AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_aquae_reg_300.orf -o00760_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.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 nadC 145 quinolinate phosphoribosyl transferase #2 mbhS2 300 hydrogenase small subunit #3 trpS 48 tryptophanyl-tRNA synthetase #4 pncA 37 pyrazinamidase/nicotinamidase #5 aq_1771 300 putative protein Motif number 1 TATAGAAAGAACTTTTCTCAAGAAATC 1 7 0 ACTTTTTCAA 0.928058 -139 AACCTTTATCCTCATTCTTCGG 2 2 1 ACCTTTTCCT 0.965923 -299 GCCTTTCTTGAGCTTTATCATATAAATT 3 8 0 AGCTTTTCAT 0.985225 -41 ATTTAATAGAAGTTTTATCAAGGAGGTGGGA 4 15 1 AGTTTTTCAA 0.961585 -23 ACTTGAGTATACCTTTATAAAATTTCCATCC 5 33 0 ACCTTTTAAA 0.865272 -268 CAAAAAATAACGCTTTATCAATAACTTATTA 5 119 0 CGCTTTTCAA 0.967428 -182 CGGTTGCTTTAGCTCTTTCAACTTTCAACTC 5 185 0 AGCTCTTCAA 0.967428 -116 TTGTTTTTGCAGCATTTTCCACTTTCAACTC 5 250 0 AGCATTTCCA 0.942953 -51 TAGGAACCTCAGCTTTTTCCTTTTTGTTTTT 5 273 0 AGCTTTTCCT 0.982144 -28 ****** **** Masking position 6 Map Score: 10.5464 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 232 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 GAATTGGCAGACGCGGGGGACTTAAAATCCCCTGGGCGA 1 73 1 AGGGATAATC 0.919557 -73 ACACGATAGTATACAGGGGAAGGGAAGTTCCCGAAGAAT 2 24 0 AGGGAGAATT 0.987873 -277 GAAGGGAACGAGGTTATTGACGTTAAGGTTACTTACGCA 2 97 0 AATGATAAGT 0.762037 -204 AATCAAGTTTATGGAAAGGATAGGAGCTTTAGTTGTAGA 2 200 0 AAGGAGAGTT 0.970956 -101 ATTATTTTTAACTTAAAGGAGGGGCACTT 2 282 1 AAGGAGCATT 0.942539 -19 TATATGATAAAGCTCAAGAAAGGCAAATTGTAAAATAAT 3 15 1 AAGAAGAATT 0.955705 -34 AAAAGATTGAAAATCAAGGATGGAAATTTTATAAAGGTA 5 16 1 AAGGAGAATT 0.988639 -285 CCTAACCTTCACGAAACGAATGTTAATTTCCGCTAACCC 5 76 0 AAGAATAATT 0.941438 -225 TTTCTAATGTACCGTGTGGAGTTGAAAGTTGAAAGAGCT 5 167 1 AGGGATAAGT 0.974371 -134 TTTCTAATGTACCGTGTGGAGTTGAAAGTGGAAAATGCT 5 232 1 AGGGATAAGT 0.974371 -69 GGTACATTAGGAACCTCAGCTTTTTCCTTTTT 5 279 0 AAGAATAGTT 0.820877 -22 * * *** * ** ** Masking position 10 Map Score: 9.66277 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 264 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 AGATCTACAACTAAAGCTCCTATCCTTTCC 2 197 1 CTAAAGCTCC 0.973241 -104 CACAGGGTTTCTAATGTACCGTGTGGAGTT 5 160 1 CTAATGTACC 0.993743 -141 GTTGAAAGAGCTAAAGCAACCGCACCGATG 5 194 1 CTAAAGCAAC 0.958212 -107 TTATGAGTTTCTAATGTACCGTGTGGAGTT 5 225 1 CTAATGTACC 0.993743 -76 GCTGAGGTTCCTAATGTACC 5 291 1 CTAATGTACC 0.993743 -10 ********** Masking position 4 Map Score: 8.51326 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 4 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 GGGACTTAAAATCCCCTGGGCGAAAAGCCC 1 89 1 ATCCCCTGGG 0.99075 -57 CTGGGCGAAAAGCCCGTGAGGGTTCGACTC 1 104 1 AGCCCGTGAG 0.949625 -42 CTTTTCCGTTATCTCGTGGGTCGTCCCTTC 2 166 1 ATCTCGTGGG 0.948043 -135 AAACTTGATTATACCCTTTGACTTCAAAAA 2 229 1 ATACCCTTTG 0.932785 -72 GGTACATTAGAAACCCTGTGTGCCTGTGTC 5 150 0 AAACCCTGTG 0.963497 -151 GGTTTCTAATGTACCGTGTGGAGTTGAAAG 5 165 1 GTACCGTGTG 0.989533 -136 AGTTTCTAATGTACCGTGTGGAGTTGAAAG 5 230 1 GTACCGTGTG 0.989533 -71 ********** Masking position 7 Map Score: 6.36085 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 124 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CGCGTCTGCCAATTCCGCCACACCCCCTAACTAAAGA 1 51 0 ACCGCAACCC 0.996099 -95 TGAGGGTTCGACTCCCTCCACCCCCACCACCCAACC 1 120 1 ACCTCACCCC 0.99794 -26 CTTAACGTCAATAACCTCGTTCCCTTCTTCGTAAATG 2 109 1 ACCTCTCCCC 0.996162 -192 TTCTTCGTAAATGCCCTCTATAACTTCGTTTAACTTT 2 133 1 ACCTCAAACC 0.979445 -168 ACGAATGTTAATTTCCGCTAACCCGAGGTTCTGCAAA 5 63 0 ACCGCACCCG 0.989255 -238 ACGGTACATTAGAAACTCATAACCATCGGTGCGGTTG 5 210 0 AACTCTACCC 0.962319 -91 * **** * *** * Masking position 1 Map Score: 3.63756 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 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 6 TCTGCCAATTCCGCCACACCCCCTAACTAA 1 54 0 CCGCCACACC 0.995645 -92 GGTTCGACTCCCTCCACCCCCACCACCCAA 1 124 1 CCTCCACCCC 0.99173 -22 TCCACCCCCACCACCCAACC 1 136 1 CCACCCAACC 0.96802 -10 ATGTTAATTTCCGCTAACCCGAGGTTCTGC 5 66 0 CCGCTAACCC 0.849646 -235 AACTTATTAGACACCTAACCTTCACGAAAC 5 98 0 ACACCTAACC 0.88868 -203 TCAACTTTCAACTCCACACGGTACATTAGA 5 169 0 ACTCCACACG 0.966984 -132 AGAGCTAAAGCAACCGCACCGATGGTTATG 5 200 1 CAACCGCACC 0.896345 -101 TCCACTTTCAACTCCACACGGTACATTAGA 5 234 0 ACTCCACACG 0.966984 -67 ********** Masking position 4 Map Score: 6.1517 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 264 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TTAAGGTTACTTACGCAAAAGAGCACGGAAT 2 83 0 TTACGAAAAG 0.985189 -218 ACGAGGTTATTGACGTTAAGGTTACTTACGC 2 98 0 TGACGTAAGG 0.938531 -203 TAGAGGGCATTTACGAAGAAGGGAACGAGGT 2 122 0 TTACGAGAAG 0.953417 -179 ACCCACGAGATAACGGAAAAGTTAAACGAAG 2 156 0 TAACGAAAAG 0.972716 -145 ATAATCAAGTTTATGGAAAGGATAGGAGCTT 2 210 0 TTATGAAAGG 0.946865 -91 TCATTATTTTTAACTTAAAGGAGGGGCACTT 2 280 1 TAACTAAAGG 0.905221 -21 TTAACATTCGTTTCGTGAAGGTTAGGTGTCT 5 89 1 TTTCGGAAGG 0.912502 -212 ***** ***** Masking position 9 Map Score: 2.50473 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 476 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTTTCTATAAGTATAATATATTTCTTTAGTTA 1 29 1 GTATATATTT 0.947532 -117 CCCTTCCCCTGTATACTATCGTGTAGACTATC 2 39 1 GTATATATGT 0.965983 -262 AAGTCAAAGGGTATAATCAAGTTTATGGAAAG 2 221 0 GTATATCAGT 0.97774 -80 AAGGCAAATTGTAAAATAATTTCCC 3 34 1 GTAAATAATT 0.892619 -15 TTTTATAAAGGTATACTCAAGTTTGCAGAACC 5 42 1 GTATATCAGT 0.97774 -259 AAGGTTAGGTGTCTAATAAGTTATTGATAAAG 5 106 1 GTCTATAATT 0.924927 -195 ***** *** ** Masking position 7 Map Score: 1.59075 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 8 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AAAAGTTCTTTCTATAAGTATAATATATTT 1 22 1 TCTATAAGTA 0.919922 -124 AACCTTAACGTCAATAACCTCGTTCCCTTC 2 106 1 TCAATAACCT 0.947975 -195 GTAAATGCCCTCTATAACTTCGTTTAACTT 2 139 1 TCTATAACTT 0.983039 -162 CCCTTCCAGATCTACAACTAAAGCTCCTAT 2 190 1 TCTACAACTA 0.947975 -111 TAACGCTTTATCAATAACTTATTAGACACC 5 113 0 TCAATAACTT 0.975874 -188 ********** Masking position 6 Map Score: 2.00045 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 76 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ********** No masking Map Score: -1.65313e-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 11 ********** No masking Map Score: -1.65313e-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 12 ********** No masking Map Score: -1.65313e-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