AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i319_mixed4_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 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 0.994064 -36 TTCACCGAGCCTCTTTAATAACCTGGCTT 1 34 0 ACCGCTCTAT 0.992943 -19 TGACCAAATGACCGGTATTGTTGCATTAGGCGATCT 2 20 1 ACCTTTGTAT 0.982638 -281 AGACATGGTCACCATGCCTGCTAGATTCCATTTTCA 2 99 0 ACCGCTGTAT 0.997831 -202 AGGCATGGTGACCATGTCTGCTTTTTTATTTATAGG 2 116 1 ACCGCTGTTT 0.997987 -185 CTGTTTGATTACCTTTTCTTCTTTTTCTACAATATG 2 252 1 ACCTCTTTTT 0.969786 -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 0.973544 -225 TGCCTGCTAGATTCCATTTTCATTATGCTGT 2 90 0 ATTCCTTTTC 0.996654 -211 TTCAGTTGAAAGTCTTTTTTCTTGCCAGAAA 2 176 1 AGTCTTTTTC 0.968717 -125 GCCAGAAAGAATTGGTTTTTCAGCATATAAC 2 199 1 ATTGGTTTTC 0.960038 -102 ATCTCACAAAATCACGTTTTCCCTGTTTGAT 2 230 1 ATCACTTTTC 0.973544 -71 TCCCTGTTTGATTACCTTTTCTTCTTTTTCT 2 249 1 ATTACTTTTC 0.990161 -52 TTTGATTCCCTCTCCTTTCAACGCA 2 286 0 ATTCCTCTCC 0.965752 -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 0.987653 -49 TAAAGGATCAAGCCAGGTTATTAAAGAGGCTCG 1 25 1 ACGGTTATTA 0.9944 -28 TAATGCAACAATACCGGTCATTTGGTCATTTTC 2 15 0 ACGGTCATTT 0.991843 -286 GTTGAGAAAGATACTGGTCAATAAGCGAAAACA 2 60 1 ACGGTCAATA 0.991844 -241 AACTGAATGTACCCCTGTCATTATAATTTTCCC 2 150 0 ACTGTCATTA 0.987125 -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 CTGGTTGTTAAAGGATCAAGCCAGGTTATT 1 17 1 AAGGATCAAG 0.911695 -36 AAAACAGCATAATGAAAATGGAATCTAGCA 2 87 1 AATGAAAATG 0.964259 -214 TTTCCCTATAAATAAAAAAGCAGACATGGT 2 126 0 AATAAAAAAG 0.928965 -175 TTTTATTTATAGGGAAAATTATAATGACAG 2 139 1 AGGGAAAATT 0.911095 -162 TCTTTCTGGCAAGAAAAAAGACTTTCAACT 2 179 0 AAGAAAAAAG 0.974813 -122 GTAATCAAACAGGGAAAACGTGATTTTGTG 2 234 0 AGGGAAAACG 0.982362 -67 ********** Masking position 5 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 0.991583 -268 AGATACTGGTCAATAAGCGAAAACAGCATA 2 68 1 CAATAAGCGA 0.987576 -233 ATTCCATTTTCATTATGCTGTTTTCGCTTA 2 81 0 CATTATGCTG 0.966808 -220 TCTTTTTCTACAATATGCGTTGAAAGGAGA 2 271 1 CAATATGCGT 0.987574 -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 AAAAGTCTGGTTGTTAAAGGATCAAGCCAG 1 11 1 TTGTTAAAGG 0.906815 -42 TCTTGAAAATGACCAAATGACC 2 3 1 TTGAAAATGA 0.981239 -298 GATCTTTCCGTTGAGAAAGATACTGGTCAA 2 51 1 TTGAGAAAGA 0.977758 -250 AAACAGCATAATGAAAATGGAATCTAGCAG 2 88 1 ATGAAAATGG 0.944937 -213 ACGCATATTGTAGAAAAAGAAGAAAAGGTA 2 261 0 TAGAAAAAGA 0.957946 -40 ********** Masking position 6 Map Score: 2.20305 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 752 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 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