AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_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 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) Motif number 1 GAAACAGAAGTATTATGCTTTCTTGAAACGT 1 188 1 TATTATGTTT 0.838804 -113 GCTGAATCGATTTTATGATTTGGTTCAATTC 2 92 1 TTTTATGTTT 0.969912 -209 ACATTTTTGTTTTGATGGTTTGTTGAA 5 7 0 TTTGATGTTT 0.967018 -294 AAATCGCCGCCTTGTTGCTTTTTTACACAAG 5 72 1 CTTGTTGTTT 0.875265 -229 TCTTGCTCCTTAATAATTTAAAAAGAAAG 8 53 0 CTTAATATTT 0.603928 -19 ACCTCAAATTTTTTATGGTTTTATAACATAA 10 46 0 TTTTATGTTT 0.969912 -26 GGTCGTTTTCTTTTATATTTTTGAGTA 11 34 1 TTTTATATTT 0.940175 -17 CCCCTTTATTTTTGATACTTTG 14 2 0 TTTGATATTT 0.934615 -68 AATTGCCCCTTTTGTTGTTTTTTATTTTCTC 14 36 1 TTTGTTGTTT 0.947214 -34 GGCGTATTTTCTTTATACTTTGTGCATTGAA 16 87 1 CTTTATATTT 0.860049 -45 AATGTTATTTTTTGTTAATTTTAGTGATAAA 17 103 1 TTTGTTATTT 0.897418 -56 ACAAAATTATTTGATTTTACGTTAAAA 18 7 1 TTATTTGTTT 0.627991 -53 CTATTGTTTATTTATTACTTTGTTAATTGTT 19 46 1 TTTATTATTT 0.70471 -34 TTTAGCTTATTTTTATGATTTAATTCAGGCT 20 41 1 TTTTATGTTT 0.969912 -118 TATTCTTGATTATTTTGCTTTGAAAAAGGAT 20 82 1 TATTTTGTTT 0.761038 -77 AATTTTCTGGTTTTATATTTTTAATTATTGA 20 121 1 TTTTATATTT 0.940175 -38 ******* *** Masking position 6 Map Score: 19.6567 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 213 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 TGCTGACGCTGCTGAAATGAAATTGCTGAT 1 64 1 GCTGAAATGA 0.953018 -237 TTCCTTGCGTGCTGAAACAGAAGTATTATG 1 175 1 GCTGAAACAG 0.957839 -126 ACAAGATCGCGCTGAAACGTTTCAAGAAAG 1 205 0 GCTGAAACGT 0.978173 -96 TCTCATAGAGGCTGAATCGTTTCAATTCAG 1 266 1 GCTGAATCGT 0.98221 -35 CTCCTCTCTTGCTGAATTGAAACGATTCAG 1 277 0 GCTGAATTGA 0.961526 -24 GTTCCGACAGGCTGAATCAA 2 1 0 GCTGAATCAA 0.976523 -300 AAAAGCCAAAGCTGAATCGATTTTATGATT 2 82 1 GCTGAATCGA 0.992182 -219 GAAATCTGGCACTGAATCGGTTAACTGTCC 5 184 0 ACTGAATCGG 0.893304 -117 GAAAGCTGCGGATGAAACAAATCGACCAGC 8 28 0 GATGAAACAA 0.767972 -44 ********** Masking position 5 Map Score: 12.3507 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 3 AAATCAAAAGCGCCACGAATAGTCAAA 1 7 1 AAACGCCACG 0.969127 -294 TATGAGAAAAAAAGCGCCAACCTGGCTTAGG 1 242 0 AAACGCCAAC 0.943625 -59 AATGACGTACGAAACGTCAGCGGTCAACACC 2 145 1 GAACGTCAGC 0.915424 -156 GGCTAAAGTCGAACCGCCAGGCTAGACTTTA 2 243 1 GAACGCCAGG 0.91582 -58 TTTTTAGCGAAAATCGCCGCCTTGTTGCTTT 5 62 1 AAACGCCGCC 0.987499 -239 ACATTAACAAAAAACCTCGGGCTTCCAGCCT 5 248 1 AAACCTCGGG 0.877153 -53 TCCCTCACCCAAACCCTCTCCGTGAGGAGAG 7 17 0 AAACCTCTCC 0.727849 -72 GGGTGAGGGAAAAGCCTCACCCCAGCCCTCT 7 38 1 AAACCTCACC 0.915545 -51 CGGATGAAACAAATCGACCAGCAGCTTATTG 8 19 0 AAACGACCAG 0.692539 -53 TAAAGTTAATAAAACGCCGCCATTATACTGT 9 59 0 AAACGCCGCC 0.987499 -28 AATATAAAAGAAAACGACCGCACTTTGCGAC 11 22 0 AAACGACCGC 0.941655 -29 ATACGCCTAAAAAGCGACGGCATTTGCACCA 16 63 0 AAACGACGGC 0.968631 -69 *** ******* Masking position 3 Map Score: 9.46328 Number of sites scoring better than the average of aligned sites = 1555 Number in coding regions = 1426 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 4 AGGCTAGACTTTAGTTCCACAACACTAAACCTATAAGTT 2 261 1 TTCCCCATAA 0.9662 -40 GATCTTCTCCTAAGCAGTAAATTGGGCCGCA 4 20 0 TTCCACATAA 0.989329 -21 TCCAATCCCACCCTCTCCACATGGAGAAG 6 1 1 TTCCACTTCA 0.970877 -41 TGCGGTAAATTTTTATCCATTTCTCTACAAAATTATGTT 10 14 1 TTCCTCTTCA 0.873754 -58 TTGTTCGTTATACTATCCAAAACATTCCATCAAAGGAAA 16 18 0 TTCCACATCA 0.989138 -114 TTTATCTGTATATTAGCCGATACAATAAATTAAATCTGA 17 40 1 TGCCACATAA 0.961054 -119 TTTAATCTCCTATCCATTCAAGATGGTTGCT 18 39 0 TTCCACATAA 0.989351 -21 AGATACCTTCCGAAACAATTAACAAAGTAATA 19 58 0 TTCCACATAA 0.989351 -22 * *** * ** * ** Masking position 19 Map Score: 6.37443 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 5 TCATTAAACATTATGCCGCTAAAGGAAGAA 2 120 0 TTATGCCGCT 0.916055 -181 TTGTTTTTCAATAAGCTGCTGGTCGATTTG 8 11 1 ATAAGCTGCT 0.874016 -61 GCTTCCTTGCTTAATCCCCTTTAGACAGTA 9 35 1 TTAATCCCCT 0.981759 -52 AAAGGGGCAATTAAGCCCCTTTATTTTTGA 14 18 0 TTAAGCCCCT 0.988322 -52 TTTTAATCTCCTAATAGATCTT 17 3 1 TTAATCTCCT 0.971613 -156 TTTAATCTCCTATCCATTCAA 18 49 0 TTAATCTCCT 0.971613 -11 ********** Masking position 3 Map Score: 3.58514 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 6 TAGTCAAAATGCCATTTCACTGTTGCTGATTGG 1 30 1 GCCATTATGT 0.986375 -271 TAGGAAAAATGGCAAAAAATTGTGCAGCACATC 1 116 1 GGCAAAATGT 0.94736 -185 AACACCCGCCAGCAATGGACTGTATTGCGCTCT 2 170 1 AGCAATATGT 0.842919 -131 CGCTAAAAATGGCATTTAAATGTGAGTAGTGTC 5 38 0 GGCATTATGT 0.989592 -263 ATAAAACGCCGCCATTATACTGTCTAAAGGGGA 9 49 0 GCCATTATGT 0.986367 -38 TTCTTACTTAGCCATAAAATTGTGAAATTTTAT 19 11 1 GCCATAATGT 0.968796 -69 ATTTAATTCAGGCTTTTTAGTGTTTATTCTTGA 20 58 1 GGCTTTATGT 0.951791 -101 ****** * *** Masking position 9 Map Score: 4.5162 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 31 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 AAGCGCCACGAATAGTCAAAATGCCATTTCA 1 18 1 AATAGCAAAA 0.877665 -283 AATTAGGAAAAATGGCAAAAAATTGTGCAGC 1 113 1 AATGGAAAAA 0.776026 -188 TTAAATTATTAAGGAGCAAGA 8 61 1 AAGGACAAGA 0.872398 -11 TTTGTAGAGAAATGGATAAAAATTTACCGCA 10 14 0 AATGGTAAAA 0.683523 -58 CCTTAGGCATAAGGAAAAATAATT 13 41 1 AAGGAAAATA 0.678481 -14 CAAAGTATCAAAAATAAAGGGGC 14 3 1 AAGTACAAAA 0.625764 -67 AGCTATAAGAAAGAGAAAATAAAAAACAACA 14 48 0 AAGAGAAATA 0.62975 -22 GAAGGTTCACAATAGATAAGAT 15 2 0 AATAGTAAGA 0.624336 -69 TCATCCAAAAAAGAGTCAATAACGTTGGTTA 15 49 0 AAGAGCAATA 0.810616 -22 TGGATAGTATAACGAACAAGAAAAATGGTGC 16 38 1 AACGACAAGA 0.610532 -94 TAGATCACAGAATGATAAAAAATGTTATTTT 17 83 1 AATGAAAAAA 0.779591 -76 TTATCACTAAAATTAACAAAAAATAACATTT 17 102 0 AATTACAAAA 0.670603 -57 CAAAGTAATAAATAAACAATAGCCATAAAAT 19 37 0 AATAACAATA 0.841771 -43 TGAGATTGTGAATAATAAATAAACTATTTAG 20 15 1 AATAAAAATA 0.678876 -144 TTCAAAGCAAAATAATCAAGAATAAACACTA 20 75 0 AATAACAAGA 0.872599 -84 TCGACTAATCAATAATTAAAAATATAAAACC 20 129 0 AATAATAAAA 0.644653 -30 ***** ***** Masking position 8 Map Score: 4.46379 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 305 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 8 TGTATTTCCCCAACTTATAGGTTTAG 2 285 0 TCCCCAACTT 0.933748 -16 AACCCTACCTTACTTGTGACT 3 34 0 ACCCTACCTT 0.929455 -11 TCCAATCCCACCCTCTCCACATGG 6 5 1 ATCCCACCCT 0.938582 -37 AATTAACCCCACCTTCTCCATGTGG 6 27 0 ACCCCACCTT 0.991596 -15 GAAAAGCCTCACCCCAGCCCTCTCGGGTAA 7 46 1 ACCCCAGCCC 0.931086 -43 ATTTGTTTCATCCGCAGCTTTCTTTTTAAA 8 36 1 TCCGCAGCTT 0.951949 -36 AAAGAAAACGACCGCACTTTGCGACCGTTT 11 17 0 ACCGCACTTT 0.823371 -34 TTTTCCCAGCTTTATCAATAGT 16 120 0 TTCCCAGCTT 0.927576 -12 ********** Masking position 6 Map Score: 3.45567 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 238 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 AAATCAAAAGCGCCACGAATAGTCAAAATG 1 11 1 CGCCACGAAT 0.765012 -290 AGAAAAAAAGCGCCAACCTGGCTTAGGGTT 1 239 0 CGCCAACCTG 0.83119 -62 ATACCAGTTCCGACAGGCTGAATCAA 2 7 0 CGACAGGCTG 0.877861 -294 GGTCAACACCCGCCAGCAATGGACTGTATT 2 166 1 CGCCAGCAAT 0.942983 -135 GTATTGTTAGCGCCAGTTTTTAACAGACGC 2 212 0 CGCCAGTTTT 0.668554 -89 AAAGTCGAACCGCCAGGCTAGACTTTAGTT 2 247 1 CGCCAGGCTA 0.896721 -54 TAGCGAAAATCGCCGCCTTGTTGCTTTTTT 5 66 1 CGCCGCCTTG 0.860761 -235 ACTGTCCAGTCGACGGCCTTTTGTGTGATA 5 161 0 CGACGGCCTT 0.948367 -140 CCAGCCTGCGCGACAGCAAACATAAGAAGG 5 272 1 CGACAGCAAA 0.689869 -29 GTTAATAAAACGCCGCCATTATACTGTCTA 9 56 0 CGCCGCCATT 0.94514 -31 GCCTAAAAAGCGACGGCATTTGCACCATTT 16 60 0 CGACGGCATT 0.934497 -72 ********** Masking position 4 Map Score: 3.85617 Number of sites scoring better than the average of aligned sites = 3845 Number in coding regions = 3674 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 10 GCAACAGTGAAATGGCATTTTGACTATTCG 1 26 0 AATGGCATTT 0.974535 -275 CGTTATCAGCAATTTCATTTCAGCAGCGTC 1 68 0 AATTTCATTT 0.719005 -233 GCCTGTCGGAACTGGTATTTAACCAGACTA 2 19 1 ACTGGTATTT 0.9022 -282 TTTCGCTAAAAATGGCATTTAAATGTGAGT 5 44 0 AATGGCATTT 0.974535 -257 CAGCTTTATCAATAGTATTTCAATGCACAA 16 106 0 AATAGTATTT 0.828574 -26 AATGATAAAAAATGTTATTTTTTGTTAATT 17 93 1 AATGTTATTT 0.895012 -66 ********** Masking position 7 Map Score: 0.982953 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 67 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CAATCACATAAATATAGGGGGTAGAGAGGT 5 130 0 AATATAGGGG 0.921678 -171 ACAGCAAACATAAGAAGGGGTGTTTTT 5 284 1 TAAGAAGGGG 0.894678 -17 CATTATACTGTCTAAAGGGGATTAAGCAAG 9 40 0 TCTAAAGGGG 0.966853 -47 AAGTATCAAAAATAAAGGGGCTTAATTGCC 14 13 1 AATAAAGGGG 0.974822 -57 ATAAAAAACAACAAAAGGGGCAATTAAGCC 14 31 0 ACAAAAGGGG 0.966853 -39 ********** Masking position 6 Map Score: 0.668385 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 19 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 ********** No masking Map Score: 5.77204e-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 TGAGCAAAAGTTTGATGTGCTGCACAATTTTTTGCC 1 126 0 TTGATGCACA 0.942938 -175 CCGGGTTCTTTTAAAAATCAGTCACAAGTAAGGTAG 3 15 1 TTAATTCACA 0.778614 -30 GGCATTTAAATGTGAGTAGTGTCACATTTTTGTTTT 5 25 0 TGGAATCACA 0.530473 -276 AGGTAATTGACGTGACGTTCATCACAAAACGCTTGT 5 98 0 CGGATTCACA 0.647546 -203 CGGCCTTTTGTGTGATATCAATCACATAAATATAGG 5 142 0 TGGATTCACA 0.543014 -159 TTGTAGATACTGCGAAATCTGGCACTGAATCGGTTA 5 191 0 TGGATGCACT 0.932459 -110 AAATTAAATCTGAGATCTAGATCACAGAATGATAAA 17 66 1 TGGATTCACA 0.549466 -93 ** ** * ***** Masking position 5 Map Score: 0.869027 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 26 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 14 CGTCAGCAGCCAATCAGCAACAGTGAAATG 1 42 0 CAATCAGCAA 0.93611 -259 GGAAAATCCGTTATCAGCAATTTCATTTCA 1 76 0 TTATCAGCAA 0.942159 -225 ACGGATTTTCCCATCAGCAATTAGGAAAAA 1 95 1 CCATCAGCAA 0.955978 -206 AGCCGTAAAGTTATGAGCAAAAGTTTGATG 1 145 0 TTATGAGCAA 0.917916 -156 GATTCAGCCTCTATGAGAAAAAAAGCGCCA 1 254 0 CTATGAGAAA 0.917916 -47 AAGCTATAAGAAAGAGAAAATAA 14 57 0 CTATAAGAAA 0.803915 -13 ********** Masking position 6 Map Score: 0.387385 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 249 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ********** No masking Map Score: 5.77204e-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