AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_hpyl_reg_300.orf -o110_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 RHP00355 67 AE000511 #2 RHP00357 40 AE000511 #3 RHP00358 21 AE000511 #4 RHP00359 300 AE000511 #5 RHP00568 212 AE000511 #6 RHP00571 48 AE000511 Motif number 1 TTTTCAAACATTCTAACACAAAATAAAAATTTTGCATG 1 19 0 TTTAAACATA 0.932076 -49 TTTATATTTTAACCTGAATTTTTTCAAACATTC 1 44 0 TTTAACCATT 0.9811 -24 GGAATTTCTTTTTTAAACCCTAGTTTATTAAGGAGTTT 2 11 1 TTTAACCATT 0.981077 -30 TTTATTAAAGGGACTATCAGC 3 2 1 TTTTAAGATA 0.931335 -20 CTTTTGAGCATTTTTACAGACACTCATTGCCACTAAAA 4 32 0 TTTTAAGATT 0.974461 -269 TTATTATGGCTTATTATAGAAAATGCTTTTGAGCATTT 4 57 0 TTTTAAGATT 0.974461 -244 TATTTAGAAATTCTTAAACGGGTTTTGTTTGAGTTTTA 4 143 0 TTTTAACGTT 0.962752 -158 TATTGTATATTTTTTACCCATATTTAGAAATTCTTAAA 4 163 0 TTTTACCATA 0.972664 -138 AGTTTTTTTATTATAATCCAAAATTTCTTTGAATAGTG 5 58 1 TTTAACCATT 0.9811 -155 ACCCAAGCCCTTATTATGGGAAGTTTATGAGCCGTTTT 5 98 0 TTTTAGGATT 0.921508 -115 AAAACAGCTCTTATTCACCCCAATTGTTAGAAGTTTGG 5 139 0 TTTTCCCATT 0.944999 -74 ATAAGAGCTGTTTTTAAACATGGTGCTTTAAAGCGTCA 5 163 1 TTTTAACGTT 0.962753 -50 ** *** ** * * * Masking position 14 Map Score: 16.2047 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 173 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 AATAAACTAGGGTTTAAAAAAGAAATTCC 2 10 0 GGTTTAAAAA 0.817715 -31 AAAAACTCCTTAATAAACTAGGGTTT 2 25 0 TCCTTAATAA 0.966579 -16 GCTGATAGTCCCTTTAATAAA 3 2 0 CCTTTAATAA 0.971148 -20 GCAATGAGTGTCTGTAAAAATGCTCAAAAG 4 40 1 TCTGTAAAAA 0.777794 -261 AAAAGCATTTTCTATAATAAGCCATAATAA 4 65 1 TCTATAATAA 0.964592 -236 TCTATAATAAGCCATAATAAAAGGGCTTGC 4 75 1 GCCATAATAA 0.916562 -226 AAACAAAACCCGTTTAAGAATTTCTAAATA 4 151 1 CGTTTAAGAA 0.79622 -150 TATACAATACCTTATAATAAGATGAAAATT 4 192 1 CTTATAATAA 0.815503 -109 ATTTTTTATTTCTTTATTAATTTGATTGCA 4 239 1 TCTTTATTAA 0.766392 -62 TTAATTTGATTGCATAATAATAGCTGACAT 4 255 1 TGCATAATAA 0.93398 -46 ATTTAATGATTGTTTAATCATTGTTGTTAA 5 20 1 TGTTTAATCA 0.728997 -193 GAAATTTTGGATTATAATAAAAAAACTGGC 5 55 0 ATTATAATAA 0.599071 -158 TCATAAACTTCCCATAATAAGGGCTTGGGT 5 106 1 CCCATAATAA 0.95458 -107 TAAAGCACCATGTTTAAAAACAGCTCTTAT 5 163 0 TGTTTAAAAA 0.721758 -50 AACGCTATACCTTAAAAATTAATGACGC 5 195 0 ACCTTAAAAA 0.795916 -18 ********** Masking position 6 Map Score: 12.9973 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 793 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 AAAAACTCCTTAATAAACTAG 2 30 0 AAAACTCCTT 0.965755 -11 GAGTGTCTGTAAAAATGCTCAAAAGCATTT 4 45 1 AAAAATGCTC 0.87441 -256 AAGCCATAATAAAAGGGCTTGCAAGCGAGT 4 83 1 AAAAGGGCTT 0.982852 -218 AAATGAGCGCAAAACGCCATGAATTTTCAT 4 213 0 AAAACGCCAT 0.937346 -88 GAATAGTGGCAAAACGGCTCATAAACTTCC 5 88 1 AAAACGGCTC 0.992542 -125 ACTTCCCATAATAAGGGCTTGGGTTTTCCA 5 112 1 ATAAGGGCTT 0.911311 -101 ACCATGTTTAAAAACAGCTCTTATTCACCC 5 157 0 AAAACAGCTC 0.978263 -56 AAAAACACCTTTTTTTGAAAT 6 38 0 AAAACACCTT 0.965773 -11 ********** Masking position 4 Map Score: 10.5781 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 436 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 GAGTGTCTGTAAAAATGCTCAAAAGCATTT 4 45 1 AAAAATGCTC 0.809923 -256 TGGTAGCTTTAAAATTGATGACAACAAAGC 4 112 1 AAAATTGATG 0.954015 -189 TAATAAGATGAAAATTCATGGCGTTTTGCG 4 206 1 AAAATTCATG 0.799533 -95 TAATAAAGAAATAAAAAATGAGCGCAAAAC 4 228 0 ATAAAAAATG 0.847404 -73 TGATTGCATAATAATAGCTGACATAACACA 4 261 1 ATAATAGCTG 0.946542 -40 GGATTATAATAAAAAAACTGGCTGAAATTA 5 47 0 AAAAAAACTG 0.940438 -166 ATTGGGGTGAATAAGAGCTGTTTTTAAACA 5 153 1 ATAAGAGCTG 0.888596 -60 CTATACCTTAAAAATTAATGACGCTTTAAA 5 189 0 AAAATTAATG 0.871784 -24 TAAAGTTTGCTAAAAAGATGATTCTAATTT 6 12 1 TAAAAAGATG 0.840392 -37 TCTAATTTCAAAAAAAGGTGTTTTT 6 34 1 AAAAAAGGTG 0.931892 -15 ********** Masking position 4 Map Score: 5.6506 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 586 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 AAATAAAAATTTTGCATGGTTTGATT 1 5 0 TTTGCTGTTT 0.764755 -63 ACCTGAATTTTTTCAAACATTCTAACACAAA 1 35 0 TTTTCACATT 0.819772 -33 AGATTGCGGCTTTGCCCTCTTTTAGTGGCAAT 4 13 1 TTTGCCCTTT 0.983535 -288 AGAAAATGCTTTTGAGCATTTTTACAGACACT 4 46 0 TTTGACTTTT 0.802121 -255 TTGTATATTTTTTACCCATATTTAGAAATTCT 4 167 0 TTTACCTATT 0.819772 -134 TTCATGGCGTTTTGCGCTCATTTTTTATTTCT 4 220 1 TTTGCCCATT 0.983529 -81 ATGTGTTATGTCAGCTATTATTATGCAATCAA 4 260 0 TCAGCATATT 0.875258 -41 GTTGTTAATTTCAGCCAGTTTTTTTATTATAA 5 42 1 TCAGCATTTT 0.875259 -171 TATGAGCCGTTTTGCCACTATTCAAAGAAATT 5 79 0 TTTGCATATT 0.973001 -134 AATCATCTTTTTAGCAAACTTTAT 6 3 0 TTAGCACTTT 0.954564 -46 ***** * **** Masking position 11 Map Score: 5.32497 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 936 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 ********** No masking Map Score: -1.42576e-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: -1.42576e-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: -1.42576e-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