AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_mjan_reg_300.orf -o00010_mjan_300.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 MJ0634 300 conserved hypothetical protein #6 MJ0635 219 M. jannaschii predicted coding region MJ0635 #7 MJ0636 239 dihydrolipoamide dehydrogenase #8 MJ0641 166 phosphoglycerate kinase (pgk) #9 MJ1146 66 glyceraldehyde 3-phosphate dehydrogenase #10 MJ1605 37 glucose-6-phosphate isomerase #11 MJ1606 167 glycogen synthase (glgA) Motif number 1 TAAATTTTCTTTAAAAAATTTATTTCTACGA 1 116 1 TTAAAAATTT 0.927582 -52 ATAGATATTTTTAAATACTTTAATTATGAAT 2 40 0 TTAAATATTT 0.871763 -32 ATTAAATATTAACTACTAAAAT 3 2 1 TTAAATATAA 0.799325 -281 ATCTCAATTAATAAAAATTTATTTTAGTAGT 3 22 0 ATAAAAATTA 0.901516 -261 TATTCTTATTTTAAAAATTTTCGTCCTTCTT 3 145 0 TTAAAAATTT 0.927579 -138 ATTTTCTTTAATAAATAGATAACTATGTTTA 3 216 0 ATAAATAATA 0.811223 -67 AAATAATACTATAAAAAGAATAAAATTTAGC 3 243 1 ATAAAAAAAT 0.922563 -40 TAAAATTAAATTAAAAAGAGGAA 4 3 0 TTAAAAAAGG 0.805868 -45 CTAATACAACATAAAAATAAGAAATGGTCTT 5 47 1 ATAAAAAAAG 0.880628 -254 TGATAATCATATAAAAATTTTTTTATTATTT 5 90 0 ATAAAAATTT 0.935403 -211 CTTAGAGCTTTTAAAAATTAGCATTTTCTCA 5 133 0 TTAAAAATAG 0.880622 -168 AAATCTTTAAATAAAAATAGGAAAAATTCCT 5 175 0 ATAAAAAAGG 0.824358 -126 ACCATTTAATTTAAATAATTTGATATTCTAT 5 266 0 TTAAATATTT 0.871763 -35 ATAAATTAGAATAAAAAAAGTAGAAAGT 6 8 0 ATAAAAAAGT 0.883444 -212 TGCGCAATTGATAAAAATTAGATAAAATAAA 6 34 0 ATAAAAATAG 0.892933 -186 ATACAATAATATAAATAAAAAAGAGTGCGCA 6 59 0 ATAAATAAAA 0.799878 -161 ATTTAACTATATAAATACAATAATATAAATA 6 73 0 ATAAATAAAT 0.863444 -147 ATTTATATAGTTAAATAAATTTATAGACGAA 6 88 1 TTAAATAATT 0.8574 -132 TAGATATTATTTAAAAAATTTTAA 7 4 0 TTAAAAATTT 0.927582 -236 TAAAAAGAAAATAAAAAGAAAATAGATATTA 7 26 0 ATAAAAAAAA 0.88278 -214 TAACTTTCTCTTAAAAAGAAAATAAAAAGAA 7 37 0 TTAAAAAAAA 0.869466 -203 TTTTAATCAAATAAAAAATAAGAACAACAAC 7 154 0 ATAAAAATAA 0.894895 -86 TTTTATTTGATTAAAAAATTTAATTGTAATT 7 169 1 TTAAAAATTT 0.927582 -71 AATTAAAAATTGGTTTAATGTTA 7 227 0 TTAAAAATGG 0.824358 -13 TAAAGAAATCTTAAATAATTATTAAGTTAAT 8 24 0 TTAAATATTA 0.811223 -143 TGCAGAAAGAATAAATATAAAGAAATCTTAA 8 41 0 ATAAATAAAA 0.79987 -126 TGCAAAAACCTTAAAAACTTTAAAATGATAA 8 68 1 TTAAAAATTT 0.927582 -99 ATTATAAAAATATATATTGCCAAA 9 4 1 ATAAAAAATA 0.890071 -63 ATTTAGATTTTTAAATATAGTATAAATCTTA 11 20 1 TTAAATAAGT 0.780603 -148 TTAGAAAGGTATAAAAACTATCTAATAGATA 11 48 1 ATAAAAATAT 0.930886 -120 ATTAGATAATATAAAAACATTGTGATATATG 11 85 1 ATAAAAAATT 0.927582 -83 GATTTTAACAATAAATATTATATTATGATGT 11 117 0 ATAAATATAT 0.876201 -51 ******* *** Masking position 5 Map Score: 48.045 Number of sites scoring better than the average of aligned sites = 2521 Number in coding regions = 1651 Number in noncoding regions = 870 Number of orfs with sites within 600 bp upstream = 598 Fraction of orfs with sites within 600 bp upstream = 0.0960488 Motif number 2 AGTTTATTATAAAAATTCATAATTAAAGTATTT 2 26 1 AAAATATAAT 0.878774 -46 TAAAGTATTTAAAAATATCTATTAGGTGATAAT 2 49 1 AAAATCTATT 0.974585 -23 CTCAATTAATAAAAATTTATTTTAGTAGTTAAT 3 18 0 AAAATATTTT 0.699417 -265 AATGAACTTTAATAATCTCAATTAATAAAAATT 3 34 0 AAAATCAATT 0.974615 -249 AGATTGCCATTAAAATTTCTAATATCAAAGTTT 3 100 1 TAAATCTAAT 0.893074 -183 ATACTATAAAAAGAATAAAATTTAGCAGTTCTG 3 248 1 AAAATAATTT 0.699438 -35 AATTTAATTTTAAAATCTCTTTTGTGAGGGGAA 4 22 1 TAAATCTTTT 0.728353 -26 AATACAACATAAAAATAAGAAATGGTCTTATTA 5 49 1 AAAATGAAAT 0.72607 -252 TGGTCTTATTAACAATCTCAAATAATAAAAAAA 5 71 1 AAAATCAAAT 0.969331 -230 AGGTCGTTAATAGAATATCAAATTATTTAAATT 5 257 1 TAAATCAAAT 0.893074 -44 GTTTATATATTAGAATCGCAAATTTGTGGGGCT 6 121 1 TAAATCAAAT 0.893074 -99 AAATTTTTTAAATAATATCTATTTTCTTTTTAT 7 14 1 AAAATCTATT 0.974494 -226 ATTTTTGCAGAAAAATAGCTTATTGCAATGGTA 7 73 1 AAAATCTTAT 0.893073 -167 TAAGAACAACAACAATAACAATTGAAATAAAAC 7 134 0 AAAATCAATT 0.974615 -106 AATGGTTAATAACAATTACAATTAAATTTTTTA 7 180 0 AAAATCAATT 0.974615 -60 ATTATAAAAATATATATTGCCAAAGTAA 9 6 1 AAAATATATT 0.897995 -61 TTAATCCTACAAAAATTTCAAATGGTGAATCT 9 45 1 AAAATCAAAT 0.969331 -22 GAAAGGTATAAAAACTATCTAATAGATACTTTA 11 51 1 AAACTCTAAT 0.760647 -117 TTCAGATTTTAACAATAAATATTATATTATGAT 11 119 0 AAAATATATT 0.897884 -49 ACCCCTTTAAAGCAATTTCAATTTCAGATTTTA 11 141 0 AGAATCAATT 0.794268 -27 ** *** ***** Masking position 6 Map Score: 28.713 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 514 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 AAATGTAATTAAATTAAAACATAATTTATACT 1 20 0 AAATAAACAT 0.935519 -148 GAAAGTCTTAAAATGAAAACTATAAATGTAAT 1 43 0 AAATAAACTA 0.832006 -125 AAAATTTTTAAAATAAGAATATGGACGAAACT 3 155 1 AAATAAATAT 0.924668 -128 TTATTAAAGAAAATAATACTATAAAAAGAATA 3 233 1 AAATAACTAT 0.806757 -50 AGAGATTTTAAAATTAAATTAAAAAGAGGAA 4 10 0 AAATAATTAA 0.899202 -38 ATCTAATACAACATAAAAATAAGAAATGGTCT 5 45 1 ACATAAATAA 0.868271 -256 TAACAATCTCAAATAATAAAAAAATTTTTATA 5 80 1 AAATAAAAAA 0.882733 -221 TCAAATCTTTAAATAAAAATAGGAAAAATTCC 5 176 0 AAATAAATAG 0.765361 -125 ATTTCATCGAAAATTACATCAAATCTTTAAAT 5 194 0 AAATAATCAA 0.913344 -107 ATTTTCGATGAAATTCTAACAAAAAAAGTTTA 5 212 1 AAATCAACAA 0.725623 -89 TAGATAAAATAAATTAGAATAAAAAAAGTAGA 6 15 0 AAATAAATAA 0.962542 -205 CAATTGATAAAAATTAGATAAAATAAATTAGA 6 29 0 AAATAATAAA 0.723052 -191 AAAATTTTTTAAATAATATCTATTTTCTTTTT 7 13 1 AAATAATCTA 0.632045 -227 CTTAAAAAGAAAATAAAAAGAAAATAGATATT 7 27 0 AAATAAAGAA 0.815345 -213 TTTTCTGCAAAAATGAGAATAACTTTCTCTTA 7 55 0 AAATAAATAA 0.962576 -185 ATAACAATTGAAATAAAACCATGCAAAAACTT 7 121 0 AAATAACCAT 0.831442 -119 ATCAAATAAAAAATAAGAACAACAACAATAAC 7 148 0 AAATAAACAA 0.968142 -92 ATATTCAATAACATTAAACCAATTTTTAATT 7 219 1 ACATAACCAA 0.725836 -21 AAAAACTTTAAAATGATAATTAGGAAATATCT 8 80 1 AAATAAATTA 0.807078 -87 AAGTTTCTACAAATGACGATAATCTATTAAAA 8 117 1 AAATAGATAA 0.811774 -50 TTAAAAATCTAAATGATGATATT 11 2 0 AAATAGATAT 0.672818 -166 TAGATACTTTAAATTAGATAATATAAAAACAT 11 73 1 AAATAATAAT 0.554875 -95 TGATATATGTACATCATAATATAATATTTATT 11 107 1 ACATAAATAT 0.758507 -61 **** * ***** Masking position 4 Map Score: 25.6579 Number of sites scoring better than the average of aligned sites = 892 Number in coding regions = 640 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 4 TCTAAATGCCTTTTAATATATAATACTGCGAA 1 72 0 TTTAAATATA 0.841595 -96 AGAAATAAATTTTTTAAAGAAAATTTATGCTT 1 111 0 TTTTAAGAAA 0.903772 -57 AATTATGAATTTTTATAATAAACTTGGAGGTG 2 18 0 TTTATATAAA 0.838337 -54 TAAAAATTTATTTTAGTAGTTAATATTTAAT 3 10 0 TTTAGAGTTA 0.697958 -273 TTAAAGTTCATTATTGGATATATCAAACTGCG 3 55 1 TTTTGATATA 0.871583 -228 GTCCATATTCTTATTTTAAAAATTTTCGTCCT 3 149 0 TTTTTAAAAA 0.434762 -134 AGTTATCTATTTATTAAAGAAAATAATACTAT 3 223 1 TTTTAAGAAA 0.91387 -60 ACAAAAGAGATTTTAAAATTAAATTAAAAAGA 4 15 0 TTTAAATTAA 0.752401 -33 TAGATAAAGATTTTATGAGAAATATACGATTA 5 18 0 TTTATAGAAA 0.854007 -283 TATTTTTATGTTGTATTAGATAAAGATTTTAT 5 34 0 TTTATAGATA 0.76955 -267 AAGCTCTAAGTTTTTAGCTAAAGGAATTTTTC 5 154 1 TTTTACTAAA 0.606705 -147 TTCGATGAAATTCTAACAAAAAAAGTTTATGA 5 215 1 TTTAAAAAAA 0.697877 -86 TTTATTTATATTATTGTATTTATATAGTTAAA 6 71 1 TTTTGATTTA 0.689155 -149 TTAAATAAATTTATAGACGAAAAGTTTATATA 6 98 1 TTTAGCGAAA 0.655058 -122 AAATTTGCGATTCTAATATATAAACTTTTCGT 6 114 0 TTTAAATATA 0.841599 -106 AAAATAGATATTATTTAAAAAATTTTAA 7 7 0 TTTTTAAAAA 0.463966 -233 TTTATTTTCTTTTTAAGAGAAAGTTATTCTCA 7 42 1 TTTAAAGAAA 0.912925 -198 GTTATTCTCATTTTTGCAGAAAAATAGCTTAT 7 64 1 TTTTGAGAAA 0.899186 -176 TTCTTATTTTTTATTTGATTAAAAAATTTAAT 7 161 1 TTTTTATTAA 0.647062 -79 TGGTTTAATGTTATTGAATATAAAGTTAATGG 7 208 0 TTTTGATATA 0.871526 -32 GTTTTTAAGGTTTTTGCAGAAAGAATAAATAT 8 54 0 TTTTGAGAAA 0.899186 -113 TTTGAAATTTTTGTAGGATTAATAATAATTAC 9 35 0 TTTAGATTAA 0.782305 -32 CCCAAATCTTTTATTACATAAAGTGGAAAG 10 9 0 TTTTAATAAA 0.899113 -29 ATCATTTAGATTTTTAAATATAGTATAAATCT 11 17 1 TTTTAATATA 0.851557 -151 TTTTATACCTTTCTAAGATTTATACTATATTT 11 32 0 TTTAAATTTA 0.634527 -136 ** *** ***** Masking position 4 Map Score: 28.193 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 996 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 5 ATAACTTCACCTCCAAGTTTAT 2 3 1 AACTTCACCT 0.936284 -69 ATTATCACCTAATAGATATT 2 62 0 ATTATCACCT 0.955633 -10 AATTTCCCCTCACAAAAGAG 4 38 0 AATTTCCCCT 0.970861 -10 AATATCACCTCTACACCATT 5 291 0 AATATCACCT 0.975721 -10 ATCTCTTCATATTATCACCTCCATTTGTGA 6 154 0 ATTATCACCT 0.955633 -66 AATTACCCCTTTAAAGCAAT 11 158 0 AATTACCCCT 0.891536 -10 ********** Masking position 1 Map Score: 4.3746 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 41 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AATAAACTTGGAGGTGAAGTTAT 2 4 0 GAGGTGAAGT 0.927023 -68 AAATATCTATTAGGTGATAAT 2 61 1 TAGGTGATAA 0.842642 -11 ATTTAAACATGGGTTGATAAACATAGTTAT 3 199 1 GGGTTGATAA 0.782769 -84 TCTCTTTTGTGAGGGGAAATT 4 37 1 GAGGGGAAAT 0.965254 -11 AAATGGTGTAGAGGTGATATT 5 290 1 GAGGTGATAT 0.981737 -11 TTCACAAATGGAGGTGATAATATGAAGAGA 6 153 1 GAGGTGATAA 0.97635 -67 TAAAAGATTTGGGGGGAAAT 10 28 1 GGGGGGAAAT 0.949223 -10 ********** Masking position 7 Map Score: 3.59969 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 55 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ATTTAGCTAAGTATAAATTATGTT 1 5 1 AGCTAAGTAT 0.355071 -163 TTCATAGTCAATATAAGATTTAGGACTTTC 1 145 0 ATATAAGATT 0.815643 -23 ATAACTTCACCTCCAAGTTTATTATAAAAA 2 11 1 CTCCAAGTTT 0.692544 -61 ATCTCAATTAATAAAAATTTATTTTAGTAG 3 23 0 ATAAAAATTT 0.571591 -260 CGAAGTCCTATTCAAAGATTGCCATTAAAA 3 85 1 TTCAAAGATT 0.539421 -198 AATTTCTAATATCAAAGTTTTACAAATAGA 3 113 1 ATCAAAGTTT 0.923638 -170 AAAAGAAGGACGAAAATTTTTAAAATAAGA 3 143 1 CGAAAATTTT 0.345972 -140 TGATAATCATATAAAAATTTTTTTATTATT 5 91 0 ATAAAAATTT 0.571591 -210 TTTTTAAAAGCTCTAAGTTTTTAGCTAAAG 5 147 1 CTCTAAGTTT 0.915261 -154 AATTCTAACAAAAAAAGTTTATGAAGATGT 5 223 1 AAAAAAGTTT 0.47876 -78 AATTTATTTTATCTAATTTTTATCAATTGC 6 32 1 ATCTAATTTT 0.546861 -188 AACTTTTCGTCTATAAATTTATTTAACTAT 6 94 0 CTATAAATTT 0.543674 -126 AATTTATAGACGAAAAGTTTATATATTAGA 6 105 1 CGAAAAGTTT 0.841315 -115 CGAAAGTTTTAGATAAGTTTTTGCATGGTT 7 107 1 AGATAAGTTT 0.855851 -133 CTTAATAATTATTTAAGATTTCTTTATATT 8 29 1 ATTTAAGATT 0.359858 -138 GAAATATCTAAGAAAAGTTTCTACAAATGA 8 103 1 AGAAAAGTTT 0.855851 -64 CCCTCTAAGATTTTTATGTTTT 8 155 0 CTCTAAGATT 0.836614 -12 ACTTTATGTAATAAAAGATTTGGGGGGAAA 10 17 1 ATAAAAGATT 0.815643 -21 TTTTATACCTTTCTAAGATTTATACTATAT 11 34 0 TTCTAAGATT 0.539421 -134 ********** Masking position 10 Map Score: 8.80982 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1008 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 8 TTTTAAGACTTTCGCAGTATTATATATTAA 1 62 1 TTCGCAGTAT 0.847892 -106 TGAATAGGACTTCGCAGTTTGATATATCCA 3 69 0 TTCGCAGTTT 0.972498 -214 AACTTTGATATTAGAAATTTTAATGGCAAT 3 102 0 TTAGAAATTT 0.729168 -181 AGAATAAAATTTAGCAGTTCTGTATGGTGG 3 259 1 TTAGCAGTTC 0.954452 -24 CTTTTAAAAATTAGCATTTTCTCATATCAA 5 127 0 TTAGCATTTT 0.964321 -174 ACTTTTTTTGTTAGAATTTCATCGAAAATT 5 211 0 TTAGAATTTC 0.812376 -90 GAGAAAGTTATTCTCATTTTTGCAGAAAAA 7 58 1 TTCTCATTTT 0.814466 -182 TATTTCCTAATTATCATTTTAAAGTTTTTA 8 79 0 TTATCATTTT 0.841824 -88 TTTTATGTTTTTAGAAGTTTTAATAGATTA 8 136 0 TTAGAAGTTT 0.933555 -31 ********** Masking position 6 Map Score: 5.3254 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 188 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 ********** No masking Map Score: 5.70866e-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 10 ********** No masking Map Score: 5.70866e-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 11 ********** No masking Map Score: 5.70866e-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