AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_bbur_reg_300.orf -o078_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00315 172 3615 #2 RBB00314 240 3615 #3 RBB00313 90 3615 #4 RBB00312 91 3615 #5 RBB00307 45 3615 Motif number 1 GTAATAGATATTATTTTTTTTTTAATGTAGAATTTAT 1 32 0 TTTTTTAATG 0.956936 -141 TGTGAATTTTTAAAAGTTTTTGGTATTTCCTATGTAA 1 65 0 TATTTGTATT 0.857375 -108 TAACATTATATAGTATAATGTTAAATTAGGATTCTAT 1 112 0 TTATTTAATT 0.955216 -61 TTTAAAATAATTTTTGATTCTTCAATTAAGT 2 5 0 TTATTTAATT 0.955241 -236 AATTATTTGGTTCAATTGTTTAAAATAATTTTTGATT 2 23 0 TATTTAAATA 0.813409 -218 AATTGTAGGTTGTTTTTTTGTTGTATTTTTGATAAAT 2 57 0 TTTTTTTATT 0.965305 -184 TTTACTTGCATCATATAGTATTAAATACAATTAAACA 2 104 1 TTATTTAATA 0.955216 -137 AGTAAGCTACTGTTTGATTGTTTAATTGTATTTAATA 2 122 0 TTATTTAATT 0.955241 -119 GTGGATTTTGTATTTTTATTTTTTATAGATATATAGT 2 168 0 TTTTTTTATA 0.964593 -73 GATGCCTCCTTATATATTCTATTACATTTTATC 2 218 0 TTTTTTTATT 0.965306 -23 AGTGAGTTATTAATGCTATTTTGAATATTAAAATAAG 3 11 1 TTTTTTAATA 0.97841 -80 AATAAGCTTTTCTAGGTTTATTCAATATTGTTTTTTG 3 42 1 TATTTTAATA 0.955242 -49 CAATATTGTTTTTTGCATTGTGGTATAAAAAATTGAT 3 64 1 TTATTGTATA 0.855952 -27 TATTGACAATTGCATTTATATGCTATACCATGTTAGT 4 15 1 TATTTGTATA 0.857375 -77 CTTGGCAGCATAAAATTGTTTTTAATGGAGGAGCGTT 4 65 1 TATTTTAATG 0.912532 -27 ACTATTATTCCTCTTTAAAATTCAATACAAAG 5 24 0 TTTTTAAATT 0.902711 -22 * * * * ** **** Masking position 9 Map Score: 23.1834 Number of sites scoring better than the average of aligned sites = 1404 Number in coding regions = 890 Number in noncoding regions = 514 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TTAATTAAAATCTAGACACAGATAAATTCT 1 7 1 AAAACTAACA 0.893616 -166 AGACACAGATAAATTCTACATTAAAAAAAAAATA 1 24 1 AAATCTAAAA 0.957888 -149 AAACTTTTAAAAATTCACAAACAATTTAGATAGA 1 83 1 AAATCACAAA 0.945736 -90 GTATAGTGCTAAAACCAACAAGGACAAAAAA 1 152 1 AAAACAAAGA 0.9626 -21 AATTTATCAAAAATACAACAAAAAAACAACCTAC 2 56 1 AAATCAAAAA 0.990246 -185 ATATAGTATTAAATACAATTAAACAATCAAACAG 2 116 1 AAATCAATAC 0.871752 -125 TAAAAAATAAAAATACAAAATCCACAAAATCTTA 2 180 1 AAATCAAACA 0.986355 -61 CCACAATGCAAAAAACAATATTGAATAAACCTAG 3 53 0 AAAACAAAGA 0.9626 -38 TATAGCATATAAATGCAATTGTCAATAATAA 4 8 0 AAATCAATCA 0.962546 -84 GCCAAGCTACAAATTAAACACTAACATGGTATAG 4 37 0 AAATAAAAAA 0.879292 -55 CTCCTCCATTAAAAACAATTTTATGCTGCCAAGC 4 64 0 AAAACAATAT 0.704024 -28 TTCCTCTTTAAAATTCAATACAAAGCAAGCCCAT 5 15 0 AAATCAAAAA 0.990246 -31 **** *** * ** Masking position 3 Map Score: 15.7001 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 605 Number in noncoding regions = 305 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TTTCCTATGTAATAGATATTATTTTTTTTTTAATGT 1 41 0 AAAAAATTTT 0.73909 -132 TACATAGGAAATACCAAAAACTTTTAAAAATTCACA 1 66 1 ATCAACTTTA 0.946246 -107 ATTTAACATTATACTATATAATGTTAAAAGTATAGT 1 123 1 ATCAAATTTA 0.990342 -50 TAATTGAAGAATCAAAAATTATTTTAAACAATTGAA 2 14 1 ATAAAATTTA 0.970652 -227 ACAACCTACAATTTAACAAGATATTTACTTGCATCA 2 81 1 ATTAAATTTT 0.838393 -160 GTTTAATTGTATTTAATACTATATGATGCAAGTAAA 2 104 0 ATTAAATTGA 0.721124 -137 CAATTAAACAATCAAACAGTAGCTTACTACTATTAC 2 131 1 ATAAAAGTTA 0.912656 -110 AAAAATACAAAATCCACAAAATCTTATTAAGATAAA 2 188 1 AACAAATTTA 0.967752 -53 CTCCTTATATATTCTATTACATTTTATCTTAATAAG 2 210 0 ATCATATTTA 0.909848 -31 TTATTTTAATATTCAAAATAGCATTAATAACTCACT 3 11 0 ATCAAGCTTA 0.847593 -80 ATATTGAATAAACCTAGAAAAGCTTATTTTAATATT 3 34 0 AACAAAGTTA 0.90459 -57 TTCTAGGTTTATTCAATATTGTTTTTTGCATTGTGG 3 51 1 ATCAAGTTTT 0.904589 -40 TTGCATTTATATGCTATACCATGTTAGTGTTTAATT 4 24 1 ATCAAATTTA 0.990342 -68 ACGCTCCTCCATTAAAAACAATTTTATGCTGCCAAG 4 65 0 ATAAAATTTA 0.970652 -27 ** * * * ** *** Masking position 6 Map Score: 17.8737 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 313 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ACAGATAAATTCTACATTAAAAAAAAAATA 1 28 1 TCTACATTAA 0.84598 -145 AAATTAGGATTCTATCTAAATTGTTTGTGA 1 97 0 TCTATCTAAA 0.94648 -76 AACCAAATAATTTATCAAAAATACAACAAA 2 48 1 TTTATCAAAA 0.809892 -193 CTACTATATATCTATAAAAAATAAAAATAC 2 166 1 TCTATAAAAA 0.935964 -75 TCTATTACATTTTATCTTAATAAGATTTTG 2 204 0 TTTATCTTAA 0.753536 -37 AATGCTATTTTGAATATTAAAATAAGCTTT 3 22 1 TGAATATTAA 0.677796 -69 AATGCAATTGTCAATAATAA 4 1 0 TCAATAATAA 0.907911 -91 TCTTTAAAATTCAATACAAAGCAAGCCCAT 5 15 0 TCAATACAAA 0.85261 -31 ********** Masking position 4 Map Score: 1.6169 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 324 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 AAATTCTACATTAAAAAAAAAATAATATCT 1 34 1 TTAAAAAAAA 0.841087 -139 TAGTATAATGTTAAATTAGGATTCTATCTA 1 109 0 TTAAATTAGG 0.904496 -64 TTTTTGATTCTTCAATTAAGT 2 2 0 TTCAATTAAG 0.903106 -239 GTTCAATTGTTTAAAATAATTTTTGATTCT 2 21 0 TTAAAATAAT 0.924004 -220 CAAAATCTTATTAAGATAAAATGTAATAGA 2 204 1 TTAAGATAAA 0.886766 -37 ATTTTGAATATTAAAATAAGCTTTTCTAGG 3 28 1 TTAAAATAAG 0.979651 -63 ********** Masking position 4 Map Score: 0.762298 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 331 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 ********** No masking Map Score: 2.65333e-13 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 7 ********** No masking Map Score: 2.65333e-13 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: 2.65333e-13 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