AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_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 codB 152 cytosine permease/transport #2 thiM 222 hydoxyethylthiazole kinase #3 thiC 232 thiamin biosynthesis, pyrimidine moiety #4 HI0354 300 ABC transporter, ATP-binding protein #5 HI0357 21 thiamine biosynthesis protein, putative #6 HI0415 300 hydroxyethylthiazole kinase Motif number 1 CACGCAGAAGGGCACCCCGAGTCGTTTGGT 2 101 0 GGCACCCCGA 0.997937 -122 AGCCAGTTAAGGCACTCCGACAAGAAATTA 3 61 0 GGCACTCCGA 0.98182 -172 TCAGGTTCCGCGGATCCCGAATAAACGGTC 3 93 0 CGGATCCCGA 0.970404 -140 TCGGGATCCGCGGAACCTGATCAGGCTAAT 3 103 1 CGGAACCTGA 0.970045 -130 TCAGCCTTTCGGCACCCCGACTAAAAACTG 4 148 0 GGCACCCCGA 0.997937 -153 GATGATACCCGTGAACCTGAAACAGTTAGC 4 178 1 GTGAACCTGA 0.954412 -123 TCAGCCTTTCGGCACCCCGACTAAAAGTCG 6 98 0 GGCACCCCGA 0.997937 -203 GATGATACCCGTGAACCTGAAACAGTTAGC 6 128 1 GTGAACCTGA 0.954412 -173 ********** Masking position 4 Map Score: 16.5922 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 107 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 ATGAGTGCAAAAAGGTGGGGGAAAAATTATCG 1 26 0 AAAGGGGGGA 0.910362 -127 TCAAACAGCAAAAAGGGGGAATTTC 1 138 1 AAAGGGGAAT 0.798353 -15 CACGCGTTGTAAACGAGGAAAAACGGCAGTTT 2 29 0 AAAGGGAAAA 0.972087 -194 CCTTCTGCGTGAAGGCTGAGAAATACCCGTAT 2 120 1 GAAGTGAGAA 0.933611 -103 GCTCCTGCCATAACGTGAAGAAGCAATGACCT 2 196 0 TAAGGAAGAA 0.876738 -27 GCTCATTCCAAAAAGTTAAGGACGTGGCTTGT 3 210 0 AAAGTAAGGA 0.844654 -23 CGGGGTGCCGAAAGGCTGAGATGATACCCGTG 4 159 1 AAAGTGAGAT 0.922892 -142 ATAAGAAATGGAATGAAAAGAAAATGGATTTT 4 234 0 GAAGAAAGAA 0.684193 -67 AATAAAAAAGAAAGGATAAGAAATGGAATGAA 4 249 0 AAAGTAAGAA 0.949321 -52 CTTTTCATTAAAGGAGAAAAA 5 10 1 AAAGGAAAAA 0.936124 -12 ATTTTGCAAATAATGAGAAGAATTTGACCGCT 6 13 0 TAAGGAAGAA 0.876738 -288 ATTATTTGCAAAATGAGGGAAAAATTTGACCG 6 31 1 AAAGGGGAAA 0.936404 -270 CGGGGTGCCGAAAGGCTGAGATGATACCCGTG 6 109 1 AAAGTGAGAT 0.922892 -192 CGTGATAGAGAAAGGTTGAATATGTGGCATAT 6 175 0 AAAGTGAATA 0.665934 -126 AGGTGTAATAAAATGTAGAAAATTGGGAAAAT 6 221 0 AAAGAGAAAA 0.872734 -80 *** * ****** Masking position 3 Map Score: 14.4394 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 667 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 3 CCACTGTTTTTACACCGATAATTTTTCCCCCACCTTTT 1 7 1 TTTACCGTTC 0.923389 -146 TAAAAAATATATTTCCCCACGAAAACGATTGCTTTTTATCTT 1 63 1 ATCCCCGCTC 0.994498 -90 TGAAACCCAAAAAATCCGCCGCATTCTATTCATCTGAAGATA 1 99 0 AATCCCGCTA 0.894014 -54 GGAGGATGGTAATGTCCAGCGCACGCGTTGTAAACGAGGAAA 2 40 0 ATTCCCGCTA 0.979197 -183 GTGGTCCGTGACTTCCCTACGCTGGCATTATCCAGATCAGGT 2 153 0 ATCCCCGCTC 0.994498 -70 GATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGT 3 117 0 TTCCCCGTTC 0.986935 -116 TGCTATCGCATCGCCCCTGCGGCGATCGTCTCTTGCTTCATC 3 159 1 TGCCCCGTTC 0.973631 -74 TTCTCTTGCTAAGATACAACGGAGATCGTACAACTGATATTA 4 25 0 AGTACCGTTA 0.785922 -276 TTGGCATATTAGTTTCCTACGTCAGTGCTAACTGTTTCAGGT 4 192 0 ATTCCCGTTC 0.993548 -109 GTGGCATATTAGTTTCCTACGTCAGTGCTAACTGTTTCAGGT 6 142 0 ATTCCCGTTC 0.993548 -159 * * *** ** * * * Masking position 19 Map Score: 11.1992 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 371 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CAATCGTTTTCGTGGGGAAATATATTTTTT 1 64 0 CGTGGGGAAA 0.938162 -89 GCCTTCACGCAGAAGGGCACCCCGAGTCGT 2 106 0 AGAAGGGCAC 0.90714 -117 ATAATGCCAGCGTAGGGAAGTCACGGACCA 2 164 1 CGTAGGGAAG 0.9865 -59 CTAATACCTGCGAAGGGAACAAGAGTTAAT 3 128 1 CGAAGGGAAC 0.995931 -105 GGTTTCTATCCGAATGGAACAAGAAAAGCA 4 76 0 CGAATGGAAC 0.969464 -225 TTAGCACTGACGTAGGAAACTAATATGCCA 4 203 1 CGTAGGAAAC 0.988629 -98 TTAGCACTGACGTAGGAAACTAATATGCCA 6 153 1 CGTAGGAAAC 0.988629 -148 ********** Masking position 9 Map Score: 9.33675 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 85 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TCATCTGAAGATAAAAAGCAATCGTTTTCG 1 82 0 ATAAAAAGCA 0.784486 -71 GTTTGAAACCCAAAAAATCCGCCGCATTCT 1 114 0 CAAAAAATCC 0.881738 -39 CATCCGTCGTCTGACAAGCCACGTCCTTAA 3 197 1 CTGACAAGCC 0.869056 -36 CGAATGGAACAAGAAAAGCATTTTTAAATT 4 66 0 AAGAAAAGCA 0.849183 -235 TTTGGTAGAAAAAACAAGCAATTAGGTTTC 4 100 0 AAAACAAGCA 0.944005 -201 TTTTTTCTACCAAACAAGCGTAAACTTACC 4 116 1 CAAACAAGCG 0.976892 -185 ACTAATATGCCAAAAAATCCATTTTCTTTT 4 221 1 CAAAAAATCC 0.881738 -80 TTTTCAAGAAAAAACAAGCGGTCAAATTTT 6 51 0 AAAACAAGCG 0.963649 -250 TTTTTTCTTGAAAAGAAGCGTAAACTTCTT 6 67 1 AAAAGAAGCG 0.882751 -234 ATAAAATAAACAAAAATGCCCGCTATTCAC 6 267 0 CAAAAATGCC 0.858531 -34 ********** Masking position 6 Map Score: 6.81079 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 573 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 6 ATGGTAATGTCCAGCGCACGCGTTGTAAAC 2 47 0 CCAGCGCACG 0.843086 -176 CTGGCATTATCCAGATCAGGTGATACGGGT 2 144 0 CCAGATCAGG 0.632621 -79 CTGGATAATGCCAGCGTAGGGAAGTCACGG 2 160 1 CCAGCGTAGG 0.843054 -63 TTACGCGTTAACAGCGCAGAAC 3 3 0 ACAGCGCAGA 0.871323 -230 ACGGTCTCAGCCAGTTAAGGCACTCCGACA 3 69 0 CCAGTTAAGG 0.927496 -164 ATCCGCGGAACCTGATCAGGCTAATACCTG 3 108 1 CCTGATCAGG 0.499492 -125 CAGGCTAATACCTGCGAAGGGAACAAGAGT 3 124 1 CCTGCGAAGG 0.540888 -109 ********** Masking position 8 Map Score: 6.68413 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 958 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 TGCGATTTATCATCGCAACCAAACGACTCG 2 84 1 CATCGCAACC 0.966055 -139 GATACGGGTATTTCTCAGCCTTCACGCAGA 2 123 0 TTTCTCAGCC 0.970465 -100 CCGAATAAACGGTCTCAGCCAGTTAAGGCA 3 77 0 GGTCTCAGCC 0.986307 -156 TCACGGGTATCATCTCAGCCTTTCGGCACC 4 162 0 CATCTCAGCC 0.996978 -139 TCACGGGTATCATCTCAGCCTTTCGGCACC 6 112 0 CATCTCAGCC 0.996978 -189 ********** Masking position 7 Map Score: 5.78419 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 35 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AAATATATTTCCCCACGAAAACGATTGCTT 1 67 1 CCCCACGAAA 0.981514 -86 TTCCGCGGATCCCGAATAAACGGTCTCAGC 3 88 0 CCCGAATAAA 0.98389 -145 CTTTCGGCACCCCGACTAAAAACTGTTGGT 4 143 0 CCCGACTAAA 0.995896 -158 CTTTCGGCACCCCGACTAAAAGTCGAAAGA 6 93 0 CCCGACTAAA 0.995896 -208 ********** Masking position 5 Map Score: 5.02241 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 7 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 9 TTTTTCCCCCACCTTTTTGCACTCATTCAT 1 32 1 ACCTTTTTGC 0.84169 -121 ACGGACCACCAGGTCATTGCTTCTTCACGT 2 186 1 AGGTCATTGC 0.981807 -37 TTGCTTCTTCACGTTATGGCAGGAGCAAAC 2 202 1 ACGTTATGGC 0.887386 -21 AGCTCATTCCAAAAAGTTAA 3 223 0 AGCTCATTCC 0.899314 -10 TCGGATAGAAACCTAATTGCTTGTTTTTTC 4 93 1 ACCTAATTGC 0.967393 -208 TTAGTTTCCTACGTCAGTGCTAACTGTTTC 4 196 0 ACGTCAGTGC 0.980284 -105 TTAGTTTCCTACGTCAGTGCTAACTGTTTC 6 146 0 ACGTCAGTGC 0.980284 -155 TTATTACACCTGCTAATTGCTCACAGTGAA 6 242 1 TGCTAATTGC 0.765693 -59 ********** Masking position 4 Map Score: 4.53166 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 353 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 CACCGATAATTTTTCCCCCACCTTTTTGCA 1 23 1 TTTTCCCCCA 0.784655 -130 CCCCCACCTTTTTGCACTCATTCATATAAA 1 37 1 TTTGCACTCA 0.840557 -116 ACGATTGCTTTTTATCTTCAGATGAATAGA 1 87 1 TTTATCTTCA 0.865112 -66 AAACGGCAGTTTTACAATCGCGTTAATAAA 2 11 0 TTTACAATCG 0.840718 -212 AAAACTGCCGTTTTTCCTCGTTTACAACGC 2 28 1 TTTTTCCTCG 0.916815 -195 TCCTCTGCGATTTATCATCGCAACCAAACG 2 79 1 TTTATCATCG 0.788321 -144 TAACGCGTAATTTACATTCAATGCCCCATT 3 23 1 TTTACATTCA 0.90089 -210 TTACCAACAGTTTTTAGTCGGGGTGCCGAA 4 141 1 TTTTTAGTCG 0.699925 -160 ATCCATTTTCTTTTCATTCCATTTCTTATC 4 237 1 TTTTCATTCC 0.736629 -64 GCGGTCAAATTTTTCCCTCATTTTGCAAAT 6 34 0 TTTTCCCTCA 0.950856 -267 TTTTGTTTATTTTATATTCAACACAAGGA 6 282 1 TTTATATTCA 0.826963 -19 ********** Masking position 3 Map Score: 3.9267 Number of sites scoring better than the average of aligned sites = 1040 Number in coding regions = 917 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 11 CCAGATCAGGTGATACGGGTATTTCTCAGC 2 134 0 TGATACGGGT 0.973546 -89 AAGGCTGAGATGATACCCGTGAACCTGAAA 4 170 1 TGATACCCGT 0.978946 -131 CAGTGCTAACTGTTTCAGGTTCACGGGTAT 4 182 0 TGTTTCAGGT 0.955207 -119 AAGGCTGAGATGATACCCGTGAACCTGAAA 6 120 1 TGATACCCGT 0.978946 -181 CAGTGCTAACTGTTTCAGGTTCACGGGTAT 6 132 0 TGTTTCAGGT 0.955207 -169 ********** Masking position 4 Map Score: 2.56538 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 104 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 GAAATTCCCCCTTTTTGCTGTTTGAAA 1 136 0 CCCCTTTTTG 0.595759 -17 ACATTACCATCCTCCTCTGCGATTTATCATC 2 67 1 CCTCTCTGCG 0.976553 -156 GACTCGGGGTGCCCTTCTGCGTGAAGGCTGA 2 108 1 GCCCTCTGCG 0.995925 -115 ACATTCAATGCCCCATTTGCGGGGCTAATTT 3 36 1 CCCCTTTGCG 0.98856 -197 TATCGCATCGCCCCTGCGGCGATCGTCTCTT 3 162 1 CCCCGCGGCG 0.991128 -71 TATCATCTCAGCCTTTCGGCACCCCGACTAA 4 154 0 GCCTTCGGCA 0.956464 -147 TATCATCTCAGCCTTTCGGCACCCCGACTAA 6 104 0 GCCTTCGGCA 0.956464 -197 **** ****** Masking position 2 Map Score: 3.38236 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 904 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 13 GTTTTACAATCGCGTTAATAAA 2 3 0 CGCGTTAATA 0.892525 -220 ATGTAAATTACGCGTTAACAGCGCAGAAC 3 10 0 CGCGTTAACA 0.977445 -223 ATTCGGGATCCGCGGAACCTGATCAGGCTA 3 101 1 CGCGGAACCT 0.947524 -132 CTACCAAACAAGCGTAAACTTACCAACAGT 4 122 1 AGCGTAAACT 0.975087 -179 CTTGAAAAGAAGCGTAAACTTCTTTCGACT 6 73 1 AGCGTAAACT 0.975087 -228 ********** Masking position 7 Map Score: 0.731837 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 369 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 14 ********** No masking Map Score: -1.72419e-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: -1.72419e-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