AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_mjan_reg_300.orf -o00660_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 MJ0161 300 acetolactate synthase small subunit (ilvN) #2 MJ0210 86 succinyl-CoA synthetase, beta subunit #3 MJ0277 183 acetolactate synthase large subunit (ilvB) #4 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #5 MJ0663 27 acetolactate synthase large subunit (ilvB) #6 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) Motif number 1 TAGGAAACCAAAAATTAAGTTAAGATT 1 5 1 AAAAAAATTA 0.943528 -296 AGTTAAGATTAAAAGAAAATTTTCATAGTTTTT 1 28 1 AAAAAATTTT 0.95131 -273 TCAATTTTTCATAACTAAATTTAACAACTTTAC 1 62 0 ATATAATTTA 0.904685 -239 ATATTTGCAAAAACCAATAATTTAGATGCCAAT 1 139 1 AAAAAAATTT 0.94333 -162 ATTAATTAACAAAAGAAAAATTAAGCCTTGTCA 1 170 1 AAAAAAATTA 0.943203 -131 AAAAATATGCAAATCAAAAATTTCAGGTATCAT 1 212 1 AAAAAAATTT 0.941914 -89 AAAAATAATAAAATAGATATTTAGTAGAACTCA 1 258 0 AAAGAATTTA 0.904351 -43 TCCTTTTTATAGTAAGATTTAAAAATAATAA 1 280 0 ATAAAATTTA 0.959663 -21 TAAAATTATCATATAAAAAATTTGGTGATAAAT 2 22 0 ATAAAAATTT 0.918537 -65 ATTTCTTTTTAATGCAAAATTTTAAAATTATCA 2 44 0 AATAAATTTT 0.870781 -43 ATTTTGCATTAAAAAGAAATTTATCATTTAAGG 2 57 1 AAAGAATTTA 0.90436 -30 ACTAAAAATAAAAAATAGAATTAAAGAAAGAAA 3 11 0 AAATAAATTA 0.869546 -173 TAAATATTAAATACCAACACTTTTTTATATCAA 3 60 1 ATAAAACTTT 0.776314 -124 ACACTTTTTTATATCAAACTTTTTAAAGTTCTT 3 76 1 ATAAACTTTT 0.705187 -108 TTGAAATCATATATAAAAATTTTTATACTAAGG 3 121 0 ATAAAATTTT 0.959639 -63 AAATAATAACAAAAAACTATTTATATACCCTTC 4 33 1 AAAACATTTA 0.779805 -50 CTCACCGTTTAAATCAATATTTTT 5 14 1 AAAAAATTTT 0.968258 -14 TCGTCATTCCAATAGTAGATTTATTCCTGTGAA 6 173 0 AATTAATTTA 0.728895 -128 AACTTTCACAATTTATATATTTATAAGGCACTT 6 222 0 ATTTAATTTA 0.644757 -79 GTAAAAGGGGATATATAAATTTTACGGTTTAAT 6 276 1 ATATAATTTT 0.904662 -25 *** ** ***** Masking position 11 Map Score: 28.4837 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 928 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 2 AAGATAAAGGACATAATAAATGTCTTTCGA 1 105 0 ACATAATAAA 0.741265 -196 TTGTCATATCCTATCAAAAATATGCAAATC 1 197 1 CTATCAAAAA 0.810699 -104 AAAAATATGCAAATCAAAAATTTCAGGTAT 1 212 1 AAATCAAAAA 0.757391 -89 AGAACTCACCATATAATAATTATGATACCT 1 236 0 ATATAATAAT 0.804911 -65 TAAGATTTAAAAATAATAAAATAGATATTT 1 269 0 AAATAATAAA 0.809798 -32 TTAAATCTTACTATAAAAAGGA 1 289 1 CTATAAAAAG 0.94372 -12 TAAAATTATCATATAAAAAATTTGGTGATA 2 25 0 ATATAAAAAA 0.972253 -62 TAAAATTTTGCATTAAAAAGAAATTTATCA 2 53 1 CATTAAAAAG 0.598549 -34 TAAAGACTAAAAATAAAAAATAGAATTAAA 3 19 0 AAATAAAAAA 0.937979 -165 ATTAGTAATTAAATATTAAATACCAACACT 3 51 1 AAATATTAAA 0.463531 -133 AAAAAGTTTGATATAAAAAAGTGTTGGTAT 3 70 0 ATATAAAAAA 0.972253 -114 ATTTGAAGAACTTTAAAAAGTTTGATATAA 3 84 0 CTTTAAAAAG 0.766217 -100 TTGAAATCATATATAAAAATTTTTATACTA 3 124 0 ATATAAAAAT 0.935407 -60 ACGCTTTTGTCCATAAAAAATAATAACAAA 4 16 1 CCATAAAAAA 0.857593 -67 TGTGAAGGGTATATAAATAGTTTTTTGTTA 4 39 0 ATATAAATAG 0.67172 -44 GATTTAAGTTATTTAAAAAATGGTGGGGGT 6 26 1 ATTTAAAAAA 0.876571 -275 TGCCTTATAAATATATAAATTGTGAAAGTT 6 225 1 ATATATAAAT 0.719036 -76 ACAACGACACATATAAAAAGTAAAAGGGGA 6 257 1 ATATAAAAAG 0.965997 -44 GTAAAAGGGGATATATAAATTTTACGGTTT 6 276 1 ATATATAAAT 0.719036 -25 ********** Masking position 4 Map Score: 22.6425 Number of sites scoring better than the average of aligned sites = 2141 Number in coding regions = 1505 Number in noncoding regions = 636 Number of orfs with sites within 600 bp upstream = 468 Fraction of orfs with sites within 600 bp upstream = 0.0751686 Motif number 3 CTTAACTTAATTTTTGGTTTCCTA 1 5 0 TTTTTGGTTT 0.967316 -296 AACTATGAAAATTTTCTTTTAATCTTAACT 1 28 0 ATTTTCTTTT 0.797974 -273 AAGTTGTTAAATTTAGTTATGAAAAATTGA 1 65 1 ATTTAGTTAT 0.585959 -236 GGCATCTAAATTATTGGTTTTTGCAAATAT 1 139 0 TTATTGGTTT 0.880143 -162 CAAGGCTTAATTTTTCTTTTGTTAATTAAT 1 170 0 TTTTTCTTTT 0.940895 -131 ATACCTGAAATTTTTGATTTGCATATTTTT 1 212 0 TTTTTGATTT 0.850102 -89 GGTGATAAATTTATAGGTTTA 2 2 0 TTATAGGTTT 0.860715 -85 TATTTTTTATTTTTAGTCTTTAAGATTAGT 3 27 1 TTTTAGTCTT 0.82741 -157 TATAAATAGTTTTTTGTTATTATTTTTTAT 4 28 0 TTTTTGTTAT 0.871431 -55 ATATATCCCCTTTTACTTTTTATATGTGTC 6 262 0 TTTTACTTTT 0.930538 -39 GATATATAAATTTTACGGTTTAATAC 6 285 1 TTTTACGGTT 0.751664 -16 ********** Masking position 4 Map Score: 6.64408 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 1047 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 4 TTTTCATAGTTTTTCGTAAAGTTGTTAAATTTA 1 47 1 TTTTCAAAGT 0.75173 -254 GTTTTTGCAAATATTCTAAAGATAAAGGACATA 1 120 0 ATATTAAAGT 0.826933 -181 TTTTGATAGGATATGACAAGGCTTAATTTTTCT 1 183 0 ATATGAAGGT 0.965823 -118 AATTTCTTTTTAATGCAAAATTTTAAAATTATC 2 45 0 TAATGAAATT 0.711156 -42 CTATCACCTTAAATGATAAATTTCTTTTTAATG 2 63 0 AAATGAAATT 0.793663 -24 TTTATATCAAACTTTTTAAAGTTCTTCAAATGC 3 83 1 ACTTTAAAGT 0.478672 -101 ATAAAAATTTTTATACTAAGGATTTAGCATTTG 3 109 0 TTATAAAGGT 0.639023 -75 AAGGGTAAAGTAATGATAAAATTGAAATCATAT 3 142 0 TAATGAAAAT 0.582684 -42 AATCACCAAAAAATGTTAAGGGTAAAGTAATGA 3 159 0 AAATGAAGGT 0.965819 -25 TCCAAATACTTTTTGTGAAGGGTATATAAATAG 4 49 0 TTTTGAAGGT 0.920246 -34 CACAAAAAGTATTTGGAAAGGTTAGGAG 4 65 1 ATTTGAAGGT 0.947527 -18 AAAATAAATCAGAAAGATTTAAGTTATT 6 6 1 AAATCAAAGT 0.881162 -295 TAAATATATAAATTGTGAAAGTTCTACAACGAC 6 232 1 AATTGAAAGT 0.946273 -69 ***** **** * Masking position 8 Map Score: 5.2128 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 872 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 TTATATGGTGAGTTCTACTAAATATCTATT 1 250 1 AGTTCTACTA 0.982927 -51 AACTTTTTAAAGTTCTTCAAATGCTAAATC 3 92 1 AGTTCTTCAA 0.957956 -92 TCACAGGAATAAATCTACTATTGGAATGAC 6 174 1 AAATCTACTA 0.851517 -127 AAATTGTGAAAGTTCTACAACGACACATAT 6 241 1 AGTTCTACAA 0.982927 -60 ********** Masking position 6 Map Score: 0.937395 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 8 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CTACTAAATATCTATTTTATTATTTTTAAA 1 264 1 TCTATTTTAT 0.596698 -37 TTTCTTTAATTCTATTTTTTATTTTTAGTC 3 15 1 TCTATTTTTT 0.903711 -169 ATTAAATACCAACACTTTTTTATATCAAAC 3 65 1 AACACTTTTT 0.922907 -119 CTTTACCCTTAACATTTTTTGGTGATTGG 3 165 1 AACATTTTTT 0.924319 -19 GTTTTTTGTTATTATTTTTTATGGACAAAA 4 20 0 ATTATTTTTT 0.888148 -63 AGGGTATATAAATAGTTTTTTGTTATTATT 4 34 0 AATAGTTTTT 0.844135 -49 AACCTTTCCAAATACTTTTTGTGAAGGGTA 4 58 0 AATACTTTTT 0.935533 -25 CAGCACCCCCACCATTTTTTAAATAACTTA 6 30 0 ACCATTTTTT 0.936538 -271 TATATCCCCTTTTACTTTTTATATGTGTCG 6 261 0 TTTACTTTTT 0.803263 -40 ********** Masking position 6 Map Score: 5.97612 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 473 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 7 ACCTGGGTTCAAATCCCAGCACCCCCACCATTT 6 43 0 AACCCGCACC 0.997476 -258 ACGGCAGGAGAAATCCCTGGACCTGGGTTCAAA 6 63 0 AACCCGGACC 0.997476 -238 AGTTGCCTATAGGGCGCTGGACCACGGCAGGAG 6 86 0 AGCGCGGACC 0.988549 -215 TGGCTACACCACACCCCCGCATCAATGTAGAAT 6 139 1 AACCCGCATC 0.990041 -162 * * *** ***** Masking position 11 Map Score: 0.0920988 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 ********** No masking Map Score: 3.56936e-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: 3.56936e-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: 3.56936e-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