AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_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 yqgH 68 alternate gene name: yzmC; similar to phosphate ABC transporter (permease) #2 yqgG 153 alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein) #3 pbpA 113 penicillin-binding protein 2A #4 yqgE 33 similar to hypothetical proteins #5 sodA 178 superoxide dismutase #6 yqgC 109 yqgC Motif number 1 CACATCATGTGAGCGTTTTTT 2 1 0 GGCGTTTTTT 0.995669 -153 CACATGATGTGGGCGTTTTTTTTATACAAAA 2 21 1 GGCGTTTTTT 0.995669 -133 TTGTAAATCAGTGCGTTTTTTTGTATAAAAA 2 39 0 GGCGTTTTTT 0.995669 -115 AAAGGTTTTTTCGACTTTTTTCTACAGATAA 3 30 0 TGACTTTTTT 0.926657 -84 TCAAGTAAGAGTGCCAGTTTTCATTTTAAAG 3 57 0 GGCCAGTTTT 0.943225 -57 GCACTCTTACTTGAGTGTCTTTTCTTTCTGT 3 74 1 TGAGTGTCTT 0.868262 -40 GAGCCAAATCGTGAGCTTTTTCATTGATTAC 5 75 1 GGAGCTTTTT 0.9651 -104 GCTTCACAGCGAGCCTTTCTTCATTCAATGT 5 122 0 GGCCTTTCTT 0.987649 -57 * ********* Masking position 8 Map Score: 11.6887 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 335 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 GTTAAGAGGAGAAACGGTTGTCCCCGCACTC 1 26 0 GAAACGGTTT 0.959754 -43 TGAACCGAATGTTAAGGTTTTGTAAATCAGT 2 58 0 GTTAAGGTTT 0.942114 -96 GGTTCTATGTAAAAAGGGTTTGAACCGAATG 2 78 0 AAAAAGGGTT 0.960328 -76 CACGTATAGAGTAAAGGTTCTATGTAAAAAG 2 93 0 GTAAAGGTTT 0.9891 -61 TTTTTTTGCCAAAAAGGGGTTATCTGTAGAA 3 11 1 AAAAAGGGGT 0.959682 -103 AGTTTTCATTTTAAAGGTTTTTTCGACTTTT 3 42 0 TTAAAGGTTT 0.933424 -72 TCTGTAAATAGAAAAGGTGATGTT 3 100 1 GAAAAGGTGT 0.988887 -14 CTAAGGGATAGTAAAGGGGAGTCAGTA 4 17 1 GTAAAGGGGG 0.958641 -17 ********* * Masking position 4 Map Score: 8.4191 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 176 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TTACACTCCTATGAATGTGTTAAGAGGAGAA 1 44 0 ATGAAGTGTT 0.942264 -25 CGCCCACATCATGTGAGCGTTTTTT 2 5 0 ATGTGGCGTT 0.996134 -149 CGCTCACATGATGTGGGCGTTTTTTTTATAC 2 17 1 ATGTGGCGTT 0.996134 -137 GGTTTTGTAAATCAGTGCGTTTTTTTGTATA 2 43 0 ATCAGGCGTT 0.989659 -111 ***** ***** Masking position 2 Map Score: 2.18754 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 21 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGAGTAAAGGTTCTATGTAAAAAGGGTTTG 2 87 0 TTCTATGTAA 0.92691 -67 CCCCTGCGTATAATGTGTAATTTGTCCTAC 2 123 0 TAATGTGTAA 0.87486 -31 AAAAAACCTTTAAAATGAAAACTGGCACTC 3 50 1 TAAAATGAAA 0.940128 -64 GATTATCGGTTAAAGTGAAATATGTCCGCT 5 40 1 TAAAGTGAAA 0.928832 -139 ATGCTTTGTAATCAATGAAAAAGCTCACGA 5 83 0 ATCAATGAAA 0.859293 -96 CCTTTCTTCATTCAATGTAACAAAAGAATG 5 110 0 TTCAATGTAA 0.958067 -69 ********** Masking position 6 Map Score: 1.01091 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 267 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 TCTTAATAAAAAGAGGAGTGCGGGGACAA 1 10 1 AAAGAGGAGT 0.977699 -59 ATGAATGTGTTAAGAGGAGAAACGGTTGTC 1 35 0 TAAGAGGAGA 0.953013 -34 AAAGACACTCAAGTAAGAGTGCCAGTTTTC 3 66 0 AAGTAAGAGT 0.819869 -48 CTATTTACAGAAAGAAAAGACACTCAAGTA 3 81 0 AAAGAAAAGA 0.838078 -33 AAGGGATAGTAAAGGGGAGTCAGTA 4 19 1 AAAGGGGAGT 0.901408 -15 TGTTACATTGAATGAAGAAAGGCTCGCTGT 5 118 1 AATGAAGAAA 0.769738 -61 CATATATACTAAGGAGGAATTATC 5 165 1 AAGGAGGAAT 0.928107 -14 TTAGTTTAGCTAGGAAGTGAAGATA 6 6 0 TAGGAAGTGA 0.772281 -104 GTGTGAATACAAGGAAGACATGAAGAAGAC 6 65 1 AAGGAAGACA 0.964266 -45 AGGAAGACATGAAGAAGACAGAGTAAAATG 6 76 1 GAAGAAGACA 0.847724 -34 ********** Masking position 2 Map Score: 4.97505 Number of sites scoring better than the average of aligned sites = 2294 Number in coding regions = 1726 Number in noncoding regions = 568 Number of orfs with sites within 600 bp upstream = 591 Fraction of orfs with sites within 600 bp upstream = 0.0949245 Motif number 6 CACATGATGTGGGCGTTTTTTTTATACAAA 2 21 1 GGGCGTTTTT 0.888587 -133 TATACGTGTAGGACAAATTACACATTATAC 2 116 1 GGACAAATTA 0.964088 -38 ATTATACGCAGGGGGAATTCAGGAA 2 139 1 GGGGGAATTC 0.953163 -15 AGGTTTAATGGGGCAGATTATCGGTTAAAG 5 25 1 GGGCAGATTA 0.961182 -154 TCATTTCAGCGGACATATTTCACTTTAACC 5 47 0 GGACATATTT 0.928951 -132 TATATACTAAGGAGGAATTATC 5 167 1 GGAGGAATTA 0.956642 -12 ********** Masking position 8 Map Score: 0.956625 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 272 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: 1.5372e-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 8 ********** No masking Map Score: 1.5372e-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 9 ********** No masking Map Score: 1.5372e-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