AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -ilexA_mgen_opreg_300.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #2 MG070 110 ribosomal protein S2 (rpS2) #3 MG244 300 DNA helicase II, putative #4 MG298 202 P115 protein #5 MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) #6 MG304 176 ABC transporter, ATP binding protein #7 MG305 87 heat shock protein 70 (dnaK) #8 MG309 53 lipoprotein, putative Motif number 1 GCTCTTTTAGTTGTTTTTGGAATTTTATTAGTTCT 1 33 1 TTGTTTGTTT 0.990549 -268 GACTAGGATTTTTATTTTGAGCTTTAAAAATTTCA 1 73 1 TTTTTTGTTT 0.980806 -228 TAATTTGACCTTTCTTTTGTTCTTTAAGTGAAATT 1 101 0 TTTTTTGTTT 0.980806 -200 TTATTTTTGCTTGCAATAGTTTTTTTAATGCTAGG 1 216 1 TTGAATGTTT 0.960102 -85 TGGCTTTTAGTTATTATCGAGTTTTATTGA 2 6 0 TTATATGTTT 0.747808 -105 CCATAAAACCTTGGTTTTGTGGTTTTTAGCTTGTT 2 38 1 TTGTTTGTTT 0.990549 -73 GTTATCGCTATTGCATTAGGCTTATCTAAATTAGT 3 39 0 TTGATTGTAT 0.962989 -262 CTAATCAAAATTGTTATGGTTCTAATTGTTATCGC 3 66 0 TTGTATGTAA 0.793727 -235 CCATAACAATTTTGATTAGTTTTTTACAACTGATT 3 82 1 TTTATTGTTT 0.97314 -219 TACAACTGATTTTTATTGGTTATTTTTGTTTTAGT 3 106 1 TTTATTGTTT 0.97314 -195 TTGGTTATTTTTGTTTTAGTTCTGAAAAACAAGCT 3 121 1 TTGTTTGTGA 0.842598 -180 TTTAAGCTAGTTGGTTTTGATTTTAAAGTGTGTTT 3 195 0 TTGTTTGTTA 0.971379 -106 TCTAAAAAGCTTTAATTTGGATGTTGTTATTAGAT 4 174 0 TTTATTGGTT 0.811778 -29 TGCTGCTCTTTTTTATTTGGAATATGTTCTATATG 6 17 0 TTTATTGTAT 0.926926 -160 ATTGTTTTGGTGTTTTGGGTATTTAA 6 161 0 TTGTTTGTTT 0.990549 -16 AACAAACTTTAATTAGCACTTTTAGTGTTTGA 7 8 1 TTTATTGTTT 0.97314 -80 TACTGAGTAATTGTTATTGATCTAAAAAAAAAGT 7 64 1 TTGTATGTAA 0.793726 -24 *** *** * *** Masking position 7 Map Score: 27.7453 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 199 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 AAAAGAAACAACAAATTAGTTTTATTTTTGCTT 1 195 1 AAAAAGTTTT 0.960968 -106 AATTTTATTAACCAAACAGCTTAGGAAGGGAAA 1 265 0 ACAAAGCTTA 0.956004 -36 GGTTAATAAAATTTAGTAGTTTTAAA 1 285 1 ATTAAGTTTT 0.722839 -16 TAATATTGTTATAAACAAGCTAAAAACCACAAA 2 53 0 AAAAAGCTAA 0.907629 -58 AATAACCAATAAAAATCAGTTGTAAAAAACTAA 3 97 0 AAAAAGTTGT 0.868197 -204 TTTAGTTCTGAAAAACAAGCTTTACAAGAGATA 3 135 1 AAAAAGCTTT 0.98763 -166 TAAAATCAAAACCAACTAGCTTAAAAACCAACA 3 205 1 ACAAAGCTTA 0.956004 -96 TGTTATTAATTAATGAGTTTTTCCACTTCAT 3 280 0 ATAAAGTTTT 0.945295 -21 ATGTTTTAATAGTAACTAGTTTATTTAATTTAA 4 57 0 ATAAAGTTTA 0.92456 -146 TACTATTAAAACATAGAAGCTTTTTTAAATGAA 4 76 1 AATAAGCTTT 0.92336 -127 TAGGTTACTAAAAAATAAGCTAATAACGCTTCA 4 105 0 AAAAAGCTAA 0.907622 -98 TTAGTAACCTAATAATTAGCCTAGTTTAGTTTA 4 127 1 ATAAAGCCTA 0.8204 -76 TTGTTCTAAAAAGCTTTAATTTGGATG 4 186 0 TTAAAGCTTT 0.812975 -17 ACTTTAATTTAATAATTAGATTTTAATACT 5 8 0 ATAAAGATTT 0.88261 -23 ATAAAAAACAAAAAAGCAGCTGTTGTGCTGCTC 6 44 0 AAAAAGCTGT 0.955428 -133 TTTATCTACCAAAAAACAGATTTTTAGCTCTGA 6 72 1 AAAAAGATTT 0.917306 -105 TTTAAAATTTATAAATAAGCTTAGTTTGCTACA 6 111 1 AAAAAGCTTA 0.982642 -66 * *** ****** Masking position 8 Map Score: 22.5423 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 178 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TTCCAAAAACAACTAAAAGAGCATATGTTG 1 25 0 AACTAAAAGA 0.667916 -276 GTCCAATTAGAACTAATAAAATTCCAAAAA 1 46 0 AACTAATAAA 0.855778 -255 CTTTAAGTGAAATTTTTAAAGCTCAAAATA 1 85 0 AATTTTTAAA 0.863623 -216 TTAAAAATTTCACTTAAAGAACAAAAGAAA 1 96 1 CACTTAAAGA 0.809759 -205 TCCAATAACTCACTTAAAAATGAAGTTCCT 1 150 1 CACTTAAAAA 0.95105 -151 CTATTCCTAGCATTAAAAAAACTATTGCAA 1 226 0 CATTAAAAAA 0.844901 -75 TAAAATTTAGTAGTTTTAAA 1 291 1 TAGTTTTAAA 0.615834 -10 AAGAAAAACACACTTTAAAATCAAAACCAA 3 190 1 CACTTTAAAA 0.95105 -111 AAACTTTTAAATGATATTGCT 4 2 1 AACTTTTAAA 0.920484 -201 TAGTTTATTTAATTTAAAAATTACATTAAT 4 44 0 AATTTAAAAA 0.907372 -159 ATAAACTAGTTACTATTAAAACATAGAAGC 4 66 1 TACTATTAAA 0.67842 -137 AATAACGCTTCATTTAAAAAAGCTTCTATG 4 87 0 CATTTAAAAA 0.913988 -116 ATTATTAGGTTACTAAAAAATAAGCTAATA 4 113 0 TACTAAAAAA 0.765466 -90 ATTAAAATCTAATTATTAAATTAAAGT 5 14 1 AATTATTAAA 0.764487 -17 CTTATTTATAAATTTTAAAAATAAGTCAGA 6 100 0 AATTTTAAAA 0.90738 -77 AGTTTGCTACAAGTTAAAAACCTCAGTTTT 6 133 1 AAGTTAAAAA 0.874625 -44 TTAAAAACCTCAGTTTTAAATACCCAAAAC 6 146 1 CAGTTTTAAA 0.830255 -31 TAAAAATATAAATTTTAAAATTATTGAAAT 8 21 1 AATTTTAAAA 0.90738 -33 ********** Masking position 4 Map Score: 18.4269 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 554 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 ATGCTCTTTTAGTTGTTTTTGGAATTTTAT 1 31 1 AGTTGTTTTT 0.767886 -270 TTGACCTTTCTTTTGTTCTTTAAGTGAAAT 1 102 0 TTTTGTTCTT 0.852725 -199 AAAACTAATTTGTTGTTTCTTTTTCATCAA 1 188 0 TGTTGTTTCT 0.855723 -113 AACAAATTAGTTTTATTTTTGCTTGCAATA 1 204 1 TTTTATTTTT 0.862614 -97 TCCTAAGCTGTTTGGTTAATAAAATTTAGT 1 272 1 TTTGGTTAAT 0.70736 -29 TTTTATGGCTTTTAGTTATTATCGAGTTTT 2 16 0 TTTAGTTATT 0.779302 -95 ACCTTGGTTTTGTGGTTTTTAGCTTGTTTA 2 45 1 TGTGGTTTTT 0.960437 -66 TATTGGTTATTTTTGTTTTAGTTCTGAAAA 3 119 1 TTTTGTTTTA 0.718506 -182 AGCTAGTTGGTTTTGATTTTAAAGTGTGTT 3 196 0 TTTTGATTTT 0.742661 -105 TCAGGTTGATTGTTGGTTTTTAAGCTAGTT 3 218 0 TGTTGGTTTT 0.910733 -83 TGTTATTAATTAATGAGTTT 3 291 0 TGTTATTAAT 0.512233 -10 AAGCAATTAATGTAATTTTTAAATTAAATA 4 39 1 TGTAATTTTT 0.604286 -164 TTAATTTGGATGTTGTTATTAGATTATACT 4 168 0 TGTTGTTATT 0.960612 -35 ACAGCTGCTTTTTTGTTTTTTATCTACCAA 6 54 1 TTTTGTTTTT 0.971205 -123 TATTTAAAACTGAGGTTTTTAACTTGTAGC 6 138 0 TGAGGTTTTT 0.647541 -39 GTTTTGGTGTTTTGGGTATTTAAAACTGAG 6 154 0 TTTGGGTATT 0.70921 -23 GAGTGCTAATTTTTGTTTATAATTACTGAG 7 41 1 TTTTGTTTAT 0.886383 -47 AAATTTATATTTTTATTATTACCAC 8 6 0 TTTTATTATT 0.777926 -48 ********** Masking position 7 Map Score: 15.7445 Number of sites scoring better than the average of aligned sites = 978 Number in coding regions = 891 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CCCTCTAGGAACTTCATTTTTAAGTGAGTT 1 156 0 ACTTCATTTT 0.522669 -145 CAAAAATAAAACTAATTTGTTGTTTCTTTT 1 195 0 ACTAATTTGT 0.740012 -106 TTTAAAACTACTAAATTTTATTAACCAAA 1 282 0 ACTAAATTTT 0.729111 -19 GCAGCGAAGCGCTTAATTTTTTCACTAATT 3 16 1 GCTTAATTTT 0.932509 -285 GTTTTTTACAACTGATTTTTATTGGTTATT 3 100 1 ACTGATTTTT 0.818501 -201 GATTTTTATTGGTTATTTTTGTTTTAGTTC 3 113 1 GGTTATTTTT 0.811649 -188 CTCTTGTAAAGCTTGTTTTTCAGAACTAAA 3 135 0 GCTTGTTTTT 0.906339 -166 AGCGTTATTAGCTTATTTTTTAGTAACCTA 4 108 1 GCTTATTTTT 0.980911 -95 ACTAAACTAGGCTAATTATTAGGTTACTAA 4 127 0 GCTAATTATT 0.685256 -76 CTGTTGTGCTGCTCTTTTTTATTTGGAATA 6 28 0 GCTCTTTTTT 0.774796 -149 CACAACAGCTGCTTTTTTGTTTTTTATCTA 6 50 1 GCTTTTTTGT 0.827243 -127 TTTAGCTCTGACTTATTTTTAAAATTTATA 6 94 1 ACTTATTTTT 0.955798 -83 AGCAAACTAAGCTTATTTATAAATTTTAAA 6 111 0 GCTTATTTAT 0.845399 -66 GTGTTTGAGTGCTAATTTTTGTTTATAATT 7 35 1 GCTAATTTTT 0.959657 -53 ACTTTTTTTTTAGATCAATA 7 78 0 ACTTTTTTTT 0.874093 -10 ********** Masking position 7 Map Score: 17.1539 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 196 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AAACCAAGGTTTTATGGCTTTTAGTTATTATC 2 23 0 TTTATGCTTT 0.962475 -88 TTATAACAATATTATTGCAGTTTTACTGCATA 2 72 1 ATTATGCATT 0.821316 -39 GGTTCTAATTGTTATCGCTATTGCATTAGGCT 3 52 0 GTTATGCTTT 0.98699 -249 TTTACCAGGCGTAATAGCTCTTGATGAAGTGG 3 257 1 GTAATGCTTT 0.979303 -44 ACTTTTAAATGATATTGCTTTTCTAAAAGCAA 4 13 1 GATATGCTTT 0.931518 -190 AAAAATTACATTAATTGCTTTTAGAAAAGCAA 4 27 0 TTAATGCTTT 0.941136 -176 CAACATCCAAATTAAAGCTTTTTAGAACAA 4 183 1 ATTAAGCTTT 0.821307 -20 TAATTACTGAGTAATTGTTATTGATCTAAAAA 7 60 1 GTAATGTTTT 0.840861 -28 ***** *** ** Masking position 4 Map Score: 5.77569 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 89 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ATGTTGCATGCAAACAACATATGC 1 5 1 TGCATGCAAA 0.932791 -296 AGTGAGTTATTGGAAGTCAAATCATTAGTA 1 134 0 TGGAAGTCAA 0.850987 -167 CTAGAGGGAGTTGATGAAAAAGAAACAACA 1 178 1 TTGATGAAAA 0.870069 -123 AAAAAACTATTGCAAGCAAAAATAAAACTA 1 211 0 TGCAAGCAAA 0.969608 -90 ACCTTTATGGTTCAAGAAAAACACACTTTA 3 177 1 TTCAAGAAAA 0.921407 -124 ATTATACTAGTTGAAGTAAACTAAACTAGG 4 146 0 TTGAAGTAAA 0.938718 -57 GGTTTTTAACTTGTAGCAAACTAAGCTTAT 6 125 0 TTGTAGCAAA 0.878096 -52 ********** Masking position 9 Map Score: 1.31412 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 88 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTAGAACTAATAAAATTCCAAAAACAACTA 1 40 0 TAAAATTCCA 0.90051 -261 AAGCTCAAAATAAAAATCCTAGTCCAATTA 1 67 0 TAAAAATCCT 0.874399 -234 AAAAGAAAGGTCAAATTACTAATGATTTGA 1 118 1 TCAAATTACT 0.865524 -183 TTCCTAGCATTAAAAAAACTATTGCAAGCA 1 223 0 TAAAAAAACT 0.694953 -78 TTTAAAACTACTAAATTTTATT 1 289 0 TAAAACTACT 0.904734 -12 CTGCATAATGTAAAATTACACAGC 2 97 1 TAAAATTACA 0.954107 -14 TATTTAATTTAAAAATTACATTAATTGCTT 4 39 0 AAAAATTACA 0.74719 -164 AATTTTTGTTTATAATTACTGAGTAATTGT 7 48 1 TATAATTACT 0.810897 -40 GTGGTAATAATAAAAATATAAATTTTAAAA 8 11 1 TAAAAATATA 0.656189 -43 ATATAAATTTTAAAATTATTGAAATTTTTG 8 26 1 TAAAATTATT 0.83991 -28 ********** Masking position 5 Map Score: 4.61907 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 125 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAAATTTCACTTAAAGAACAAAAGAAAGGT 1 99 1 TTAAAGAACA 0.714151 -202 TTTTTCACTAATTTAGATAAGCCTAATGCA 3 33 1 ATTTAGATAA 0.845341 -268 CATTAATTGCTTTTAGAAAAGCAATATCAT 4 21 0 TTTTAGAAAA 0.919189 -182 ATAACGCTTCATTTAAAAAAGCTTCTATGT 4 86 0 ATTTAAAAAA 0.66742 -117 AATTAAAGCTTTTTAGAACAA 4 192 1 TTTTAGAACA 0.956627 -11 CCTGTTCATATAGAACATATTCCAAAT 6 8 1 ATATAGAACA 0.896796 -169 TTTTTAAAATTTATAAATAAGCTTAGTTTG 6 109 1 TTATAAATAA 0.552759 -68 ACTTTTTTTTTAGATCAATAACAATTA 7 71 0 TTTTAGATCA 0.932724 -17 ********** Masking position 5 Map Score: 2.40321 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 133 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GAGCATATGTTGTTTGCATGCAACAT 1 7 0 TGTTTGCATG 0.55702 -294 AGGAACTTCATTTTTAAGTGAGTTATTGGA 1 150 0 TTTTTAAGTG 0.495103 -151 ACAACAAATTAGTTTTATTTTTGCTTGCAA 1 202 1 AGTTTTATTT 0.453752 -99 TTGCAATAGTTTTTTTAATGCTAGGAATAG 1 226 1 TTTTTTAATG 0.655304 -75 GTTATTATCGAGTTTTATTGA 2 2 0 AGTTTTATTG 0.885567 -109 CATAAAACCTTGGTTTTGTGGTTTTTAGCT 2 39 1 TGGTTTTGTG 0.618125 -72 ATATTATTGCAGTTTTACTGCATAATGTAA 2 80 1 AGTTTTACTG 0.924669 -31 TTTACAACTGATTTTTATTGGTTATTTTTG 3 104 1 ATTTTTATTG 0.646252 -197 TGGTTATTTTTGTTTTAGTTCTGAAAAACA 3 122 1 TGTTTTAGTT 0.760121 -179 TTGTAAAGCTTGTTTTTCAGAACTAAAACA 3 132 0 TGTTTTTCAG 0.45794 -169 ACCATAAAGGTGTTTGACAGTATCTCTTGT 3 158 0 TGTTTGACAG 0.790011 -143 TAGCTGGATCAGGTTGATTGTTGGTTTTTA 3 226 0 AGGTTGATTG 0.653931 -75 ATTGTTTTGGTGTTTTGGGTAT 6 165 0 TGTTTTGGTG 0.835197 -12 GCACTTTTAGTGTTTGAGTGCTAATTTTTG 7 26 1 TGTTTGAGTG 0.964094 -62 ATTATTGAAATTTTTGACTGTGCA 8 40 1 TTTTTGACTG 0.83653 -14 ********** Masking position 5 Map Score: 3.89941 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 390 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ********** No masking Map Score: 1.21746e-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: 1.21746e-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: 1.21746e-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