AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i243_regulatory_hpyl_reg_300.orf -o243_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 RHP00155 93 AE000511 #2 RHP00156 41 AE000511 #3 RHP00158 91 AE000511 #4 RHP00160 119 AE000511 #5 RHP00163 146 AE000511 Motif number 1 GTTTTTAAAGCGCTTTTTAACCTTGATTGTG 1 38 1 CGCTTTTAAC 0.996307 -56 AGTTTTTTGCCGTATTTTGACACAATCAAGG 1 58 0 CGTTTTTGAC 0.928517 -36 TGGCGCATTCGGTATTTTAACACAAAT 3 7 0 GGTTTTTAAC 0.909269 -85 AAAACTAGCAAGCGTTTTAGCGTTGGCGCAT 3 30 0 AGCTTTTAGC 0.990387 -62 TTTAAAACACCGCTTACTAGCCAAAAACTAG 3 53 0 CGCTACTAGC 0.928568 -39 CCGTGCTTTTAGCCTTATGGCTAACTT 4 7 0 AGCTTATGGC 0.819386 -113 ACGCTTTAGCCACGCTTTAGCCGTGCTTTTA 4 27 0 CACCTTTAGC 0.978538 -93 ACGCTCCAGCCACGCTTTAGCCACGCTTTAG 4 38 0 CACCTTTAGC 0.978538 -82 AATTTTCTGACGCATTTTAACAAAAAAAAAA 4 83 0 CGCTTTTAAC 0.996307 -37 TTTAAATCATGGCATTTTAGCATTTTATTTG 5 29 1 GGCTTTTAGC 0.993762 -118 TTAAGAAAATCGCTTTTTAATGCAAATAAAA 5 51 0 CGCTTTTAAT 0.974013 -96 TAATTTTAAGCACGTTTTAGTATGATAACTT 5 93 1 CACTTTTAGT 0.94813 -54 *** ******* Masking position 8 Map Score: 23.2251 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 811 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 TAAGTTTTTAAAGCGCTTTTTAACCTTGAT 1 35 1 AAGCGCTTTT 0.967062 -59 ATTTTGACACAATCAAGGTTAAAAAGCGCT 1 46 0 AATCAAGGTT 0.847493 -48 AAAAACTAGCAAGCGTTTTAGCGTTGGCGC 3 32 0 AAGCGTTTTA 0.87896 -60 TTTGGCTAGTAAGCGGTGTTTTAAATCTTT 3 59 1 AAGCGGTGTT 0.964945 -33 ATAAGGCTAAAAGCACGGCTAAAGCGTGGC 4 20 1 AAGCACGGCT 0.984655 -100 AGCACGGCTAAAGCGTGGCTAAAGCGTGGC 4 31 1 AAGCGTGGCT 0.99204 -89 AGCGTGGCTAAAGCGTGGCTGGAGCGTGGG 4 42 1 AAGCGTGGCT 0.99204 -78 ATTCTTTTTAAATCATGGCATTTTAGCATT 5 23 1 AATCATGGCA 0.761176 -124 TTGCATTAAAAAGCGATTTTCTTAAACAAT 5 57 1 AAGCGATTTT 0.933288 -90 GCTTAATTTTAAGCACGTTTTAGTATGATA 5 90 1 AAGCACGTTT 0.887276 -57 ********** Masking position 2 Map Score: 15.4427 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 886 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 GATTGTGTCAAAATACGGCAAAAAACTTTG 1 62 1 AAATACGGCA 0.990866 -32 TTAAAATACCGAATGCGCCAACGCTAAAAC 3 18 1 GAATGCGCCA 0.989507 -74 TTTTTTGTTAAAATGCGTCAGAAAATTCGG 4 87 1 AAATGCGTCA 0.990858 -33 ATGCGTCAGAAAATTCGGCATGAGGGCAAA 4 99 1 AAATTCGGCA 0.990866 -21 ********** Masking position 4 Map Score: 4.05818 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 48 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 AAGAGCTTCATTTTAATCAAGCGAT 1 4 1 AGCTTATTTA 0.946371 -90 TTTTAATCAAGCGATAAGTTTTTAAAGCGCTT 1 21 1 GCGATATTTT 0.827887 -73 CAACCCATTCAGCATGCGTTTAACACAGATTT 2 16 1 AGCATCTTTA 0.909329 -26 CGCCTTTCCTTTAAAAGATTTAA 3 79 0 GCCTTCTTTA 0.990109 -13 CCACGCTTTAGCCGTGCTTTTAGCCTTATGGC 4 17 0 GCCGTCTTTA 0.968555 -103 GGAGCGTGGGGGTTTGCGTTTTTTTTTTTTTG 4 62 1 GGTTTCTTTT 0.819405 -58 TCATTGCCTTAAATTCTTTTTAAATCA 5 6 1 GCCTTATTCT 0.936489 -141 ATGCTAAAATGCCATGATTTAAAAAGAATTTA 5 20 0 GCCATATTAA 0.884265 -127 TAAACAATAAGGCTTAATTTTAAGCACGTTTT 5 79 1 GGCTTATTTA 0.984262 -68 TAAAATTAACCTTTAATTTTTGAGAGAATT 5 127 0 ACCTTATTTT 0.946828 -20 ***** * **** Masking position 5 Map Score: 8.27002 Number of sites scoring better than the average of aligned sites = 890 Number in coding regions = 803 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 TTATTCTCATATCAAAGTTTTTTGCCGTATT 1 73 0 TATAAGTTTT 0.919797 -21 AGCATGCGTTTAACACAGATTTGATA 2 26 1 TAAAAGATTT 0.963413 -16 CGCCTTTCCTTTAAAAGATTTAAAACACCGC 3 71 0 TTTAAGATTT 0.98184 -21 ATGCCATGATTTAAAAAGAATTTAAGGCAATG 5 12 0 TTAAAGAATT 0.963413 -135 ACCTTTAATTTTTGAGAGAATTTAAAAGTTAT 5 117 0 TTTAAGAATT 0.974181 -30 *** * ****** Masking position 7 Map Score: 1.61314 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 193 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 AATACCGAATGCGCCAACGCTAAAACGCTT 3 22 1 GCGCCAACGC 0.973303 -70 CAGCCACGCTTTAGCCACGCTTTAGCCGTG 4 33 0 TTAGCCACGC 0.940108 -87 CCCCCACGCTCCAGCCACGCTTTAGCCACG 4 44 0 CCAGCCACGC 0.991817 -76 AAAAACGCAAACCCCCACGCTCCAGCCACG 4 55 0 ACCCCCACGC 0.994608 -65 TTTTGCCCTCATGCCGAATTTTCT 4 106 0 GCCCTCATGC 0.948257 -14 ********** Masking position 7 Map Score: 0.832362 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 242 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AGTTTTTAAAGCGCTTTTTAACCTTGATTG 1 37 1 GCGCTTTTTA 0.926507 -57 AAAGTTTTTTGCCGTATTTTGACACAATCA 1 61 0 GCCGTATTTT 0.95239 -33 GTTGGCGCATTCGGTATTTTAACACAAAT 3 10 0 TCGGTATTTT 0.918808 -82 TGGCTAGTAAGCGGTGTTTTAAATCTTTTA 3 61 1 GCGGTGTTTT 0.986547 -31 GTGGGGGTTTGCGTTTTTTTTTTTTTGTTA 4 67 1 GCGTTTTTTT 0.986348 -53 TGGCATTTTAGCATTTTATTTGCATTAAAA 5 38 1 GCATTTTATT 0.698829 -109 GCATTAAAAAGCGATTTTCTTAAACAATAA 5 59 1 GCGATTTTCT 0.926507 -88 ********** Masking position 5 Map Score: 3.39502 Number of sites scoring better than the average of aligned sites = 1293 Number in coding regions = 1184 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 ********** No masking Map Score: -4.16788e-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 9 ********** No masking Map Score: -4.16788e-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 10 ********** No masking Map Score: -4.16788e-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