AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_mjan_reg_100.orf -o00010_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 Input sequences: #1 MJ0107 167 dihydropteroate synthase #2 MJ0232 71 enolase (eno) #3 MJ0487 282 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #4 MJ0490 47 L-lactate dehydrogenase EGAD|7256|705 #5 MJ0636 239 dihydrolipoamide dehydrogenase #6 MJ0641 166 phosphoglycerate kinase (pgk) #7 MJ1146 66 glyceraldehyde 3-phosphate dehydrogenase #8 MJ1605 37 glucose-6-phosphate isomerase #9 MJ1606 167 glycogen synthase (glgA) Motif number 1 AGTATAAATTATGTTTTAATTTAATTACATT 1 20 1 ATTTTTAATT 0.801821 -148 TCGCAGTATTATATATTAAAAGGCATTTAGA 1 73 1 ATTATTAAAA 0.519451 -95 CGTAGAAATAAATTTTTTAAAGAAAATTTAT 1 115 0 AATTTTTAAA 0.953409 -53 CTTTAATTATGAATTTTTATAATAAACTTGG 2 23 0 GATTTTTATA 0.753168 -49 CACCTAATAGATATTTTTAAATACTTTAATT 2 46 0 ATTTTTTAAA 0.924176 -26 TTTTAGTAGTTAATATTTAAT 3 1 0 TATATTTAAT 0.692051 -282 CTACTAAAATAAATTTTTATTAATTGAGATT 3 23 1 AATTTTTATT 0.953985 -260 TTGATATTAGAAATTTTAATGGCAATCTTTG 3 97 0 AATTTTAATG 0.848007 -186 AGAAGGACGAAAATTTTTAAAATAAGAATAT 3 146 1 AATTTTTAAA 0.95341 -137 AAACATAGTTATCTATTTATTAAAGAAAATA 3 217 1 ATTATTTATT 0.769725 -66 CTAAATTTTATTCTTTTTATAGTATTATTTT 3 242 0 TTTTTTTATA 0.906109 -41 CTTTTTAATTTAATTTTAAAATCTCTTTTGT 4 16 1 TATTTTAAAA 0.790596 -32 TTAAAATTTTTTAAATAATATCTAT 5 5 1 AATTTTTAAA 0.953409 -235 AATATCTATTTTCTTTTTATTTTCTTTTTAA 5 27 1 TTTTTTTATT 0.874262 -213 TCTTTTTATTTTCTTTTTAAGAGAAAGTTAT 5 38 1 TTTTTTTAAG 0.802418 -202 TTGTTGTTCTTATTTTTTATTTGATTAAAAA 5 155 1 TATTTTTATT 0.921094 -85 ATTACAATTAAATTTTTTAATCAAATAAAAA 5 168 0 AATTTTTAAT 0.936481 -72 ACATTAAACCAATTTTTAATT 5 229 1 AATTTTAATT 0.8715 -11 ATTATTAAGTTAATTTTAATAACTGAT 6 7 0 TATTTTAATA 0.841495 -160 TTAACTTAATAATTATTTAAGATTTCTTTAT 6 25 1 AATATTTAAG 0.766244 -142 TAAGATTTCTTTATATTTATTCTTTCTGCAA 6 42 1 TTTATTTATT 0.653039 -125 TATCATTTTAAAGTTTTTAAGGTTTTTGCAG 6 67 0 AATTTTTAAG 0.923719 -100 ATGTTTTTAGAAGTTTTAATAGATTATCGTC 6 131 0 AATTTTAATA 0.904108 -36 CCCTCTAAGATTTTTATGTTTTTAGAAG 6 149 0 AGTTTTTATG 0.778512 -18 TTGGCAATATATATTTTTATAAT 7 3 0 ATTTTTTATA 0.94487 -64 ATCATCATTTAGATTTTTAAATATAGTATAA 9 14 1 AGTTTTTAAA 0.808582 -154 ATCTATTAGATAGTTTTTATACCTTTCTAAG 9 47 0 TATTTTTATA 0.94187 -121 ATATATCACAATGTTTTTATATTATCTAATT 9 84 0 ATTTTTTATA 0.94487 -84 CATCATAATATAATATTTATTGTTAAAATCT 9 118 1 TATATTTATT 0.759619 -50 ** ******** Masking position 6 Map Score: 38.6604 Number of sites scoring better than the average of aligned sites = 2774 Number in coding regions = 1842 Number in noncoding regions = 932 Number of orfs with sites within 600 bp upstream = 637 Fraction of orfs with sites within 600 bp upstream = 0.102313 Motif number 2 GTTTTAATTTAATTACATTTATAGTTTTCAT 1 32 1 AATTAATTTA 0.890041 -136 AAAGTCTTAAAATGAAAACTATAAATGTAAT 1 43 0 AATGAAACTA 0.855859 -125 AAATTTTTTAAAGAAAATTTATGCTTAAGGG 1 106 0 AAGAAATTTA 0.72719 -62 TCATAGTCAATATAAGATTTAGGACTTTCGT 1 143 0 TATAAATTTA 0.826319 -25 TAAAGTATTTAAAAATATCTATTAGGTGATA 2 49 1 AAAAAATCTA 0.454064 -23 AATCTCAATTAATAAAAATTTATTTTAGTAG 3 23 0 AATAAAATTT 0.833111 -260 TATATCCAATAATGAACTTTAATAATCTCAA 3 46 0 AATGACTTTA 0.682818 -237 AAATTTTTAAAATAAGAATATGGACGAAACT 3 156 1 AATAAAATAT 0.717789 -127 CTATAAAAAGAATAAAATTTAGCAGTTCTGT 3 251 1 AATAAATTTA 0.968385 -32 GAGATTTTAAAATTAAATTAAAAAGAGGAA 4 10 0 AATTAATTAA 0.804844 -38 AAATTTTTTAAATAATATCTATTTTCTTTTT 5 14 1 AATAAATCTA 0.934062 -226 TTAAAAAGAAAATAAAAAGAAAATAGATATT 5 27 0 AATAAAAGAA 0.623338 -213 TTTCTGCAAAAATGAGAATAACTTTCTCTTA 5 55 0 AATGAAATAA 0.867399 -185 GAACAACAACAATAACAATTGAAATAAAACC 5 133 0 AATAAAATTG 0.745432 -107 TCAAATAAAAAATAAGAACAACAACAATAAC 5 148 0 AATAAAACAA 0.87831 -92 TAACAATTACAATTAAATTTTTTAATCAAAT 5 173 0 AATTAATTTT 0.568809 -67 GTTAATGGTTAATAACAATTACAATTAAATT 5 185 0 AATAAAATTA 0.968385 -55 CTTTATATTCAATAACATTAAACCAATTTTT 5 215 1 AATAAATTAA 0.939783 -25 CAGTTATTAAAATTAACTTAATAATTATTTA 6 13 1 AATTACTTAA 0.408812 -154 TTGCAGAAAGAATAAATATAAAGAAATCTTA 6 42 0 AATAATATAA 0.489636 -125 AAAACTTTAAAATGATAATTAGGAAATATCT 6 81 1 AATGAAATTA 0.92774 -86 TTGTAGGATTAATAATAATTACTTTGGCAAT 7 26 0 AATAAAATTA 0.968385 -41 CTTAGAAAGGTATAAAAACTATCTAATAGAT 9 47 1 TATAAAACTA 0.687533 -121 TACATCATAATATAATATTTATTGTTAAAAT 9 116 1 TATAAATTTA 0.826319 -52 ***** ***** Masking position 5 Map Score: 22.3892 Number of sites scoring better than the average of aligned sites = 1897 Number in coding regions = 1336 Number in noncoding regions = 561 Number of orfs with sites within 600 bp upstream = 452 Fraction of orfs with sites within 600 bp upstream = 0.0725988 Motif number 3 TAATTTAATTACATTTATAGTTTTCATTTTA 1 36 1 ACATTATAGT 0.685765 -132 TCATTTTAAGACTTTCGCAGTATTATATATT 1 59 1 ACTTTGCAGT 0.971874 -109 AAGATTTAGGACTTTCGTAGAAATAAATTTT 1 130 0 ACTTTGTAGA 0.931803 -38 ACTTTCATAGTCAATATAAGA 1 157 0 ACTTTATAGT 0.951995 -11 TTAATTATGAATTTTTATAATAAACTTGGAG 2 21 0 ATTTTATAAT 0.859927 -51 ATAAAAATTTATTTTAGTAGTTAATATTTAA 3 12 0 ATTTTGTAGT 0.968657 -271 CCAATAATGAACTTTAATAATCTCAATTAAT 3 41 0 ACTTTATAAT 0.87855 -242 TATTTGTAAAACTTTGATATTAGAAATTTTA 3 110 0 ACTTTATATT 0.660155 -173 AAATTTTATTCTTTTTATAGTATTATTTTCT 3 240 0 CTTTTATAGT 0.744957 -43 AAAAGAATAAAATTTAGCAGTTCTGTATGGT 3 256 1 AATTTGCAGT 0.795561 -27 AGTTATTCTCATTTTTGCAGAAAAATAGCTT 5 63 1 ATTTTGCAGA 0.906398 -177 AGTTTTTAAGGTTTTTGCAGAAAGAATAAAT 6 56 0 GTTTTGCAGA 0.707431 -111 GTTTTTAGAAGTTTTAATAGATTATCGTCAT 6 129 0 GTTTTATAGA 0.653569 -38 GGCAATATATATTTTTATAAT 7 1 0 ATTTTATAAT 0.859927 -66 AATAATAATTACTTTGGCAATATATATTTTT 7 16 0 ACTTTGCAAT 0.910029 -51 ACCATTTGAAATTTTTGTAGGATTAATAATA 7 40 0 ATTTTGTAGG 0.830075 -27 TCAATTTCAGATTTTAACAATAAATATTATA 9 126 0 ATTTTACAAT 0.845992 -42 ***** ***** Masking position 5 Map Score: 17.5966 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 380 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 ATTAAAACATAATTTATACTTAGCTAAAT 1 10 0 AATTTATACT 0.569639 -158 AATGCCTTTTAATATATAATACTGCGAAAG 1 70 0 AATATATAAT 0.607312 -98 AGTATTTAAAAATATCTATTAGGTGATAAT 2 52 1 AATATCTATT 0.802499 -20 TACTAAAATAAATTTTTATTAATTGAGATT 3 24 1 AATTTTTATT 0.382303 -259 GAACTTTAATAATCTCAATTAATAAAAATT 3 34 0 AATCTCAATT 0.592005 -249 TTGCCATTAAAATTTCTAATATCAAAGTTT 3 103 1 AATTTCTAAT 0.898818 -180 CACAAAAGAGATTTTAAAATTAAATTAAAA 4 18 0 ATTTTAAAAT 0.282336 -30 TTTTTTAAATAATATCTATTTTCTTTTTAT 5 17 1 AATATCTATT 0.802499 -223 AATGAGAATAACTTTCTCTTAAAAAGAAAA 5 46 0 ACTTTCTCTT 0.464947 -194 TGCATGGTTTTATTTCAATTGTTATTGTTG 5 128 1 TATTTCAATT 0.655496 -112 TTTTTAATCAAATAAAAAATAAGAACAACA 5 156 0 AATAAAAAAT 0.462069 -84 GGTTAATAACAATTACAATTAAATTTTTTA 5 180 0 AATTACAATT 0.796602 -60 TTAACCATTAACTTTATATTCAATAACATT 5 204 1 ACTTTATATT 0.821955 -36 AATTAAAAATTGGTTTAATG 5 230 0 AATTAAAAAT 0.643607 -10 ATCAGTTATTAAAATTAACTTAATAA 6 7 1 TATTAAAATT 0.341549 -160 ATTAAAATTAACTTAATAATTATTTAAGAT 6 18 1 ACTTAATAAT 0.651397 -149 ATTTAAGATTTCTTTATATTTATTCTTTCT 6 39 1 TCTTTATATT 0.564024 -128 AACCTTAAAAACTTTAAAATGATAATTAGG 6 74 1 ACTTTAAAAT 0.808387 -93 ATTATAAAAATATATATTGCCAAAGTAA 7 9 1 AATATATATT 0.487012 -58 ATCCTACAAAAATTTCAAATGGTGAATCT 7 48 1 AATTTCAAAT 0.877523 -19 AGGTATAAAAACTATCTAATAGATACTTTA 9 54 1 ACTATCTAAT 0.752493 -114 TCTAATAGATACTTTAAATTAGATAATATA 9 68 1 ACTTTAAATT 0.747963 -100 AGATTTTAACAATAAATATTATATTATGAT 9 119 0 AATAAATATT 0.499672 -49 CCTTTAAAGCAATTTCAATTTCAGATTTTA 9 141 0 AATTTCAATT 0.810296 -27 ********** Masking position 3 Map Score: 18.6943 Number of sites scoring better than the average of aligned sites = 1549 Number in coding regions = 1139 Number in noncoding regions = 410 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 5 ATTTAGCTAAGTATAAATTATGTTTTAAT 1 8 1 TAAATAAATT 0.473001 -160 AATTTAATTACATTTATAGTTTTCATTTTAAG 1 37 1 CATATAGTTT 0.466664 -131 ATAAATTTTTTAAAGAAAATTTATGCTTAAGG 1 107 0 TAAAAAATTT 0.810117 -61 TAAAAATTCATAATTAAAGTATTTAAAAATAT 2 35 1 TAAAAAGTAT 0.935059 -37 TAATCTCAATTAATAAAAATTTATTTTAGTAG 3 23 0 TAAAAAATTT 0.810103 -260 TGCGAAGTCCTATTCAAAGATTGCCATTAAAA 3 83 1 TATAAAGATT 0.918748 -200 CGAAAATTTTTAAAATAAGAATATGGACGAAA 3 153 1 TAATAAGAAT 0.429954 -130 CATGGGTTGATAAACATAGTTATCTATTTATT 3 206 1 TAAATAGTTA 0.413397 -77 AAAATAATACTATAAAAAGAATAAAATTTAGC 3 242 1 TATAAAGAAT 0.873757 -41 ATTGCAATGGTATCGAAAGTTTTAGATAAGTT 5 94 1 TATAAAGTTT 0.948598 -146 AGGAAATATCTAAGAAAAGTTTCTACAAATGA 6 101 1 TAAAAAGTTT 0.959219 -66 CCACTTTATGTAATAAAAGATTTGGGGGGAAA 8 15 1 TAAAAAGATT 0.935063 -23 TTTAGATTTTTAAATATAGTATAAATCTTAGA 9 21 1 TAAATAGTAT 0.834494 -147 CTTAGAAAGGTATAAAAACTATCTAATAGATA 9 47 1 TATAAACTAT 0.688787 -121 TATATTATCTAATTTAAAGTATCTATTAGATA 9 66 0 AATAAAGTAT 0.508591 -102 AATTAGATAATATAAAAACATTGTGATATATG 9 84 1 TATAAACATT 0.688787 -84 *** ******* Masking position 8 Map Score: 10.0604 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 572 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 6 AATAAACTTGGAGGTGAAGTTAT 2 4 0 GAGGTGAAGT 0.956249 -68 TCTCTTTTGTGAGGGGAAATT 4 37 1 GAGGGGAAAT 0.99329 -11 TAAAAGATTTGGGGGGAAAT 8 28 1 GGGGGGAAAT 0.988615 -10 AATTGCTTTAAAGGGGTAATT 9 157 1 AAGGGGTAAT 0.936495 -11 ********** Masking position 8 Map Score: 0.327584 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 ATATTAAAAGGCATTTAGATGCCCTTAAGC 1 85 1 GCATTTAGAT 0.906807 -83 TTTAAAAATATCTATTAGGTGATAAT 2 56 1 TCTATTAGGT 0.851609 -16 AAATTTTTATTAATTGAGATTATTAAAGTT 3 33 1 TAATTGAGAT 0.84845 -250 ACTTAATAATTATTTAAGATTTCTTTATAT 6 28 1 TATTTAAGAT 0.743651 -139 AATATCATCATTTAGATTTTTAAATAT 9 8 1 TCATTTAGAT 0.969347 -160 ATTTAAAGTATCTATTAGATAGTTTTTATA 9 57 0 TCTATTAGAT 0.949112 -111 ATAGATACTTTAAATTAGATAATATAAAAA 9 72 1 TAAATTAGAT 0.921622 -96 ********** Masking position 7 Map Score: 0.469491 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 206 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 ********** No masking Map Score: -3.62844e-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 9 ********** No masking Map Score: -3.62844e-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 10 ********** No masking Map Score: -3.62844e-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