AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -imalT_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #2 HP0474 21 molybdenum ABC transporter, permease protein (modB) #3 HP0745 300 conserved hypothetical protein #4 HP0813 132 conserved hypothetical protein #5 HP0818 68 osmoprotection protein (proWX) Motif number 1 CTAAGATCGGTTATTTTTCTAAAAGTTTTAATTT 1 44 1 TTTTTTAAAA 0.976965 -182 TTAACCAACATTTTCACTCTAAAATCTTCATCTT 1 85 0 TTCACTAAAA 0.893953 -141 ATCTTAAAAATTTGTATTTTAAAAGTTTGAGGCG 1 153 0 TTTATTAAAA 0.97597 -73 ATTATACCTATTTGTATCTTAAAAATTTGTATTT 1 168 0 TTTATTAAAA 0.97597 -58 ACCAATTCCAATCATTTAATCAAAGGGAGTTCT 1 203 1 ATTTTTCAAA 0.886589 -23 TCGCGCAATTTTTCCATATTCAATCCTCCTTCTT 3 47 1 TTCATTCAAT 0.823684 -254 TTTTCGTTGTTTTCCATTATAAAACCCCTTTTAA 3 143 1 TTCATTAAAA 0.980008 -158 TTAAAAACCATTATTTTACTCAAAACCTTAAAAA 3 257 0 TTTTTTCAAA 0.972085 -44 AAACTCTTTTTTGCTTTTTTAAAAACCATTATTT 3 275 0 TTTTTTAAAA 0.976965 -26 GATTTTCCTTTCATCAAACTCATCTCAA 4 5 1 TTTTTTCAAA 0.972138 -128 TTCAATAATAATGACTTTTTAAAACTAGTTTGAA 4 96 1 ATCTTTAAAA 0.916725 -37 AAGAATGCCTTTAGCATTTTAAAACCCCTTTATC 5 27 1 TTCATTAAAA 0.980028 -42 ** *** ***** Masking position 12 Map Score: 19.8552 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 341 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 GTTACACCCTAAGATCGGTTATTTTTCTAA 1 36 1 AAGATCGGTT 0.959551 -190 TTAGAGTGAAAATGTTGGTTAAATACTAAT 1 97 1 AATGTTGGTT 0.990134 -129 AAAATATTCATGATTGGTTTTTCTTTTTT 3 10 1 ATGATTGGTT 0.971048 -291 TTTTGAGTAAAATAATGGTTTTTAAAAAAG 3 266 1 AATAATGGTT 0.929789 -35 CGCTTCTATTATTGTTGGTTGAGATGAGTT 4 27 0 ATTGTTGGTT 0.977615 -106 GGCATTCTTTAATGTTGGTTGCAGG 5 6 0 AATGTTGGTT 0.990134 -63 TTATCCAAATAAGTTTGGTTATA 5 56 1 AAGTTTGGTT 0.968264 -13 ********** Masking position 1 Map Score: 11.2037 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 TCTAAAAGTTTTAATTTTTTATCAAAGATGA 1 61 1 TTATTTTTTA 0.965463 -165 ATCCCACTTATTAGTATTTAACCAACATTTT 1 105 0 TTGTATTTAA 0.892758 -121 ATCTTAAAAATTTGTATTTTAAAAGTTTGAG 1 156 0 TTGTATTTTA 0.955198 -70 ATTATACCTATTTGTATCTTAAAAATTTGTA 1 171 0 TTGTATCTTA 0.816394 -55 ATGATTGGTTTTTCTTTTTTAATGGCTTCGC 3 20 1 TTCTTTTTTA 0.949751 -281 TGTGGCTCAAATCATTTTTAAAAGGGGTTTT 3 163 0 ATATTTTTAA 0.816723 -138 TTTTTATTTATTAATTTATTAGTTGGTTTAA 3 221 0 TTATTTATTA 0.798064 -80 AAATAAAAACATGATTTTTAAGGTTTTGAGT 3 243 1 ATATTTTTAA 0.816723 -58 AAACTCTTTTTTGCTTTTTTAAAAACCATTA 3 278 0 TTCTTTTTTA 0.949751 -23 TTCAATAATAATGACTTTTTAAAACTAGTTT 4 96 1 ATACTTTTTA 0.811104 -37 AAGAATGCCTTTAGCATTTTAAAACCCCTTT 5 27 1 TTGCATTTTA 0.891051 -42 ** ******** Masking position 11 Map Score: 8.38322 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 618 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 4 TTTCTAAAAGTTTTAATTTTTTATCAAAGAT 1 59 1 TTTTATTTTT 0.936157 -167 TCATGATTGGTTTTTCTTTTTTAATGGCTTC 3 18 1 TTTTCTTTTT 0.974035 -283 TTCGCGCAATTTTTCCATATTCAATCCTCCT 3 46 1 TTTTCATATT 0.932125 -255 ATTTTCGTTGTTTTCCATTATAAAACCCCTT 3 142 1 TTTTCATTAT 0.958989 -159 AAAAATCATGTTTTTATTTATTAATTTATTA 3 231 0 TTTTATTTAT 0.901385 -70 CCAAACTCTTTTTTGCTTTTTTAAAAACCAT 3 280 0 TTTTCTTTTT 0.974035 -21 TGCGCTATGATTTTCAATAATAATGACTTTT 4 84 1 TTTTAATAAT 0.769912 -49 AAAGAATGCCTTTAGCATTTTAAAACCCCTT 5 26 1 TTTACATTTT 0.870509 -43 **** ****** Masking position 8 Map Score: 8.32851 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 367 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 ATTTTTTATCAAAGATGAAGATTTTAGAGT 1 74 1 AAAGATGAAG 0.670396 -152 TTGTATTTTAAAAGTTTGAGGCGGTTTGTT 1 146 0 AAAGTTTGAG 0.816886 -80 AACGCATAAAAAAGGCGAGCA 2 8 1 AAAAAAGGCG 0.971645 -14 TTGAATATGGAAAAATTGCGCGAAGCCATT 3 40 0 AAAAATTGCG 0.95576 -261 GCTTGATGGGAAAGAAGGAGGATTGAATAT 3 62 0 AAAGAAGGAG 0.971496 -239 GCATCGCCTAAAAACTTGCGCAAAACGCCA 3 98 1 AAAACTTGCG 0.946865 -203 AAAACAACGAAAATCATGAGAAATTGAATG 3 126 0 AAATCATGAG 0.897627 -175 TTAATAAATAAAAACATGATTTTTAAGGTT 3 238 1 AAAACATGAT 0.615948 -63 CATAGCGCAAAAATAAGGCGATTTTGACTA 4 63 0 AAATAAGGCG 0.948363 -70 AACCAACATTAAAGAATGCCTTTAGCATTT 5 16 1 AAAGAATGCC 0.879365 -53 ********** Masking position 3 Map Score: 6.93841 Number of sites scoring better than the average of aligned sites = 1331 Number in coding regions = 1229 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 CATTTAATCAAAGGGAGTTCT 1 215 1 AAGGGAGTTC 0.966214 -11 AACGCATAAAAAAGGCGAGCA 2 11 1 AAAGGCGAGC 0.885063 -11 TGAGAAATTGAATGGCGTTTTGCGCAAGTT 3 110 0 AATGGCGTTT 0.94346 -191 ATCATTTTTAAAAGGGGTTTTATAATGGAA 3 154 0 AAAGGGGTTT 0.983714 -147 AAAAAAGCAAAAAAGAGTTTGG 3 289 1 AAAAGAGTTT 0.855996 -12 AGCGCAAAAATAAGGCGATTTTGACTAGAA 4 60 0 TAAGGCGATT 0.862412 -73 AACTAGTTTGAAGGGAGTTTGGAGT 4 118 1 AAGGGAGTTT 0.97191 -15 TTAAAATGCTAAAGGCATTCTTTAATGTTG 5 19 0 AAAGGCATTC 0.908622 -50 TTATTTGGATAAAGGGGTTTTAAAATGCTA 5 38 0 AAAGGGGTTT 0.983714 -31 ********** Masking position 2 Map Score: 10.8073 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 703 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 7 ACACCCTAAGATCGGTTATTTTTCTAAAAG 1 39 1 ATCGGTTATT 0.882772 -187 TATCCCACTTATTAGTATTTAACCAACATT 1 107 0 ATTAGTATTT 0.915108 -119 TATCTTAAAAATTTGTATTTTAAAAGTTTG 1 158 0 ATTTGTATTT 0.950019 -68 GATTATACCTATTTGTATCTTAAAAATTTG 1 173 0 ATTTGTATCT 0.853996 -53 AATGATTGGAATTGGTGATTATACCTATTT 1 189 0 ATTGGTGATT 0.934876 -37 AATATTCATGATTGGTTTTTCTTTTTTAAT 3 13 1 ATTGGTTTTT 0.982535 -288 TGAGTAAAATAATGGTTTTTAAAAAAGCAA 3 269 1 AATGGTTTTT 0.921127 -32 ********** Masking position 1 Map Score: 3.12427 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 267 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TAAAAGTTTGAGGCGGTTTGTTTTGTGGGT 1 138 0 AGGCGGTTTG 0.995206 -88 ATGGGAAAGAAGGAGGATTGAATATGGAAA 3 57 0 AGGAGGATTG 0.876973 -244 GCAAGTTTTTAGGCGATGCGTTCACGCTTG 3 87 0 AGGCGATGCG 0.866655 -214 AGAAATTGAATGGCGTTTTGCGCAAGTTTT 3 108 0 TGGCGTTTTG 0.959444 -193 CATTTTTAAAAGGGGTTTTATAATGGAAAA 3 152 0 AGGGGTTTTA 0.96481 -149 CGCAAAAATAAGGCGATTTTGACTAGAATA 4 58 0 AGGCGATTTT 0.934437 -75 ACTAGTTTGAAGGGAGTTTGGAGT 4 119 1 AGGGAGTTTG 0.946375 -14 ATTTGGATAAAGGGGTTTTAAAATGCTAAA 5 36 0 AGGGGTTTTA 0.96481 -33 ********** Masking position 3 Map Score: 6.55254 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 618 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 TTTTAATGGCTTCGCGCAATTTTTCCATAT 3 36 1 TTCGCGCAAT 0.930996 -265 AGGCGATGCGTTCACGCTTGATGGGAAAGA 3 77 0 TTCACGCTTG 0.92194 -224 TGAATGGCGTTTTGCGCAAGTTTTTAGGCG 3 102 0 TTTGCGCAAG 0.746538 -199 TCGCCTTATTTTTGCGCTATGATTTTCAAT 4 72 1 TTTGCGCTAT 0.924511 -61 ********** Masking position 2 Map Score: 0.620718 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 71 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GAGTGAAAATGTTGGTTAAATACTAATAAG 1 100 1 GTTGGTTAAA 0.967082 -126 GTTTGAGGCGGTTTGTTTTGTGGGTGTATC 1 133 0 GTTTGTTTTG 0.81519 -93 TAATTTATTAGTTGGTTTAATACGCTATAA 3 211 0 GTTGGTTTAA 0.981063 -90 GTTGAGATGAGTTTGATGAAAGGAAAATC 4 10 0 GTTTGATGAA 0.906807 -123 TTCTATTATTGTTGGTTGAGATGAGTTTGA 4 24 0 GTTGGTTGAG 0.989772 -109 ATTCTTTAATGTTGGTTGCAGG 5 3 0 GTTGGTTGCA 0.981337 -66 ********** Masking position 7 Map Score: 4.85878 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 87 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 GTATTTAACCAACATTTTCACTCTAAAATC 1 93 0 AACATTTTCA 0.82704 -133 TCAATTTCTCATGATTTTCGTTGTTTTCCA 3 129 1 ATGATTTTCG 0.952286 -172 TGTGGCTCAAATCATTTTTAAAAGGGGTTT 3 164 0 ATCATTTTTA 0.950182 -137 AAATAAAAACATGATTTTTAAGGTTTTGAG 3 243 1 ATGATTTTTA 0.978355 -58 GAGTAAAATAATGGTTTTTAAAAAAGCAAA 3 270 1 ATGGTTTTTA 0.932922 -31 TTTTTGCGCTATGATTTTCAATAATAATGA 4 80 1 ATGATTTTCA 0.982009 -53 TTCAATAATAATGACTTTTTAAAACTAGTT 4 96 1 ATGACTTTTT 0.774326 -37 ********** Masking position 1 Map Score: 5.68713 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 346 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 ********** No masking Map Score: 1.65857e-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 13 ********** No masking Map Score: 1.65857e-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 14 ********** No masking Map Score: 1.65857e-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