AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_aful_reg_100.orf -o00350_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0025 300 cyanate transport protein (cynX) #2 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #3 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #4 AF0885 48 4-hydroxyphenylacetate-3-hydroxylase (hpaA-2) #5 AF0886 128 S-adenosylhomocysteinase hydrolase (ahcY-1) #6 AF1215 101 cell division protein, putative #7 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #8 AF1306 77 conserved hypothetical protein #9 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #10 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #11 AF1420 216 membrane protein #12 AF1778 105 stage V sporulation protein (spoVG) #13 AF1779 57 2-hydroxyacid dehydrogenase, putative #14 AF2013 275 coenzyme F390 synthetase (ftsA-3) #15 AF2014 63 sugar transporter, putative #16 AF2100 106 acetolactate synthase, large subunit (ilvB-4) Motif number 1 GGAGAATCGTTTGATTAAATATTGATAA 1 283 0 CTTTGATTAA 0.771201 -18 AATTTTCGCTCCTTTGCTTAAATCGCCCATT 2 16 1 CTTTGCTTAA 0.931542 -108 ATCCTTAAGCCCTTTTCTTCT 2 113 1 CTTTTCTTCT 0.875584 -11 AAGTTGAAATATTTTGCTGCAGAAACTGTAT 5 77 1 ATTTGCTGCA 0.962799 -52 GACCCTTTTCTTCATCTCCAATCC 9 36 0 CTTTTCTTCA 0.982265 -14 TTCGTGGATTCGTTTTCTGCAATATCTCAAT 11 149 1 CTTTTCTGCA 0.990597 -68 TTTAATCTAACGTTTCCTGCAATCAAAATTC 12 35 1 CTTTCCTGCA 0.974696 -71 AAGAGTTTGGCTTTTGCTTCAAAACCTTTTT 13 13 1 CTTTGCTTCA 0.988805 -45 CTTTTAAAGCCTTTTGCTGCAAACGCATTCG 14 193 1 CTTTGCTGCA 0.994083 -83 AGTGTGCATTTTATGCATATTTATTTG 15 7 1 CTTTTATGCA 0.963092 -57 AAAAGCTAAAAATTTTATGCAAATAAATATG 15 26 0 ATTTTATGCA 0.800801 -38 * ********* Masking position 5 Map Score: 16.3853 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 282 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 CTAATTTGTTTTTAAATCCTGTAATACGTCAG 1 118 0 TTTAAACCTT 0.972108 -183 TTTTAAATTTTCGCTCCTTTGC 2 1 1 TTTTAATTTC 0.822705 -123 TAAGGATTCATTTATACCTTTCGTTTACCATC 2 88 0 TTTATACTTC 0.690088 -36 ATTGACTTTATTTAAATTTTTTGGATTTTCAG 3 42 1 TTTAAATTTT 0.820137 -56 GCGTTGCTGTTTTTAAACTTGCCTTTATCGAG 6 24 1 TTTTAACTTC 0.951589 -78 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 6 61 0 TTTAAACTTT 0.950777 -41 CAACCGCCATTTTAAAATTTTTTTTCGTTAAG 8 46 0 TTTAAATTTT 0.820137 -32 AAAACTTTTATGCCTACCTGAATTTGG 9 6 1 TTTTATCCTC 0.740172 -44 GTCACTCAGCTTCAAAGCTTCCCGGATAGTCT 11 55 1 TTCAAACTTC 0.909775 -162 TTCTAACCCTCCTTTCAAATTT 12 94 0 TTCTAACCTC 0.928058 -12 TGGCTTTTGCTTCAAAACCTTTTTATCTTTTC 13 20 1 TTCAAACCTT 0.92688 -38 GAAAACCGTTTTTTAATACTGCCAGATACTGT 14 49 0 TTTTAAACTC 0.817768 -227 GGCAGTGGCTTTTAAAGCCTTTTGCTGCAAAC 14 185 1 TTTAAACCTT 0.972108 -91 TGGTGAAGTATTTAAATCCTGCCTCCCTCATG 14 234 1 TTTAAACCTC 0.980401 -42 ATTTTTAGCTTTTTAATTCTTTAAATTTCC 15 44 1 TTTTAATCTT 0.853662 -20 GCTGCAAGAGTTTAAAACCCATCGAATACGAT 16 33 0 TTTAAACCCT 0.805783 -74 TTAGCAAACTTTTTAAAATTATAATCATAAAT 16 80 1 TTTTAAATTT 0.63407 -27 ****** *** * Masking position 2 Map Score: 17.734 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 300 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 AATAAAACCGCAGTCCGACAATAAAAAAGA 1 85 0 CAGTCCGACA 0.913917 -216 AAAAAACATGCAGCCTGTAAATTCAATGGG 2 41 0 CAGCCTGTAA 0.967445 -83 TTTCGTTTACCATCCTGGCATCTTTTTACC 2 72 0 CATCCTGGCA 0.955736 -52 TAAATAAAGTCAATCTGACACAAGCTCAAG 3 26 0 CAATCTGACA 0.931065 -72 GCTATCACCTCAGCCTGAAGGTCGGTTTAT 5 31 1 CAGCCTGAAG 0.947763 -98 AGAATCAACCTGTCAGCTTTTCTGG 14 6 1 CAACCTGTCA 0.962531 -270 AATACTTCACCATCCTGAAAAACGAATGCG 14 216 0 CATCCTGAAA 0.958475 -60 TAAACTCTTGCAGCCTGACAAAATCAACCT 16 51 1 CAGCCTGACA 0.99431 -56 ********** Masking position 2 Map Score: 8.18402 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 195 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GCAGTCCGACAATAAAAAAGATATACTGCT 1 76 0 AATAAAAAAG 0.831335 -225 AATCTATCTTTATCAAAAAGCGGTTTTTAT 1 230 0 TATCAAAAAG 0.876153 -71 TCTTACTGAAAATCCAAAAAATTTAAATAA 3 49 0 AATCCAAAAA 0.855018 -49 TATTAGCGTAAATCAAAAAGTCCTTC 8 7 0 AATCAAAAAG 0.980498 -71 CTTCATCTCCAATCCAAATTCAGGTAGGCA 9 21 0 AATCCAAATT 0.701392 -29 GAATCAAAAAAAGAGGAAGGG 10 14 0 AATCAAAAAA 0.932044 -11 CGTTTCCTGCAATCAAAATTCTTATATACC 12 45 1 AATCAAAATT 0.845203 -61 AAATTTAAAGAATTAAAAAGCTAAAAATTT 15 42 0 AATTAAAAAG 0.831333 -22 GAATACGATTAATCAAAAAGAATAAATAAT 16 12 0 AATCAAAAAG 0.980498 -95 TTAAAATTATAATCATAAATCGAGT 16 92 1 AATCATAAAT 0.734369 -15 ********** Masking position 7 Map Score: 8.51762 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 113 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TGGCCAAAAGTTCAGGCATTCTTCGGAAATGAC 1 190 1 TTCGGCATTT 0.923628 -111 TCGTTTACCATCCTGGCATCTTTTTACCCAAAA 2 67 0 TCCGGCATTT 0.94196 -57 AGCTCAAGAAATCTGGAGGTGTT 3 1 0 ATCGGAGGTT 0.815124 -97 TTTTTGGATTTTCAGTAAGATTTATTTAACTGA 3 59 1 TTCGTAAGTT 0.913765 -39 AAAAAAGAAATTCTATCAGGATTGATTGAGGTG 4 21 1 TTCATCAGTT 0.850282 -28 TTCGAGCAGAGTTTCCAAAGGCT 5 1 1 TTCAGCAGTT 0.939238 -128 AAATAGACTATCCGGGAAGCTTTGAAGCTGAGT 11 58 0 TCCGGAAGTT 0.974814 -159 AGAAAACGAATCCACGAAGTCTTGAAGCGTTGC 11 134 0 TCCCGAAGTT 0.921807 -83 AGAATCAACCTGTCAGCTTTTCTGGAACTG 14 8 1 ACCGTCAGTT 0.939086 -268 CTCAGACAGTATCTGGCAGTATTAAAAAACGGT 14 44 1 ATCGGCAGTT 0.969009 -232 AGCCTGGTGATCCTCTCGGCTTTGGGAGCCGGT 14 124 0 TCCCTCGGTT 0.81899 -152 *** ***** ** Masking position 12 Map Score: 6.82368 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 533 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 AAATATTGATAAAAGTTATTGACTTACTGAAGT 1 262 0 AAAATTATTC 0.906084 -39 CTTTTTATTTAAACCTTTTTCCCAACTTTGCAA 6 57 0 AAACTTTTTC 0.983602 -45 GCGAACTCCAAAAAATTTATTACATATCCGGAG 7 40 1 AAAATTTATC 0.906083 -33 CCGCCATTTTAAAATTTTTTTTCGTTAAGCAAA 8 42 0 AAAATTTTTC 0.968282 -36 AAAACTTTTATGCCTACCTGAATT 9 2 1 AAACTTTATC 0.949887 -48 AACTCATGAAAAACCTTATTAGCCTCTTGTTAT 11 184 1 AAACTTATTC 0.949887 -33 TTTTGCTTCAAAACCTTTTTATCTTTTCTGGGT 13 24 1 AAACTTTTTC 0.983602 -34 CAGTATTAAAAAACGGTTTTCCCGCCAGTTCAA 14 60 1 AAACGTTTTC 0.933399 -216 TTAAAAAGCTAAAAATTTTATGCAAATAAATAT 15 27 0 AAAATTTTAC 0.827968 -37 **** ***** * Masking position 7 Map Score: 9.63535 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 29 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 TTTAAAAAAGAAATTCTATCAGGATTGATTGAG 4 18 1 AATCTATCGG 0.97971 -31 TTTGCTGCAGAAACTGTATCGTGATATCTGTTG 5 89 1 AATGTATCTG 0.968462 -40 AAGCTGAGTGACAGAGTATCGTGAGATTTTCCG 11 34 0 AAAGTATCTG 0.959321 -183 GGAGTGTGAAATAGACTATCCGGGAAGCTTTGA 11 66 0 AAACTATCGG 0.973741 -151 AGTCTATTTCACACTCCATCAGGGCTATTCGTT 11 82 1 AATCCATCGG 0.936938 -135 ACTGCAGCTCAGACAGTATCTGGCAGTATTAAA 14 37 1 AAAGTATCGG 0.979882 -239 GATAAAGTGTATCTTTCTGTCATGAG 14 260 0 AATGTATCTT 0.799312 -16 * * ****** ** Masking position 8 Map Score: 3.0679 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CTGTAATACGTCAGTGAAATAAAACCGCAG 1 102 0 TCAGTGAAAT 0.767371 -199 AATGCCCCTTTAAGTTAAATTGCATTCGCA 1 161 0 TAAGTTAAAT 0.81695 -140 TTGACTTACTGAAGTTAAATCTATCTTTAT 1 247 0 GAAGTTAAAT 0.89763 -54 ATGCAGCCTGTAAATTCAATGGGCGATTTA 2 34 0 TAAATTCAAT 0.611045 -90 AACTCTAAACTCAGTTAAATAAATCTTACT 3 72 0 TCAGTTAAAT 0.940538 -26 ATTGAGTTTGGCAAATCAATTCGGCGAACT 7 17 1 GCAAATCAAT 0.832025 -56 TTCCGAGCCCGCAGTTGAATTTGGACAG 11 9 0 GCAGTTGAAT 0.905323 -208 ACGCAAATAAATAACAAGAGGC 11 205 0 GCAAATAAAT 0.857248 -12 GGTTTTCCCGCCAGTTCAATGATGGGGCCG 14 74 1 CCAGTTCAAT 0.854595 -202 AAAATTTTATGCAAATAAATATGCATAAAA 15 19 0 GCAAATAAAT 0.857248 -45 ********** Masking position 3 Map Score: 2.94533 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 84 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 TGACGTATTACAGGATTTAAAAACAAATTAGAT 1 119 1 CAGATTAAAA 0.774154 -182 AAAGTTCAGGCATTCTTCGGAAATGACCACTAC 1 196 1 CATCTTGAAA 0.858344 -105 CAATCTGACACAAGCTCAAGAAATCTGGAGGTG 3 13 0 CAACTCAAAA 0.960878 -85 GCTGAGGTGATAGCCTTTGGAAACTCTGCTCGA 5 12 0 TAGCTTGAAA 0.713592 -117 CCCAACTTTGCAATCTCGATAAAGGCAAGTTTA 6 37 0 CAACTCAAAA 0.960878 -65 ATCGAGATTGCAAAGTTGGGAAAAAGGTTTAAA 6 50 1 CAAGTTGAAA 0.809189 -52 ATCAATTCGGCGAACTCCAAAAAATTTATTACA 7 31 1 CGACTCAAAA 0.904091 -42 AATTCAACTGCGGGCTCGGAAAATCTCACGATA 11 18 1 CGGCTCGAAA 0.942151 -199 ATCTCAATATCAAACTCATGAAAAACCTTATTA 11 172 1 CAACTCTAAA 0.858344 -45 CAGTATCTGGCAGTATTAAAAAACGGTTTTCCC 14 50 1 CAGATTAAAA 0.774154 -226 CTGACAAAATCAACCTTAGCAAACTTTTTAAAA 16 65 1 CAACTTGAAA 0.966873 -42 *** *** * *** Masking position 11 Map Score: 4.65189 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 302 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ACATCTTCGATGGAACTTGTCAACATAATT 1 36 1 TGGAACTTGT 0.855964 -265 TCCAGATTTCTTGAGCTTGTGTCAGATTGA 3 17 1 TTGAGCTTGT 0.941216 -81 AGGAAAATTGAGTTTGGCAAATCAATT 7 8 1 TTGAGTTTGG 0.964764 -65 TTATGCCTACCTGAATTTGGATTGGAGATG 9 18 1 CTGAATTTGG 0.910327 -32 GAGCCCGCAGTTGAATTTGGACAG 11 5 0 TTGAATTTGG 0.970611 -212 CCGCCGAGATTTGAACTCGGGTCACCGGCT 14 101 1 TTGAACTCGG 0.924523 -175 TTTGCTAAGGTTGATTTTGTCAGGCTGCAA 16 58 0 TTGATTTTGT 0.829383 -49 ********** Masking position 4 Map Score: 2.5317 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 98 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 AAGTTCCATCGAAGATGTAACGGAGTACCT 1 24 0 GAAGATGTAA 0.887766 -277 ATAGTGCGAATGCAATTTAACTTAAAGGGG 1 157 1 TGCAATTTAA 0.672797 -144 GCAAAGGAGCGAAAATTTAAAA 2 3 0 GAAAATTTAA 0.857968 -121 AAATTCAATGGGCGATTTAAGCAAAGGAGC 2 23 0 GGCGATTTAA 0.943082 -101 CTCAACGCTAAGATTTAATACGCTTTTT 6 84 0 TAAGATTTAA 0.653663 -18 TTACGTCTCCGGATATGTAATAAATTTTTT 7 49 0 GGATATGTAA 0.822217 -24 TTACATATCCGGAGACGTAAGGCC 7 59 1 GGAGACGTAA 0.849375 -14 ATGAGAGCGTGGTAATTTAATCTAACGTTT 12 20 1 GGTAATTTAA 0.792949 -86 GGAAATTTAAAGAATTAAAA 15 54 0 GGAAATTTAA 0.948462 -10 ********** Masking position 5 Map Score: 2.12351 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 96 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 ********** No masking Map Score: 2.35433e-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 13 ********** No masking Map Score: 2.35433e-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 14 ********** No masking Map Score: 2.35433e-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