AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_mthe_reg_300.orf -o00600_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH331 208 mannosyltransferase #2 MTH332 119 LPS biosynthesis RfbU related protein #3 MTH338 190 LPS biosynthesis RfbU related protein #4 MTH343 48 rhamnosyl transferase #5 MTH347 60 O-antigen transporter #6 MTH348 194 rhamnosyl transferase #7 MTH442 195 excinuclease ABC subunit B #8 MTH443 41 excinuclease ABC subunit A #9 MTH444 133 sensory transduction histidine kinase #10 MTH446 97 sensory transduction regulatory protein #11 MTH447 109 sensory transduction regulatory protein #12 MTH448 74 unknown #13 MTH449 38 unknown #14 MTH1639 163 cell division control protein Cdc48 Motif number 1 AGCTGAACATTTATTACATATTGATGAGGTTTTTATGTAGGA 1 81 1 TTTACATGTT 0.893298 -128 GACATTCTACTTTTAACAGTTAAATGAACCTCTCTTAAATAT 1 126 0 TTTACATGCC 0.911816 -83 TTTTTAGCAGTCTTTACCCCCCACTCGCATTTTGAGGGGCTA 3 61 1 TCTACCTCTT 0.973077 -130 TCATGTCCTCTTTTTACTAGGTGCTCGGCCTCAATCTGAGCA 3 110 0 TTTACCTCCC 0.942531 -81 GGACTTGTAGTTATTACGAAAACCTCATGTCCTCTTTTTACT 3 134 0 TTTACCTCTC 0.967037 -57 GGCATCATCTCCTCACGCTTAACTCCCTTGCATGTGAAGAC 4 18 0 TCTACCTCTC 0.987631 -31 TTTATCATTACCATCCTCTGATTTATGTTTAAAACA 7 5 1 TCTACCTGTT 0.986043 -191 AGTGGGGGTATCATCACAGGATTATGGAACACGTGGGATACC 7 52 1 TCTACATGCC 0.964761 -144 AACGCATGGCTCTTCACGGATCTCTGCTCTTCCAGAGGTCCG 9 72 1 TCTACCTGTC 0.993634 -62 TATTGTGGGCTCTTCACTGGTGTCTGGTCTTCAAGACATGC 10 10 0 TCTACCTGTC 0.993634 -88 GCGTGTACCATCATAACTTCAGCCTGACGTCTCTTTATACTT 12 43 0 TCTACCTGTT 0.986043 -32 CATTTATATATGATTACCTGTACATGTATTATAGTAACCTAA 14 69 1 TGTACATGTT 0.790411 -95 ** * ** *** * * Masking position 6 Map Score: 16.9832 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 122 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 TAGGATAGGATGGACTGGACTGGACTGGAC 6 101 1 TGGACTGGAC 0.997465 -94 TGGACTGGACTGGACTGGACTGGACTGGAC 6 111 1 TGGACTGGAC 0.997465 -84 TGGACTGGACTGGACTGGACTGGACTGATA 6 121 1 TGGACTGGAC 0.997465 -74 TAAAAGATCCTGGAGTAGACAGTGAATGCA 6 149 1 TGGAGTAGAC 0.955388 -46 TTGACTTCAATGTCCTGGAC 13 29 1 TGTCCTGGAC 0.971403 -10 ********** Masking position 6 Map Score: 9.13209 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 10 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TCAATCATCCTTTCTCTGATG 5 50 0 CAATCATCCT 0.840153 -11 CCTATTCCTCCCTTAAACCTACAGCAGTAA 6 75 0 CCTTAAACCT 0.979825 -120 CCCACGTGTTCCATAATCCTGTGATGATAC 7 59 0 CCATAATCCT 0.976117 -137 TTTAATCCTGCCTTAATTCTCATTACCAGA 8 17 0 CCTTAATTCT 0.925744 -25 AACTCTTTAATCCTGCCTTAATTC 8 28 0 CTTTAATCCT 0.955344 -14 GCTCAAGACACCTTAAGCCTGGAAATTTTA 10 50 0 CCTTAAGCCT 0.976089 -48 CACGGCGTCACATTAAACCTTATTCTGCAG 11 17 1 CATTAAACCT 0.959209 -93 AATGTCCAGACATTAGTCCTCAGTGATAGC 11 68 1 CATTAGTCCT 0.934884 -42 ********** Masking position 4 Map Score: 7.49407 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 78 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AGAGATTTTCATGTATCTCATTAACAGGGAA 1 29 0 AGTATCTCAT 0.704985 -180 TATCCTACATAAAAACCTCATCAATATGTAA 1 94 0 AAAACCTCAT 0.979308 -115 TAACAGTTAAATGAACCTCTCTTAAATATTT 1 124 0 AGAACCTCTC 0.851681 -85 TCCTTAATGAGAACACCTCACACATAATCAT 1 187 0 GACACCTCAC 0.930313 -22 TAGTTATTACGAAAACCTCATGTCCTCTTTT 3 138 0 GAAACCTCAT 0.97118 -53 ATATTCCTCACGATAGTGTTC 3 180 0 AATTCCTCAC 0.920445 -11 GGAGGTCCCGGCATTCCTCATAGGGATTAAC 5 18 1 GATTCCTCAT 0.88377 -43 CACTTAAAATAAGAACCTCATTCTATTGTGG 7 171 0 AGAACCTCAT 0.971107 -25 AGAGTGGATCAGATACCTCACTGATGCAGGG 9 12 0 AATACCTCAC 0.976538 -122 GATAAACCTCCTTTATGGAACC 11 98 0 AAAACCTCCT 0.917063 -12 * ********* Masking position 8 Map Score: 6.58742 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 255 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TGTTAATGAGATACATGAAAATCTCTACGT 1 34 1 ATACATGAAA 0.959454 -175 AATATTTATCCTACATAAAAACCTCATCAA 1 101 0 CTACATAAAA 0.843 -108 AAGGTATAAACTACAGGAAAGCACCTAAGA 2 34 1 CTACAGGAAA 0.792701 -86 TTCTGGGTGAATCCATGAAAATATGTCTTT 3 34 1 ATCCATGAAA 0.978357 -157 CTTTGCCAGGATACATAAAGTTGAGTCTGG 7 111 0 ATACATAAAG 0.868385 -85 GGAACCTCTTATCCATGAAATGATAAGAGT 9 38 0 ATCCATGAAA 0.978357 -96 GGATAAGAGGTTCCATGAAACGCATGGCTC 9 54 1 TTCCATGAAA 0.931197 -80 AAGAGCAGAGATCCGTGAAGAGCCATGCGT 9 73 0 ATCCGTGAAG 0.902317 -61 GTGATAGCGGTTCCATAAAGGAGGTTTATC 11 90 1 TTCCATAAAG 0.84873 -20 ********** Masking position 8 Map Score: 7.34558 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 213 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 AGTATGTTCACATTCCCTGTTAATGAGATAC 1 17 1 CTTCCCTGTT 0.913267 -192 TCAATCATCCTTTCTCTGATGAGTTAATCC 5 41 0 CTTCTCTGAT 0.980014 -20 CGAGGATCTGCATTCACTGTCTACTCCAGGA 6 156 0 CTTCACTGTC 0.859622 -39 TTATCATTACCATCCTCTGATTTATGTTTAA 7 12 1 CTCCTCTGAT 0.979618 -184 ACATTTTCTGGTAATGAGAATT 8 2 1 CTTTTCTGGT 0.95225 -40 TTCTGACTCTCCTCTTCTGGTC 9 122 1 CTCTTCTGGT 0.951331 -12 TATTGTGGGCTCTTCACTGGTGTCTGGTCTT 10 21 0 TTTCACTGGT 0.784234 -77 TCTCTTTATACTTGCTCTGATACGCTCAACA 12 25 0 CTGCTCTGAT 0.947172 -50 AGTCAAAGAGCGTCCTCTGGCCCG 13 4 0 CTCCTCTGGC 0.979807 -35 * ********* Masking position 8 Map Score: 6.30762 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 334 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TCTTAAGGTTTTTCAGAGGCTCTCTTGAAA 2 82 0 TTTCAGAGGC 0.951684 -38 CCACTCGCATTTTGAGGGGCTACAGGAGTT 3 81 1 TTTGAGGGGC 0.925049 -110 ATGCCGGGACCTCCAGAAGTG 5 2 0 CTCCAGAAGT 0.783762 -59 TCACTGTCTACTCCAGGATCTTTTATCAGT 6 144 0 CTCCAGGATC 0.949687 -51 TCTCTCCATGTTCGAGGATCTGCATTCACT 6 169 0 TTCGAGGATC 0.876374 -26 AGATATGAGACTCCAGACTCAACTTTATGT 7 99 1 CTCCAGACTC 0.896861 -97 TGGGATTATATTTCAGGGTCAACTTATATA 7 144 0 TTTCAGGGTC 0.966603 -52 ATCTCTGCTCTTCCAGAGGTCCGGCTGATT 9 91 1 TTCCAGAGGT 0.92869 -43 ACAATAAAATTTCCAGGCTTAAGGTGTCTT 10 46 1 TTCCAGGCTT 0.889805 -52 GACATCAAAGTATCAGGGGCAATGTCCAGA 11 48 1 TATCAGGGGC 0.866569 -62 ********** Masking position 5 Map Score: 4.83773 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 1234 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 TGCTTAAGTATGTTCACATTCCCTGTTAATGAG 1 9 1 TATTACTTCC 0.991826 -200 AATCTCTACGTATATTAACAGTACCTGAAGCTGAA 1 53 1 TATTACGTCC 0.977957 -156 TAAGTAATATTATTTAAACTTTTCGTATGATGATG 6 23 1 TATTACTTCG 0.965303 -172 AGGGTCAACTTATATATACCTTTGCCAGGATACAT 7 125 0 TATTACTTGC 0.965303 -71 TGAGGACTAATGTCTGGACATTGCCCCTGATACTT 11 55 0 TGTTACTTCC 0.977957 -55 CATCTAATAGTATATAAACTTTACCGAAACATTTA 14 40 1 TATTACTTCC 0.991826 -124 *** * ** ** ** Masking position 8 Map Score: 3.38926 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 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 9 AAAACTTGATTTCTGGGTGAATCCATGAAA 3 24 1 TTCTGGGTGA 0.944275 -167 GGGATTATATTTCAGGGTCAACTTATATAT 7 143 0 TTCAGGGTCA 0.894582 -53 TCTTCCAGAGGTCCGGCTGATTTTTCTGAC 9 99 1 GTCCGGCTGA 0.983473 -35 TTCCTCTTCATTACGGTTAATGAGCTCAAG 10 73 0 TTACGGTTAA 0.781439 -25 ATAAAGAGACGTCAGGCTGAAGTTATGATG 12 47 1 GTCAGGCTGA 0.952622 -28 TACTAGAATATTCCGGTTAAATTAAATATC 14 114 1 TTCCGGTTAA 0.965095 -50 ATTATTATGATTCCGGTTGATATTTAATTT 14 132 0 TTCCGGTTGA 0.987938 -32 ********** Masking position 10 Map Score: 3.32112 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 106 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TTTAAGGGAGGAATAGGATAGGATGGACTGG 6 88 1 GAATAGGAAG 0.907135 -107 AGAGATCCGTGAAGAGCCATGCGTTTCATGG 9 66 0 GAAGAGCCTG 0.942595 -68 CGGACCTCTGGAAGAGCAGAGATCCGTGAAG 9 83 0 GAAGAGCAAG 0.989992 -51 GACCAGAAGAGGAGAGTCAGAAAAAT 9 118 0 GAAGAGGAAG 0.986896 -16 GCATGTCTTGAAGACCAGACACCAGTGAAG 10 10 1 GAAGACCAAC 0.935387 -88 AGACACCAGTGAAGAGCCCACAATAAAATTT 10 27 1 GAAGAGCCAC 0.980641 -71 TAACCGTAATGAAGAGGAACCGGA 10 84 1 GAAGAGGACC 0.954472 -14 ******** ** Masking position 5 Map Score: 4.7115 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 91 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 GAGATTTATCATGATTATGTGTGAGGTGTTCTC 1 177 1 ATGTTGTGTG 0.831517 -32 GCCCCTCAAAATGCGAGTGGGGGGTAAAGACTG 3 68 0 ATGATGGGGG 0.988638 -123 AACTTTTCGTATGATGATGTGGGGTGCGACAGA 6 39 1 ATGGTGTGGG 0.979289 -156 GTTTAAAACAAGTTCAGTGGGGGTATCATCACA 7 37 1 AGTATGGGGG 0.952907 -159 TAAGAACCTCATTCTATTGTGGGATTATATTTC 7 160 0 ATTATGTGGG 0.98524 -36 AAGCCTGGAAATTTTATTGTGGGCTCTTCACTG 10 33 0 ATTATGTGGG 0.98524 -65 *** * ****** Masking position 8 Map Score: 1.01546 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 GTTCCTCTTCATTACGGTTAATGAGCTCAA 10 74 0 ATTACGGTTA 0.966405 -24 ATTCTAGTAAATTTAGGTTACTATAATACA 14 93 0 ATTTAGGTTA 0.878647 -71 TTACTAGAATATTCCGGTTAAATTAAATAT 14 113 1 ATTCCGGTTA 0.987402 -51 TATTATTATGATTCCGGTTGATATTTAATT 14 133 0 ATTCCGGTTG 0.978721 -31 ********** Masking position 3 Map Score: 0.191832 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 3 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: 1.64379e-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 14 ********** No masking Map Score: 1.64379e-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 15 ********** No masking Map Score: 1.64379e-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