AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_hpyl_reg_100.orf -o210_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 RHP00445 140 AE000511 #2 RHP00454 53 AE000511 #3 RHP00455 72 AE000511 #4 RHP00458 63 AE000511 #5 RHP00461 148 AE000511 #6 RHP00489 66 AE000511 #7 RHP00612 35 AE000511 #8 RHP00614 48 AE000511 #9 RHP00615 119 AE000511 #10 RHP00809 24 AE000511 #11 RHP00810 101 AE000511 #12 RHP00894 101 AE000511 Motif number 1 ATAAGCCTAAAAAGACAAACCACCTACCAG 1 33 0 AAAGACAAAC 0.872824 -108 AACTTTATATTATAATAAGCCTAAAAAGAC 1 47 0 TATAATAAGC 0.878448 -94 CATTATAGCGTAAAATAAGCTTTTTTGTAT 1 87 0 TAAAATAAGC 0.938999 -54 CTTTCATTTTTAAAACTAGCATTATACA 2 9 0 TAAAACTAGC 0.920768 -45 TCCAATTCCAAAAAATAAACCCTAATTCAG 3 13 0 AAAAATAAAC 0.94473 -60 ATAACCCCCTAAAATTAAAACGACTAACG 4 45 0 TAAAATTAAA 0.866332 -19 ATTATACTAAAATAATTAAAATGACCGGTT 5 87 0 AATAATTAAA 0.588283 -62 GAAAGAAACTTTTAACAAACAATTCAAGGG 5 118 1 TTTAACAAAC 0.701653 -31 AAATCTATATTATAACTAAAAGGGGGTTTT 6 11 0 TATAACTAAA 0.830337 -56 CATTTTTAGCTAAAATAAAATCTATATTAT 6 28 0 TAAAATAAAA 0.93251 -39 GGTTAAAGTTTAAGACAAACCAAAGAGTTT 8 12 1 TAAGACAAAC 0.935971 -37 TCAAAAACAAACAAGACAAACT 8 37 0 AAAAACAAAC 0.964895 -12 ATCTGGGTTTAAAAACAACCACATTGCAGG 9 94 1 AAAAACAACC 0.812564 -26 GCTAACATGCTAAAACTAAAACCCTTATAA 11 42 1 TAAAACTAAA 0.912522 -60 AAGAATAGGGTAAAATAAACGC 11 90 1 TAAAATAAAC 0.973267 -12 AAATTCGCTATAATAAAATTTCTTTTAA 12 9 1 TATAATAAAA 0.866317 -93 ********** Masking position 5 Map Score: 18.6788 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 812 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 AATAAAGTTCGCATTATAGCGTAAAATAAGC 1 97 0 GCATTTAGCG 0.988211 -44 TTTTTGGAATTGGATTTAGCGCTTATCTCTT 3 29 1 TGGATTAGCG 0.96513 -44 AAATATAGTGGCATTGTAGCATGACTTTATT 5 28 1 GCATTTAGCA 0.977099 -121 AACAATTCAAGGGATTTGGCGATT 5 135 1 GGGATTGGCG 0.985654 -14 AAAATGGCATGGGTTTTAGCAAGGA 6 52 1 GGGTTTAGCA 0.992719 -15 AGGCGGGTTTTAGCAACGACTTTGG 7 5 1 GGGTTTAGCA 0.992719 -31 TTTAGTTTTAGCATGTTAGCATTCAGCCACC 11 31 0 GCATGTAGCA 0.908833 -71 AAAAGAAATTTTATTATAGCGAATTT 12 6 0 TTATTTAGCG 0.806001 -96 CGTTTTGTGGGGGATATGGCGCGTTTAAAAG 12 32 0 GGGATTGGCG 0.985654 -70 ***** ***** Masking position 7 Map Score: 11.5115 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 397 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 TTAATCTGGTAGGTGGTTTGTCTTTTTAGG 1 28 1 AGGTGGTTTG 0.84488 -113 ATTACCAATTAGGAGGTCGTT 1 130 1 AGGAGGTCGT 0.898179 -11 GGTATCAACAATAGGGGTTTAAAAT 2 39 1 ATAGGGGTTT 0.862284 -15 TCCTGAATTAGGGTTTATTTTTTGGA 3 7 1 ATTAGGGTTT 0.643784 -66 TCTTTAGGCGAGGGGGTCTTGCTCGGG 3 56 1 AGGGGGTCTT 0.975791 -17 TTTTAATTTTAGGGGGTTAT 4 54 1 AGGGGGTTAT 0.969997 -10 TATAACTAAAAGGGGGTTTT 6 1 0 AGGGGGTTTT 0.991475 -66 AGGCGGGTTTTAGCAACGAC 7 1 1 AGGCGGGTTT 0.966545 -35 TAATAAGGCTAGGAGGATTTTCTTAGGGGC 9 22 0 AGGAGGATTT 0.955891 -98 CTTTCCTGCAATGTGGTTGTTTTTAAACCC 9 98 0 ATGTGGTTGT 0.81482 -22 TCCATAACTTATAAGGGTTTTAGTTTTAGC 11 50 0 ATAAGGGTTT 0.761154 -52 TAGCGTTTTGTGGGGGATATGGCGCGTTTA 12 36 0 TGGGGGATAT 0.578217 -66 ********** Masking position 5 Map Score: 9.84115 Number of sites scoring better than the average of aligned sites = 1193 Number in coding regions = 1012 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 4 GGTGGTTTGTCTTTTTAGGCTTATTATAAT 1 39 1 CTTTTTAGGC 0.924481 -102 TTATAATATAAAGTTTAAGCGTATGATACA 1 62 1 AAGTTTAAGC 0.767733 -79 ATTTTAAACCCCTATTGTTG 2 44 0 ATTTTAAACC 0.916532 -10 TAGCGCTTATCTCTTTAGGCGAGGGGGTCT 3 45 1 CTCTTTAGGC 0.794558 -28 TAACGCTAAAATTTTAAACCTTAACTCCAA 4 20 0 ATTTTAAACC 0.916532 -44 TAGTCGTTTTAATTTTAGGGGGTTAT 4 48 1 AATTTTAGGG 0.784639 -16 AATGGAGTAAAATTTTTACCCACCCTAATA 5 55 0 AATTTTTACC 0.783228 -94 AATTTTACTCCATTTTAACCGGTCATTTTA 5 71 1 CATTTTAACC 0.963766 -78 AAACCCATGCCATTTTTAGCTAAAATAAAA 6 38 0 CATTTTTAGC 0.833108 -29 GTTTGTCTTAAACTTTAACCT 8 2 0 AACTTTAACC 0.858818 -47 AATGTGGTTGTTTTTAAACCCAGATGACCG 9 89 0 TTTTTAAACC 0.663069 -31 AGCCACCACTCTTTTTAAGGAATTTGT 11 8 0 CTTTTTAAGG 0.916098 -94 AATAAAATTTCTTTTAAACGCGCCATATCC 12 22 1 CTTTTAAACG 0.855918 -80 ACAGAACATCAATTTAAAGGAACTTAAGA 12 83 1 AATTTAAAGG 0.818437 -19 ********** Masking position 5 Map Score: 11.2529 Number of sites scoring better than the average of aligned sites = 1962 Number in coding regions = 1739 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 5 TTATTAAATTACCAATTAGGAGGTCGTT 1 123 1 ACCAATTAGG 0.961126 -18 AAAGGGTATCAACAATAGGGGTTTAAAAT 2 35 1 AACAATAGGG 0.932698 -19 TAAAATTAAAACGACTAACGCTAAAATTTT 4 35 0 ACGACTAACG 0.889683 -29 CACTATATTTAACACTTAGGATTTTTA 5 8 0 AACACTTAGG 0.963867 -141 GGTTTTAGCAACGACTTTGGCTATTTTTCC 7 16 1 ACGACTTTGG 0.939663 -20 AAACAAGACAAACTCTTTGGTTTGTCTTAA 8 21 0 AACTCTTTGG 0.7308 -28 ACAAACCTACACTAATAAGGCTAGGAGGAT 9 34 0 ACTAATAAGG 0.92826 -86 AGACAAAAGACTAAGGATTAATCA 10 7 1 AAGACTAAGG 0.975035 -18 TTTATCCATAACTTATAAGGGTTTTAGTTT 11 54 0 ACTTATAAGG 0.784188 -48 TAAAAACTTAAAGAATAGGGTAAAATAAAC 11 80 1 AAGAATAGGG 0.932739 -22 ********** Masking position 6 Map Score: 7.77072 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 203 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATTTTTAAAACTAGCATTATACA 2 4 0 CTAGCATTAT 0.955195 -50 TGTTGATACCCTTTCATTTTTAAAACTAGC 2 19 0 CTTTCATTTT 0.909189 -35 CCATTTTAACCGGTCATTTTAATTATTTTA 5 80 1 CGGTCATTTT 0.893648 -69 GAAAATCCTCCTAGCCTTATTAGTGTAGGT 9 30 1 CTAGCCTTAT 0.905696 -90 CTATCATTCTCTAGCGTTTTGTGGGGGATA 12 47 0 CTAGCGTTTT 0.970566 -55 CTGTCGTTTTCTATCATTCTCTAGCGTTTT 12 57 0 CTATCATTCT 0.936864 -45 AATTGATGTTCTGTCGTTTTCTATCATTCT 12 67 0 CTGTCGTTTT 0.957698 -35 ********** Masking position 7 Map Score: 3.39305 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 219 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 CGTATGATACAAAAAAGCTTATTTTACGCT 1 81 1 AAAAAAGCTT 0.861697 -60 AGTATAATTGAAAGAAACTTTTAACAAACA 5 109 1 AAAGAAACTT 0.980549 -40 CCACTCTTTTTAAGGAATTTGT 11 3 0 TAAGGAATTT 0.777043 -99 TAAGTTATGGATAAAAACTTAAAGAATAGG 11 69 1 ATAAAAACTT 0.80784 -33 GGCGCGTTTAAAAGAAATTTTATTATAGCG 12 16 0 AAAGAAATTT 0.944419 -86 ACATCAATTTAAAGGAACTTAAGA 12 88 1 AAAGGAACTT 0.976633 -14 ********** Masking position 6 Map Score: 1.79573 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 258 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 ********** No masking Map Score: -1.60339e-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 9 ********** No masking Map Score: -1.60339e-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 10 TAAAATCAATGCCTTAATCTGGTAGGTGGTTT 1 15 1 GCTTATCTGG 0.983336 -126 TCCTGAATTAGGGTTTATTTTTTGGAATTGGA 3 11 1 GGTTATTTTT 0.793881 -62 AGGCGAGGGGGTCTTGCTCGGG 3 61 1 GCTTCTCGGG 0.949803 -12 GGCTTGATCTTGGAGTTAAGGT 4 1 1 GCTTATCTTG 0.973686 -63 TAAAATTTTAGCGTTAGTCGTTTTAATTTTAG 4 34 1 GGTTGTCGTT 0.743198 -30 ATTGTAGCATGACTTTATTAGGGTGGGTAAAA 5 40 1 GCTTATTAGG 0.902141 -109 ACAAACCAAAGAGTTTGTCTTGTTTGTTTTTG 8 26 1 GGTTGTCTTG 0.9629 -23 AGGCTAGGAGGATTTTCTTAGGGGCAGATTTA 9 15 0 GTTTCTTAGG 0.500084 -105 TGTAAAAGTAGCGGTCATCTGGGTTTAAAAAC 9 78 1 GGGTATCTGG 0.938435 -42 GCGTTTATTTTACCCTATTCTT 11 90 0 GGTTATTTTA 0.685952 -12 * *** ****** Masking position 5 Map Score: 0.320224 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 364 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 ********** No masking Map Score: -1.60339e-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: -1.60339e-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 13 ********** No masking Map Score: -1.60339e-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