AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i091_Sugar_Transport_3_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 xylF 300 xylose binding protein transport system #2 xylG 77 putative ATP-binding protein of xylose transport system #3 HI1110 50 D-xylose ABC transporter, ATP-binding protein (xylG) #4 HI1111 233 D-xylose ABC transporter, periplasmic-binding protein (xylF) Motif number 1 TCTCAATAGCAGTGTGAAATAACATAATTGA 1 19 0 ATGTGAAATA 0.800092 -282 AATAAAATGGAATGATGAAACTGGGTAATTC 1 78 1 ATGATGAAAC 0.824163 -223 GTAATTCCTCGAAGAGAAAAATGCAATAAGT 1 102 1 GAGAGAAAAA 0.976692 -199 ATCGTAATCGAAAGATAAAAATCTGTAATTG 1 187 1 AAGATAAAAA 0.91424 -114 TAGCAACTAAACAGGGGAAAACAATTACAGA 1 208 0 AAGGGGAAAA 0.864331 -93 CCCCTGTTTAGTTGCTAAAAATTGGTTACGT 1 222 1 GTGCTAAAAA 0.717334 -79 CACGCGGCATGGAGAGAAATCACGCCCCCGC 2 31 0 GAGAGAAATC 0.839073 -47 CTTTAAGAGGGAAGAGAAAACTCTTCCCTTA 3 11 1 GAGAGAAAAC 0.96526 -40 TTCATCACCTAGAGAGGAAAATGTT 4 5 0 AAGAGGAAAA 0.964624 -229 TTTTCGTATTTTTGTGAAAAACTAACTTTTC 4 38 1 TTGTGAAAAA 0.770696 -196 AAATAACATAATTGATGAAAAGTTAGTTTTT 4 54 0 ATGATGAAAA 0.876064 -180 CAAATAATCAACATAGAAAAATTAAATAACA 4 77 0 AATAGAAAAA 0.714548 -157 GTGGATCACAGTTGTGAAAAAACGTAATAAT 4 118 1 GTGTGAAAAA 0.95596 -116 CCTTTTTTAAAGTGTGAAAACTAACAACTGG 4 173 1 ATGTGAAAAC 0.933959 -61 * ********* Masking position 8 Map Score: 13.9682 Number of sites scoring better than the average of aligned sites = 1926 Number in coding regions = 1588 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 367 Fraction of orfs with sites within 600 bp upstream = 0.0589464 Motif number 2 TCAGTTGCTCAATTATGTTATTTCACACTGC 1 9 1 TCATTATTAT 0.967534 -292 GTTTCATCATTCCATTTTATTTTGCGAGCGAGC 1 66 0 TCATTTTTTT 0.895477 -235 TTTTTATCTTTCGATTACGATTTTTGGTTTATT 1 175 0 TCATTACATT 0.960909 -126 GGAAGAGTTTTCTCTTCCCTCTTAAAG 3 5 0 TCCTTCCTTT 0.911239 -46 AGAAAACTCTTCCCTTACCTCTTAGGGAGTTAC 3 25 1 TCCTTACTTT 0.974781 -26 TAACTTTTCATCAATTATGTTATTTAATTTTTC 4 60 1 TCATTATTAT 0.967534 -174 AAAATCTTTCTCCATTATTACGTTTTTTCACAA 4 129 0 TCATTATAGT 0.901669 -105 AAAAAGGCTTTCAATTATAAAATCTTTCTCCAT 4 147 0 TCATTATAAT 0.939877 -87 AACTAGTCCTTCACTTAACTATTGAGGTATCAA 4 210 1 TCCTTAATTT 0.90679 -24 ** ***** * ** Masking position 6 Map Score: 5.45269 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 92 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TTGAGATAATTCACAAGTGTGCGCTCGCTCG 1 44 1 TCCAAGTGTG 0.991043 -257 TTGTTACTTATTAAAACTGTCCTCTAACTAC 1 265 1 TTAAACTGTC 0.949545 -36 TGTTGATTATTTGCAACTGTGGCGTGGATCA 4 95 1 TTCAACTGTG 0.993347 -139 TTACGTTTTTTCACAACTGTGATCCACGCCA 4 114 0 TCCAACTGTG 0.993834 -120 GAAAGCCTTTTTTAAAGTGTGAAAACTAACA 4 168 1 TTAAAGTGTG 0.978491 -66 ** ******** Masking position 6 Map Score: 5.14931 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GCGTTACGCCCCAGCGCGGAGCGG 2 5 1 TACGCCCCAG 0.996633 -73 GGAGAGAAATCACGCCCCCGCTCCGCGCTG 2 22 0 CACGCCCCCG 0.998404 -56 AACTGTGATCCACGCCACAGTTGCAAATAA 4 101 0 CACGCCACAG 0.996633 -133 ********** Masking position 2 Map Score: 3.36254 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 TTGCATTTTTCTCTTCGAGGAATTACCCAG 1 98 0 CTCTTCGAGG 0.966732 -203 GCGTTACGCCCCAGCGCGGAGCGGGGGCG 2 10 1 CCCAGCGCGG 0.980232 -68 CTTTAAGAGGGAAGAGAAAA 3 1 1 CTTTAAGAGG 0.955255 -50 ATCGTAACTCCCTAAGAGGTAAGGGAAGA 3 32 0 CCCTAAGAGG 0.990295 -19 AATTTCATCACCTAGAGAGGAAAATGTT 4 9 0 CCTAGAGAGG 0.89845 -225 ********** Masking position 7 Map Score: 2.13594 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 193 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 TTCTTGATTTATGACCGAGATCTTACTTTT 1 146 0 ATGACCGAGA 0.99135 -155 ATAAGTAACAATCACCGCGATAAACGTAAC 1 246 0 ATCACCGCGA 0.994391 -55 GAAAAATTTCATCACCTAGAGAGGAAAATG 4 13 0 ATCACCTAGA 0.987233 -221 ********** Masking position 4 Map Score: 0.873514 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 55 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 CAATAGCAGTGTGAAATAACATAATTGAGCA 1 16 0 GTGAATAACA 0.817787 -285 CTGCTATTGAGATAATTCACAAGTGTGCGCT 1 38 1 GATAATCACA 0.957559 -263 AGAAAAATGCAATAAGTACAATTGCGCAACA 1 116 1 AATAATACAA 0.71177 -185 TAAATCAAGAAATAAACCAAAAATCGTAATC 1 165 1 AATAACCAAA 0.748827 -136 GGACAGTTTTAATAAGTAACAATCACCGCGA 1 256 0 AATAATAACA 0.97599 -45 ACATAGAAAAATTAAATAACATAATTGATGA 4 67 0 ATTAATAACA 0.93703 -167 CACAGTTGCAAATAATCAACATAGAAAAATT 4 85 0 AATAACAACA 0.958365 -149 TTTAAAGTGTGAAAACTAACAACTGGAGCAA 4 178 1 GAAAATAACA 0.892145 -56 ***** ***** Masking position 5 Map Score: 2.37198 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 344 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 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