AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iphoB_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH478 49 sulfate transport system permease protein #2 MTH479 136 conserved protein #3 MTH604 116 adhesion protein #4 MTH676 151 unknown #5 MTH777 48 conserved protein #6 MTH778 68 unknown #7 MTH779 300 conserved protein #8 MTH877 275 unknown #9 MTH922 67 unknown #10 MTH923 21 unknown #11 MTH925 32 conserved protein #12 MTH927 139 ferredoxin #13 MTH1727 117 phosphate-binding protein PstS #14 MTH1728 83 phosphate-binding protein PstS homolog #15 MTH1734 21 phosphate transport system regulator Motif number 1 GAACATGGGATCGTCCTGAAAGATAAAGAAGGACT 2 36 0 TGTCCTGAAA 0.707732 -101 ATATGTATATATGTCCATGTCGATATAGGTGTTCT 2 90 1 AGTCCATTAA 0.913925 -47 ATTCTGTGTTAAATCCAGATAAAGTAATACATGAT 4 92 0 AATCCAGTAT 0.899463 -60 CCAGCGATAACATCCATCACCAGTAAGTAATAAT 4 128 0 AATCCATAAT 0.946263 -24 CAGTAAAAATAAATGCAGGACAATAAAAACAGTTT 7 117 1 AATGCAGAAA 0.771965 -184 CTTTTTTGTAATTTCCTTTAATAAAACAGAATAAA 8 57 1 ATTCCTTAAA 0.782029 -219 AGAGATCCATTTATCCATCAAAACATCCATTCAGA 8 143 1 TATCCATAAA 0.852803 -133 CTTACCGGTCAGATCCATGATTAATTTTCAGATAA 8 189 0 AATCCATAAT 0.946263 -87 GGTATCAGATCCTGGTTTAAA 10 1 0 AATCCTGTAA 0.867679 -21 ATCCTCACGTATTTCCTGAAAAATAAAAAAATTGA 12 13 0 ATTCCTGAAA 0.813445 -127 ATACGTGAGGATATCCATTATAACTGCGGGGGTCC 12 36 1 AATCCATAAT 0.946263 -104 TGTTTTCATGAGGTCCATTAAGAAAGATTTATATA 12 94 1 AGTCCATAAA 0.96212 -46 TATATTCCACAGGTCCATATATAAATCTTTCTTAA 12 111 0 AGTCCATTAA 0.913925 -29 TAAAATCCAGGAGGACTTTTA 15 3 1 AATCCAGAAT 0.955359 -19 * ****** * * * Masking position 13 Map Score: 12.0541 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 192 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 ATAAAGTAGTATGTTAACTGTTT 1 1 0 AGTTACTGTT 0.860826 -49 TAAGACCCCGACTTTTTCTGAAG 1 37 1 ATTTTCTGAG 0.685031 -13 ATGTCGATATAGGTGTTCTGAGTTAATGGAGGT 2 106 1 AGTGTCTGAT 0.961224 -31 AAGTCTTATAAAGTGTGCTGTTCAATAACATTA 4 33 0 AGTGTCTGTC 0.896399 -119 AGTAAGTAATAATTATTCTGTGTTAAATCCAGA 4 108 0 ATTATCTGTT 0.906253 -44 GAAGTTTTTCAGGTTTCCTTATTAAAATAAAAA 7 77 0 AGTTTCTTAT 0.903929 -224 TCCTGCATTTATTTTTACTGATTAAATGAAGTT 7 104 0 ATTTTCTGAT 0.937145 -197 CAAAACTGTTTTTTAAACTGTTTTTATTGTCCT 7 133 0 TTTAACTGTT 0.419978 -168 AAAAGGCTTAATGTATACTTTGTTGGGGCTGGT 7 234 0 AGTATCTTTT 0.859167 -67 TAATATTTAAAGTTAACCTTATTAAATCTTCGA 7 266 1 ATTAACTTAT 0.606605 -35 TCTTTGACTTATTTATTCTGTTTTATTAAAGGA 8 70 0 ATTATCTGTT 0.906253 -206 CAAAGAACTAATTTTTCCTTATTCTCTGGTTTC 8 97 1 ATTTTCTTAT 0.867645 -179 AAGATGAACATTTTTTTCTGAGCTGGGGAGTAT 8 221 1 TTTTTCTGAC 0.57421 -55 CGCTCCTGAAAGGTGTGCTGAATTACTTTCAGA 9 35 1 AGTGTCTGAT 0.961224 -33 TTTACTATTTTTGTGTACTTAATTACCTATTTT 13 53 0 TGTGTCTTAT 0.715998 -65 CAACCACAACATTTTTTCTTTCCGTCACCTTCA 14 20 1 ATTTTCTTTC 0.695872 -64 CGTCACCTTCAAGTGAACTTTATTAACCAATAG 14 42 1 AGTGACTTTT 0.759054 -42 * **** **** * Masking position 9 Map Score: 10.5197 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 238 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 ATCCTATCTTAATAAATGTTTATATATTTT 3 16 1 AATAAATGTT 0.942875 -101 GATAAAATTTAATAAATTTTAACATAAAAT 3 41 0 AATAAATTTT 0.907173 -76 GCAACCATATAATAATTGTTAATATAAACG 3 70 0 AATAATTGTT 0.85154 -47 TTTAACACAGAATAATTATTACTTACTGGT 4 114 1 AATAATTATT 0.474011 -38 GGAAGTGCCCAATGATTTTTAAGTTTAAAG 7 29 0 AATGATTTTT 0.83231 -272 TGTGGCCTGGAATGATTTTTTTATTTTAAT 7 60 1 AATGATTTTT 0.83231 -241 AAGTCAAAGAACTAATTTTTCCTTATTCTC 8 93 1 ACTAATTTTT 0.742048 -183 CCAGCTCAGAAAAAAATGTTCATCTTACCG 8 217 0 AAAAAATGTT 0.818487 -59 ACACAAAAATAGTAAATTTTAAATAGTTCT 13 70 1 AGTAAATTTT 0.761651 -48 TGACGGAAAGAAAAAATGTTGTGGTTGTGA 14 17 0 AAAAAATGTT 0.818487 -67 ********** Masking position 5 Map Score: 6.70046 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 16 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 CCTTCTTTATCTTTCAGGACGATCCCATGT 2 39 1 CTTTCAGGAC 0.950768 -98 CATATCTCTGGTTTCAGGGTCCGGATTTTT 6 39 1 GTTTCAGGGT 0.950768 -30 GTTTCAGGGCAAAAATCCGG 6 59 0 GTTTCAGGGC 0.968119 -10 TAAATGAAGTTTTTCAGGTTTCCTTATTAA 7 85 0 TTTTCAGGTT 0.905119 -216 TTATTCTCTGGTTTCAGATGTCCCTGATAG 8 115 1 GTTTCAGATG 0.886547 -161 AAATGGATCTCTATCAGGGACATCTGAAAC 8 125 0 CTATCAGGGA 0.827339 -151 CCATGATTAATTTTCAGATAATGCCCTGCA 8 180 0 TTTTCAGATA 0.778017 -96 TTCAGCACACCTTTCAGGAGCGTTTCCAGT 9 27 0 CTTTCAGGAG 0.929864 -41 TGCTGAATTACTTTCAGATTACCTTGAA 9 50 1 CTTTCAGATT 0.878622 -18 GGTATCAGATCCTGGTTTAAA 10 11 0 GTATCAGATC 0.738507 -11 ATTTTTTTATTTTTCAGGAAATACGTGAGG 12 16 1 TTTTCAGGAA 0.856043 -124 ********** Masking position 6 Map Score: 8.13309 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 548 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 AACATACTACTTTATTTTTAAGACCCCGAC 1 19 1 TTTATTTTTA 0.941581 -31 GTTTATATATTTTATGTTAAAATTTATTAA 3 33 1 TTTATGTTAA 0.805133 -84 TTAAAATTTATTAAATTTTATCGTTTATAT 3 49 1 TTAAATTTTA 0.758924 -68 AATTTTATCGTTTATATTAACAATTATTAT 3 62 1 TTTATATTAA 0.75122 -55 CCCAATGATTTTTAAGTTTAAAGGGAGTCA 7 22 0 TTTAAGTTTA 0.786154 -279 GAATGATTTTTTTATTTTAATAAGGAAACC 7 69 1 TTTATTTTAA 0.85988 -232 TTGTCCTGCATTTATTTTTACTGATTAAAT 7 110 0 TTTATTTTTA 0.941581 -191 ATTAAGCCTTTTAATATTTAAAGTTAACCT 7 255 1 TTAATATTTA 0.78862 -46 AGATCCATGATTAATTTTCAGATAATGCCC 8 184 0 TTAATTTTCA 0.701708 -92 TTTCAATTTTTTTATTTTTCAGGAAATACG 12 11 1 TTTATTTTTC 0.754355 -129 CTAGAACTATTTAAAATTTACTATTTTTGT 13 72 0 TTAAAATTTA 0.606287 -46 ********** Masking position 4 Map Score: 6.64814 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 30 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 GTGTTCTGAGTTAATGGAGGTTAAAGACC 2 118 1 TTAATGGATT 0.972628 -19 ATTTTTAAGTTTAAAGGGAGTCACCGGGATGT 7 13 0 TTAAAGGGTC 0.860017 -288 TTTTTACTGATTAAATGAAGTTTTTCAGGTTT 7 94 0 TTAAATGATT 0.679535 -207 GGAAATTACAAAAAAGGAGTTTTCGGTGAGAC 8 41 0 AAAAAGGATT 0.776429 -235 TTCTGTTTTATTAAAGGAAATTACAAAAAAGG 8 56 0 TTAAAGGATT 0.960429 -220 TTTTGATGGATAAATGGATCTCTATCAGGGAC 8 134 0 TAAATGGATC 0.924043 -142 CCTGCAGTTCTGAATGGATGTTTTGATGGATA 8 154 0 TGAATGGATT 0.904195 -122 TAGCACCAGTATAATGGCAATTTCGGGCAT 11 9 0 ATAATGGCTT 0.789883 -24 CCCCGCAGTTATAATGGATATCCTCACGTATT 12 35 0 ATAATGGATC 0.945745 -105 TAAATCTTTCTTAATGGACCTCATGAAAACAG 12 93 0 TTAATGGATC 0.974682 -47 ******** ** Masking position 4 Map Score: 5.77386 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 107 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GGAATGAGAACATGGGATCGTCCTGAAAGATAA 2 45 0 CATGGGCGCC 0.9746 -92 TGTTCAATAACATTACCATGACCTAAGGAGAAC 4 15 0 CATTACTGCC 0.853197 -137 TAAAGGGAGTCACCGGGATGTCC 7 1 0 CACCGGTGCC 0.937192 -300 TTCCAGGCCACAGGGAAGTGCCCAATGATTTTT 7 39 0 CAGGGATGCC 0.991067 -262 AAACAGTTTTGAGTGGACTGGCCGGGATTTGAA 7 155 1 GAGTGGTGCC 0.928642 -146 GTCGCCTTGGCATGGCGGAGGCCCCGGGTTCAA 7 183 0 CATGGCAGCC 0.931183 -118 GAAAATTAATCATGGATCTGACCGGTAAGATGA 8 195 1 CATGGATGCC 0.985905 -81 GTTTCCAGTGCAGTGAACTGTCCTA 9 3 0 CAGTGATGCC 0.977461 -65 GCACACCTTTCAGGAGCGTTTCCAGTGCAGTGA 9 20 0 CAGGAGTTCC 0.815613 -48 ****** ** ** Masking position 2 Map Score: 3.44677 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 467 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ACATTACCATGACCTAAGGAGAACCGCT 4 9 0 GACCTAAGGA 0.950032 -143 GCGGTCCCAGCTGGTGAATGATCAAGA 5 8 1 CAGCTGGTGA 0.949792 -41 ATTTTTTTCTGAGCTGGGGAGTATTAATAA 8 230 1 GAGCTGGGGA 0.99075 -46 TTTTACATGGCAGCTGAGGACCCCCGCAGT 12 58 0 CAGCTGAGGA 0.981083 -82 TTTCTTAATGGACCTCATGAAAACAGTACT 12 89 0 GACCTCATGA 0.904963 -51 TTTATATATGGACCTGTGGAATATACGAT 12 121 1 GACCTGTGGA 0.975167 -19 ********** Masking position 5 Map Score: 2.54009 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 108 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 CATGTTCTCATTCCTTCACAGAACCGATATGTATA 2 64 1 TCTCACAACC 0.890238 -73 CCTGTTAAGTTATGTCAACGCAACCATATAATAAT 3 84 0 TTTAACAACC 0.986114 -33 ACATATGTCATATATGAAGACAATCATGTATTACT 4 70 1 TTTAAGAATC 0.826002 -82 AGGGTCCGGATTTTTGCCCTGAAAC 6 54 1 TTTCCCAAAC 0.867534 -15 ATTTTTTTATTTTAATAAGGAAACCTGAAAAACTT 7 74 1 TTAAAGAACC 0.852277 -227 AGCCTTTTAATATTTAAAGTTAACCTTATTAAATC 7 259 1 TTTAAGAACC 0.973403 -42 CTAACCCTCTTGTCTCACCGAAAACTCCTTTTTTG 8 30 1 TTTACCAAAC 0.930547 -246 AATTACCTATTTTGTGAACTAAACCCTGTGCGCAG 13 31 0 TTTAACAACC 0.986114 -87 TTTATCACCTCAACCTTTACCTTAT 13 103 0 TTTACCAACC 0.983215 -15 * * * *** **** Masking position 12 Map Score: 5.15596 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 61 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CTGGTTTCAGGGTCCGGATTTTTGCCCTGA 6 46 1 GGTCCGGATT 0.900529 -23 ACTTCCCTGTGGCCTGGAATGATTTTTTTA 7 53 1 GGCCTGGAAT 0.943078 -248 TGTTTTTATTGTCCTGCATTTATTTTTACT 7 118 0 GTCCTGCATT 0.948242 -183 TGAGTGGACTGGCCGGGATTTGAACCCGGG 7 164 1 GGCCGGGATT 0.968004 -137 CATGGCGGAGGCCCCGGGTTCAAATCCCGG 7 176 0 GCCCCGGGTT 0.954693 -125 TTCAGATAATGCCCTGCAGTTCTGAATGGA 8 168 0 GCCCTGCAGT 0.965249 -108 CAGCTGAGGACCCCCGCAGTTATAATGGAT 12 48 0 CCCCCGCAGT 0.922245 -92 TAAAAGTCCTCCTGGATTTTA 15 4 0 CTCCTGGATT 0.913386 -18 ********** Masking position 10 Map Score: 3.03504 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 232 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 AACCCCATATCTCTGGTTTCAGGGTCCGGA 6 34 1 CTCTGGTTTC 0.992669 -35 AATGAAGTTTTTCAGGTTTCCTTATTAAAA 7 83 0 TTCAGGTTTC 0.930983 -218 TCTACTAACCCTCTTGTCTCACCGAAAACT 8 26 1 CTCTTGTCTC 0.952364 -250 TTTCCTTATTCTCTGGTTTCAGATGTCCCT 8 110 1 CTCTGGTTTC 0.992669 -166 ********** Masking position 7 Map Score: 1.69663 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 29 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 ********** No masking Map Score: 1.51646e-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: 1.51646e-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: 1.51646e-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