AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_ecoli_reg_100.orf -o00740_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 b0024 102 orf, hypothetical protein #2 ybaD 90 orf, hypothetical protein #3 ribH 88 riboflavin synthase, beta chain #4 appA 184 phosphoanhydride phosphorylase; pH 2.5 acid phosphatase; periplasmic #5 ymfA 48 orf, hypothetical protein #6 potA 249 ATP-binding component of spermidine/putrescine transport #7 ribA 169 GTP cyclohydrolase II #8 ribE 214 riboflavin synthase, alpha chain #9 cobU 300 cobinamide kinase/cobinamide phosphate guanylyltransferase #10 aceB 268 malate synthase A #11 aceA 29 isocitrate lyase #12 BIME206 22 BIME #13 aceK 27 isocitrate dehydrogenase kinase/phosphatase #14 aphA 300 diadenosine tetraphosphatase Motif number 1 GCTAAAATCCGCCCCCCTGCGGGGCCATACTCG 3 50 1 GCCCCTGCGG 0.996417 -39 CGATGCTAATGCGCCGCATCAGGCCTACGTTCG 4 116 0 GCCCCATCGG 0.928195 -69 TAATACCACCGCCCGCTTGCTGAA 5 2 0 GCCGTTGCGA 0.988796 -47 TGATAAATATTCCCGCTTGCAGGGGTAAAAGTG 6 77 0 TCCGTTGCGG 0.964059 -173 ATTCTGTTCAGCACAATAGCAGGTGGAAAACGC 8 164 0 GCCATAGCGG 0.979528 -51 AGAACACAATGCCCGTTTGCTGGTTGTTCCGGC 9 21 1 GCCGTTGCGG 0.995854 -280 AATGGATCCCCCACCGTTGCTGACCGCAAAACA 9 233 0 CCCCTTGCGA 0.979781 -68 TTTCCGAAACGTACCTCAGCAGGTGAATAAATT 10 79 1 GTCCCAGCGG 0.934782 -190 GCAACAACAACCGTTGCTGACT 12 8 1 CACCTTGCGA 0.809059 -15 ATCAAATTTCGCTCATTTGCCGAGGATTCATCA 14 55 1 GCCATTGCGA 0.967553 -246 TCCTTCCTTTCCCCGGCAGCTGGCGTTATGGTC 14 214 1 CCCGCAGCGG 0.983266 -87 ** ** **** ** Masking position 4 Map Score: 14.5909 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1059 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 CGTCCTGACCAGGTGGTTAACGGAAATCTAT 2 66 0 AGTGGTTAAC 0.958267 -25 ATCAGGCCTACGTTCGTTAACTTTTCAGACG 4 101 0 CGTCGTTAAC 0.995012 -84 AGAGTCACCAAGGTGGTTAACCACAAACCCC 6 201 1 AGTGGTTAAC 0.958267 -49 CACGACGCGTCGATCGTTCACGGAATGGCAC 7 81 0 CGTCGTTCAC 0.992605 -89 CGCATTTTGTCGGACGTTAACACGAGAAAGT 9 114 1 CGACGTTAAC 0.976422 -187 CTGTGATAGTCGATCGTTAAGCGATTCAGCA 10 15 1 CGTCGTTAAG 0.974586 -254 GCACAACGATCCTTCGTTCACAGTGGGGAAG 10 219 1 CCTCGTTCAC 0.962694 -50 ** ******** Masking position 10 Map Score: 6.74515 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 127 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 GGCCCCGCAGGGGGGCGGATTTTAGCATAATA 3 44 0 GGGGGGATTT 0.81602 -45 CAGCAAGCGGGCGGTGGTATTACCGCCCGTTT 5 13 1 GCGGTGATTA 0.955246 -36 ATTCCCGCTTGCAGGGGTAAAAGTGACCTGAC 6 70 0 GCAGGGAAAA 0.949504 -180 ACCCCTGCAAGCGGGAATATTTATCAGCATTA 6 84 1 GCGGGAATTT 0.770536 -166 CAAGCGGTTTGCCGTAGAATTACCGCCCTCAT 6 167 1 GCCGTGATTA 0.888421 -83 AAAAGAAGAAGCAGGGGAAATTCAGTCTATTG 8 70 1 GCAGGGAATT 0.949504 -145 CAGCACAATAGCAGGTGGAAAACGCCCTTACC 8 157 0 GCAGGGAAAA 0.949504 -58 GGTTGTTCCGGCAGTAGCATTAATTCATTATC 9 42 1 GCAGTGATTA 0.962793 -259 ACGTACCTCAGCAGGTGAATAAATTTTATTCA 10 87 1 GCAGGGATAA 0.976485 -182 GTGATGAAAAGCAGGATGATTATATTTAACCC 14 167 0 GCAGGTATTA 0.899908 -134 ***** * **** Masking position 9 Map Score: 6.29345 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 650 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 ATGCCCTTTTAGCCTTCTTTTGTCAATGGATTT 1 61 1 AGCTTTTTGT 0.929024 -42 TTGGTTCGTCGGCATTTTGTTGATGTGTTCGCT 4 37 1 GGCTTTTTGA 0.976925 -148 TTACTGGCTTAGCTTTATATTCATTAAGGTAAT 6 112 0 AGCTTTTTCA 0.948853 -138 ATACAGAACCAGCATTATCTGGAGAATTTC 7 150 1 AGCTTTTGGA 0.745495 -20 CCATTCAGGCGGCTTTTTAGTCTCTCATATAAC 8 31 0 GGCTTTGTCT 0.963786 -184 GGGTAAGAATGGCTATTTTTTCACTGGAGAATT 8 117 0 GGCATTTTCA 0.865152 -98 AATCAGTTAAGACATTCTGTTCAGCACAATAGC 8 177 0 GACTTTTTCA 0.925967 -38 CCAGCAAACGGGCATTGTGTTCTGAAATCCAGG 9 11 0 GGCTTTTTCT 0.977007 -290 GGAATAGCCAGACTTTCTCGTGTTAACGTCCGA 9 123 0 GACTTTGTGT 0.846797 -178 CCCGGCAGCTGGCGTTATGGTCAGATGGTTTTT 14 225 1 GGCTTTGTCA 0.969349 -76 AGTATGTTGAAACTTTTTATTGTGAGATTTGTT 14 260 0 AACTTTTTGT 0.764279 -41 *** ** * **** Masking position 6 Map Score: 8.81505 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 305 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 ACGGCGTCCTGACCAGGTGGTTAACGG 2 74 0 GCTCTACAGG 0.987476 -17 GTCTTTTCTTGCTTCTTAATAATGTTGTCACAAA 6 27 0 GCTCTATATG 0.969631 -223 CCACCTTGGTGACTCTTAATGAGGGCGGTAATTC 6 183 0 GATCTATAGG 0.969662 -67 AACGATCGACGCGTCGTGATTAGGTGAACCCCTT 7 94 1 GCTCTATAGG 0.991538 -76 GAAGTTTTCGGATCCATGACGAGGAGCTGCACG 10 246 1 GACCTACAGG 0.962927 -23 GTGCAGATGCTCCATAGTTATGTGGTGGT 11 8 0 GCCCTGTATG 0.922343 -22 TTAGCGCCCTCATCAGGAGCAGAGAAT 13 11 0 GCCCTATAGG 0.992982 -17 ** ** * ** *** Masking position 12 Map Score: 5.25789 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 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 Motif number 6 CCTTGCTAACTAAAAAACGG 5 39 0 CCTTGCTAAC 0.959823 -10 TGGTTAACCACCTTGGTGACTCTTAATGAG 6 194 0 CCTTGGTGAC 0.9662 -56 GATCCCCCACCGTTGCTGACCGCAAAACAT 9 232 0 CGTTGCTGAC 0.992043 -69 CAACAACAACCGTTGCTGACT 12 12 1 CGTTGCTGAC 0.992043 -11 CCAGTAAATACGTTCCTGTCTTTTTTTGTA 14 139 0 CGTTCCTGTC 0.972164 -162 CGCAGATAATCCTTCCTTTCCCCGGCAGCT 14 205 1 CCTTCCTTTC 0.870001 -96 ********** Masking position 4 Map Score: 4.49312 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 242 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GCGCTGCTTCCCTTTCGAGCCGGGAGA 3 8 0 CCTTTCGAGC 0.802051 -81 AAATCCGCCCCCCTGCGGGGCCATACTCGA 3 54 1 CCCTGCGGGG 0.649096 -35 GCTAATGCGCCGCATCAGGCCTACGTTCGT 4 115 0 CGCATCAGGC 0.954971 -70 GCATTAGCATCGCATCAGGCAATCAATAAT 4 137 1 CGCATCAGGC 0.954971 -48 TTCAGCAAGCGGGCGGTGGTATTA 5 5 1 GCAAGCGGGC 0.799139 -44 TCACTTTTACCCCTGCAAGCGGGAATATTT 6 76 1 CCCTGCAAGC 0.70835 -174 CAAAGATTGGCGATTCAAGCGGTTTGCCGT 6 152 1 CGATTCAAGC 0.893237 -98 GATGGCTTACCGATGCGGGGTTTGTGGTTA 6 218 0 CGATGCGGGG 0.927431 -32 TTTTTGCTGCCCATTCAGGCGGCTTTTTAG 8 44 0 CCATTCAGGC 0.967595 -171 ********** Masking position 6 Map Score: 4.53866 Number of sites scoring better than the average of aligned sites = 2116 Number in coding regions = 1810 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 8 GAACCAAAGTAAATACCACATTGTTTCTGCTC 4 12 0 AAATACCATT 0.717535 -173 TCCGCTTTTCATATCTGACATTATTGATTGCC 4 154 0 ATATCGCATT 0.78699 -31 CCTTTTTGATAAGTCCCACAATCATAACTGAA 7 18 1 AAGTCCCAAT 0.903924 -152 GGAATGGCACAAATCTGTCAATTTTTCCTGGA 7 59 0 AAATCGCAAT 0.980125 -111 CGTTATGGCAAAATAAGCCAATACAGAACCAG 7 130 1 AAATAGCAAT 0.90664 -40 AAGCAGGGGAAATTCAGTCTATTGTAGCGAGG 8 78 1 AATTCGCTAT 0.658582 -137 TATCTGAATGAAATGTGTCAATCCACAGAAAC 9 70 1 AAATGGCAAT 0.937583 -231 ACGTCCGACAAAATGCGTCATTGACAGCGGTT 9 99 0 AAATGGCATT 0.898454 -202 TAACACGAGAAAGTCTGGCTATTCCGTAATGC 9 131 1 AAGTCGCTAT 0.840291 -170 ATATAATTAAAAATCCAGCATTCTCAATCCAT 9 177 0 AAATCACATT 0.764142 -124 TTTTTGCAACAAATCTCACAATAAAAAGTTTC 14 253 1 AAATCCCAAT 0.956295 -48 ***** * **** Masking position 1 Map Score: 4.62916 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 245 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 AACTGACGATACAACAAAGGCGCAACGCTTT 2 26 0 ACAACAAAGC 0.914462 -65 TAATGTTGTCACAAAAAGTGAGGGTGACTAC 6 11 0 ACAAAAAGGA 0.799683 -239 GTGGTTAACCACAAACCCCGCATCGGTAAGC 6 213 1 ACAAACCCGC 0.798204 -37 CACAATCATAACTGAAAACGCCAGTTCCAGG 7 34 1 ACTGAAAAGC 0.710552 -136 ATAAGCCAATACAGAACCAGCATTATCTGGA 7 142 1 ACAGAACCGC 0.929355 -28 GTGTCAATCCACAGAAACCGCTGTCAATGAC 9 84 1 ACAGAAACGC 0.971652 -217 CGTTTCGGAAATAAAAAAGGCACCCGAAGGT 10 59 0 ATAAAAAAGC 0.686991 -210 GTTGTGCTGAACGAAAAGAGCACAACGATCC 10 200 1 ACGAAAAGGC 0.82806 -69 GCAACAACAACCGTTGCTGACT 12 4 1 ACAACAACGT 0.67311 -19 CATTTTTTATACAAAAAAAGACAGGAACGTA 14 130 1 ACAAAAAAGA 0.82804 -171 GCTTTTCATCACAAAAACCGCAGATAATCCT 14 187 1 ACAAAAACGC 0.982055 -114 ******** ** Masking position 1 Map Score: 3.53815 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 648 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 10 GGAGCAGAAACAATGTGGTATTTA 4 5 1 CAGAAACAAT 0.828329 -180 TGGTTAACCACAAACCCCGCATCGGTAAGC 6 214 1 CAAACCCCGC 0.884873 -36 TAAGCCAATACAGAACCAGCATTATCTGGA 7 143 1 CAGAACCAGC 0.917268 -27 TGTCAATCCACAGAAACCGCTGTCAATGAC 9 85 1 CAGAAACCGC 0.980427 -216 AATGCAAAATCAAAAACAATTTCCATTTTA 10 153 0 CAAAAACAAT 0.831158 -116 GCAACAACAACCGTTGCTGACT 12 5 1 CAACAACCGT 0.895368 -18 CTTTTCATCACAAAAACCGCAGATAATCCT 14 188 1 CAAAAACCGC 0.980807 -113 AGATTTGTTGCAAAAACCATCTGACCATAA 14 239 0 CAAAAACCAT 0.926436 -62 ********** Masking position 2 Map Score: 3.99104 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 653 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 CGCCGCATCAGGCCTACGTTCGTTAACTTTT 4 107 0 GGCCACGTTC 0.945845 -78 ATCACGACGCGTCGATCGTTCACGGAATGGC 7 83 0 GTCGTCGTTC 0.988906 -87 GACGCATTTTGTCGGACGTTAACACGAGAAA 9 112 1 GTCGACGTTA 0.941672 -189 ACGGTGGGGGATCCATTGTTCTGTTCAATGA 9 249 1 ATCCTTGTTC 0.823321 -52 TTCTGTGATAGTCGATCGTTAAGCGATTCAG 10 13 1 GTCGTCGTTA 0.967869 -256 GAGCACAACGATCCTTCGTTCACAGTGGGGA 10 217 1 ATCCTCGTTC 0.967869 -52 **** ****** Masking position 9 Map Score: 0.545967 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 103 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 ********** No masking Map Score: 5.4955e-13 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 ********** No masking Map Score: 5.4955e-13 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: 5.4955e-13 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