTGATTTCAC 2 7 1 TAATCTGTGA 0.921223 -273 GAAAACGGCTTTAATTGTTGTTATGACGCTG 2 126 0 TAATTGTTGT 0.911144 -154 TAATTTAGTATAAATTAATGTAATCGTTTAC 3 34 0 TAATTAATGT 0.908007 -174 TAATTTATACTAAATTATTGTAAATAAACCG 3 48 1 TAATTATTGT 0.955797 -160 GCTTATTTTCTTATTTTGTGACAAAGATCAC 3 78 0 TATTTTGTGA 0.794592 -130 CAATTTATCGTAAATTATTTATGATCAAAAT 3 154 1 TAATTATTTA 0.623803 -54 TAAAAAATTATGAATTTGTGATCCATGTCAC 4 14 0 TAATTTGTGA 0.964887 -77 ATTATCGTAATTAATCTATGAGCAAATTTGC 4 64 0 TAATCTATGA 0.839853 -27 AAATAAATTATCGTAATTAATCTA 4 77 0 TAATTATCGT 0.825969 -14 TTTCCCATCAATTTTTGTTGTAATCTAA 5 8 1 TAATTTTTGT 0.964835 -58 * ********* Masking position 5 Map Score: 6.94469 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 208 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 GCAGTAATAGACTGCGCCCAATCAGTC 1 8 0 ACTGCGCCCA 0.977285 -53 GCAGTCTATTACTGCGCCCTTATTGTATGG 1 23 1 ACTGCGCCCT 0.985218 -38 GATAGCTATGATTGCACCGTTTTAACGTTG 2 54 1 ATTGCACCGT 0.897948 -226 CATTAACTCTACTGCCCCGCCGAGCATTTA 2 221 1 ACTGCCCCGC 0.989914 -59 GGGAAGATCCACTTCCCCTTAGATTACAAC 5 27 0 ACTTCCCCTT 0.980256 -39 GGGAAGTGGATCTTCCCCTTTTTAAAGAGG 5 40 1 TCTTCCCCTT 0.924546 -26 ********** Masking position 3 Map Score: 4.22677 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 351 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 CACTCACAGATTGAAAGCGG 2 1 0 TTGAAAGCGG 0.992501 -279 GGGTTACAACGTTAAAACGGTGCAATCATA 2 60 0 GTTAAAACGG 0.960182 -220 GGTAACGCTCCAGAAAACGGCTTTAATTGT 2 139 0 CAGAAAACGG 0.903422 -141 AAGAACGAATTTTAAAAAGTGAGCTTCGGC 2 177 1 TTTAAAAAGT 0.736717 -103 TTACGATAAATTGAAAGCGGTTACTTTCAT 3 137 0 TTGAAAGCGG 0.992501 -71 TCTTCCCCTTTTTAAAGAGGTTGGAT 5 50 1 TTTAAAGAGG 0.966034 -16 ********** Masking position 5 Map Score: 4.03951 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 547 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 6 CCGCCGAGCATTTATCTCAAGCACTACCCT 2 237 1 TTTATCTCAA 0.888148 -43 GTATCTCCGGTTTTTCTTATGCAGGGTAGT 2 259 0 TTTTTCTTAT 0.925687 -21 TGACTCCTGTTTTTTATCAATGTAAACGAT 3 13 1 TTTTTATCAA 0.870295 -195 TCATAAAAAATTTTGCTTATTTTCTTATTT 3 93 0 TTTTGCTTAT 0.96239 -115 TTTTTTATGATTTAGTTCATACTTATGAAA 3 113 1 TTTAGTTCAT 0.887037 -95 AAATCTTATATTTTGATCATAAATAATTTA 3 164 0 TTTTGATCAT 0.969493 -44 ATTTTTGCAAATTTGCTCATAGATTAATTA 4 58 1 ATTTGCTCAT 0.950926 -33 ********** Masking position 9 Map Score: 3.50907 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 507 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 7 ATAATTTTACCTTGTTGGCCAT 1 49 0 AATTTTACCT 0.887489 -12 GTGATTATTCACTGTTACATACGGGTTACA 2 82 0 ACTGTTACAT 0.877087 -198 GTGAATAATCACTTTTGCCGAGGTAACAGC 2 100 1 ACTTTTGCCG 0.921023 -180 TTGTTATGACGCTGTTACCTCGGCAAAAGT 2 110 0 GCTGTTACCT 0.970451 -170 CGTTTTCTGGAGCGTTACCGGGCATGGAAG 2 150 1 AGCGTTACCG 0.825063 -130 GAGTTAATGAAGTGTTACTGAACGCCGAAG 2 200 0 AGTGTTACTG 0.911303 -80 GGTATCTCCGGTTTTTCTTATGCAGGGTA 2 261 0 GGTTTTTCTT 0.702258 -19 AATCATAAAAAATTTTGCTTATTTTCTTAT 3 95 0 AATTTTGCTT 0.694581 -113 TAAATTGAAAGCGGTTACTTTCATAAGTAT 3 131 0 GCGGTTACTT 0.79615 -77 AACTTTTTCCTTGTTATAATC 3 197 0 ACTTTTTCCT 0.91371 -11 ********** Masking position 5 Map Score: 2.41104 Number of sites scoring better than the average of aligned sites = 1305 Number in coding regions = 1169 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 8 ********** No masking Map Score: -1.36181e-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 9 ********** No masking Map Score: -1.36181e-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 ********** No masking Map Score: -1.36181e-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