AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_hpyl_reg_100.orf -o156_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 RHP01009 51 AE000511 #2 RHP01011 174 AE000511 #3 RHP00289 58 AE000511 #4 RHP00290 207 AE000511 #5 RHP00314 108 AE000511 Motif number 1 AACACAATCTCATTCAAATAGCGTTT 1 7 0 CATTCAAATA 0.90083 -45 TCAAAATATCCTTTTAAATAACTATAACAC 1 32 0 CTTTTAAATA 0.868345 -20 TGTCATAGGGCTTTAAAAAAAGGATCTAGC 2 24 1 CTTTAAAAAA 0.966765 -151 GCGAAGAGGAGTTTCAAAAACGCTTGATTA 2 52 1 GTTTCAAAAA 0.969823 -123 GATTGAGAATGTTTCTAATCAAGCGTTTTT 2 67 0 GTTTCTAATC 0.671345 -108 AAAATCATCGGTTTCAAAACGCAATTGCGC 2 120 0 GTTTCAAAAC 0.874851 -55 ATCAATAAGCGTTGAAAAATCATCGGTTTC 2 135 0 GTTGAAAAAT 0.579913 -40 TTCAAGCTTTCACAAATACGATCAAT 2 159 0 CTTTCACAAA 0.936974 -16 AAACCTTAATCTTTAAATTAGCCCCTATTA 3 36 0 CTTTAAATTA 0.786288 -23 GAGCGATAACCTTTAAAAAGCGTTATGGGG 4 33 1 CTTTAAAAAG 0.69552 -175 ATGGGGTGGTGTTGCAAAACCCCCTATTTT 4 57 1 GTTGCAAAAC 0.846138 -151 CGATCTTTTTGATTAACAAAACTTTAAAAT 4 101 1 GATTAACAAA 0.581893 -107 ATTAACAAAACTTTAAAATCCGCAACCAAT 4 112 1 CTTTAAAATC 0.893343 -96 CGCAACCAATCATTCTAAAAAGCTATTTAG 4 132 1 CATTCTAAAA 0.704491 -76 GATTGAATTTCTTTAAATTAAAGGATAACC 4 188 1 CTTTAAATTA 0.786288 -20 TTGTTCCTTTCTTTTAAAATTTTCGTATCG 5 88 0 CTTTTAAAAT 0.71413 -21 ********** Masking position 3 Map Score: 13.8555 Number of sites scoring better than the average of aligned sites = 3780 Number in coding regions = 3270 Number in noncoding regions = 510 Number of orfs with sites within 600 bp upstream = 322 Fraction of orfs with sites within 600 bp upstream = 0.0517186 Motif number 2 TTTCTAATCAAGCGTTTTTGAAACTCCTCT 2 56 0 AGCGTTTTTG 0.988238 -119 TTTGCGCAATTGCGTTTTGAAACCGATGAT 2 117 1 TGCGTTTTGA 0.933696 -58 ACGCTTATTGATCGTATTTGTGAAAGCTTG 2 153 1 ATCGTATTTG 0.894129 -22 ACCTTTAAAAAGCGTTATGGGGTGGTGTTG 4 41 1 AGCGTTATGG 0.980996 -167 AATTTGGTCGATCTTTTTGATTAACAAAAC 4 93 1 ATCTTTTTGA 0.940833 -115 GTTCCTAAATAGCTTTTTAGAATGATTGGT 4 136 0 AGCTTTTTAG 0.958454 -72 GACTTTTTTTATCTTTTTGGCTGATTTTTT 5 26 0 ATCTTTTTGG 0.983134 -83 ********** Masking position 5 Map Score: 6.44794 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 692 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 AGGGCTTTAAAAAAAGGATCTAGCGAAGAG 2 30 1 AAAAAGGATC 0.930992 -145 ATAAGCGTTGAAAAATCATCGGTTTCAAAA 2 131 0 AAAAATCATC 0.955306 -44 AACAAAACTTTAAAATCCGCAACCAATCAT 4 115 1 TAAAATCCGC 0.940684 -93 TTTTTAGATCAGAAATCCGC 5 1 0 AGAAATCCGC 0.980917 -108 TTCTGATCTAAAAAATCAGCCAAAAAGATA 5 17 1 AAAAATCAGC 0.984437 -92 AAAAAGATAAAAAAAGTCGCTAAATCATAG 5 38 1 AAAAAGTCGC 0.946457 -71 AAATTTTAAAAGAAAGGAACAAC 5 96 1 AGAAAGGAAC 0.837354 -13 ********** Masking position 5 Map Score: 4.84997 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 549 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AAACGCTATTTGAATGAGATTGT 1 4 1 CGCTATTTGA 0.952136 -48 AACTCCTCTTCGCTAGATCCTTTTTTTAAA 2 35 0 CGCTAGATCC 0.890973 -140 GTTTCAAAAACGCTTGATTAGAAACATTCT 2 62 1 CGCTTGATTA 0.966106 -113 GATTTTTCAACGCTTATTGATCGTATTTGT 2 144 1 CGCTTATTGA 0.973764 -31 ATATAATAGGGGCTAATTTAAAGATTAAGG 3 33 1 GGCTAATTTA 0.850534 -26 CACCCCATAACGCTTTTTAAAGGTTATCGC 4 35 0 CGCTTTTTAA 0.879417 -173 TAAAAAAAGTCGCTAAATCATAGTCGTTTA 5 45 1 CGCTAAATCA 0.973743 -64 AAATCATAGTCGTTTAATTAAGTGCGCTAC 5 59 1 CGTTTAATTA 0.793363 -50 ********** Masking position 4 Map Score: 4.16026 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 839 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 TTTTAAATAACTATAACACAATCTCATTCAAA 1 19 0 CTATACCAAT 0.975796 -33 GATCCTTTTTTTAAAGCCCTATGACAAGTAGG 2 18 0 TTAAACCTAT 0.888112 -157 TAGAAACATTCTCAATCGCAATAAAGACAATT 2 80 1 CTCAACCAAT 0.990587 -95 ATCATCGGTTTCAAAACGCAATTGCGCAAACT 2 115 0 TCAAACCAAT 0.854433 -60 TAAAAGATTACTCTAATACAATATAATAGGGG 3 13 1 CTCTATCAAT 0.787844 -46 ACTAAACCTTAATCTTTAAATTA 3 46 0 CTAAACTAAT 0.976539 -13 AAGGTTATCGCTCAAGCTTAAGAATCTAACTC 4 14 0 CTCAACTAAG 0.872246 -194 ACCAATCATTCTAAAAAGCTATTTAGGAACAA 4 136 1 CTAAAACTAT 0.81824 -72 AAAAAAGTCGCTAAATCATAGTCGTTTAATTA 5 47 1 CTAAACTAGT 0.907141 -62 ***** * **** Masking position 5 Map Score: 3.77648 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 508 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 ********** No masking Map Score: 1.24588e-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 7 ********** No masking Map Score: 1.24588e-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 8 ********** No masking Map Score: 1.24588e-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