AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00072_bsub_reg_100.orf -o00072_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mmgA 137 acetyl-CoA acetyltransferase #2 yxjD 78 similar to 3-oxoadipate CoA-transferase #3 yxjC 153 similar to hypothetical proteins from B. subtilis Motif number 1 AATAGTTGTTAGAAGGAGGCTGTTTGACGC 1 17 1 AGAAGGAGGC 0.974868 -121 GAATGAAAAAAGAAGGCTGCGTCAAACAGC 1 35 0 AGAAGGCTGC 0.973887 -103 ATGTATGCTTTGAAACGGGCATGAATGAAT 1 61 0 TGAAACGGGC 0.981652 -77 TAGAAGAAAACGAAAGGGGCATCAAT 2 63 1 CGAAAGGGGC 0.991536 -16 ATGGTAGAGGAAAGCTCCGAAAAAAGGA 3 9 1 GGAAAGCTCC 0.983323 -145 GATTAAAAAAGGAAAGCTCCTTTTTTCGGA 3 26 0 GGAAAGCTCC 0.983323 -128 CATATGTACGAGAAGCGTGGGCCAACTATT 3 58 0 AGAAGCGTGG 0.925982 -96 TCGTACATATGGAAAGGGGACGGAAACAGC 3 77 1 GGAAAGGGGA 0.982775 -77 GAAAGGGGACGGAAACAGCCGATGCGGACA 3 88 1 GGAAACAGCC 0.976598 -66 TCTAGTTCGCGGAAACGGGGGATGTGTGT 3 135 1 GGAAACGGGG 0.990596 -19 ********** Masking position 4 Map Score: 17.4619 Number of sites scoring better than the average of aligned sites = 1468 Number in coding regions = 1311 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 CAGAAGATAGACAGCGCTTACAATTTCTAGT 1 103 0 ACAGCGTTAC 0.996677 -35 AATCGCGATCACAGCAAATACGGCAGCCGTT 2 11 0 ACAGCAATAC 0.991001 -68 GGGGACGGAAACAGCCGATGCGGACAGGTTT 3 92 1 ACAGCCATGC 0.986227 -62 CGCGAACTAGAAAGCGTTTACAAAAACCTGT 3 115 0 AAAGCGTTAC 0.986946 -39 ****** **** Masking position 3 Map Score: 2.49509 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 107 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 CTCCTTCTAACAACTATTCATTTT 1 5 0 CAACTATTCA 0.97452 -133 CTTCTTTTTTCATTCATTCATGCCCGTTTC 1 50 1 CATTCATTCA 0.969331 -88 CGTTTCAAAGCATACATTCATAGAAGACAA 1 74 1 CATACATTCA 0.982373 -64 AAGCGTGGGCCAACTATTCCGATTAAAAAA 3 46 0 CAACTATTCC 0.976351 -108 ACACACATCCCCCGTTTCCGC 3 143 0 CACACATCCC 0.957948 -11 ********** Masking position 6 Map Score: 2.44933 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 300 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 CATGAATGAATGAAAAAAGAAGGCTGCGTC 1 42 0 TGAAAAAAGA 0.981605 -96 AGGAAAGCTCCGAAAAAAGGAGCTTTCCTT 3 18 1 CGAAAAAAGG 0.991892 -136 ACTATTCCGATTAAAAAAGGAAAGCTCCTT 3 34 0 TTAAAAAAGG 0.981605 -120 ********** Masking position 5 Map Score: 1.06113 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 124 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TCATTCATGCCCGTTTCAAAGCATACATTC 1 63 1 CCGTTTCAAA 0.943499 -75 AAGATAGACAGCGCTTACAATTTCTAGTTG 1 101 0 GCGCTTACAA 0.990315 -37 GCTGTAAATCGCGATCACAGCAAATACGGC 2 18 0 GCGATCACAG 0.961069 -61 GCCAACTATTCCGATTAAAAAAGGAAAGCT 3 38 0 CCGATTAAAA 0.973732 -116 GAACTAGAAAGCGTTTACAAAAACCTGTCC 3 113 0 GCGTTTACAA 0.991843 -41 ********** Masking position 5 Map Score: 3.18876 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 252 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AATAGTTGTTAGAAGGAGGCTGTTTGACGC 1 17 1 AGAAGGAGGC 0.980879 -121 GAATGAAAAAAGAAGGCTGCGTCAAACAGC 1 35 0 AGAAGGCTGC 0.958832 -103 ATACATTCATAGAAGACAACTAGAAATTGT 1 85 1 AGAAGACAAC 0.978408 -53 CACCTCATTCAGAAGATAGACAGCGCTTAC 1 113 0 AGAAGATAGA 0.890243 -25 GGTCTAGTGTAGAAGAAAACGAAAGGGGCA 2 54 1 AGAAGAAAAC 0.985367 -25 ATGGTAGAGGAAAGCTCCGAAAAAA 3 6 1 AGAGGAAAGC 0.994038 -148 TCCGATTAAAAAAGGAAAGCTCCTTTTTTC 3 29 0 AAAGGAAAGC 0.955801 -125 GTTTCCGCGAACTAGAAAGCGTTTACAAAA 3 121 0 ACTAGAAAGC 0.910259 -33 ********** Masking position 1 Map Score: 10.4461 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 911 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 ********** No masking Map Score: -4.23894e-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 8 ********** No masking Map Score: -4.23894e-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 9 ********** No masking Map Score: -4.23894e-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