AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_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 fruB 300 PTS system, fructose-specific IIA/fpr component #2 ptsH 300 PTS system protein HPr #3 ptsI 44 PEP-protein phosphotransferase system enzyme I #4 crr 40 PTS system, glucose-specific IIA component #5 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #6 BIME180 41 BIME #7 mtlD 88 mannitol-1-phosphate dehydrogenase #8 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #9 HI0449 86 H. influenzae predicted coding region HI0449 #10 HI0451 71 conserved hypothetical protein #11 HI0452 50 conserved hypothetical protein #12 HI0453 26 conserved hypothetical protein #13 HI0454 54 conserved hypothetical protein #14 HI0457 69 conserved hypothetical protein #15 HI0458 70 stationary phase survival protein SurA, putative #16 HI0459 131 pyrimidine operon regulatory protein (pyrR) #17 HI1009 158 glycerol-3-phosphate regulon repressor (glpR) #18 HI1711 59 PTS system, glucose-specific IIA component (crr) #19 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #20 HI1713 158 phosphocarrier protein HPr (ptsH) #21 HI1714 70 conserved hypothetical protein Motif number 1 GAAACAGAAGTATTATGCTTTCTTGAAACGT 1 188 1 TATTATGTTT 0.832944 -113 GCTGAATCGATTTTATGATTTGGTTCAATTC 2 92 1 TTTTATGTTT 0.970628 -209 ACATTTTTGTTTTGATGGTTTGTTGAA 5 7 0 TTTGATGTTT 0.964465 -294 AAATCGCCGCCTTGTTGCTTTTTTACACAAG 5 72 1 CTTGTTGTTT 0.874988 -229 TCTTGCTCCTTAATAATTTAAAAAGAAAG 8 53 0 CTTAATATTT 0.567637 -19 ACCTCAAATTTTTTATGGTTTTATAACATAA 10 46 0 TTTTATGTTT 0.970628 -26 GGTCGTTTTCTTTTATATTTTTGAGTA 11 34 1 TTTTATATTT 0.941557 -17 CCCCTTTATTTTTGATACTTTG 14 2 0 TTTGATATTT 0.929736 -68 AATTGCCCCTTTTGTTGTTTTTTATTTTCTC 14 36 1 TTTGTTGTTT 0.950602 -34 GGCGTATTTTCTTTATACTTTGTGCATTGAA 16 87 1 CTTTATATTT 0.854219 -45 AATGTTATTTTTTGTTAATTTTAGTGATAAA 17 103 1 TTTGTTATTT 0.903677 -56 ACAAAATTATTTGATTTTACGTTAAAA 18 7 1 TTATTTGTTT 0.653005 -53 CTATTGTTTATTTATTACTTTGTTAATTGTT 19 46 1 TTTATTATTT 0.719046 -34 TTTAGCTTATTTTTATGATTTAATTCAGGCT 20 41 1 TTTTATGTTT 0.970628 -118 TATTCTTGATTATTTTGCTTTGAAAAAGGAT 20 82 1 TATTTTGTTT 0.779502 -77 AATTTTCTGGTTTTATATTTTTAATTATTGA 20 121 1 TTTTATATTT 0.941557 -38 ATGCAAAAATTTTTTTCATTTTACCAAAAAC 21 26 1 TTTTTTCTTT 0.752103 -45 ******* *** Masking position 6 Map Score: 19.4006 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 246 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 2 AAATCAAAAGCGCCACGAATAGTCAAA 1 7 1 AAAGCGCCCG 0.96024 -294 TTTCATTTCAGCAGCGTCAGCAGCCAATCAG 1 55 0 GCAGCGTCGC 0.842149 -246 TATGAGAAAAAAAGCGCCAACCTGGCTTAGG 1 242 0 AAAGCGCCAC 0.922688 -59 AATGACGTACGAAACGTCAGCGGTCAACACC 2 145 1 GAAACGTCGC 0.954986 -156 GGCTAAAGTCGAACCGCCAGGCTAGACTTTA 2 243 1 GAACCGCCGG 0.876954 -58 TTTTTAGCGAAAATCGCCGCCTTGTTGCTTT 5 62 1 AAATCGCCCC 0.922688 -239 ACATTAACAAAAAACCTCGGGCTTCCAGCCT 5 248 1 AAAACCTCGG 0.804633 -53 TCCCTCACCCAAACCCTCTCCGTGAGGAGAG 7 17 0 AAACCCTCCC 0.864689 -72 GGGTGAGGGAAAAGCCTCACCCCAGCCCTCT 7 38 1 AAAGCCTCCC 0.938059 -51 TAAAGTTAATAAAACGCCGCCATTATACTGT 9 59 0 AAAACGCCCC 0.979747 -28 AATATAAAAGAAAACGACCGCACTTTGCGAC 11 22 0 AAAACGACGC 0.963231 -29 ATACGCCTAAAAAGCGACGGCATTTGCACCA 16 63 0 AAAGCGACGC 0.976622 -69 AACAAGGGAAAAAACGACCGCACTTTT 21 54 1 AAAACGACGC 0.963231 -17 ******** ** Masking position 3 Map Score: 12.4005 Number of sites scoring better than the average of aligned sites = 1720 Number in coding regions = 1612 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 ATCAGCAATTTCATTTCAGCAGCGTCAGCA 1 64 0 TCATTTCAGC 0.938795 -237 CATAATACTTCTGTTTCAGCACGCAAGGAA 1 175 0 CTGTTTCAGC 0.944991 -126 CTTTCTTGAAACGTTTCAGCGCGATCTTGT 1 205 1 ACGTTTCAGC 0.971335 -96 CTGAATTGAAACGATTCAGCCTCTATGAGA 1 266 0 ACGATTCAGC 0.976607 -35 CTGAATCGTTTCAATTCAGCAAGAGAGGAG 1 277 1 TCAATTCAGC 0.949742 -24 TTGATTCAGCCTGTCGGAAC 2 1 1 TTGATTCAGC 0.969186 -300 AATCATAAAATCGATTCAGCTTTGGCTTTT 2 82 0 TCGATTCAGC 0.989687 -219 GGACAGTTAACCGATTCAGTGCCAGATTTC 5 184 1 CCGATTCAGT 0.86359 -117 GCTGGTCGATTTGTTTCATCCGCAGCTTTC 8 28 1 TTGTTTCATC 0.714509 -44 ********** Masking position 5 Map Score: 12.0811 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 280 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 AAATGCCATTTCACTGTTGCTGATTGGCTGCTG 1 36 1 TCGTTGCTGA 0.916779 -265 TTGCCATTTTTCCTAATTGCTGATGGGAAAATC 1 98 0 TCATTGCTGA 0.910905 -203 TTACGGCTTTCCTTGCGTGCTGAAACAGAAGTA 1 167 1 CCCGTGCTGA 0.97192 -134 AAAAAAAGCGCCAACCTGGCTTAGGGTTAAAGA 1 234 0 CCCTGGCTTA 0.935685 -67 GCTTTTTTTCTCATAGAGGCTGAATCGTTTCAA 1 258 1 TCGAGGCTGA 0.962186 -43 AGTTCTCCTCTCTTGCTGAATTGAAACGA 1 282 0 CCCTTGCTGA 0.976509 -19 AAATACCAGTTCCGACAGGCTGAATCAA 2 6 0 TCCAGGCTGA 0.95231 -295 ATGTTTGCTGTCGCGCAGGCTGGAAGCCCGAGG 5 262 0 TCCAGGCTGG 0.962501 -39 ATGTTTTTACCCGAGAGGGCTGGGGTGAGGCTT 7 49 0 CCAGGGCTGG 0.93166 -40 AGCAAGGAAGCCTGTAAGGCTTATCTAGGCAAA 9 13 0 CCAAGGCTTA 0.868535 -74 ** ******** Masking position 11 Map Score: 6.86655 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 945 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TGCACAATTTTTTGCCATTTTTCCTAATTGCTGA 1 108 0 TTTGCCTTTC 0.859408 -193 TGTATTTCCCCAACTTATAGGTTTAGTG 2 283 0 TTTCCCCTTT 0.94474 -18 TTTCCCGGGTTCTTTTAAAAATCA 3 1 1 TTTCCCTTCT 0.894385 -44 CTACCTTACTTGTGACTGATTTTTAAAAGAACCC 3 17 0 TGTGACTTTT 0.819298 -28 ATGTGAGTAGTGTCACATTTTTGTTTTGATGGTT 5 18 0 TGTCACTTTT 0.86266 -283 AAGGGGCTTAATTGCCCCTTTTGTTGTTTTTTAT 14 27 1 ATTGCCTTTT 0.888618 -43 TGTTTTTTATTTTCTCTTTCTTATAGCTT 14 51 1 TTTCTCCTTT 0.656255 -19 AACCAACGTTATTGACTCTTTTTTGGATGAG 15 50 1 ATTGACTTTT 0.745622 -21 AGCGACGGCATTTGCACCATTTTTCTTGTTCGTT 16 48 0 TTTGCATTTT 0.718701 -84 TTTTCCCAGCTTTATCAATAGTATT 16 117 0 TTTCCCTTTT 0.980131 -15 AGCCATAAAATTTCACAATTTTATGGCTAAGTAA 19 14 0 TTTCACTTTT 0.947709 -66 GCGGTCGTTTTTTCCCTTGTTTTTGGTAAAATGA 21 41 0 TTTCCCTTTT 0.980131 -30 ****** *** * Masking position 11 Map Score: 6.91332 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 277 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 GCAACAGTGAAATGGCATTTTGACTATTCG 1 26 0 AATGGCATTT 0.870833 -275 TTTCGCTAAAAATGGCATTTAAATGTGAGT 5 44 0 AATGGCATTT 0.870833 -257 CTGTCCAGTCGACGGCCTTTTGTGTGATAT 5 160 0 GACGGCCTTT 0.956927 -141 GATAAAAATTTACCGCACTT 10 1 0 TACCGCACTT 0.92845 -71 AAAAGAAAACGACCGCACTTTGCGACCGTT 11 18 0 GACCGCACTT 0.985443 -33 CCTAAAAAGCGACGGCATTTGCACCATTTT 16 59 0 GACGGCATTT 0.986568 -73 GGGAAAAAACGACCGCACTTTT 21 59 1 GACCGCACTT 0.985443 -12 ********** Masking position 2 Map Score: 6.18984 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 121 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AGGCTAGACTTTAGTTCCACAACACTAAACCTATAAGTT 2 261 1 TTCCCCATAA 0.961043 -40 GATCTTCTCCTAAGCAGTAAATTGGGCCGCA 4 20 0 TTCCACATAA 0.987662 -21 TCCAATCCCACCCTCTCCACATGGAGAAG 6 1 1 TTCCACTTCA 0.966408 -41 TGCGGTAAATTTTTATCCATTTCTCTACAAAATTATGTT 10 14 1 TTCCTCTTCA 0.856584 -58 TTGTTCGTTATACTATCCAAAACATTCCATCAAAGGAAA 16 18 0 TTCCACATCA 0.987435 -114 TTTATCTGTATATTAGCCGATACAATAAATTAAATCTGA 17 40 1 TGCCACATAA 0.955148 -119 TTTAATCTCCTATCCATTCAAGATGGTTGCT 18 39 0 TTCCACATAA 0.987681 -21 AGATACCTTCCGAAACAATTAACAAAGTAATA 19 58 0 TTCCACATAA 0.987681 -22 * *** * ** * ** Masking position 19 Map Score: 6.1498 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 6 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 TCATTAAACATTATGCCGCTAAAGGAAGAA 2 120 0 TTATGCCGCT 0.899898 -181 TTGTTTTTCAATAAGCTGCTGGTCGATTTG 8 11 1 ATAAGCTGCT 0.851096 -61 GCTTCCTTGCTTAATCCCCTTTAGACAGTA 9 35 1 TTAATCCCCT 0.977943 -52 AAAGGGGCAATTAAGCCCCTTTATTTTTGA 14 18 0 TTAAGCCCCT 0.985859 -52 TTTTAATCTCCTAATAGATCTT 17 3 1 TTAATCTCCT 0.96575 -156 TTTAATCTCCTATCCATTCAA 18 49 0 TTAATCTCCT 0.96575 -11 ********** Masking position 3 Map Score: 3.40543 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 43 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 AAGCGCCACGAATAGTCAAAATGCCATTTCAC 1 18 1 AATAGAAAAT 0.71981 -283 AATTAGGAAAAATGGCAAAAAATTGTGCAGCA 1 113 1 AATGGAAAAA 0.91217 -188 TTCAGCCTCTATGAGAAAAAAAGCGCCAACCT 1 250 0 ATGAGAAAAA 0.529884 -51 CTGCCGCCACATTAACAAAAAACCTCGGGCTT 5 240 1 ATTAAAAAAA 0.523383 -61 CTTGCTCCTTAATAATTTAAAAAGAAAGCTGC 8 49 0 AATAATAAAA 0.371265 -23 TTTGTAGAGAAATGGATAAAAATTTACCGCAC 10 13 0 AATGGAAAAA 0.91217 -59 TACTCAAAAATATAAAAGAAAACGACCGCA 11 31 0 AATATAAGAA 0.301907 -20 CCTTAGGCATAAGGAAAAATAATT 13 41 1 AAGGAAATAA 0.620064 -14 CAAAGTATCAAAAATAAAGGGGCT 14 3 1 AAGTAAAAAA 0.535481 -67 AGCTATAAGAAAGAGAAAATAAAAAACAACAA 14 47 0 AAGAGAATAA 0.74313 -23 GAAGGTTCACAATAGATAAGAT 15 1 0 AATAGAAGAT 0.501144 -70 TCATCCAAAAAAGAGTCAATAACGTTGGTTAG 15 48 0 AAGAGAATAA 0.74313 -23 TAGATCACAGAATGATAAAAAATGTTATTTTT 17 83 1 AATGAAAAAA 0.877167 -76 TTATCACTAAAATTAACAAAAAATAACATTTT 17 101 0 AATTAAAAAA 0.620257 -58 ATAAATAAACAATAGCCATAAAATTTCACAAT 19 29 0 AATAGATAAA 0.462012 -51 TGAGATTGTGAATAATAAATAAACTATTTAGC 20 15 1 AATAAAATAA 0.738121 -144 TTCAAAGCAAAATAATCAAGAATAAACACTAA 20 74 0 AATAAAAGAA 0.772917 -85 TCGACTAATCAATAATTAAAAATATAAAACCA 20 128 0 AATAAAAAAA 0.896951 -31 TTTTTGGTAAAATGAAAAAAATTTTTGCATAG 21 24 0 AATGAAAAAT 0.591711 -47 TACCAAAAACAAGGGAAAAAACGACCGCACTT 21 47 1 AAGGGAAAAC 0.46597 -24 ***** ***** Masking position 11 Map Score: 6.23833 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 507 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 281 Fraction of orfs with sites within 600 bp upstream = 0.0451333 Motif number 10 TGATAACGGATTTTCCCATCAGCAATTAGG 1 90 1 TTTTCCCATC 0.954045 -211 CTGCACAATTTTTTGCCATTTTTCCTAATT 1 113 0 TTTTGCCATT 0.760934 -188 TTGGCGCTTTTTTTCTCATAGAGGCTGAAT 1 253 1 TTTTCTCATA 0.844389 -48 GGGGTGAGGCTTTTCCCTCACCCAAACCCT 7 31 0 TTTTCCCTCA 0.81796 -58 ACTTTTCCCTTGTTAGAACTGT 12 15 0 TTTTCCCTTG 0.954045 -12 AATTATTTTTCCTTATGCCTAAGGC 13 40 0 TTTTTCCTTA 0.791098 -15 TTGTTTTTTATTTTCTCTTTCTTATAGCTT 14 50 1 TTTTCTCTTT 0.844389 -20 TTTTCCCAGCTTTATCAATA 16 122 0 TTTTCCCAGC 0.829076 -10 ATGCAAAAATTTTTTTCATTTTACCAAAAA 21 26 1 TTTTTTCATT 0.51656 -45 TGCGGTCGTTTTTTCCCTTGTTTTTGGTAA 21 46 0 TTTTCCCTTG 0.954045 -25 ********** Masking position 4 Map Score: 3.13225 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 362 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 11 TCCACGAGATGCGGCCCAATTTAC 4 5 1 CGAGATGCGG 0.929451 -36 GCAGTATCTACAAGGTCCGGCTACCTCTGC 5 214 1 CAAGGTCCGG 0.97733 -87 TCCACATGGAGAAGGTGGGGTTAATT 6 26 1 GAAGGTGGGG 0.941463 -16 ATTTAAAAAGAAAGCTGCGGATGAAACAAA 8 37 0 AAAGCTGCGG 0.959517 -35 CAAACGGTCGCAAAGTGCGGTCGTTTTCTT 11 16 1 CAAAGTGCGG 0.984505 -35 AAAAGTGCGGTCGTTTTTTC 21 61 0 AAAAGTGCGG 0.965752 -10 ********** Masking position 6 Map Score: 1.02108 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 213 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 TTATTTTGATGCGCGAAATTAATCGTTACAGG 2 50 1 GCGCAAATAA 0.928899 -251 AAACATTATGCCGCTAAAGGAAGAATTGAACC 2 113 0 CCGCAAAGAA 0.918836 -188 GACTTTAGTTCCACAACACTAAACCTATAAGT 2 267 1 CCACACATAA 0.936393 -34 GCTACCTCTGCCGCCACATTAACAAAAAACCT 5 233 1 CCGCACATAA 0.991266 -68 CTTCCAGCCTGCGCGACAGCAAACATAAGAAG 5 269 1 GCGCACACAA 0.945978 -32 TGTATATTAGCCGATACAATAAATTAAATCTG 17 46 1 CCGAACATAA 0.968712 -113 AGATACCTTCCGAAACAATTAACAAAGTAAT 19 59 0 CCGAACATTA 0.865369 -21 **** *** *** Masking position 6 Map Score: 1.13823 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 241 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 ********** No masking Map Score: 6.376e-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 14 ********** No masking Map Score: 6.376e-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 15 ********** No masking Map Score: 6.376e-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