AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_ecoli_bsub_300.orf -o348_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 csrA 234 carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties #2 alaS 128 alanyl-tRNA synthetase #3 oraA 68 regulator, OraA protein #4 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #5 ygaD 144 orf, hypothetical protein #6 mltB 255 membrane-bound lytic murein transglycosylase B #7 yviE 46 yviE #8 flgM 80 anti-sigma factor repressor of sigma-D-dependent transcription #9 yvyF 73 alternate gene name: yviB; similar to flagellar protein #10 comFB 59 late competence gene #11 comFA 105 late competence protein #12 yviA 97 alternate gene name: degV, sacU; similar to hypothetical proteins #13 degU 82 two-component response regulator #14 degS 216 two-component sensor histidine kinase Motif number 1 GAAGCGAGTCCACGGCATTGCCTGACGCTTAT 1 12 0 CACGGCATTC 0.995888 -223 GGACTCGCTTCACGGCATTCGCATTAACGCTA 1 33 1 CACGGCATTC 0.995888 -202 TCTAAGCAGTCATGGCATTACATTCTGTTAAA 1 115 0 CATGGCATTA 0.938312 -120 CTCTCTGTATCCCGGCATTATCCATCATATAA 1 180 0 CCCGGCATTC 0.996593 -55 CAGTTACCAGCCCGGCGGTTAAGACACGCTGG 2 66 1 CCCGGCGGTA 0.96702 -63 TCCGGTATTACCCGGCATGACAGGAGTAAAA 4 59 1 CCCGGCATGA 0.977565 -21 TTCCCTCCGTCACGGCGTTGTCATATATTTTT 14 192 0 CACGGCGTTC 0.993901 -25 ********* * Masking position 6 Map Score: 9.74122 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 224 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 GACCCGACTCTTTTAATCTTTCAAGGAGCAAAGA 1 211 1 TTTATTAGAA 0.96264 -24 ATAAGATAAGTTTTCTTGACTGGGAAGGTAAAATACCGTATG 2 14 0 TTTTTTGGAA 0.809113 -115 TGAGCATACAGTATAATTGCTTCAACAGAACATATTGACTAT 4 18 1 GTTATTAGAA 0.815621 -62 TCAGGATTTATTGTTTTATTACCAAACGGCAACCTAATCTAA 6 22 1 TTTTTAAGCA 0.820146 -234 AAGATAAATATTTTAATTTGAAAGTTTGAATAAAAGGATAGC 6 107 1 TTTATAGGAA 0.967122 -149 GAGTTCGCTTTTTTTATAGTTCAGGAGGTAGAGTG 7 22 1 TTTATTGGAA 0.949803 -25 CTGTGTCAATTTCTAGTGATTATATCGGCATAAAAACAGAAT 9 14 0 TTTGTTAGAA 0.829138 -60 TGACACAGGCATATTATCTAATAAGGAGAAAAAAAG 9 48 1 ATTATAAGAA 0.823659 -26 TTTTTTTATATTCTTATTTTAATAGTTGGACAGAAAATATTC 11 39 1 TTTATAAGAA 0.975802 -67 TATAACTCTATTGTAAGGGAAACGGCAGCCTAAAAAAAGACC 12 41 0 TTTAGAGGCA 0.702183 -57 TATCTACTCTTTATGATACCAAAATACGCACAAAAATTCTAA 14 67 0 TTTATAAGAA 0.975802 -150 TTATGTCGAATTATAATGAAAGAATGCGTATATTCTAGAAAA 14 125 0 TTTATAAGAA 0.975803 -92 TCAATTACATTTATAATAAAAATATATGACAACGCCGTGACG 14 175 1 TTTATAAGCA 0.952825 -42 ** * ** * * * * * Masking position 22 Map Score: 9.72678 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 50 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TCTTTGCTCCTTGAAAGATTAAAAGAGTCGGGTCTCT 1 208 0 CTCCTAAAAG 0.978186 -27 GCAGATGCGACCCTTGTGTATCAAACAAGACGA 3 3 0 CCCTTAAAAC 0.865256 -66 GGCATATCCTTACAACTTAAAAAAGCAAAAGGGCCG 3 43 0 ATCCTAAAAC 0.942089 -26 TTTCTGAATCCTCCTCGTAAAATTGCAACGCCAACACCATC 5 58 1 CTCCTAGAAC 0.989132 -87 CACTCTACCTCCTGAACTATAAAAAAAGCGAACTCCTAA 7 18 0 CTCCTTAAAC 0.963231 -29 CTTTTTTTCTCCTTATTAGATAATATGCCTGTGTCAATT 9 45 0 CTCCTAAATC 0.988278 -29 TTTTACAGCTCCTCATCATCGGTTATATGAGTATACTGT 10 31 0 CTCCTATATG 0.801599 -29 ATAGCACGCCTCCTTTCGAAACAGTATGCCTGAATGAATA 11 76 0 CTCCTAGATC 0.976306 -30 CTAGCTGACCCTCCTGCTAAGCATAAAAGACTGCCTATACA 14 12 1 CTCCTAAAAC 0.994536 -205 ATACTATCTACTCTTTATGATACCAAAATACGCACAAAAAT 14 72 0 CTCTTAAAAC 0.969789 -145 ***** * * ** * Masking position 5 Map Score: 8.14992 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 61 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 TCGTCTTGTTTGATACACAAGGGTC 3 6 1 TTGTTTGATA 0.820175 -63 TCAGGATTTATTGTTTTATTACCAAACGGC 6 22 1 TTGTTTTATT 0.858748 -234 AGGAGTTCGCTTTTTTTATAGTTCAGGAGG 7 20 1 TTTTTTTATA 0.952799 -27 AGAGCGGAGATTTTTTTATATTCTTATTTT 11 29 1 TTTTTTTATA 0.952799 -77 ACCTGCCTTATTGCTTTATAACTCTATTGT 12 69 0 TTGCTTTATA 0.903881 -29 CCACGCCTCCTTGTATTATTGTTCTATATA 13 60 0 TTGTATTATT 0.733535 -23 GAAAAAAACATTTTTATATACTATCTACTC 14 100 0 TTTTTATATA 0.739612 -117 TATAAAAATGTTTTTTTCTAGAATATACGC 14 112 1 TTTTTTTCTA 0.808057 -105 ATACGCATTCTTTCATTATAATTCGACATA 14 136 1 TTTCATTATA 0.797123 -81 TGTCATATATTTTTATTATAAATGTAATTG 14 176 0 TTTTATTATA 0.901378 -41 ********** Masking position 2 Map Score: 6.5336 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 44 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TATCGTTGTCGATAGCGTTAATGCGAATGC 1 47 0 GATAGCGTTA 0.810962 -188 CGCTGGAGCTGGTGGCGATATTTCGTTAGC 2 92 1 GGTGGCGATA 0.949214 -37 TTTACAAGAGGGGGGCGTGAGCTTCCCTCT 5 14 1 GGGGGCGTGA 0.984063 -131 GGAAGATGGTGTTGGCGTTGCAATTTTACG 5 73 0 GTTGGCGTTG 0.71648 -72 AATAAATCCTGAAGGAGAGAACA 6 4 0 GAAGGAGAGA 0.678201 -252 TGAATAAAAGGATAGCGAGGGGAATGAGTT 6 133 1 GATAGCGAGG 0.850275 -123 CCCCGCACAAGGAAGCGGTAGTCACTGCCC 6 184 0 GGAAGCGGTA 0.792153 -72 CTTCCTTGTGCGGGGCGTGATGCTTTACCA 6 199 1 CGGGGCGTGA 0.878211 -57 GACTGCAACGGAAAGCGAGAGGAATCCT 8 63 1 GAAAGCGAGA 0.907637 -18 TGTTTCGAAAGGAGGCGTGCTAT 11 93 1 GGAGGCGTGC 0.960578 -13 AATAATACAAGGAGGCGTGGCTT 13 70 1 GGAGGCGTGG 0.984924 -13 ********** Masking position 5 Map Score: 6.17421 Number of sites scoring better than the average of aligned sites = 2506 Number in coding regions = 2378 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 6 CAACGATAAAGTCAGGTTGAAGTTGTGTATATCGGC 1 69 1 GCAGGAAGTT 0.985589 -166 AAGCTGATTAGCCAGAGGGAAGCTCACGCCCCCCTC 5 21 0 GCAGGAAGTA 0.91512 -124 TAGCACTTTCGTCAGGAAGATGGTGTTGGCGTTGCA 5 81 0 GCAGGATGTT 0.934204 -64 ATAAATTTTTGACTGACAGAGGTTGTG 5 128 1 GCTGGAGGTT 0.986636 -17 CCATACTTGCCCCTGGTTGAATCTGTTAAATGGACC 6 226 1 CCTGGAATTT 0.936363 -30 TAGATAATATGCCTGTGTCAATTTCTAGTGATTATA 9 32 0 GCTGCAATTT 0.936363 -42 GAAACAGTATGCCTGAATGAATATTTTCTGTCCAAC 11 63 0 GCTGGAATTT 0.990222 -43 CATATTGACCGAATGCTAGAGTATATAGAACAATAA 13 39 1 GATGGAGTTT 0.848984 -44 AAATTCTAAAGACTGTACGAATTTGTATAGGCAGTC 14 40 0 GCTGGAATTT 0.990222 -177 * *** **** * * Masking position 10 Map Score: 6.65836 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 292 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TGTCATTGCTTACTTTTTGGCGTTATATGA 1 158 1 TACTTTTTGG 0.842691 -77 GAAGGTAAAATACCGTATGCGT 2 3 0 TACCGTATGC 0.961468 -126 TACTGTATGAGCATACAGTA 4 1 1 TACTGTATGA 0.622263 -79 GAAGCAATTATACTGTATGCTCATACAGTA 4 11 0 TACTGTATGC 0.914152 -69 TAGATTAGGTTGCCGTTTGGTAATAAAACA 6 33 0 TGCCGTTTGG 0.979674 -223 GGGCAGTGACTACCGCTTCCTTGTGCGGGG 6 184 1 TACCGCTTCC 0.855543 -72 CATTCAGGCATACTGTTTCGAAAGGAGGCG 11 80 1 TACTGTTTCG 0.907272 -26 ATAGGAGACTTGCCTTTTACTAGGCAGGTC 12 15 1 TGCCTTTTAC 0.68603 -83 TTTTTTAGGCTGCCGTTTCCCTTACAATAG 12 46 1 TGCCGTTTCC 0.968521 -52 TCGGTCAATATGCCTTTTGGCTCTATTTTA 13 21 0 TGCCTTTTGG 0.931506 -62 ********** Masking position 8 Map Score: 5.75485 Number of sites scoring better than the average of aligned sites = 1325 Number in coding regions = 1252 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 8 ATACGGTATTTTACCTTCCCAGTCAAGAAA 2 15 1 TTACCTTCCC 0.955381 -114 CACTTTTCAGTTACCAGCCCGGCGGTTAAG 2 59 1 TTACCAGCCC 0.919174 -70 GAGGGGGGCGTGAGCTTCCCTCTGGCTAAT 5 21 1 TGAGCTTCCC 0.848968 -124 ATGCTTTACCATACTTGCCCCTGGTTGAAT 6 218 1 ATACTTGCCC 0.926085 -38 TATAATAGGAGACTTGCCTTTTACTAGGC 12 10 1 AGACTTGCCT 0.925805 -88 GCCTAAAAAAAGACCTGCCTAGTAAAAGGC 12 26 0 AGACCTGCCT 0.982002 -72 AGCTTCGATACCTGCCTTATTGCTTTA 12 81 0 ATACCTGCCT 0.971857 -17 GCTAGCTGACCCTCCTGCTAAGCATA 14 7 1 TGACCCTCCT 0.868221 -210 ********** Masking position 3 Map Score: 5.61186 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 417 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 TCATGGCATTACATTCTGTTAAACCTAAGTTT 1 106 0 ACATTCTTAA 0.929023 -129 AACTGAAAACGCAGTCGATAAAAGGGTTAAGA 8 22 1 GCAGTCGTAA 0.985225 -59 GCTTTCCGTTGCAGTCTTTAAACAATCTTAAC 8 47 0 GCAGTCTTAA 0.99001 -34 ATATACTCTAGCATTCGGTCAATATGCCTTTT 13 33 0 GCATTCGTAA 0.969958 -50 ATTTGTATAGGCAGTCTTTTATGCTTAGCAGG 14 24 0 GCAGTCTTAT 0.97733 -193 ACAAATTCGTACAGTCTTTAGAATTTTTGTGC 14 50 1 ACAGTCTTGA 0.892683 -167 TAGAATATACGCATTCTTTCATTATAATTCGA 14 130 1 GCATTCTTAT 0.954282 -87 ******* * ** Masking position 3 Map Score: 5.32101 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 CCCGACTCTTTTAATCTTTCAAGGAGCAAAG 1 213 1 TAATCTTTCA 0.981656 -22 ATAACACTTTTAAATCTTTCAATCTGATTAG 6 60 0 TAATCTTTCA 0.981656 -196 AATTAAAATATTTATCTTTCATTTTGCGATC 6 94 0 TTATCTTTCA 0.946101 -162 ATCCTTTTATTCAAACTTTCAAATTAAAATA 6 115 0 TAAACTTTCA 0.924915 -141 TAGAATATACGCATTCTTTCATTATAATTCG 14 130 1 GATTCTTTCA 0.887879 -87 * ********* Masking position 7 Map Score: 1.40007 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ********** No masking Map Score: 3.61199e-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 12 ********** No masking Map Score: 3.61199e-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 ********** No masking Map Score: 3.61199e-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