AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i039_Mannose_Metabolism_hpyl_reg_300.orf -o039_hpyl_300.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 RHP00993 108 AE000511 #2 RHP01659 30 AE000511 #3 RHP00999 126 AE000511 #4 RHP01003 62 AE000511 #5 RHP01004 69 AE000511 #6 RHP00650 116 AE000511 #7 RHP00654 69 AE000511 #8 RHP00655 101 AE000511 Motif number 1 TTATTTGGTATAATACCAAAACTTCATTTAAG 1 77 1 TAAACAAAAC 0.969405 -32 ACAAGTCCCATAATAACAAAAAAAATTCTCAT 3 26 0 TAAACAAAAA 0.91216 -101 ACCTTACTGGTGCAACCAAAAAACACAAGTCC 3 50 0 TGCACAAAAA 0.968805 -77 GTAAGGTGCATGAGATGAAAAAAAGCCCTTGC 3 75 1 TGAAGAAAAA 0.98097 -52 CCTTGCACATTGTTATGAAAACAGGTTAAATC 3 101 1 TGTAGAAAAC 0.974877 -26 CCCTAAAAATTACGAAGAAAACCTGATTTTCC 4 39 1 TACAGAAAAC 0.980593 -24 AAAGAGAGCCTGACAAGAAAACGC 5 56 1 TGAAGAAAAC 0.993682 -14 GCACCACGCTTGAAATTAAAACTAAATTTTAG 6 26 1 TGAATAAAAC 0.960525 -91 ATCTAAAATTTGCTAAGAATACACTAAAATTT 6 49 0 TGCAGAATAC 0.96048 -68 *** * ****** Masking position 5 Map Score: 12.7361 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 135 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 AAAGCGCTACAATCTCGCTTAGAAAAAGGA 1 17 0 AATCTCGCTT 0.960431 -92 AAGAACCAACCTTAAATGAAGTT 1 96 0 AACCAACCTT 0.91934 -13 CCGCTCGCATCACCCCTTTCAAACAAG 4 8 1 CATCACCCCT 0.904897 -55 GGGGAAAATCAGGTTTTCTTCGTAAT 4 47 0 AATCAGGTTT 0.858971 -16 ACCACCGCCTTTAACGCACCAC 6 3 1 CACCGCCTTT 0.863296 -114 GCCTTTAACGCACCACGCTTGAAATTAAAA 6 17 1 CACCACGCTT 0.99371 -100 ATTTAGAAAAAATCACGCTTGATCTTATCT 6 77 0 AATCACGCTT 0.985635 -40 CTGAAATACCAGCCCCGCTTAAGATTACTA 7 17 0 AGCCCCGCTT 0.962267 -53 TAAAGGTTTTAATCCCGCTTTCTGCTGAAA 7 41 0 AATCCCGCTT 0.976961 -29 AAGCCAATTAAACCATGTTTTTGCTAATCG 8 45 0 AACCATGTTT 0.858128 -57 ********** Masking position 10 Map Score: 9.78474 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 864 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CTTTTTCTAAGCGAGATTGTAGCGCTTTATCTT 1 19 1 GCGGATTTAC 0.996253 -90 GCGAGATTTAACCTGTTTTCATA 3 114 0 GCGGATTAAC 0.995833 -13 TGTTTGAAAGGGGTGATGCGAGCGG 4 3 0 GGGGATGGAC 0.977516 -60 TTGTTTTTTAGGGTTATTATAGCGTTTTTAATT 5 24 0 GGGTATTTAC 0.966989 -46 ATAAGATCAAGCGTGATTTTTTCTAAATTTTAG 6 79 1 GCGGATTTTC 0.990178 -38 TCAGCAGAAAGCGGGATTAAAACCTTTAGAGAC 7 43 1 GCGGATTAAC 0.996497 -27 *** **** ** * Masking position 7 Map Score: 7.80044 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 74 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 ACTGGTGCAACCAAAAAACACAAGTCCCAT 3 47 0 CCAAAAAACA 0.588597 -80 AAACAAGGCCCTAAAAATTACGAAGAAAAC 4 31 1 CTAAAAATTA 0.987621 -32 TATAATAACCCTAAAAAACAAAAGAGAGCC 5 36 1 CTAAAAAACA 0.883683 -34 ACGCACCACGCTTGAAATTAAAACTAAATT 6 24 1 CTTGAAATTA 0.883683 -93 TAAGAATACACTAAAATTTAGTTTTAATTT 6 38 0 CTAAAATTTA 0.969491 -79 TTGATCTTATCTAAAATTTGCTAAGAATAC 6 59 0 CTAAAATTTG 0.856798 -58 CCTTAAATGCCTAAAATTTAGAAAAAATCA 6 92 0 CTAAAATTTA 0.969491 -25 ACCAGCCCCGCTTAAGATTACTAAATTTT 7 10 0 CTTAAGATTA 0.883683 -60 AGCTGAAAAAATAAAAATTATTTTAACATT 8 13 0 ATAAAAATTA 0.862752 -89 ATTTTTTCAGCTAACGATTAGCAAAAACAT 8 31 1 CTAACGATTA 0.8646 -71 TTGTCATTTGCTAGTAATTAAAGGAGTTTG 8 74 1 CTAGTAATTA 0.811618 -28 ********** Masking position 2 Map Score: 9.14662 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 472 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 GAGATTGTAGCGCTTTATCTTTGAGCTTTCAGCGGGTCA 1 31 1 CCTTCTTTTT 0.977585 -78 TTTGAGCTTTCAGCGGGTCATTAGGGTTTATTTGGTATA 1 50 1 CGGTCTTTTT 0.985876 -59 GCCGCTTATCCATGCTATTTGGCTACTTGG 2 11 0 CGTTCATTTT 0.994293 -20 GGGGAAAATCAGGTTTTCTTCGTAATTTTTAGGGCCTT 4 35 0 CGTTCTCTTT 0.99031 -28 GTTTTCTTGTCAGGCTCTCTTTTGTTTTTTAGGGTTATT 5 39 0 CGTTCTTTTT 0.995611 -31 CAGCGTCTCTAAAGGTTTTAATCCCGCTT 7 51 0 CGTTCAATTT 0.989404 -19 CAGACTCTCAAACTCCTTTAATTACTAGC 8 83 0 CGTTCAATTT 0.989404 -19 * * * ** ** *** Masking position 8 Map Score: 8.32141 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 31 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TTTGTGTCCTTTTTCTAAGCGAGA 1 5 1 TGTCCTTTTT 0.747102 -104 TTGTTATTATGGGACTTGTGTTTTTTGGTT 3 39 1 GGGACTTGTG 0.975886 -88 CAATGTGCAAGGGCTTTTTTTCATCTCATG 3 83 0 GGGCTTTTTT 0.985742 -44 GTAATTTTTAGGGCCTTGTTTGAAAGGGGT 4 22 0 GGGCCTTGTT 0.990179 -41 TTTTTAATTGGGGATTTTTGAG 5 3 0 GGGATTTTTG 0.965219 -67 AAGATCAAGCGTGATTTTTTCTAAATTTTA 6 81 1 GTGATTTTTT 0.812801 -36 ATGGTTTAATTGGCTTTGTCATTTGCTAGT 8 59 1 TGGCTTTGTC 0.911189 -43 ********** Masking position 6 Map Score: 4.96724 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 767 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AGGTTTTCTTCGTAATTTTTAGGGCCTTGT 4 33 0 CGTAATTTTT 0.959912 -30 TGAAATTAAAACTAAATTTTAGTGTATTCT 6 36 1 ACTAAATTTT 0.97409 -81 GTGTATTCTTAGCAAATTTTAGATAAGATC 6 57 1 AGCAAATTTT 0.920485 -60 TAAGATCAAGCGTGATTTTTTCTAAATTTT 6 80 1 CGTGATTTTT 0.880567 -37 CGTGATTTTTTCTAAATTTTAGGCATTTAA 6 90 1 TCTAAATTTT 0.919606 -27 GCTTAAGATTACTAAATTTT 7 1 0 ACTAAATTTT 0.97409 -69 GAAATGTTAAAATAATTTTTATTTTTTCAG 8 11 1 AATAATTTTT 0.866243 -91 ********** Masking position 5 Map Score: 4.60207 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 138 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TGGTATTATACCAAATAAACCCTAATGACC 1 65 0 CCAAATAAAC 0.986172 -44 CCAAGTAGCCAAATAGCATGGATAAGCG 2 9 1 CCAAATAGCA 0.932195 -22 ACTGGTGCAACCAAAAAACACAAGTCCCAT 3 47 0 CCAAAAAACA 0.952723 -80 TCAAAAATCCCCAATTAAAAACGCTATAAT 5 12 1 CCAATTAAAA 0.960486 -58 CTATAATAACCCTAAAAAACAAAAGAGAGC 5 35 1 CCTAAAAAAC 0.904119 -35 AATGACAAAGCCAATTAAACCATGTTTTTG 8 52 0 CCAATTAAAC 0.974504 -50 ********** Masking position 4 Map Score: 5.04089 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 110 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AACCAACCTTAAATGAAGTTTTGGTATTAT 1 86 0 AAATGAAGTT 0.905628 -23 CATTGTTATGAAAACAGGTTAAATCTCGC 3 108 1 AAAACAGGTT 0.973259 -19 GGGGAAAATCAGGTTTTCTTCGTAA 4 48 0 AAATCAGGTT 0.989177 -15 AATTTAGAAAAAATCACGCTTGATCTTATC 6 78 0 AAATCACGCT 0.957637 -39 AAAGCCAATTAAACCATGTTTTTGCTAATC 8 46 0 AAACCATGTT 0.951865 -56 ********** Masking position 6 Map Score: 1.42056 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 68 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 10 ********** No masking Map Score: 1.57984e-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 11 ********** No masking Map Score: 1.57984e-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 12 ********** No masking Map Score: 1.57984e-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