AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_hpyl_reg_100.orf -o216_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00546 21 AE000511 #2 RHP00549 16 AE000511 #3 RHP00550 73 AE000511 #4 RHP00552 130 AE000511 #5 RHP01673 21 AE000511 #6 RHP00716 174 AE000511 Motif number 1 TTAACCTCACAAAACC 2 3 0 TAACCCAAAA 0.986635 -14 TTATACAACAAAAGCACCCAAAACATGCTTAAA 3 13 0 AAACCCAAAA 0.974547 -61 GCTTTTGTTGTATAATCTCAAATTTAATACGAA 3 31 1 TATACCAAAT 0.900246 -43 TACAAAAATCTCCTAAAATATTCGTATT 3 56 0 AAACCTAAAA 0.978966 -18 ATTATACAACAAAGCATTTAAATTAAAAAGGAT 4 17 0 AAACTTAAAT 0.803627 -114 TGCTTTGTTGTATAATTTTGAAAAAATACGCAA 4 34 1 TATATTGAAA 0.699972 -97 ACGCAACAATTAAAAGCGTAAAAGCAAAAGGCG 4 61 1 TAAACTAAAA 0.987254 -70 TATTATCCTAAAATAGAGCGTTC 4 118 0 TATACTAAAA 0.964615 -13 ACCTTCTACTTAAAAACCCTAATTTTTTAAACA 6 97 0 TAAACCTAAT 0.781264 -78 AACCTTAAAAAAATAGCATAAACTCTTATACCT 6 126 0 AAAACTAAAC 0.903728 -49 AATTTGATTTTAAAACCTTAAAAAAATAGCATA 6 139 0 TAAACTAAAA 0.987254 -36 GCTAATCCTTTGAAATTTGATTTTA 6 160 0 TAACTTGAAA 0.883758 -15 *** * * ***** Masking position 11 Map Score: 12.7146 Number of sites scoring better than the average of aligned sites = 2009 Number in coding regions = 1675 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 CTTTTAAGCATGTTTTGGGT 3 1 1 CTTTTAAGCA 0.915546 -73 TTGGGTGCTTTTGTTGTATAATCTCAAATT 3 25 1 TTGTTGTATA 0.715757 -49 TTTAAATGCTTTGTTGTATAATTTTGAAAA 4 28 1 TTGTTGTATA 0.715757 -103 TGTTGCGTATTTTTTCAAAATTATACAACA 4 39 0 TTTTTCAAAA 0.50943 -92 ACGCTTTTAATTGTTGCGTATTTTTTCAAA 4 50 0 TTGTTGCGTA 0.942739 -81 ACGCCTTTTGCTTTTACGCTTTTAATTGTT 4 65 0 CTTTTACGCT 0.724952 -66 ATCCAACCATTTTTTAAGGAACGCTCTATT 4 100 1 TTTTTAAGGA 0.938244 -31 AAGAAAATTCTTGTTGCGAACGGATAATAA 6 37 1 TTGTTGCGAA 0.898203 -138 ATTTCCACAATTTTTACACAAAAGAGGGTT 6 65 0 TTTTTACACA 0.936056 -110 AAACCCTAATTTTTTAAACACCATTTCCAC 6 87 0 TTTTTAAACA 0.84394 -88 AAAATTAGGGTTTTTAAGTAGAAGGTATAA 6 104 1 TTTTTAAGTA 0.947567 -71 TTATGCTATTTTTTTAAGGTTTTAAAATCA 6 138 1 TTTTTAAGGT 0.785714 -37 ********** Masking position 5 Map Score: 8.36019 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1078 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 3 CATTTAAATTAAAAAGGATAGTCCA 4 6 0 AAAAAGGATA 0.928281 -125 AAATTATACAACAAAGCATTTAAATTAAAA 4 22 0 ACAAAGCATT 0.93321 -109 ACGCAACAATTAAAAGCGTAAAAGCAAAAG 4 61 1 TAAAAGCGTA 0.897343 -70 GCGTAAAAGCAAAAGGCGTTCCAAATCCAA 4 76 1 AAAAGGCGTT 0.971381 -55 GCGTTCCTTAAAAAATGGTTGGATTTGGAA 4 94 0 AAAAATGGTT 0.874478 -37 TTATCCTAAAATAGAGCGTTCCTTAAAAAA 4 109 0 ATAGAGCGTT 0.887581 -22 TTTTTACACAAAAGAGGGTTATTATCCGTT 6 55 0 AAAGAGGGTT 0.980416 -120 AAAATTGTGGAAATGGTGTTTAAAAAATTA 6 81 1 AAATGGTGTT 0.73367 -94 GTGTTTAAAAAATTAGGGTTTTTAAGTAGA 6 96 1 AATTAGGGTT 0.854967 -79 AACCTTAAAAAAATAGCATAAACTCTTATA 6 129 0 AAATAGCATA 0.871622 -46 AAATCAAATTTCAAAGGATTAGC 6 162 1 TCAAAGGATT 0.77613 -13 ********** Masking position 9 Map Score: 8.85226 Number of sites scoring better than the average of aligned sites = 3542 Number in coding regions = 3057 Number in noncoding regions = 485 Number of orfs with sites within 600 bp upstream = 291 Fraction of orfs with sites within 600 bp upstream = 0.0467395 Motif number 4 GTGTTTTCCTTAATGTCAATT 1 11 0 TGTTTTCCTT 0.961259 -11 TGGACTATCCTTTTTAATTTAA 4 3 1 GACTATCCTT 0.938822 -128 TATTATCCTAAAATAGAGCG 4 121 0 TATTATCCTA 0.981044 -10 AGAATTTTCTTGTTATCTTAATGTAAAGGT 6 18 0 TGTTATCTTA 0.916064 -157 AAAAGAGGGTTATTATCCGTTCGCAACAAG 6 46 0 TATTATCCGT 0.971481 -129 ********** Masking position 6 Map Score: 0.803182 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 113 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 ********** No masking Map Score: 6.84553e-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 6 ********** No masking Map Score: 6.84553e-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: 6.84553e-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