AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_aful_reg_300.orf -o00860_aful_300.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 AF0114 63 transcriptional regulatory protein, putative #2 AF0260 30 glutamyl-tRNA synthetase (gltX) #3 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #4 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #5 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #6 AF1778 105 stage V sporulation protein (spoVG) #7 AF1779 57 2-hydroxyacid dehydrogenase, putative #8 AF1975 99 glutamyl-tRNA reductase (hemA) #9 AF1976 93 26S protease regulatory subunit 4 Motif number 1 AAACCATTCGAAAAGTTAAAATCTTAGCTCA 1 29 1 AAAATTAAAA 0.990319 -35 CTTAGCTCAACAAGTTTAAAAGG 1 51 1 CAAGTTAAAA 0.892281 -13 GGGAAGTTGAGAAATATAAAG 2 1 0 GAAAATAAAG 0.826103 -30 GGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 3 113 0 GAAGTTAAAA 0.956906 -26 GAAAATCCAAAAAATTTAAATAAAGTCAATC 4 41 0 AAAATTAAAT 0.962095 -57 TTAATGGGAAAAAACTTAAATAAAATGA 5 8 0 AAAATTAAAT 0.962095 -74 TCAGCAAGAAAACATTTAAAACGAATTGGAG 5 51 1 AACATTAAAA 0.946124 -31 TGAGAGTAACGAAATTTGAAAGGAGGGTTAG 6 83 1 GAAATTGAAA 0.916659 -23 TTGAACCCAGAAAAGATAAAAAGGTTTTGAA 7 30 0 AAAAATAAAA 0.97324 -28 GCTGAAAAGCAAAAATTAAAATGATAAAATG 8 30 0 AAAATTAAAA 0.990319 -70 TGCTGAATAAAAAACTTAAAAAGCACTTGTG 8 63 1 AAAATTAAAA 0.990319 -37 AGAGGGAAGCAAAAAATAAAATTGAGGGATA 9 69 1 AAAAATAAAA 0.97324 -25 **** ****** Masking position 9 Map Score: 20.8972 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 65 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 TATATAAACCATTCGAAAAGTTAAAATCTTAG 1 24 1 ATCGAAAATT 0.963796 -40 TTTAGGCAATATATAAGAATTTCGAAATTTGC 3 45 1 ATTAAGAATT 0.929948 -94 TTAAACCAGAAAGCGCAAATTTCGAAATTCTT 3 59 0 AACGCAAATT 0.847355 -80 AAATATCTGCAATCGAGAAGTTTTTTAACCTT 3 101 1 AACGAGAATT 0.966485 -38 CTTACTGAAAATCCAAAAAATTTAAATAAAGT 4 46 0 ATCAAAAATT 0.973951 -52 ACAAAGTGGTATATAAGAATTTTGATTGCAGG 6 50 0 ATTAAGAATT 0.929948 -56 CAATGCTGAAAAGCAAAAATTAAAATGATAAA 8 33 0 AACAAAAATA 0.912229 -67 AGCATTGCTGAATAAAAAACTTAAAAAGCACT 8 58 1 AAAAAAAATT 0.829051 -42 ATCACTCATCATATAAGAACTTGTTGCTG 9 8 0 ATTAAGAATT 0.929948 -86 ACGTAGAGGGAAGCAAAAAATAAAATTGAGGG 9 65 1 AACAAAAATA 0.912229 -29 ** ****** ** Masking position 8 Map Score: 9.24841 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 104 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 TTTCGAATGGTTTATATAACCTTCACGAACG 1 6 0 TTTTACTCAC 0.922609 -58 AAAGCGCAAATTTCGAAATTCTTATATATTGCCTAA 3 46 0 TTTGACTATA 0.92617 -93 TGCAGATATTTTTAGGTAAGCTTAAACCAGAAAGCG 3 76 0 TTTGACTAAA 0.987091 -63 AAGGGGGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 3 113 0 TGTGATTAAA 0.77051 -26 TGCTGCAACTCTAAACTCAGTTAAAT 4 82 0 TGCGACTAAC 0.978318 -16 TCCTTTCAAATTTCGTTACTCTCAAACAAAGTGGTA 6 71 0 TTTGACTAAA 0.9889 -35 CCGTTCCGGGAGTCTCCACCATTTTATCA 8 4 1 TTCGACTCAC 0.986792 -96 AAGTTTTTTATTCAGCAATGCTGAAAAGCAAAAATT 8 44 0 TTCGACTAAA 0.989727 -56 TTAAAAAGCACTTGTGAATTCTGAACTATAAG 8 78 1 CTTTACTAAC 0.777294 -22 TCCCTCTACGTTCCGGAAGCCTCCAAATACATATAT 9 40 0 TTCGACTCAA 0.985703 -54 *** * * ** *** Masking position 8 Map Score: 9.43028 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 246 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 TTATATTTCTCAACTTCCCAGGTGGGCC 2 13 1 CAACTTCCCA 0.990674 -18 CCTGTAATTGCAAGTCCCCCTCTTTTTAGG 3 21 1 CAAGTCCCCC 0.98837 -118 GAAGTTTTTTAACCTTCCCACAACTCCCCC 3 117 1 AACCTTCCCA 0.965102 -22 AACCTTCCCACAACTCCCCCTT 3 127 1 CAACTCCCCC 0.991986 -12 TCTTGCTGAGAATGTTCCCATTTAATGGGA 5 30 0 AATGTTCCCA 0.927587 -52 ********** Masking position 5 Map Score: 3.53482 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 140 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AGTCCCCCTCTTTTTAGGCAATATATAAGA 3 33 1 TTTTTAGGCA 0.94454 -106 ATTGCAGATATTTTTAGGTAAGCTTAAACC 3 84 0 TTTTTAGGTA 0.848163 -55 AATTTTTTGGATTTTCAGTAAGATTTATTT 4 56 1 ATTTTCAGTA 0.933315 -42 CTGAGTTTAGAGTTGCAGCA 4 88 1 AGTTGCAGCA 0.829066 -10 AAATGGGAACATTCTCAGCAAGAAAACATT 5 37 1 ATTCTCAGCA 0.908902 -45 GATAAAAAGGTTTTGAAGCAAAAGCCAAAC 7 17 0 TTTTGAAGCA 0.944225 -41 TTAATTTTTGCTTTTCAGCATTGCTGAATA 8 42 1 CTTTTCAGCA 0.96161 -58 TTTAAGTTTTTTATTCAGCAATGCTGAAAA 8 53 0 TTATTCAGCA 0.915168 -47 TCACAAGTGCTTTTTAAGTTTTTTATTCAG 8 65 0 TTTTTAAGTT 0.643048 -35 ********** Masking position 8 Map Score: 4.31135 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 830 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 CGTTCGTGAAGGTTATATAAACCATTCG 1 8 1 GAAGGTTAAT 0.883091 -56 GGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 3 113 0 GAAGGTTAAA 0.953776 -26 TTCCCATTTAATGGGAAAAAACTTAAATAAA 5 15 0 ATGGGAAAAA 0.68413 -67 CTCAAACAAAGTGGTATATAAGAATTTTGAT 6 56 0 GTGGTATAAA 0.855413 -50 AATTTGAAAGGAGGGTTAGAA 6 95 1 GAGGGTTAAA 0.989037 -11 CTTATATGATGAGTGATATATATGTATTTGG 9 23 1 GAGTGATAAT 0.855413 -71 CCGGAACGTAGAGGGAAGCAAAAAATAAAAT 9 60 1 GAGGGAAGAA 0.933651 -34 AAATAAAATTGAGGGATAAAAT 9 82 1 GAGGGATAAA 0.993138 -12 ******** ** Masking position 10 Map Score: 4.82438 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 664 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 TTAAACTTGTTGAGCTAAGATTTTAACTTT 1 40 0 TGAGCTAAGA 0.930209 -24 GCAGATATTTTTAGGTAAGCTTAAACCAGA 3 81 0 TTAGGTAAGC 0.778394 -58 TTTATTTAACTGAGTTTAGAGTTGCAGCA 4 79 1 TGAGTTTAGA 0.819593 -19 CGAATTGGAGAGAGCGAAGC 5 72 1 AGAGCGAAGC 0.984133 -10 GCTTATTATGAGAGCGTGGTAATTTAATCT 6 13 1 AGAGCGTGGT 0.859986 -93 TTAAGAGTTTGGCTTTTGCTTCA 7 4 1 AGAGTTTGGC 0.921756 -54 TCCGGAACGTAGAGGGAAGCAAAAAATAAA 9 59 1 AGAGGGAAGC 0.977054 -35 ********** Masking position 3 Map Score: 1.00604 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 699 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 ********** No masking Map Score: 1.67931e-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: 1.67931e-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 10 ********** No masking Map Score: 1.67931e-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