AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_hpyl_reg_300.orf -o00910_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0004 121 carbonic anhydrase (icfA) #2 HP0380 65 glutamate dehydrogenase (gdhA) #3 HP0382 182 zinc-metallo protease (YJR117W) #4 HP0512 290 glutamine synthetase (glnA) #5 HP0640 62 poly(A) polymerase (papS) #6 HP0643 164 glutamyl-tRNA synthetase (gltX) #7 HP0649 57 aspartate ammonia-lyase (aspA) #8 HP0723 128 L-asparaginase II (ansB) #9 HP0943 21 D-amino acid dehydrogenase (dadA) #10 HP0944 300 translation initiation inhibitor, putative Motif number 1 CTAAAAGGGTAATTAAGTTTTAAT 2 1 0 AATTAGTTAT 0.595463 -65 TCCTTTATTGTTTTAAGTGTTTTTATTGTAACAC 2 34 0 TTTTAGTTTT 0.97583 -32 AAGAGACTATTTTTGAGCGTTTTTAATCCTAAAA 3 51 0 TTTTGGTTTT 0.944205 -132 ATTTATTTAATTTTATGGTTTTATGGTAAATTTT 3 96 1 TTTTAGTTAT 0.806963 -87 ATGGTAAATTTTTGAAAAATTGTTATAATTCCTA 3 118 1 TTTGAATTTT 0.648701 -65 GCAACCACACTATTAGGATTTTTTGAAGAAAATC 4 118 0 TATTAGTTTT 0.971276 -173 GTAGAATCTGTATCAAGTTTTATTAAGATGCATG 4 196 0 TATCAGTTTT 0.74613 -95 AATTGTTATGAATTGAGTTTGATTGATAGGGGTG 4 256 0 AATTGGTGTT 0.593725 -35 AATTCATAACAATTAAAGGTGGTTA 4 276 1 AATTAATGTT 0.647008 -15 TTTTTAGAATTTTTAAGGAATTTTG 5 2 0 TTTTAGATTT 0.806963 -61 TTCTTTGTGTTATTATATCTTTTTAGAATTTTTA 5 21 0 TATTAATTTT 0.946726 -42 GCTTTTTACTCTTAAAATTTCTTTGTGTTATTA 5 40 0 TCTTAATTTT 0.860314 -23 ACGCCAAGCTTTTTATGGTTGGTTATCAAAAAGC 6 22 0 TTTTAGTGTT 0.907927 -143 ACCACAACACAATTAAGTATTCTTTAGGTATAAT 6 112 1 AATTAGTTTT 0.934536 -53 TAACCCTTTTTAAATTTATTTTAACGATGT 8 7 1 TTTTTATTTT 0.848647 -122 CACCTTTTGAAATTAAAAGATTTTATAGTATAGT 8 44 0 AATTAAATTT 0.437267 -85 AATGAGAATATTTTTGAAATTGTTGATTCTTTTA 8 84 1 TTTTTATTTT 0.848647 -45 AATTGTTGATTCTTTTATTTTGTTTGAAGGGGCA 8 101 1 TCTTTATTTT 0.619415 -28 TAGAAAATGCTTTTGAGCATTTTTACAGACACTC 10 45 0 TTTTGGTTTT 0.944205 -256 CAAGCCCTTTTATTATGGCTTATTATAGAAAATG 10 70 0 TATTAGTTTT 0.971276 -231 TTTGTTTGAGTTTTAGGCTTTGTTGTCATCAATT 10 124 0 TTTTAGTTTT 0.97583 -177 TTTTACCCATATTTAGAAATTCTTAAACGGGTTT 10 156 0 ATTTAATTTT 0.899603 -145 TATTATAAGGTATTGTATATTTTTTACCCATATT 10 177 0 TATTGATTTT 0.881639 -124 AACGCCATGAATTTTCATCTTATTATAAGGTATT 10 197 0 ATTTTATTTT 0.703064 -104 ***** * ** ** Masking position 3 Map Score: 26.35 Number of sites scoring better than the average of aligned sites = 1245 Number in coding regions = 992 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 TTTTACACTTTAAAGGGCTTTC 1 2 0 TAAGGGCTTT 0.9326 -120 TTTTAAAAACAAACGAATTTTAATCAAAATG 1 83 1 AAAGAATTTT 0.909356 -39 ATTTTAATCAAAATGAGATTTAAGGGTTAAA 1 99 1 AAAGAGATTT 0.799849 -23 CGCTATAAACAAAAAGGTTTGTC 3 3 0 AAAAGGTTTG 0.868651 -180 TTTAATGGAGAAAGGAGTTTGGAAT 3 168 1 AAAGAGTTTG 0.962732 -15 AATTGTTATGAATTGAGTTTGATTGATAGGG 4 259 0 AATGAGTTTG 0.688543 -32 TTAGAATTTTTAAGGAATTTTG 5 2 0 TAAGAATTTT 0.859975 -61 ATAATAACACAAAGAAATTTTAAGAGTAAAA 5 39 1 AAAAAATTTT 0.702609 -24 TAACCAACCATAAAAAGCTTGGCGTTAGCCA 6 31 1 TAAAAGCTTG 0.692908 -134 CCTTTATTTAAAAATAGTTTTTGATTATACC 6 138 0 AAATAGTTTT 0.708329 -27 TATTTTTAAATAAAGGGTTTTT 6 153 1 TAAGGGTTTT 0.958124 -12 AATTATTACATAAGGAGCTTTT 7 46 1 TAAGAGCTTT 0.927352 -12 CTTTTGAAATTAAAAGATTTTATAGTATAGT 8 44 0 TAAAGATTTT 0.611208 -85 AAAAATGCTCAAAAGCATTTTCTATAATAAG 10 55 1 AAAGCATTTT 0.648969 -246 AAGCCATAATAAAAGGGCTTGCAAGCGAGTG 10 83 1 AAAGGGCTTG 0.944204 -218 AGAAATTCTTAAACGGGTTTTGTTTGAGTTT 10 145 0 AAAGGGTTTT 0.973926 -156 *** ******* Masking position 9 Map Score: 15.4359 Number of sites scoring better than the average of aligned sites = 2064 Number in coding regions = 1728 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 3 AAATAACGCCATTATAACAAAAAGAAATGCA 1 30 1 ATATAACAAA 0.825031 -92 TTCGTTTGTTTTTAAAACGCTTATCATAGCT 1 69 0 TTAAAACGCT 0.902234 -53 TAGTGTTACAATAAAAACACTTAAAACAATA 2 32 1 ATAAAACACT 0.942915 -34 CTTTTTAGGATTAAAAACGCTCAAAAATAGT 3 49 1 TTAAAACGCT 0.902234 -134 AAGTGTAGGAATTATAACAATTTTTCAAAAA 3 126 0 ATATAACAAT 0.945929 -57 ATGGGATGATATTATAAAAATTGGTGGGAAT 4 17 0 ATATAAAAAT 0.847589 -274 TTTGAAGAAAATCAAAACAATCAATTTGTCA 4 100 0 ATAAAACAAT 0.900355 -191 GTCTGCTTCCATAATAACACTCCTTGATTTA 4 152 1 ATATAACACT 0.969762 -139 CGCATGCATCTTAATAAAACTTGATACAGAT 4 194 1 TTATAAAACT 0.840648 -97 TCAAACTCAATTCATAACAATTAAAGGTGGT 4 268 1 TTATAACAAT 0.900317 -23 CTAAAAAGATATAATAACACAAAGAAATTTT 5 29 1 ATATAACACA 0.896087 -34 ATGGTTGGTTATCAAAAAGCTAACAGCGTTT 6 11 0 ATAAAAAGCT 0.851252 -154 TTTTAAATTTATTTTAACGATGTTTTACTAT 8 18 1 ATTTAACGAT 0.765592 -111 GTTGTCATCAATTTTAAAGCTACCACTCGCT 10 106 0 ATTTAAAGCT 0.658259 -195 TGCAATCAAATTAATAAAGAAATAAAAAATG 10 238 0 TTATAAAGAA 0.457047 -63 ** ******** Masking position 6 Map Score: 14.8051 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 675 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 GCCATTATAACAAAAAGAAATGCAAGAATT 1 37 1 CAAAAAGAAA 0.945304 -85 ATAAGCGTTTTAAAAACAAACGAATTTTAA 1 76 1 TAAAAACAAA 0.88666 -46 GAATTTTAATCAAAATGAGATTTAAGGGTT 1 97 1 CAAAATGAGA 0.881772 -25 TCCAACCCGCTATAAACAAAAAGGTTTGTC 3 11 0 TATAAACAAA 0.842357 -172 AATATGGTAGAAAAAAGAGACTATTTTTGA 3 69 0 AAAAAAGAGA 0.863519 -114 TTAAAAATTCTAAAAAGATATAATAACACA 5 20 1 TAAAAAGATA 0.735935 -43 GATATAATAACACAAAGAAATTTTAAGAGT 5 36 1 CACAAAGAAA 0.84172 -27 TCATGTTTGATAAAAACAGAACTACCACAA 6 89 1 TAAAAACAGA 0.894465 -76 ATTCTTTAGGTATAATCAAAAACTATTTTT 6 130 1 TATAATCAAA 0.680335 -35 AAAGGTGGTCCATAATGAGAATATTTTTGA 8 71 1 CATAATGAGA 0.835911 -58 CAATCAAATTAATAAAGAAATAAAAAATGA 10 237 0 AATAAAGAAA 0.799555 -64 ********** Masking position 5 Map Score: 6.11315 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 678 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 TTATTTTACACTTTAAAGGGCTTTC 1 6 0 CTTTAAAGGG 0.943824 -116 ATCAAAATGAGATTTAAGGGTTAAAGA 1 105 1 GATTTAAGGG 0.931314 -17 ACACTTAAAACAATAAAGGATGCCGCTC 2 48 1 CAATAAAGGA 0.61483 -18 AATTCCTACACTTTTATTGGTAAATTTAAT 3 144 1 CTTTTATTGG 0.539209 -39 TTTATTGGTAAATTTAATGGAGAAAGGAGT 3 156 1 AATTTAATGG 0.807008 -27 ATAATGCGAACAATTATGGGATGATATTAT 4 33 0 CAATTATGGG 0.924088 -258 GTGATTATAGCATTTATGGGGCAAAAAAAG 4 229 0 CATTTATGGG 0.963362 -62 CAATTCATAACAATTAAAGGTGGTTA 4 275 1 CAATTAAAGG 0.744977 -16 ACACAAAGAAATTTTAAGAGTAAAAAGC 5 45 1 ATTTTAAGAG 0.550014 -18 GAATAGGCATCATTTAAGAGATTAGCACTT 6 61 0 CATTTAAGAG 0.91095 -104 AACTATTTTTAAATAAAGGGTTTTT 6 150 1 AAATAAAGGG 0.89903 -15 TTTATTAAAGGGACTATCAGC 9 3 1 TATTAAAGGG 0.853927 -19 AATAAGCCATAATAAAAGGGCTTGCAAGCG 10 80 1 AATAAAAGGG 0.671784 -221 ********** Masking position 6 Map Score: 6.56368 Number of sites scoring better than the average of aligned sites = 1244 Number in coding regions = 1086 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 CAATAAAAGTGTAGGAATTATAACAATTTT 3 133 0 GTAGGAATTA 0.95064 -50 ATAAAAATTGGTGGGAATGATAAG 4 5 0 GTGGGAATGA 0.991622 -286 CCTCTGATAGATAGGAATGACAAATTGATT 4 83 1 ATAGGAATGA 0.95064 -208 CCCTCTTTTAGTGGCAATGAGTGTCTGTAA 10 27 1 GTGGCAATGA 0.977853 -274 ********** Masking position 6 Map Score: 0.331568 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 CAAGAATTTTAGCTATGATAAGCGTTTTAAAAA 1 59 1 AGCTATATAC 0.976117 -63 GCCCCATAAATGCTATAATCACCCCTATCAATC 4 237 1 TGCTATATAC 0.981902 -54 AAAATATTCTAGCTATTGTAACCAAATCTTGGA 7 11 0 AGCTATGTAC 0.92776 -47 CAAAAGCATTTTCTATAATAAGCCATAATAAAA 10 64 1 TTCTATATAC 0.911972 -237 TGAATTTTCATCTTATTATAAGGTATTGTATAT 10 191 0 TCTTATATAG 0.728691 -110 GTGTTATGTCAGCTATTATTATGCAATCAAATT 10 257 0 AGCTATATAG 0.969506 -44 GATTGAAACTCCTATGATGATGTGTTATGTCA 10 279 0 TCCTATATAG 0.955827 -22 ****** ** * * Masking position 5 Map Score: 0.611576 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 35 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 ATATTTATTTAATTTTATGGTTTTATGGTA 3 94 1 AATTTTATGG 0.899205 -89 GTTTTATGGTAAATTTTTGAAAAATTGTTA 3 113 1 AAATTTTTGA 0.53801 -70 TTTATTGGTAAATTTAATGGAGAAAGGAGT 3 156 1 AATTTAATGG 0.83496 -27 GATATTATAAAAATTGGTGGGAATGATAAG 4 11 0 AAATTGGTGG 0.938145 -280 TAGGAATGACAAATTGATTGTTTTGATTTT 4 94 1 AAATTGATTG 0.941515 -197 TTATGAATTGAGTTTGATTGATAGGGGTGA 4 255 0 AGTTTGATTG 0.69652 -36 AATATTTTTGAAATTGTTGATTCTTTTATT 8 90 1 AAATTGTTGA 0.835836 -39 GGTAGCTTTAAAATTGATGACAACAAAGCC 10 113 1 AAATTGATGA 0.94156 -188 AATAAGATGAAAATTCATGGCGTTTTGCGC 10 207 1 AAATTCATGG 0.916511 -94 TTTCTTTATTAATTTGATTGCATAATAATA 10 247 1 AATTTGATTG 0.916701 -54 ********** Masking position 5 Map Score: 5.20325 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 384 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 ********** No masking Map Score: -3.24475e-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 ATCCTAAAAAGCTGTGTTATCCAACCCGCTA 3 29 0 GCTGTGTATC 0.929242 -154 GCTTTTTACTCTTAAAATTTC 5 52 0 GCTTTTTCTC 0.956886 -11 ACAGATTGCGGCTTTGCCCTCTTTTAGTGGC 10 11 1 GCTTTGCCTC 0.992065 -290 TGAGTTTTAGGCTTTGTTGTCATCAATTTTA 10 121 0 GCTTTGTGTC 0.97738 -180 AATTCATGGCGTTTTGCGCTCATTTTTTATT 10 218 1 GTTTTGCCTC 0.959935 -83 ******* *** Masking position 5 Map Score: 0.105871 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 32 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ********** No masking Map Score: -3.24475e-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: -3.24475e-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: -3.24475e-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