AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igalR_ecoli_hinf_300.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 modF 67 ATP-binding component of molybdate transport system #3 modE 128 molybdate uptake regulatory protein #4 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #5 mglB 279 galactose-binding transport protein; receptor for galactose taxis #6 galS 141 mgl repressor, galactose operon inducer #7 folE 257 GTP cyclohydrolase I #8 galR 300 repressor of galETK operon #9 galP 300 galactose-proton symport of transport system #10 HI0351 172 UDP-glucose 4-epimerase (galE) #11 HI0352 300 conserved hypothetical protein #12 HI0819 37 galactokinase (galK) #13 HI0820_HI0821 207 HI0820: galactose-1-phosphate uridylyltransferase (galT), HI0821: galactose operon repressor (galR) #14 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #15 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) Motif number 1 GATAAAAAGCGCAATCATTCATAAACCCTCT 1 102 1 GCAATCATCA 0.992048 -159 AAGATACTGTGAAATCACTCACAGATTGAAA 5 15 0 GAAATCATCA 0.899775 -265 ATAGCCGCCAGCAAGCAGTCATTTACTGCAA 6 101 1 GCAAGCATCA 0.955514 -41 AATCAATCAATCAATCAATCAAT 11 3 1 TCAATCATCA 0.995529 -298 AATCAATCAATCAATCAATCAATCAATCAAT 11 15 1 TCAATCATCA 0.995529 -286 AATCAATCAATCAATCAATCAATCAATCAAT 11 27 1 TCAATCATCA 0.995529 -274 AATCAATCAATCAATCAATCAATCAATCAAT 11 43 1 TCAATCATCA 0.995529 -258 AATCAATCAATCAATCAATCAATCAATCAAT 11 59 1 TCAATCATCA 0.995529 -242 AATCAATCAATCAATCAATCAATCAATCAAT 11 71 1 TCAATCATCA 0.995529 -230 AATCAATCAATCAATCAATCAATCAATCAAT 11 83 1 TCAATCATCA 0.995529 -218 AATCAATCAATCAATCAATCAATCAATCAAT 11 95 1 TCAATCATCA 0.995529 -206 AATCAATCAATCAATCAATCAAAGTCTGTCA 11 107 1 TCAATCATCA 0.995529 -194 ******* *** Masking position 7 Map Score: 44.3429 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 2 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 2 TTTTATGCGCGATTAAGTGATTATAAAACAG 1 131 0 GATTAATGAT 0.964829 -130 ACGCTGTTGCGATTGACCGCTGGTGGCGTTT 8 123 0 GATTGACGCT 0.959539 -178 TATCATCATAGATTAAACGCTGTTATCTGCA 9 134 0 GATTAACGCT 0.767169 -167 TTGATTGATTGATTGATTGATT 11 2 0 GATTGATGAT 0.994961 -299 TTGATTGATTGATTGATTGATTGATTGATTG 11 14 0 GATTGATGAT 0.994961 -287 TTGATTGATTGATTGATTGATTGATTGATTG 11 26 0 GATTGATGAT 0.994961 -275 TTGATTGATTGATTGATTGATTGATTGATTG 11 42 0 GATTGATGAT 0.994961 -259 TTGATTGATTGATTGATTGATTGATTGATTG 11 58 0 GATTGATGAT 0.994961 -243 TTGATTGATTGATTGATTGATTGATTGATTG 11 70 0 GATTGATGAT 0.994961 -231 TTGATTGATTGATTGATTGATTGATTGATTG 11 82 0 GATTGATGAT 0.994961 -219 TTGATTGATTGATTGATTGATTGATTGATTG 11 94 0 GATTGATGAT 0.994961 -207 GACAGACTTTGATTGATTGATTGATTGATTG 11 106 0 GATTGATGAT 0.994961 -195 ****** **** Masking position 6 Map Score: 41.09 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 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 3 GGAATAAATTAGTGGAATCGTTTACACAAGAATTT 1 169 0 ATGAACGTTC 0.996615 -92 CATAACAACAATTAAAGCCGTTTTCTGGAGCGTTA 5 132 1 ATAAGCGTTC 0.913901 -148 GAGTCACAGCAATGGAAACGGTTACAGCCGTTTTG 6 33 0 ATGAACGTTC 0.996615 -109 ACACTGAAAGAATGTAAGCGTTTACCCACTAAGGT 8 270 1 ATGAACGTTC 0.996615 -31 TATCATCACAACTGAAACCGATTACACCAACCACA 9 20 1 ATGAACGTTC 0.996615 -281 AAATCACATCAGTGTAATCGCTTACACTAACATTT 9 205 0 ATGAACGTTC 0.996615 -96 TGATCTTCAAAATAAAATTGATTGCAACGGAAAAC 11 203 0 ATAAATGTTC 0.897945 -98 TTTACGATAAATTGAAAGCGGTTACTTTCATAAGT 13 61 1 ATGAACGTTC 0.996615 -147 GTTTTTTATCAATGTAAACGATTACATTAATTTAT 13 173 0 ATGAACGTTC 0.996615 -35 AATTTGCAAAAATGAAAATGATTACATAAAAAATT 14 36 0 ATGAATGTTC 0.980731 -55 * ** ** ** ** * Masking position 6 Map Score: 27.7912 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 AATTTAGCCGTTTTTTATGCGCGATTAAGTG 1 143 0 TTTTTTATGG 0.866945 -118 TTTTCGCATCTTTGTTATGCTATGGTTATTT 1 213 1 TTTGTTATGT 0.952052 -48 GTGTTGACAATTTGTTATGAAACACGTATCC 2 13 1 TTTGTTATGA 0.887753 -55 ATCTCCGGTTTTTCTTATGCAGGGTAGTGCT 5 256 0 TTTCTTATGA 0.84447 -24 AACATTTATCTTAGTTATGATTTAAGTGCAT 9 181 0 TTAGTTATGT 0.816473 -120 AATATGGTTATTTTTTATTGTGAATTAAGAT 9 270 0 TTTTTTATTT 0.899948 -31 TAGCAACAGGTTTTTTATTTTATTGAAAATC 10 87 1 TTTTTTATTT 0.899948 -86 AAAAAATACTTTTTTTATTTTCTTGCCAAGA 11 244 0 TTTTTTATTT 0.899948 -57 TTATCGTAAATTATTTATGATCAAAATATAA 13 40 0 TTATTTATGT 0.862036 -168 ATAAGCAAAATTTTTTATGATTTAGTTCATA 13 95 0 TTTTTTATGT 0.965383 -113 TTTTGCTTATTTTCTTATTTTGTGACAAAGA 13 116 1 TTTCTTATTT 0.814702 -92 AAATTCATAATTTTTTATGTAATCATTTTCA 14 28 1 TTTTTTATGA 0.91741 -63 ********* * Masking position 7 Map Score: 11.3923 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 75 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 GGCTAAATTCTTGTGTAAACGATTCCACTAATT 1 165 1 TGTGTAACGT 0.984557 -96 ACGTATCCCTGTCAGTAATCGCTGCACAAAGTG 2 36 1 GCAGTAACGT 0.949824 -32 GTATGTAACAGTGAATAATCACTTTTGCCGAGG 5 90 1 GGAATAACAT 0.570873 -190 TTAACAAAACGGCTGTAACCGTTTCCATTGCTG 6 29 1 GCTGTAACGT 0.957435 -113 TCACAGCACATTGAATAAACGGTATGATGAAGA 7 41 0 TGAATAACGT 0.892072 -217 AAATACCTTAGTGGGTAAACGCTTACATTCTTT 8 276 0 GGGGTAACGT 0.957849 -25 CTGTTGTGGTTGGTGTAATCGGTTTCAGTTGTG 9 26 0 TGTGTAACGT 0.984557 -275 TATATCATCATAGATTAAACGCTGTTATCTGCA 9 134 0 TGATTAACGT 0.82417 -167 AGATAAATGTTAGTGTAAGCGATTACACTGATG 9 201 1 TGTGTAACGT 0.984557 -100 TCATACTTATGAAAGTAACCGCTTTCAATTTAT 13 67 0 GAAGTAACGT 0.94605 -141 TAGTATAAATTAATGTAATCGTTTACATTGATA 13 169 1 TATGTAACGT 0.947337 -39 TCATAATTTTTTATGTAATCATTTTCATTTTTG 14 32 1 TATGTAACAT 0.714235 -59 * ****** ** * Masking position 7 Map Score: 11.1009 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 177 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TTTATATCCCACTTTGTGCAGCGATTACTGACAGG 2 43 0 ATTTGTGGCT 0.879352 -25 TGTGCGGTCAGCTTTGCGTGGCGTTCGTTTTCCGT 3 75 1 GTTTGCGGCT 0.991223 -54 CGTGGCGTTCGTTTTCCGTCACAATAAGACTTTTG 3 91 1 GTTTCCGACT 0.978654 -38 AATTAAAGCCGTTTTCTGGAGCGTTACCGGGCATG 5 141 1 GTTTCTGGCT 0.964969 -139 TGAGATAAATGCTCGGCGGGGCAGTAGAGTTAATG 5 221 0 GTCGGCGGCT 0.928048 -59 TAATTATTGTAATTGCCGCTGCCTTTCATCAGCAG 7 115 0 ATTGCCGGCT 0.957285 -143 CTTTGGTTACACTTTGCGAAACGCTGTTGCGATTG 8 139 0 ATTTGCGACT 0.923844 -162 ACCAACGGGCGTTTTCCGTAACACTGAAAGAATGT 8 250 1 GTTTCCGACT 0.978654 -51 AGATTATGATGTTTTCCGTTGCAATCAATTTTATT 11 193 1 GTTTCCGGCT 0.992902 -108 * ****** ** * Masking position 3 Map Score: 7.65958 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 440 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ATAACAAAGATGCGAAAAGTGTGACATGGAATAAA 1 196 0 TGCGAGTGAC 0.927339 -65 GCTTTCAATCTGTGAGTGATTTCACAGTATCTTAA 5 13 1 TGTGAATCAC 0.982809 -267 TTTCCATTGCTGTGACTCGATTCACGAAGTCCTGT 6 50 1 TGTGAGTCAC 0.996015 -92 GTTTATTCAATGTGCTGTGAGTAACTTTCACTTCC 7 54 1 TGTGCGTAAC 0.948343 -204 TACTGGATTATGTGCGCCGCCTCACGCACAATAAT 7 160 1 TGTGCGTCAC 0.992984 -98 ATTACACTGATGTGATTTGCTTCACATCTTTTTAC 9 222 1 TGTGAGTCAC 0.996015 -79 TTTCTTATTTTGTGACAAAGATCACGGTTTATTTA 13 126 1 TGTGAATCAC 0.982809 -82 TTTGTGACATGGATCACAAATTCATAA 14 3 1 TGTGAGTCAC 0.996015 -88 ***** * **** Masking position 14 Map Score: 11.7978 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 15 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 AAAAAACGGCTAAATTCTTGTGTAAACGATT 1 158 1 TAAATTTTGT 0.938379 -103 GAAAACGGCTTTAATTGTTGTTATGACGCTG 5 126 0 TTAATTTTGT 0.925312 -154 ATTCACAGCGATAATTATTGTAATTGCCGCT 7 130 0 ATAATTTTGT 0.715405 -128 ATGATATAACTCAATTATTTTCATGCACTTA 9 159 1 TCAATTTTTT 0.794681 -142 GATTTCCTTGTTAATTATTGAGACTAAAAAA 10 149 0 TTAATTTTGA 0.796714 -24 TAAACTATAGTCAATTGATTTTAAACTTGTT 11 154 0 TCAATTATTT 0.469822 -147 AAAGTATTTTTTAATTGTTCTACAATTTTTG 11 263 1 TTAATTTTCT 0.616057 -38 TAATTGTTCTACAATTTTTGAGCAATACTAT 11 274 1 ACAATTTTGA 0.557259 -27 CAATTTATCGTAAATTATTTATGATCAAAAT 13 44 0 TAAATTTTTA 0.507488 -164 TAATTTATACTAAATTATTGTAAATAAACCG 13 150 0 TAAATTTTGT 0.932389 -58 TAATTTAGTATAAATTAATGTAATCGTTTAC 13 164 1 TAAATTATGT 0.757052 -44 AAATAAATTATCGTAATTAATCTA 14 77 0 TAAATTTCGT 0.706454 -14 TTTCCCATCAATTTTTGTTGTAATCTAA 15 8 1 TCAATTTTGT 0.950921 -58 ****** **** Masking position 4 Map Score: 5.37078 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 85 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 GTGCTAAGGCCGCCTCCGGCAAGGTCAGCA 1 19 0 CGCCTCCGGC 0.978318 -242 GCGCAGTAATAGACTGCGCCCAATCAGTC 4 10 0 AGACTGCGCC 0.915871 -51 CTGACAAAATAGCCGCCAGCAAGCAGTCAT 6 93 1 AGCCGCCAGC 0.878764 -49 TGCTGATGAAAGGCAGCGGCAATTACAATA 7 116 1 AGGCAGCGGC 0.912501 -142 ATTGTGCGTGAGGCGGCGCACATAATCCAG 7 162 0 AGGCGGCGCA 0.867527 -96 GCAGGTGTGACGCCTCCGCCCTGCGTGGGG 7 224 0 CGCCTCCGCC 0.982421 -34 CGGCAAAAAAAACCTGCGCATCTGCGCAGG 8 12 1 AACCTGCGCA 0.729484 -289 GAATTACACCAGCCTGCGCAGATGCGCAGG 8 24 0 AGCCTGCGCA 0.964921 -277 TGAAGCCAAACGCCACCAGCGGTCAATCGC 8 116 1 CGCCACCAGC 0.794458 -185 ********** Masking position 4 Map Score: 3.03086 Number of sites scoring better than the average of aligned sites = 2969 Number in coding regions = 2873 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 10 TGGCAAAAGTCTTATTGTGACGGAAAACGAACGCC 3 94 0 CTATGAGGAA 0.91319 -35 TTCTGGAGCGTTACCGGGCATGGAAGAACGAATTT 5 154 1 TTCGGAGGAA 0.927671 -126 CTTACATTCTTTCAGTGTTACGGAAAACGCCCGTT 8 253 0 TTATGAGGAA 0.953237 -48 CAATTAAGACTTTACTGAAAAGAAATGTAACAACT 9 101 0 TTATGAGAAA 0.905264 -200 TTAGTTATGATTTAAGTGCATGAAAATAATTGAGT 9 167 0 TTAGTAGAAA 0.621781 -134 TCTGTCATTATTGCAGGTAATGGAACAAGTTTAAA 11 131 1 TTCGGAGGAA 0.968769 -170 CAAAATAAAATTGATTGCAACGGAAAACATCATAA 11 196 0 TTATGAGGAA 0.97189 -105 AGATCATTATTTTCTTGGCAAGAAAATAAAAAAAG 11 232 1 TTCTGAGAAA 0.498103 -69 ** * ** * **** Masking position 10 Map Score: 2.54379 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 55 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 AAAGTCTTATTGTGACGGAAAACGAACGCCACG 3 91 0 TGTGACAAAC 0.861371 -38 TGTTAACGAATGTGATCCAGATCG 6 2 0 TGTGATGATC 0.97833 -140 TTTCCATTGCTGTGACTCGATTCACGAAGTCCT 6 50 1 TGTGACATTC 0.955778 -92 CGGTTTCAGTTGTGATGATAATCTGCGGT 9 7 0 TGTGATAATC 0.956253 -294 ATTACACTGATGTGATTTGCTTCACATCTTTTT 9 222 1 TGTGATCTTC 0.8888 -79 CAAAATTTTTTATGATTTAGTTCATACTTATGA 13 88 0 TATGATGTTC 0.75861 -120 TTTCTTATTTTGTGACAAAGATCACGGTTTATT 13 126 1 TGTGACGATC 0.986228 -82 TTTGTGACATGGATCACAAATTCAT 14 3 1 TGTGACGATC 0.986228 -88 ****** **** Masking position 5 Map Score: 3.91948 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 43 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 TTGTATGGCCAACAAGGTAAAATTAT 4 45 1 AACAAGGTAA 0.933002 -16 ACAGTATCTTAACAATGTGATAGCTATGAT 5 36 1 AACAATGTGA 0.846788 -244 GCGTCATAACAACAATTAAAGCCGTTTTCT 5 128 1 AACAATTAAA 0.830717 -152 CAAACAACACAACAAGGAGCCACGC 7 6 0 AACAAGGAGC 0.733889 -252 CGTTTTCCGTAACACTGAAAGAATGTAAGC 8 259 1 AACACTGAAA 0.855492 -42 CTCAATAATTAACAAGGAAATCATT 10 158 1 AACAAGGAAA 0.968509 -15 AAAATTGTAGAACAATTAAAAAATACTTTT 11 262 0 AACAATTAAA 0.830717 -39 TATAGATTATAACAAGGAAAAAGTT 13 6 0 AACAAGGAAA 0.968509 -202 CCTGTTTTTTATCAATGTAAACGATTACAT 13 181 0 ATCAATGTAA 0.643955 -27 GCAAATTTGCAAAAATGAAAATGATTACAT 14 44 0 AAAAATGAAA 0.712651 -47 ********** Masking position 4 Map Score: 4.93395 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 180 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 13 TTATGAATGATTGCGCTTTTTATCTGAAAA 1 96 0 TTGCGCTTTT 0.825624 -165 CACAAGAATTTAGCCGTTTTTTATGCGCGA 1 150 0 TAGCCGTTTT 0.919222 -111 CAGAAAAGCACTCCCCTTTTGTGCGGTCAG 3 56 1 CTCCCCTTTT 0.958634 -73 ACAACAATTAAAGCCGTTTTCTGGAGCGTT 5 136 1 AAGCCGTTTT 0.8183 -144 GGTATCTCCGGTTTTTCTTATGCAG 5 265 0 CTCCGGTTTT 0.940863 -15 GAAACGGTTACAGCCGTTTTGTTAACGAAT 6 24 0 CAGCCGTTTT 0.959188 -118 TTTGACTCCTGTTTTTTATCAATGT 13 193 0 CTCCTGTTTT 0.85365 -15 GAAGTGGATCTTCCCCTTTTTAAAGAGGTT 15 42 1 TTCCCCTTTT 0.918172 -24 ********** Masking position 7 Map Score: 2.22227 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 373 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 14 CTGAAAAAAGACGCGGTTTCATGCCTGCAT 1 73 0 ACGCGGTTTC 0.976066 -188 TGTTGTTATGACGCTGTTACCTCGGCAAAA 5 112 0 ACGCTGTTAC 0.986012 -168 TATTTGCATAACGATGTTTTAACATCTGCT 7 90 1 ACGATGTTTT 0.720003 -168 ACTTTGCGAAACGCTGTTGCGATTGACCGC 8 134 0 ACGCTGTTGC 0.976385 -167 CATAGATTAAACGCTGTTATCTGCAATTAA 9 129 0 ACGCTGTTAT 0.959706 -172 GATAAATTGAAAGCGGTTACTTTCATAAGT 13 66 1 AAGCGGTTAC 0.900401 -142 ********** Masking position 7 Map Score: 2.39814 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 184 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 GTCGGTAGTGCTGACCTTGCCG 1 3 1 CGGTAGTGCT 0.988759 -258 CCGCACAAAAGGGGAGTGCTTTTCTGTGCT 3 52 0 GGGGAGTGCT 0.980986 -77 CTTCCATGCCCGGTAACGCTCCAGAAAACG 5 150 0 CGGTAACGCT 0.9285 -130 TTCTTATGCAGGGTAGTGCTTGAGATAAAT 5 246 0 GGGTAGTGCT 0.988759 -34 ********** Masking position 5 Map Score: 0.239557 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432