AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_mjan_reg_100.orf -o00660_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 MJ0161 300 acetolactate synthase small subunit (ilvN) #2 MJ0210 86 succinyl-CoA synthetase, beta subunit #3 MJ0277 183 acetolactate synthase large subunit (ilvB) #4 MJ0663 27 acetolactate synthase large subunit (ilvB) #5 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) Motif number 1 TAGGAAACCAAAAATTAAGTTAAGATT 1 5 1 AAAAAAATTA 0.946557 -296 AGTTAAGATTAAAAGAAAATTTTCATAGTTTTT 1 28 1 AAAAAATTTT 0.948624 -273 TCAATTTTTCATAACTAAATTTAACAACTTTAC 1 62 0 ATATAATTTA 0.916328 -239 ATATTTGCAAAAACCAATAATTTAGATGCCAAT 1 139 1 AAAAAAATTT 0.951242 -162 ATTAATTAACAAAAGAAAAATTAAGCCTTGTCA 1 170 1 AAAAAAATTA 0.946132 -131 AAAAATATGCAAATCAAAAATTTCAGGTATCAT 1 212 1 AAAAAAATTT 0.949313 -89 AAAAATAATAAAATAGATATTTAGTAGAACTCA 1 258 0 AAAGAATTTA 0.90926 -43 TCCTTTTTATAGTAAGATTTAAAAATAATAA 1 280 0 ATAAAATTTA 0.962104 -21 TAAAATTATCATATAAAAAATTTGGTGATAAAT 2 22 0 ATAAAAATTT 0.935081 -65 ATTTCTTTTTAATGCAAAATTTTAAAATTATCA 2 44 0 AATAAATTTT 0.88591 -43 ATTTTGCATTAAAAAGAAATTTATCATTTAAGG 2 57 1 AAAGAATTTA 0.909272 -30 ACTAAAAATAAAAAATAGAATTAAAGAAAGAAA 3 11 0 AAATAAATTA 0.884259 -173 TAAATATTAAATACCAACACTTTTTTATATCAA 3 60 1 ATAAAACTTT 0.81599 -124 ACACTTTTTTATATCAAACTTTTTAAAGTTCTT 3 76 1 ATAAACTTTT 0.748803 -108 TTGAAATCATATATAAAAATTTTTATACTAAGG 3 121 0 ATAAAATTTT 0.965619 -63 CTCACCGTTTAAATCAATATTTTT 4 14 1 AAAAAATTTT 0.969393 -14 TCGTCATTCCAATAGTAGATTTATTCCTGTGAA 5 173 0 AATTAATTTA 0.751547 -128 AACTTTCACAATTTATATATTTATAAGGCACTT 5 222 0 ATTTAATTTA 0.689687 -79 GTAAAAGGGGATATATAAATTTTACGGTTTAAT 5 276 1 ATATAATTTT 0.923792 -25 *** ** ***** Masking position 11 Map Score: 29.5148 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 792 Number in noncoding regions = 362 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 2 TCGAAAGACATTTATTATGTCCTTTATCTT 1 105 1 TTTATTATGT 0.918737 -196 ATACCTGAAATTTTTGATTTGCATATTTTT 1 212 0 TTTTTGATTT 0.822887 -89 AGGTATCATAATTATTATATGGTGAGTTCT 1 236 1 ATTATTATAT 0.871277 -65 AAATATCTATTTTATTATTTTTAAATCTTA 1 269 1 TTTATTATTT 0.943824 -32 TATCACCAAATTTTTTATATGATAATTTTA 2 25 1 TTTTTTATAT 0.975926 -62 TAAAAAGAAATTTATCATTTAAGGTGATAG 2 66 1 TTTATCATTT 0.726023 -21 TTTAATTCTATTTTTTATTTTTAGTCTTTA 3 19 1 TTTTTTATTT 0.967167 -165 AGTGTTGGTATTTAATATTTAATTACTAAT 3 51 0 TTTAATATTT 0.905505 -133 ATACCAACACTTTTTTATATCAAACTTTTT 3 70 1 TTTTTTATAT 0.975926 -114 GTATAAAAATTTTTATATATGATTTCAATT 3 126 1 TTTTATATAT 0.958257 -58 ACCCCCACCATTTTTTAAATAACTTAAATC 5 26 0 TTTTTTAAAT 0.799359 -275 AACTTTCACAATTTATATATTTATAAGGCA 5 225 0 ATTTATATAT 0.859087 -76 CCCTTTTACTTTTTATATGTGTCGTTGTAG 5 255 0 TTTTATATGT 0.91873 -46 AAACCGTAAAATTTATATATCCCCTTTTAC 5 276 0 ATTTATATAT 0.859087 -25 ********** Masking position 7 Map Score: 20.0519 Number of sites scoring better than the average of aligned sites = 1389 Number in coding regions = 953 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 3 AGTTAAGATTAAAAGAAAATTTTCATAGTT 1 28 1 AAAAGAAAAT 0.876856 -273 TTTAACAACTTTACGAAAAACTATGAAAAT 1 46 0 TTACGAAAAA 0.703826 -255 TTAAATTTAGTTATGAAAAATTGAACACCC 1 71 1 TTATGAAAAA 0.899353 -230 GCAAATATTCTAAAGATAAAGGACATAATA 1 117 0 TAAAGATAAA 0.913322 -184 ATTAATTAACAAAAGAAAAATTAAGCCTTG 1 170 1 AAAAGAAAAA 0.960521 -131 CCTATCAAAAATATGCAAATCAAAAATTTC 1 206 1 ATATGCAAAT 0.634633 -95 CAAATTTTTTATATGATAATTTTAAAATTT 2 31 1 ATATGATAAT 0.662912 -56 AATTTCTTTTTAATGCAAAATTTTAAAATT 2 48 0 TAATGCAAAA 0.915242 -39 CTATCACCTTAAATGATAAATTTCTTTTTA 2 66 0 AAATGATAAA 0.941438 -21 AAAATAGAATTAAAGAAAGAAA 3 3 0 TAAAGAAAGA 0.729363 -181 TTAAAGACTAAAAATAAAAAATAGAATTAA 3 20 0 AAAATAAAAA 0.596944 -164 AAAGTTCTTCAAATGCTAAATCCTTAGTAT 3 100 1 AAATGCTAAA 0.890288 -84 AAGGGTAAAGTAATGATAAAATTGAAATCA 3 145 0 TAATGATAAA 0.924281 -39 GACACATATAAAAAGTAAAAGGGGATATAT 5 262 1 AAAAGTAAAA 0.755588 -39 ********** Masking position 3 Map Score: 10.8456 Number of sites scoring better than the average of aligned sites = 2120 Number in coding regions = 1825 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 4 TAGAGGGTGTTCAATTTTTCATAACTAAAT 1 75 0 TCAATTTTTC 0.837771 -226 ATGACAAGGCTTAATTTTTCTTTTGTTAAT 1 174 0 TTAATTTTTC 0.336103 -127 CTACTAAATATCTATTTTATTATTTTTAAA 1 264 1 TCTATTTTAT 0.909865 -37 TCCTTTTTATAGTAAGATTT 1 291 0 TCCTTTTTAT 0.901304 -10 TTTATCACCAAATTTTTTATATGATAATTT 2 23 1 AATTTTTTAT 0.56614 -64 TTTCTTTAATTCTATTTTTTATTTTTAGTC 3 15 1 TCTATTTTTT 0.884593 -169 AAATACCAACACTTTTTTATATCAAACTTT 3 68 1 ACTTTTTTAT 0.766561 -116 CTTAGTATAAAAATTTTTATATATGATTTC 3 122 1 AAATTTTTAT 0.656387 -62 ATATATGATTTCAATTTTATCATTACTTTA 3 140 1 TCAATTTTAT 0.936622 -44 CTTTACCCTTAACATTTTTTGGTGATTGG 3 165 1 AACATTTTTT 0.733639 -19 ACCGTTTAAATCAATATTTTT 4 17 1 TCAATATTTT 0.524646 -11 CAGCACCCCCACCATTTTTTAAATAACTTA 5 30 0 ACCATTTTTT 0.873959 -271 TATCCCCTTTTACTTTTTATATGTGTCGTT 5 259 0 TACTTTTTAT 0.783966 -42 AGGGGATATATAAATTTTACGGTTTAATAC 5 281 1 TAAATTTTAC 0.729914 -20 ********** Masking position 5 Map Score: 8.37025 Number of sites scoring better than the average of aligned sites = 1543 Number in coding regions = 1227 Number in noncoding regions = 316 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 5 GTTGTTAAATTTAGTTATGAAAAATTGAACA 1 67 1 TTAGTATGAA 0.839982 -234 ATCTAAATTATTGGTTTTTGCAAATATTCTA 1 135 0 TTGGTTTTGC 0.8405 -166 AATTTTTCTTTTGTTAATTAATTGGCATCTA 1 161 0 TTGTTATTAA 0.845087 -140 ATCTATTTTATTATTTTTAAATCTTACTATA 1 273 1 TTATTTTAAA 0.520396 -28 TATAAAAAATTTGGTGATAAATTTATAGGTT 2 13 0 TTGGTATAAA 0.909143 -74 TTTTTTATTTTTAGTCTTTAAGATTAGTAAT 3 29 1 TTAGTTTTAA 0.951631 -155 GTCTTTAAGATTAGTAATTAAATATTAAATA 3 42 1 TTAGTATTAA 0.939243 -142 TAAAAAAGTGTTGGTATTTAATATTTAATTA 3 56 0 TTGGTTTTAA 0.969378 -128 TACTAAGGATTTAGCATTTGAAGAACTTTAA 3 98 0 TTAGCTTTGA 0.746803 -86 TTAACATTTTTTGGTGATTGG 3 173 1 TTGGTATTGG 0.8405 -11 ***** ***** Masking position 8 Map Score: 3.9156 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 375 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 GCTGGACCACGGCAGGAGAAATCCCTGGACCTGGG 5 69 0 GGCAGAACCC 0.9961 -232 GCGCCCTATAGGCAACTGGAGTCCCCGATGATAGA 5 102 1 GGCACTACCC 0.992095 -199 TGATAGACCTGGCTACACCACACCCCCGCATCAAT 5 130 1 GGCTCAACCC 0.99325 -171 ATCTACTATTGGAATGACGATACCCTTTAGGCATC 5 186 1 GGAAGAACCC 0.985612 -115 ATACCCTTTAGGCATCAAAGTGCCTTATAAATATA 5 205 1 GGCACAGCCT 0.978051 -96 **** ** * *** Masking position 13 Map Score: 0.614153 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AAATTTTCTTTTAATCTTAACTTAATTTTT 1 20 0 TTAATCTTAA 0.740225 -281 AGATTAAAAGAAAATTTTCATAGTTTTTCG 1 33 1 AAAATTTTCA 0.721386 -268 TTTTTATATGATAATTTTAAAATTTTGCAT 2 36 1 ATAATTTTAA 0.926897 -51 CCTATCACCTTAAATGATAAATT 2 74 0 ATCACCTTAA 0.831293 -13 TATTTAATTACTAATCTTAAAGACTAAAAA 3 36 0 CTAATCTTAA 0.812914 -148 TAGCATTTGAAGAACTTTAAAAAGTTTGAT 3 88 0 AGAACTTTAA 0.941173 -96 CATTTTTTAAATAACTTAAATCTTTCTGAT 5 18 0 ATAACTTAAA 0.720856 -283 GCATCAATGTAGAATCTTCACAGGAATAAA 5 157 1 AGAATCTTCA 0.929604 -144 GTGTCGTTGTAGAACTTTCACAATTTATAT 5 237 0 AGAACTTTCA 0.929604 -64 ********** Masking position 4 Map Score: 1.80802 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 435 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 8 TAGGAAACCAAAAATTAAGTTAAG 1 5 1 AAACCAAAAA 0.973298 -296 ATATTTGCAAAAACCAATAATTTAGATGCC 1 139 1 AAACCAATAA 0.957844 -162 AAAAATATGCAAATCAAAAATTTCAGGTAT 1 212 1 AAATCAAAAA 0.802776 -89 TAAACCTATAAATTTATCACC 2 2 1 AAACCTATAA 0.945798 -85 CCTATCACCTTAAATGATAAATTT 2 73 0 TCACCTTAAA 0.786198 -14 CCAATCACCAAAAAATGTTAAGGG 3 170 0 TCACCAAAAA 0.928974 -14 TTCTACAACGACACATATAAAAAGTAAAAG 5 253 1 ACACATATAA 0.656352 -48 GTATTAAACCGTAAAATTTATATAT 5 286 0 AAACCGTAAA 0.857371 -15 ********** Masking position 3 Map Score: 3.08465 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 528 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 9 ********** No masking Map Score: 6.77448e-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: 6.77448e-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: 6.77448e-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