AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i319_bsub_mtub_100.orf -o319_bsub_mtub_100.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 comGB 52 probably part of the DNA transport machinery #2 comGA 300 late competence gene Motif number 1 CTCTTTAATAACCTGGCTTGATCCTTTAACAACCAG 1 17 0 ACCGTTGTTT 0.994208 -36 TTCACCGAGCCTCTTTAATAACCTGGCTT 1 34 0 ACCGCTCTAT 0.993114 -19 TGACCAAATGACCGGTATTGTTGCATTAGGCGATCT 2 20 1 ACCTTTGTAT 0.983055 -281 AGACATGGTCACCATGCCTGCTAGATTCCATTTTCA 2 99 0 ACCGCTGTAT 0.997876 -202 AGGCATGGTGACCATGTCTGCTTTTTTATTTATAGG 2 116 1 ACCGCTGTTT 0.998036 -185 CTGTTTGATTACCTTTTCTTCTTTTTCTACAATATG 2 252 1 ACCTCTTTTT 0.970501 -49 *** * *** * ** Masking position 9 Map Score: 7.79922 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 56 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 CATTTTCATTATGCTGTTTTCGCTTATTGAC 2 76 0 ATGCTTTTTC 0.971522 -225 TGCCTGCTAGATTCCATTTTCATTATGCTGT 2 90 0 ATTCCTTTTC 0.996391 -211 TTCAGTTGAAAGTCTTTTTTCTTGCCAGAAA 2 176 1 AGTCTTTTTC 0.96634 -125 GCCAGAAAGAATTGGTTTTTCAGCATATAAC 2 199 1 ATTGGTTTTC 0.95703 -102 ATCTCACAAAATCACGTTTTCCCTGTTTGAT 2 230 1 ATCACTTTTC 0.971522 -71 TCCCTGTTTGATTACCTTTTCTTCTTTTTCT 2 249 1 ATTACTTTTC 0.989396 -52 TTTGATTCCCTCTCCTTTCAACGCA 2 286 0 ATTCCTCTCC 0.963158 -15 ***** ***** Masking position 1 Map Score: 6.45906 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 661 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AAAAGTCTGGTTGTTAAAGGATCAAG 1 4 1 ACGGTTGTTA 0.989557 -49 TAAAGGATCAAGCCAGGTTATTAAAGAGGCTCG 1 25 1 ACGGTTATTA 0.995269 -28 TAATGCAACAATACCGGTCATTTGGTCATTTTC 2 15 0 ACGGTCATTT 0.993105 -286 GTTGAGAAAGATACTGGTCAATAAGCGAAAACA 2 60 1 ACGGTCAATA 0.993106 -241 AACTGAATGTACCCCTGTCATTATAATTTTCCC 2 150 0 ACTGTCATTA 0.989109 -151 * * ******** Masking position 8 Map Score: 4.83583 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 43 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AATAACCTGGCTTGATCCTTTAACAACCAG 1 17 0 CTTGATCCTT 0.915227 -36 TGCTAGATTCCATTTTCATTATGCTGTTTT 2 87 0 CATTTTCATT 0.965766 -214 ACCATGTCTGCTTTTTTATTTATAGGGAAA 2 126 1 CTTTTTTATT 0.931862 -175 CTGTCATTATAATTTTCCCTATAAATAAAA 2 139 0 AATTTTCCCT 0.914651 -162 AGTTGAAAGTCTTTTTTCTTGCCAGAAAGA 2 179 1 CTTTTTTCTT 0.975889 -122 CACAAAATCACGTTTTCCCTGTTTGATTAC 2 234 1 CGTTTTCCCT 0.983121 -67 ********** Masking position 6 Map Score: 2.92571 Number of sites scoring better than the average of aligned sites = 1813 Number in coding regions = 1520 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 5 GGTATTGTTGCATTAGGCGATCTTTCCGTT 2 33 1 CATTAGGCGA 0.990516 -268 AGATACTGGTCAATAAGCGAAAACAGCATA 2 68 1 CAATAAGCGA 0.986008 -233 ATTCCATTTTCATTATGCTGTTTTCGCTTA 2 81 0 CATTATGCTG 0.962851 -220 TCTTTTTCTACAATATGCGTTGAAAGGAGA 2 271 1 CAATATGCGT 0.986006 -30 ********** Masking position 5 Map Score: 2.33926 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 123 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 GGTCATTTGGTCATTTTCAAGA 2 3 0 TCATTTTCAA 0.987431 -298 TTGACCAGTATCTTTCTCAACGGAAAGATC 2 51 0 TCTTTCTCAA 0.97876 -250 CTGCTAGATTCCATTTTCATTATGCTGTTT 2 88 0 CCATTTTCAT 0.948019 -213 TACCTTTTCTTCTTTTTCTACAATATGCGT 2 261 1 TCTTTTTCTA 0.968839 -40 ********** Masking position 5 Map Score: 1.87602 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 408 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 ********** No masking Map Score: -1.17788e-14 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: -1.17788e-14 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: -1.17788e-14 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