AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_bsub_mtub_300.orf -o348_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yviE 46 yviE #2 flgM 80 anti-sigma factor repressor of sigma-D-dependent transcription #3 yvyF 73 alternate gene name: yviB; similar to flagellar protein #4 comFB 59 late competence gene #5 comFA 105 late competence protein #6 yviA 97 alternate gene name: degV, sacU; similar to hypothetical proteins #7 degU 82 two-component response regulator #8 degS 216 two-component sensor histidine kinase Motif number 1 CCTCCTGAACTATAAAAAAAGCGAACTCCT 1 20 0 TATAAAAAAA 0.969959 -27 TATATCGGCATAAAAACAGAATCAT 3 6 0 TAAAAACAGA 0.927153 -68 ATCTCCGCTCTAAAAACGGAGATTTGGCC 5 10 0 TAAAAACGGA 0.830069 -96 AAAATAAGAATATAAAAAAATCTCCGCTCT 5 29 0 TATAAAAAAA 0.969959 -77 GTCCAACTATTAAAATAAGAATATAAAAAA 5 40 0 TAAAATAAGA 0.945805 -66 TATAATAGGAGACTTGCCTT 6 1 1 TATAATAGGA 0.90746 -97 AACGGCAGCCTAAAAAAAGACCTGCCTAGT 6 33 0 TAAAAAAAGA 0.96732 -65 GAGTAGATAGTATATAAAAATGTTTTTTTC 8 100 1 TATATAAAAA 0.804034 -117 GCGTATATTCTAGAAAAAAACATTTTTATA 8 112 0 TAGAAAAAAA 0.90856 -105 TATGTCGAATTATAATGAAAGAATGCGTAT 8 136 0 TATAATGAAA 0.81644 -81 CAATTACATTTATAATAAAAATATATGACA 8 176 1 TATAATAAAA 0.950073 -41 ********** Masking position 4 Map Score: 12.823 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 370 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 2 CTAACTGAAAACGCAGTCGATAAAAGGGTTA 2 20 1 ACGCAGCGAT 0.962165 -61 AAATTGACACAGGCATATTATCTAATAAGGA 3 44 1 AGGCATTTAT 0.894827 -30 ATATTCATTCAGGCATACTGTTTCGAAAGGA 5 75 1 AGGCATCTGT 0.973202 -31 ATAGCACGCCTCCTTTCGAAACAGTA 5 90 0 ACGCCTCTTT 0.981804 -16 GCCTTTTACTAGGCAGGTCTTTTTTTAGGCT 6 26 1 AGGCAGTCTT 0.902025 -72 GTCTTTTTTTAGGCTGCCGTTTCCCTTACAA 6 42 1 AGGCTGCGTT 0.946988 -56 AAGCCACGCCTCCTTGTATTATTGTT 7 67 0 ACGCCTCTTG 0.926507 -16 GAATTTGTATAGGCAGTCTTTTATGCTTAGC 8 27 0 AGGCAGCTTT 0.993462 -190 TCTAGAATATACGCATTCTTTCATTATAATT 8 128 1 ACGCATCTTT 0.989614 -89 ****** **** Masking position 1 Map Score: 8.02249 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 474 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 AACTGAAAACGCAGTCGATAAAAGGGTTAAG 2 22 1 GCAGTCGATA 0.982263 -59 GCTTTCCGTTGCAGTCTTTAAACAATCTTAA 2 48 0 GCAGTCTTTA 0.995471 -33 ATATACTCTAGCATTCGGTCAATATGCCTTT 7 34 0 GCATTCGGTA 0.965199 -49 ATTTGTATAGGCAGTCTTTTATGCTTAGCAG 8 25 0 GCAGTCTTTA 0.995471 -192 ACAAATTCGTACAGTCTTTAGAATTTTTGTG 8 50 1 ACAGTCTTTG 0.925552 -167 TAGAATATACGCATTCTTTCATTATAATTCG 8 130 1 GCATTCTTTA 0.986713 -87 ********* * Masking position 5 Map Score: 7.33725 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 71 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TCTAAAAACGGAGATTTGGCC 5 2 0 GAGATTTGGC 0.941961 -104 GTTTCGAAAGGAGGCGTGCTAT 5 94 1 GAGGCGTGCT 0.975497 -12 TATAATAGGAGACTTGCCTTTTACTAGG 6 9 1 GAGACTTGCC 0.995014 -89 AGCCTAAAAAAAGACCTGCCTAGTAAAAGG 6 27 0 AAGACCTGCC 0.979601 -71 AGCTTCGATACCTGCCTTATTGCTTT 6 82 0 GATACCTGCC 0.979578 -16 ATAATACAAGGAGGCGTGGCTT 7 71 1 GAGGCGTGGC 0.992584 -12 ********** Masking position 7 Map Score: 6.48844 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 104 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AAACGCAGTCGATAAAAGGGTTAAGATTGT 2 28 1 GATAAAAGGG 0.820004 -53 ATACTGTTTCGAAAGGAGGCGTGCTAT 5 89 1 GAAAGGAGGC 0.983101 -17 TATAATAGGAGACTTGCCTTTTA 6 4 1 AATAGGAGAC 0.797209 -94 AGACCTGCCTAGTAAAAGGCAAGTCTCCTA 6 16 0 AGTAAAAGGC 0.877885 -82 ACGGCAGCCTAAAAAAAGACCTGCCTAGTA 6 32 0 AAAAAAAGAC 0.747652 -66 GAGTTATAAAGCAATAAGGCAGGTATCGAA 6 75 1 GCAATAAGGC 0.890236 -23 GTAAAATAGAGCCAAAAGGCATATTGACCG 7 20 1 GCCAAAAGGC 0.947212 -63 GAACAATAATACAAGGAGGCGTGGCTT 7 66 1 ACAAGGAGGC 0.972795 -17 TTTTATGCTTAGCAGGAGGGTCAGCTAGC 8 10 0 AGCAGGAGGG 0.815402 -207 GAATTATAATGAAAGAATGCGTATATTCTA 8 130 0 GAAAGAATGC 0.824297 -87 ********** Masking position 4 Map Score: 4.16812 Number of sites scoring better than the average of aligned sites = 2623 Number in coding regions = 2229 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 373 Fraction of orfs with sites within 600 bp upstream = 0.0599101 Motif number 6 TCTACCTCCTGAACTATAAAAAAAGCGAAC 1 24 0 GAACTATAAA 0.942765 -23 CGATGATGAGGAGCTGTAAAA 4 49 1 GAGCTGTAAA 0.990218 -11 CCTTACAATAGAGTTATAAAGCAATAAGGC 6 65 1 GAGTTATAAA 0.952245 -33 CTATGATTTGTAAAATAGAGCCAA 7 5 1 GATTTGTAAA 0.966717 -78 AAATGTAATTGATCTGCAAATTATGTCGAA 8 157 0 GATCTGCAAA 0.967193 -60 ********** Masking position 5 Map Score: 3.14978 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 85 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 GTTTTTATGCCGATATAATCACTAGAAATT 3 19 1 CGATATAATC 0.881048 -55 AAACGTGGTACAGTATACTCATATAACCGA 4 22 1 CAGTATACTC 0.825117 -38 TATTATTGTTCTATATACTCTAGCATTCGG 7 47 0 CTATATACTC 0.982217 -36 TTTATGATACCAAAATACGCACAAAAATTC 8 70 0 CAAAATACGC 0.943489 -147 TTTTTATATACTATCTACTCTTTATGATAC 8 90 0 CTATCTACTC 0.954194 -127 TTTTTTTCTAGAATATACGCATTCTTTCAT 8 122 1 GAATATACGC 0.918453 -95 ********** Masking position 6 Map Score: 2.29664 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 108 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TCCTTATTAGATAATATGCCTGTGTCAATT 3 45 0 ATAATATGCC 0.958963 -29 AAAACGTGGTACAGTATACTCATATAACCG 4 21 1 ACAGTATACT 0.901007 -39 TCCTTTCGAAACAGTATGCCTGAATGAATA 5 76 0 ACAGTATGCC 0.993087 -30 TAGCATTCGGTCAATATGCCTTTTGGCTCT 7 27 0 TCAATATGCC 0.973517 -56 ********** Masking position 5 Map Score: 0.544037 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 145 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: 5.35339e-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 10 ********** No masking Map Score: 5.35339e-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 11 ********** No masking Map Score: 5.35339e-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