AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igalR_ecoli_opreg_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 galE 260 UDP-galactose-4-epimerase #2 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #3 mglB 279 galactose-binding transport protein; receptor for galactose taxis #4 galS 141 mgl repressor, galactose operon inducer #5 galR 300 repressor of galETK operon #6 galP 300 galactose-proton symport of transport system Motif number 1 ACGGTTCGACGCATGCAGGCATGAAACCGCGTCTTTT 1 61 1 GATCACTGAC 0.904673 -200 CCGCTTTCAATCTGTGAGTGATTTCACAG 3 3 1 GTTCACGTGT 0.85409 -277 TGATAGCTATGATTGCACCGTTTTAACGTTGTAACCC 3 53 1 GTTCAGTTAC 0.952545 -227 CCAGAAAACGGCTTTAATTGTTGTTATGACGCTGTTA 3 123 0 GTTAAGTGAT 0.908647 -157 CAATGGAAACGGTTACAGCCGTTTTGTTAACGAATGT 4 22 0 GTTCACTTGT 0.956152 -120 GGCTGTAACCGTTTCCATTGCTGTGACTCGATTCACG 4 39 1 GTTCAGTGAC 0.984346 -103 ACGAAGTCCTGTATTCAGTGCTGACAAAATAGCCGCC 4 73 1 GATCAGTGAA 0.851048 -69 GATCCCAGAGGTATTGATAGGTGAAGTCAACTTCGGG 5 64 0 GATGAGTGGT 0.760387 -237 CAAAAAAAGAGATTGCAAACCTTTGGTTACACTTTGC 5 157 0 GTTCACTTGT 0.956152 -144 GGGGTGGCGTGTTTTCATCGTGGGAATGTGAGCCAAA 5 209 0 GTTCAGGGAT 0.958315 -92 AACGCCCGTTGGTTCAAGGGGTGGCGTGTTTTCATCG 5 226 0 GTTAAGTGGT 0.933517 -75 GTGGGTAAACGCTTACATTCTTTCAGTGTTACGGAAA 5 262 0 GTTCACTTGT 0.956147 -39 TGGTGTAATCGGTTTCAGTTGTGATGATAATCTGCGG 6 12 0 GTTCATTGGA 0.723812 -289 TTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTC 6 83 1 GTTCAGTGAC 0.984151 -218 TAGTGTAAGCGATTACACTGATGTGATTTGCTTCACA 6 211 1 GTTCAGTGAT 0.988458 -90 * ** ** * ** ** Masking position 7 Map Score: 17.3701 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 755 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 CAGAGGGTTTATGAATGATTGCGCTTTTTATC 1 102 0 ATGATGATTC 0.845098 -159 AAATTCTTGTGTAAACGATTCCACTAATTTAT 1 169 1 GTAACGATTC 0.599797 -92 TAAGGGCGCAGTAATAGACTGCGCCCAATCAG 2 13 0 GTAAAGACTC 0.952847 -48 CTTTCAATCTGTGAGTGATTTCACAGTATCTT 3 14 1 GTGATGATTC 0.968235 -266 CAAAACGGCTGTAACCGTTTCCATTGCTGTGA 4 33 1 GTAACGTTTC 0.813351 -109 TGAGATTGCAGTAAATGACTGCTTGCTGGCGG 4 105 0 GTAATGACTC 0.968235 -37 GTAAGACAAAAAAAGAGATTGCAAACCTTTGG 5 168 0 AAAAAGATTC 0.711067 -133 CTGAAAGAATGTAAGCGTTTACCCACTAAGGT 5 273 1 GTAACGTTTC 0.527342 -28 CATCACAACTGAAACCGATTACACCAACCACA 6 23 1 GAAACGATTC 0.527342 -278 AAATGTTAGTGTAAGCGATTACACTGATGTGA 6 205 1 GTAACGATTC 0.531635 -96 **** ***** * Masking position 4 Map Score: 13.9461 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 116 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 CAAGAATTTAGCCGTTTTTTATGCGCGATT 1 148 0 GCCGTTTTTT 0.963802 -113 AACAATTAAAGCCGTTTTCTGGAGCGTTAC 3 138 1 GCCGTTTTCT 0.976295 -142 AACGGTTACAGCCGTTTTGTTAACGAATGT 4 22 0 GCCGTTTTGT 0.983604 -120 GACCGCTGGTGGCGTTTGGCTTCAGGTTGC 5 110 0 GGCGTTTGGC 0.984546 -191 CTTACTTATTTGCGTTTGGCTCACATTCCC 5 195 1 TGCGTTTGGC 0.892532 -106 TTCAAGGGGTGGCGTGTTTTCATCGTGGGA 5 221 0 GGCGTGTTTT 0.914973 -80 TGAACCAACGGGCGTTTTCCGTAACACTGA 5 247 1 GGCGTTTTCC 0.98492 -54 ********** Masking position 5 Map Score: 6.42129 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 614 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 AGTGCTGACCTTGCCGGAGGCGGCCTTAGCACC 1 17 1 TTCCGGGGGG 0.97551 -244 GTCGAACCGTTGGCCGGAGAGGGTGCTAAGGCC 1 38 0 TGCCGGGAGG 0.992879 -223 CGTTCTTCCATGCCCGGTAACGCTCCAGAAAAC 3 151 0 TGCCGGAAGC 0.969603 -129 GAAGTGTTACTGAACGCCGAAGCTCACTTTTTA 3 189 0 TGACGCGAGC 0.966623 -91 TTGAGATAAATGCTCGGCGGGGCAGTAGAGTTA 3 224 0 TGTCGGGGGC 0.991685 -56 GTTTTTCTTATGCAGGGTAGTGCTTGAGATAAA 3 247 0 TGAGGGAGGC 0.841295 -33 AGTAAATGACTGCTTGCTGGCGGCTATTTTGTC 4 95 0 TGTTGCGGGG 0.90576 -47 CTGTTGCGATTGACCGCTGGTGGCGTTTGGCTT 5 118 0 TGCCGCGGGG 0.995452 -183 ** **** ** ** Masking position 1 Map Score: 5.46515 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 782 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 AGTGATTATTCACTGTTACATACGGGTTAC 3 83 0 CACTGTTACA 0.897693 -197 AGTGAATAATCACTTTTGCCGAGGTAACAG 3 99 1 CACTTTTGCC 0.852442 -181 GTTGTTATGACGCTGTTACCTCGGCAAAAG 3 111 0 CGCTGTTACC 0.989006 -169 TAAGAAAAACCGGAGATACC 3 270 1 CGGAGATACC 0.819568 -10 CACCAGCCTGCGCAGATGCGCAGGTTTTTT 5 18 0 CGCAGATGCG 0.82745 -283 CTTTGCGAAACGCTGTTGCGATTGACCGCT 5 133 0 CGCTGTTGCG 0.990067 -168 TACATTCTTTCAGTGTTACGGAAAACGCCC 5 256 0 CAGTGTTACG 0.933098 -45 ATAGATTAAACGCTGTTATCTGCAATTAAG 6 128 0 CGCTGTTATC 0.946567 -173 TAAGCGATTACACTGATGTGATTTGCTTCA 6 216 1 CACTGATGTG 0.85844 -85 ********** Masking position 7 Map Score: 6.41338 Number of sites scoring better than the average of aligned sites = 1976 Number in coding regions = 1846 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 AAATAACCATAGCATAACAAAGATGCGAAA 1 214 0 AGCATAACAA 0.934667 -47 ATTTCACAGTATCTTAACAATGTGATAGCT 3 31 1 ATCTTAACAA 0.906111 -249 AAACGGTGCAATCATAGCTATCACATTGTT 3 46 0 ATCATAGCTA 0.931556 -234 AGGTAACAGCGTCATAACAACAATTAAAGC 3 120 1 GTCATAACAA 0.969026 -160 CGTGAATCGAGTCACAGCAATGGAAACGGT 4 46 0 GTCACAGCAA 0.866275 -96 ACCGCAGATTATCATCACAACTGAAACCGA 6 11 1 ATCATCACAA 0.934667 -290 ATGCACTTAAATCATAACTAAGATAAATGT 6 181 1 ATCATAACTA 0.952889 -120 ********** Masking position 10 Map Score: 3.63234 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AAAAGTGTGACATGGAATAAATTAGTGGAA 1 187 0 CATGGAATAA 0.971079 -74 ATGAAATAACCATAGCATAACAAAGATGCG 1 217 0 CATAGCATAA 0.971079 -44 ATGGTTATTTCATACCATAAGCCTAATGGA 1 234 1 CATACCATAA 0.946092 -27 CCTTGTTGGCCATACAATAAGGGCGCAGTA 2 32 0 CATACAATAA 0.954892 -29 CGTTACCGGGCATGGAAGAACGAATTTTAA 3 162 1 CATGGAAGAA 0.924684 -118 GTTATATCATCATAGATTAAACGCTGTTAT 6 139 0 CATAGATTAA 0.909024 -162 ********** Masking position 3 Map Score: 3.9311 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 19 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GCTAAGGCCGCCTCCGGCAAGGTCAGCACTAC 1 15 0 CCCCGGCAGG 0.869045 -246 GTTTTCTGGAGCGTTACCGGGCATGGAAGAAC 3 151 1 GCTTACCGGC 0.886024 -129 TAAAAAGTGAGCTTCGGCGTTCAGTAACACTT 3 189 1 GCTCGGCGTC 0.913435 -91 TAACTCTACTGCCCCGCCGAGCATTTATCTCA 3 224 1 GCCCGCCGGC 0.917189 -56 TTTATCTCAAGCACTACCCTGCATAAGAAAAA 3 247 1 GCCTACCCGC 0.943929 -33 GACAAAATAGCCGCCAGCAAGCAGTCATTTAC 4 95 1 CCCCAGCAGC 0.982264 -47 CACATGAATTACACCAGCCTGCGCAGATGCGC 5 27 0 ACCCAGCCGC 0.9557 -274 AAGCCAAACGCCACCAGCGGTCAATCGCAACA 5 118 1 CCCCAGCGTC 0.975604 -183 GCCACCCCTTGAACCAACGGGCGTTTTCCGTA 5 238 1 GACCAACGGC 0.833616 -63 ** ****** ** Masking position 8 Map Score: 2.32719 Number of sites scoring better than the average of aligned sites = 3730 Number in coding regions = 3598 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 9 ATAAGCCTAATGGAGCGAATT 1 250 1 TGGAGCGAAT 0.971288 -11 CGATCTGGATCACATTCGTTAACAA 4 6 1 TGGATCACAT 0.976081 -136 CAACTTCGGGTTGAGCACATGAATTACACC 5 44 0 TTGAGCACAT 0.949016 -257 TATTTGCGTTTGGCTCACATTCCCACGATG 5 201 1 TGGCTCACAT 0.937188 -100 TAAAAAGATGTGAAGCAAATCACATCAGTG 6 226 0 TGAAGCAAAT 0.863259 -75 ATAACCATATTGGAGGGCATC 6 290 1 TGGAGGGCAT 0.958256 -11 ********** Masking position 9 Map Score: 1.76543 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 355 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 GACTGATTGGGCGCAGTCTATTACTGC 2 5 1 GATTCGCAGT 0.966686 -56 CTATCACATTGTTAAGATACTGTGAAATCACTC 3 26 0 GTTATACTGT 0.739669 -254 TGATTGCACCGTTTTAACGTTGTAACCCGTATG 3 62 1 GTTTCGTTGT 0.906798 -218 CGGCAAAAGTGATTATTCACTGTTACATACGGG 3 87 0 GATTCACTGT 0.969669 -193 TTTAATTGTTGTTATGACGCTGTTACCTCGGCA 3 115 0 GTTACGCTGT 0.98192 -165 ACGCTGTTGCGATTGACCGCTGGTGGCGTTTGG 5 121 0 GATTCGCTGG 0.97377 -180 CAGTTGTGATGATAATCTGCGGT 6 1 0 GATATGCGGT 0.859783 -300 TATCATCATAGATTAAACGCTGTTATCTGCAAT 6 132 0 GATTCGCTGT 0.992896 -169 **** ****** Masking position 3 Map Score: 4.00149 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 592 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 11 TATCTGAAAAAAGACGCGGTTTCATGCCTG 1 76 0 AAGACGCGGT 0.964156 -185 TTTCAGATAAAAAGCGCAATCATTCATAAA 1 97 1 AAAGCGCAAT 0.759466 -164 GACTGATTGGGCGCAGTCTATTACTGC 2 8 1 TGGGCGCAGT 0.96094 -53 CCATACAATAAGGGCGCAGTAATAGACTGC 2 23 0 AGGGCGCAGT 0.978183 -38 AATTGTTGTTATGACGCTGTTACCTCGGCA 3 115 0 ATGACGCTGT 0.932504 -165 TACACTTTGCGAAACGCTGTTGCGATTGAC 5 137 0 GAAACGCTGT 0.90908 -164 CATCATAGATTAAACGCTGTTATCTGCAAT 6 132 0 TAAACGCTGT 0.922447 -169 ********** Masking position 10 Map Score: 0.952526 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 814 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 TTTATTCCATGTCACACTTTTCGCATCTTT 1 196 1 GTCACACTTT 0.966292 -65 TCGGCGTTCAGTAACACTTCATTAACTCTA 3 202 1 GTAACACTTC 0.973522 -78 CAAACCTTTGGTTACACTTTGCGAAACGCT 5 149 0 GTTACACTTT 0.971515 -152 ACAAAGATTTGTAATATTTTCATATTATTA 6 59 1 GTAATATTTT 0.743344 -242 TTTCACAGTTGTTACATTTCTTTTCAGTAA 6 95 1 GTTACATTTC 0.942298 -206 ********** Masking position 6 Map Score: 0.430801 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 43 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: 2.51775e-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: 2.51775e-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: 2.51775e-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