AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_mjan_reg_100.orf -o00780_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0086 36 unspecified methyltransferase Input sequences: #1 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #2 MJ0087 23 hemin permease (hemU) #3 MJ0090 80 collagenase (prtC) #4 MJ0260 94 signal sequence peptidase I, SEC11 #5 MJ0261 161 conserved hypothetical protein #6 MJ0652 300 conserved hypothetical protein #7 MJ0806 81 X-pro aminopeptidase (pepQ) #8 MJ1296_MJ1297 38 MJ1296: biotin synthetase (bioB), MJ1297: 6-carboxyhexanoate-CoA ligase (bioW) #9 MJ1299 43 dethiobiotin synthetase (bioD) Motif number 1 ATTCATAAAAATTATATAAAAAATAGAAAAAAG 1 11 0 ATATAAAAAA 0.972451 -124 AAAATACATCAATATTCATAAAAATTATATAAA 1 24 0 AAATATAAAA 0.873923 -111 TTTATCAAAAATAATCGTTAAAAATACATCAAT 1 44 0 ATATTTAAAA 0.831794 -91 AAAAATTTTTAATATCTAATATATATTTTTCGG 1 80 0 AAATAATATA 0.84025 -55 AATAATTCAAAAAATGTGATAGT 2 2 1 ATATAAAAAA 0.972613 -22 ATATGACCTCATTATATAAAAAAGA 3 3 0 ATATAAAAAA 0.972451 -78 TAAATTATATTTGAAGTATAAAATAGCAATAAC 3 38 0 TTAAATAAAA 0.446533 -43 AATATAATTTAAAATTTAAAAAAATTTCTAA 3 60 1 AAATAAAAAA 0.959869 -21 TTTTCAAAACATTATGGAATAAATATATGAGGT 4 18 1 ATATAATAAA 0.959372 -77 AGGTGGAATCATTAACCTAAAAATCAGTAAAAA 4 47 1 ATAATAAAAA 0.930923 -48 CAATATATCAATAAATTTATAAATTCAAGTTAT 5 39 1 ATAATATAAA 0.900657 -123 AATTTCACAAATAATAATATATAATGATAACTT 5 65 0 ATATTATATA 0.789485 -97 ATAATTTGCAAATAAAATATATATAAGTTAAAC 5 113 0 AAAATATATA 0.665755 -49 ACCTCGGATTATCATTGAGAAAAGTGGTTTATC 6 12 0 ATATAGAAAA 0.873921 -289 GATAGAAGTTATAAAGAAGAAAATCGTAGAGAG 6 106 0 ATAAAGAAAA 0.84564 -195 AAATATTGATAAAAAATAATAAACTATGAGGCT 6 142 0 AAAAAATAAA 0.927156 -159 ATTTTTTATCAATATTTAATAAAAAACTTAACT 6 158 1 AAATAATAAA 0.932785 -143 ATATATTATTAAGATTAAAAATAGTTAATGTAA 6 244 0 AAATAAAATA 0.886571 -57 TAATCTTAATAATATATAATAAATTTACAGTAA 6 260 1 AAATAATAAA 0.937298 -41 ATTTACAGTAATAAAATTAAAAACTATTT 6 282 1 ATAATAAAAA 0.930924 -19 ATTTTTCATTATGAATTTTAATAACTT 7 5 0 ATAATTAATA 0.560855 -77 ATAAATAAACATTAACTTTTAAAATTTA 8 6 0 ATAATTTAAA 0.724581 -33 CCTATATACAATAAATAAACATTAA 8 24 0 TAATAATAAA 0.499167 -15 TTTATTTAATAAAAACTAAAAAAGAGAAATA 9 9 0 AAAAAAAAAA 0.949761 -35 TTTAGTTTTTATTAAATAAAATAAGCATTTAT 9 22 1 ATAAAAAATA 0.901675 -22 ** ** ****** Masking position 4 Map Score: 35.7747 Number of sites scoring better than the average of aligned sites = 3067 Number in coding regions = 2228 Number in noncoding regions = 839 Number of orfs with sites within 600 bp upstream = 497 Fraction of orfs with sites within 600 bp upstream = 0.0798265 Motif number 2 CTTTTTTCTATTTTTTATATAATTTTT 1 3 1 TTTCTTTTTA 0.975142 -132 TTTTTATGAATATTGATGTATTTTTAACGATTATT 1 33 1 TTTATTTTTT 0.858111 -102 GAACAAAAATTTTTAATATCTAATATATATTTTTC 1 82 0 TTTATTTATA 0.914054 -53 TAAAAATTTTTGTTCATATCATATAGCCTAAAATG 1 102 1 TTTATTATTA 0.942359 -33 TCATATTGGTTATTGCTATTTTATACTTCAAATAT 3 30 1 TTTCTTTTTA 0.974274 -51 TTAGAAATTTTTTTAAATTTTAAATTATATTT 3 59 0 TTTTTATTTA 0.708925 -22 ACAACATCTTTTTTACTGATTTTTAGGTTAATGAT 4 54 0 TTTCTATTTA 0.926669 -41 AATAATCCCTCTTAATGTGTTTTAATCACAATAT 5 10 1 TTTATTTTTA 0.986014 -152 TTTATAAATTTATTGATATATTGTGATTAAAACAC 5 27 0 TTTATTTTTG 0.899634 -135 CTTCCTTTGATGTTTAACTTATATATATTTTATTT 5 102 1 TTTAATATTA 0.711165 -60 ACGATTTTCTTCTTTATAACTTCTATCATGAGCCT 6 112 1 TTTATATTTA 0.958137 -189 ATTTTATTACTGTAAATTTATTATATATTATTAAG 6 264 0 TTAATTTTTA 0.849783 -37 AAATAGTTTTTAATTTTATTACTGTAAATTT 6 280 0 TTTAATTATA 0.616369 -21 GTTCAATTTTTCATTATGAATTTTAATAACTT 7 8 0 TATATATTTA 0.661969 -74 TAAAAGTTAATGTTTATTTATTGTATATAGG 8 18 1 TTTATTTTTA 0.986047 -21 TATTTCTCTTTTTTAGTTTTTATTA 9 1 1 TTTCTTTTTA 0.97435 -43 ATAAATGCTTATTTTATTTAATAAAAACTA 9 24 0 TCTATTATTA 0.674609 -20 * ** ** * ** ** Masking position 14 Map Score: 23.6058 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 703 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 3 TCAATATTCATAAAAATTATATAAAAAATA 1 19 0 TAAAAATTAT 0.297188 -116 ATATTAGATATTAAAAATTTTTGTTCATAT 1 91 1 TTAAAAATTT 0.800751 -44 AAAATTTTTGTTCATATCATATAGCCTAAA 1 104 1 TTCATATCAT 0.700277 -31 AATAATTCAAAAAATGTGATAGT 2 6 1 TTCAAAAAAT 0.794951 -18 TATTTTATACTTCAAATATAATTTAAAATT 3 46 1 TTCAAATATA 0.19276 -35 AATTTAAAATTTAAAAAAATTTCTAA 3 65 1 TTAAAAAAAT 0.825341 -16 ATAGTTCTTTTCAAAACATTATGGAATAA 4 10 1 TTCAAAACAT 0.923194 -85 TAAAAATCAGTAAAAAAGATGTTGTTGAGT 4 64 1 TAAAAAAGAT 0.710428 -31 TCGATAGAGGTTAAAATCTTAGCAGGGCTT 6 52 0 TTAAAATCTT 0.877362 -249 CCTATTCCTTTTAAAAAGCTTCCTCTCTAC 6 84 1 TTAAAAAGCT 0.659422 -217 GATTTTCTTCTTTATAACTTCTATCATGAG 6 114 1 TTTATAACTT 0.573103 -187 CAATATTTAATAAAAAACTTAACTTGACAG 6 167 1 TAAAAAACTT 0.81087 -134 ATATATACCTTTAAAATCATACCTTACATT 6 221 1 TTAAAATCAT 0.865955 -80 ATTTTTAATCTTAATAATATATAATAAATT 6 255 1 TTAATAATAT 0.615406 -46 AGTAATAAAATTAAAAACTATTT 6 288 1 TTAAAAACTA 0.671794 -13 ATTATGAATTTTAATAACTT 7 1 0 TTAATAACTT 0.877362 -81 AAGGAAGGCGTTCATAAGTTCCTTATGTAC 7 52 1 TTCATAAGTT 0.788102 -30 CCTTATGTACTTCAAATGTT 7 72 1 TTCAAATGTT 0.788102 -10 TAAATTTTAAAAGTTAATGTTTATT 8 6 1 TTTAAAAGTT 0.658624 -33 TAGTTTTTATTAAATAAAATAAGCATTTAT 9 24 1 TAAATAAAAT 0.355097 -20 ********** Masking position 1 Map Score: 14.2942 Number of sites scoring better than the average of aligned sites = 2619 Number in coding regions = 2080 Number in noncoding regions = 539 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 4 CTTTTTTCTATTTTTTATATAATTT 1 6 1 TTCTATTTTT 0.83673 -129 TCTATTTTTTATATAATTTTTATGAATATT 1 17 1 ATATAATTTT 0.75407 -118 ATGAATATTGATGTATTTTTAACGATTATT 1 38 1 ATGTATTTTT 0.853263 -97 AATATCTAATATATATTTTTCGGTAGTTTA 1 73 0 ATATATTTTT 0.931748 -62 TGATATGAACAAAAATTTTTAATATCTAAT 1 93 0 AAAAATTTTT 0.472074 -42 TTAGAAATTTTTTTAAATTTTAAA 3 67 0 AAATTTTTTT 0.547916 -14 ATTCCACCTCATATATTTATTCCATAATGT 4 26 0 ATATATTTAT 0.767309 -69 CCACTCAACAACATCTTTTTTACTGATTTT 4 66 0 ACATCTTTTT 0.61061 -29 CAATATATCAATAAATTTATAAATTCAAGT 5 39 1 ATAAATTTAT 0.410893 -123 AGTTATCATTATATATTATTATTTGTGAAA 5 66 1 ATATATTATT 0.845219 -96 TGTTTAACTTATATATATTTTATTTGCAAA 5 112 1 ATATATATTT 0.65064 -50 ACCTTACATTAACTATTTTTAATCTTAATA 6 241 1 AACTATTTTT 0.881811 -60 TAAATTTATTATATATTATTAAGATTAAAA 6 257 0 ATATATTATT 0.845219 -44 AAATAGTTTTTAATTTTATT 6 291 0 AAATAGTTTT 0.598291 -10 TGGGAAGGCGTTCAATTTTTCATTATGAAT 7 22 0 TTCAATTTTT 0.560244 -60 TATTTCTCTTTTTTAGTTTTTAT 9 4 1 TTCTCTTTTT 0.579113 -40 ********** Masking position 10 Map Score: 10.7745 Number of sites scoring better than the average of aligned sites = 1959 Number in coding regions = 1449 Number in noncoding regions = 510 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 5 AATTATATAAAAAATAGAAAAAAG 1 3 0 AAAAAGAAAA 0.904682 -132 AATCGTTAAAAATACATCAATATTCATAAAAA 1 33 0 AATAATCAAA 0.952423 -102 AATAATTCAAAAAATGTGATAG 2 1 1 AATATTCAAA 0.843335 -23 ATATGACCTCATTATATAAAAAAGA 3 4 0 ATTAATAAAA 0.751977 -77 TTTGAAGTATAAAATAGCAATAACCAATATGA 3 30 0 AAAAAGCAAA 0.851563 -51 AATATAATTTAAAATTTAAAAAAATTTCTAA 3 60 1 AAAATTAAAA 0.857873 -21 TTTTAATCACAATATATCAATAAATTTATAAA 5 30 1 AATAATCAAA 0.952317 -132 CACAAATAATAATATATAATGATAACTTGAAT 5 61 0 AATAATAATA 0.944622 -101 ATTTGCAAATAAAATATATATAAGTTAAACAT 5 111 0 AAAAATATAA 0.672237 -51 AAATATTGATAAAAAATAATAAACTATGAGGC 6 143 0 AAAAATAATA 0.920392 -158 ATTTTTTATCAATATTTAATAAAAAACTTAAC 6 158 1 AATATTAATA 0.821005 -143 TAATCTTAATAATATATAATAAATTTACAGTA 6 260 1 AATAATAATA 0.944617 -41 AAGTTATTAAAATTCATAATGAAAAATTGAAC 7 11 1 AATTATAATA 0.609617 -71 CCTATATACAATAAATAAACATTAACTTTTA 8 18 0 AATAATAAAA 0.970692 -21 TAAAAACTAAAAAAGAGAAATA 9 1 0 AAAAAGAAAA 0.904681 -43 **** ***** * Masking position 1 Map Score: 20.4541 Number of sites scoring better than the average of aligned sites = 1183 Number in coding regions = 863 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 6 ATTGTCACCATTTTAGGCTATATGA 1 120 0 GCACATTTTA 0.975411 -15 TAACCAATATGACCTCATTATATAAAAAAGA 3 10 0 GCCCATTATA 0.867862 -71 ATAAATTCAAGTTATCATTATATATTATTATT 5 57 1 GTACATTATA 0.973508 -105 TAAAAGCCCTGCTAAGATTTTAACCTCTATCG 6 49 1 GTAGATTTTA 0.973139 -252 ATCGTAGAGAGGAAGCTTTTTAAAAGGAATAG 6 85 0 GAACTTTTTA 0.841877 -216 AAACTGTCAAGTTAAGTTTTTTATTAAATATT 6 168 0 GTAGTTTTTT 0.70389 -133 TTCGTCTCAGGATAACATTAGATATATATACC 6 198 1 GTACATTAGA 0.907007 -103 GTTAATGTAAGGTATGATTTTAAAGGTATATA 6 222 0 GTAGATTTTA 0.973143 -79 * ** ******* Masking position 8 Map Score: 1.36531 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 165 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 ********** No masking Map Score: -6.79689e-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 8 ********** No masking Map Score: -6.79689e-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 9 ********** No masking Map Score: -6.79689e-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