AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_mjan_reg_100.orf -o064_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: RMJ07250 117 M_jannaschii_chromosome RMJ10567 16 M_jannaschii_chromosome RMJ04312 88 M_jannaschii_chromosome Input sequences: #1 RMJ10649 118 M_jannaschii_chromosome #2 RMJ13451 62 M_jannaschii_chromosome #3 RMJ05793 41 M_jannaschii_chromosome #4 RMJ02853 151 M_jannaschii_chromosome #5 RMJ11621 200 M_jannaschii_chromosome #6 RMJ00313 27 M_jannaschii_chromosome #7 RMJ00018 300 M_jannaschii_chromosome #8 RMJ00407 205 M_jannaschii_chromosome #9 RMJ01820 25 M_jannaschii_chromosome #10 RMJ02054 97 M_jannaschii_chromosome #11 RMJ07240 80 M_jannaschii_chromosome #12 RMJ15370 178 M_jannaschii_chromosome #13 RMJ08703 34 M_jannaschii_chromosome Motif number 1 CATTAATAAATTTTTATTTTTTGAAAGACA 1 11 0 TTTTTATTTT 0.974713 -108 ATATTTATTTTAAAGACTTAA 2 2 1 TATTTATTTT 0.958141 -61 TTATACTTACTTTTTATTATATTTC 3 6 0 TTTTTATTAT 0.931015 -36 CCTATCCCTATTTTTATTATACTTACTTTT 3 22 0 TTTTTATTAT 0.931015 -20 CTACTTTCTTTTTTTATTTTTAAATATTAC 4 16 1 TTTTTATTTT 0.974713 -136 TTACATAAAATTTGTATATTTAACTTAATA 4 49 0 TTTGTATATT 0.819042 -103 TATTTAAAAGTATTTATATATAAAGTATTT 4 79 1 TATTTATATA 0.901604 -73 ATATATAAAGTATTTATATATGGGGTTTTT 4 94 1 TATTTATATA 0.901604 -58 ATATATGGGGTTTTTATATAATATCTAAGT 4 109 1 TTTTTATATA 0.939777 -43 AACCGAAAAGTATTTATAGTAGTTCTGAGT 7 124 0 TATTTATAGT 0.88035 -177 TAAAAAATTATTTTTATTTTGACGCCTATT 7 195 0 TTTTTATTTT 0.974713 -106 TAAAAATAATTTTTTATACTTTGATTTGTT 7 209 1 TTTTTATACT 0.87068 -92 AACTTCGCAGTTTTTATATTAAAAAGGTAT 8 85 0 TTTTTATATT 0.977096 -121 AACCATATGTTATTTATTTTATTATCCACA 8 153 1 TATTTATTTT 0.958141 -53 CAAAGTTATTATTTATAAAATCTTAAAAT 8 187 0 TATTTATAAA 0.763808 -19 GCTTCAAACTTTTTATTTTTTGTTGTAAA 10 10 1 TTTTTATTTT 0.974713 -88 TTGTTGTAAATATTTATAATTTATAGAACA 10 30 1 TATTTATAAT 0.898674 -68 TTTTAAATTCTTTTTATAGAGTCTTTTAAA 12 69 0 TTTTTATAGA 0.821326 -110 TTAAATTCTATTTTAATTTTAGTATTATTT 12 96 0 TTTTAATTTT 0.73389 -83 ********** Masking position 7 Map Score: 31.6589 Number of sites scoring better than the average of aligned sites = 1082 Number in coding regions = 640 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 378 Fraction of orfs with sites within 600 bp upstream = 0.0607131 Motif number 2 AAAAGTTCATTAATAAATTTTTATTTTTTGAAA 1 15 0 TATAATTTTA 0.511131 -104 ATAAGATAATTATTAAGTCTTTAAAATAAATAT 2 11 0 TATAATTTTA 0.908349 -52 TATGTAATATTTAAAAGTATTTATATATAAAGT 4 72 1 TTAAATTTTA 0.955071 -80 AGTATTTATATATAAAGTATTTATATATGGGGT 4 87 1 TAAAATTTTA 0.955071 -65 TAAATTTATCTAAAAAAGCTTTATCCTTCCCAA 5 126 0 TAAAAGTTTA 0.921847 -75 TTAGATAAATTTAAAATTATTTTTTAGTAAAAA 5 146 1 TTAAATTTTT 0.951907 -55 TCAGAACTACTATAAATACTTTTCGGTTTTATT 7 126 1 TAAAAATTTT 0.661368 -175 GGTTTTATTGTATTAAATATTTTAATTAATGTC 7 150 1 TATAATTTTT 0.887827 -151 AATCAAAGTATAAAAAATTATTTTTATTTTGAC 7 202 0 TAAAATATTT 0.710742 -99 GTTTTTATATTAAAAAGGTATTTAGATGCCTAA 8 73 0 TAAAAGATTT 0.685872 -133 TTATAAAATCTTAAAATTTATTGTGGATAATAA 8 171 0 TTAAATATTG 0.675171 -35 AATTAAAAATTTTTGGAGGGATATA 9 3 1 TTAAATTTTG 0.900071 -23 GCTTCAAACTTTTTATTTTTTGTTG 10 3 1 TTAAATTTTA 0.955071 -95 GTTCTATAAATTATAAATATTTACAACAAAAAA 10 26 0 TTTAATTTTA 0.908349 -72 ATCTCACCATTATTAAGGTTTTAAAGATAATAA 10 74 0 TATAAGTTTA 0.836845 -24 TCCTTAGTATTTCAAAATGTTTTAAAAGACTCT 12 49 1 TTAAATTTTT 0.952022 -130 TTAGTATTATTTTAAATTCTTTTTATAGAGTCT 12 75 0 TTAAATTTTT 0.952022 -104 ATTAAAATTATTCAAAGGCTTTACTAAAGGTTA 12 147 1 TTAAAGTTTA 0.928471 -32 ** *** * **** Masking position 11 Map Score: 23.8431 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 619 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 3 ATAATTATTAAGTCTTTAAAATAAATAT 2 7 0 AGTTTAAAAT 0.75963 -56 AGACTTAATAATTATCTTATATTAGATAAAGG 2 24 1 ATTTTTATAT 0.895501 -39 TTATACTTACTTTTTATTATATTTC 3 4 0 TTTTTTATAT 0.524799 -38 CTTTCTTTTTTTATTTTTAAATATTACATTTA 4 19 1 TTATTTAAAT 0.664703 -133 TATTACATTTATTAAGTTAAATATACAAATTT 4 40 1 ATTATTAAAT 0.925865 -112 ACTTTTAAATATTACATAAAATTTGTATATTT 4 58 0 ATTCTAAAAT 0.766945 -94 TTATATATAAATACTTTTAAATATTACATAAA 4 70 0 ATATTTAAAT 0.924706 -82 TAACTTAGATATTATATAAAAACCCCATATAT 4 109 0 ATTTTAAAAA 0.625631 -43 TTACTAAAAAATAATTTTAAATTTATCTAAAA 5 144 0 ATATTTAAAT 0.924706 -57 TTTCGGTTTTATTGTATTAAATATTTTAATTA 7 146 1 ATTTTTAAAT 0.886137 -155 AATTCAAGACATTAATTAAAATATTTAATACA 7 158 0 ATTATAAAAT 0.847504 -143 GTTTTATTAGATTATGTTAGATATTGTGAGAT 7 236 1 ATTTTTAGAT 0.87862 -65 TCATTCATTAATTTTGTTAAATAACATAAACC 8 125 1 ATTTTTAAAT 0.886137 -81 TAATTTTAGTATTATTTTAAATTCTTTTTATA 12 81 0 ATTTTTAAAT 0.978045 -98 AATGTTGTGTAATTTATTAAATTCTATTTTAA 12 110 0 AATTTTAAAT 0.74243 -69 CACAACATTCATTGATTAAAATTATTCAAAGG 12 133 1 ATTATAAAAT 0.847504 -46 *** * ****** Masking position 7 Map Score: 16.1516 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 590 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 4 GTTCAAAAGTTCATTAATAAATTTTTATTTT 1 21 0 TCATTAATAA 0.632372 -98 TAATATAAGATAATTATTAAGTCTTTAAAAT 2 17 0 TAATTATTAG 0.678906 -46 TTTTTATTTTTAAATATTACATTTATTAAGT 4 26 1 TAAATATTAA 0.964395 -126 TAAATACTTTTAAATATTACATAAAATTTGT 4 64 0 TAAATATTAA 0.964395 -88 ACAACTAACTTAGATATTATATAAAAACCCC 4 115 0 TAGATATTAA 0.786076 -37 TCTTCTCACGTAATTATTATAT 6 2 0 TAATTATTAA 0.879283 -26 TTTATTGTATTAAATATTTTAATTAATGTCT 7 153 1 TAAATATTTA 0.704411 -148 AGATTCACCTCAATATTATAGAACTTTCGC 8 10 1 TCAATATTAA 0.878892 -196 TTAATTTTGTTAAATAACATAAACCATATGT 8 132 1 TAAATAACAA 0.90942 -74 GATAATAAAATAAATAACATATGGTTTATGT 8 148 0 TAAATAACAA 0.90942 -58 TTATCCACAATAAATTTTAAGATTTTATAAA 8 174 1 TAAATTTTAG 0.678905 -32 TAAGATTTTATAAATAATAACTTTG 8 191 1 TAAATAATAC 0.789849 -15 AGATGTTCTATAAATTATAAATATTTACAAC 10 32 0 TAAATTATAA 0.864055 -66 TCTTATACAGTAAATAATATAAGCACTGACT 11 29 1 TAAATAATAA 0.94784 -52 TAGAATTTAATAAATTACACAACATTCATTG 12 116 1 TAAATTACAA 0.730379 -63 ********* * Masking position 5 Map Score: 12.9625 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 343 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 5 TGTCTTTCAAAAAATAAAAATT 1 3 1 TCTTTCAAAA 0.979903 -116 CCTTTGGAAGGCGTTCAAAAGTTCATTAAT 1 34 0 GCGTTCAAAA 0.949717 -85 TTTATTAGTGTCTTTCAAAACTTCTTGGAT 1 89 0 TCTTTCAAAA 0.979903 -30 ATAAATGTAATATTTAAAAATAAAAAAAGA 4 22 0 TATTTAAAAA 0.709204 -130 TACTTCAAAAATCCTCATAT 5 191 0 TACTTCAAAA 0.876295 -10 CTTTATGAAAGCGTTCAAAATTCA 12 5 0 GCGTTCAAAA 0.949717 -174 TGGTCCTTAGTATTTCAAAATGTTTTAAAA 12 46 1 TATTTCAAAA 0.95061 -133 TTTTATAGAGTCTTTTAAAACATTTTGAAA 12 58 0 TCTTTTAAAA 0.865116 -121 ********** Masking position 7 Map Score: 8.68139 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 100 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 GTTAAATATACAAATTTTATGTAATATTTAA 4 55 1 CAAATTTATG 0.969379 -97 CAATTAATGTCCAATTTTATG 5 1 0 CCAATTTATG 0.980749 -200 GGCTTTTAGCCCCAATTAATGTCCAATTTTA 5 13 0 CCCATTAATG 0.968882 -188 GCTAAAAGCCCCAACTTAATGGACGGGAGGT 5 34 1 CCAATTAATG 0.969498 -167 GGAGAAAGACCACATATTATGTTTGTTGGAG 5 94 1 CACAATTATG 0.847349 -107 TGTTATTTAACAAAATTAATGAATGAATTAA 8 120 0 CAAATTAATG 0.951965 -86 TTTTAATTGACAAAGTTTATATATAGTCAGT 11 53 0 CAAATTTATA 0.782126 -28 CCAATAAACACCCCCTTTATGAAAGCGTTCA 12 18 0 CCCCTTTATG 0.929948 -161 **** ****** Masking position 9 Map Score: 7.3692 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 93 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 TATTATATAAAAACCCCATATATAAATACTT 4 101 0 AAACCCATAT 0.980614 -51 CCATAGGAGGAGACCTCCTATTGGGATACCT 5 61 0 AGACCCCTAT 0.988496 -140 GGTTGGAGAAAGACCACATATTATGTTTGTT 5 90 1 AGACCCATAT 0.982027 -111 TACTTCAAAAATCCTCATATTCCCACCAAA 5 181 0 AATCCCATAT 0.925869 -20 GGACCAATAAACACCCCCTTTATGAAAGCGT 12 21 0 ACACCCCTTT 0.920119 -158 TTAAATCACCTATATGAATAAGT 13 22 0 AAATCCCTAT 0.924861 -13 ***** ***** Masking position 9 Map Score: 2.45033 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 17 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AGTTGTTAAATAGGTGAAAATC 4 140 1 TAGGTGAAAA 0.838028 -12 GTAAAAATGTTTGGTGGGAATATGAGGATT 5 172 1 TTGGTGGGAA 0.963284 -29 ATATAATAATTACGTGAGAAGATGATA 6 11 1 TACGTGAGAA 0.913966 -17 TATGTTAGATATTGTGAGATTACTCTCACT 7 248 1 ATTGTGAGAT 0.735808 -53 TTAAAAATTTTTGGAGGGATATA 9 13 1 TTGGAGGGAT 0.745602 -13 AACCTTAATAATGGTGAGATT 10 87 1 ATGGTGAGAT 0.947377 -11 AGAAAAAATCAAGGTGAGAAA 11 2 0 AAGGTGAGAA 0.966534 -79 TACTAAAGGTTAAGTGAGAAC 12 168 1 TAAGTGAGAA 0.877566 -11 ********** Masking position 9 Map Score: 2.08349 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 149 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 TCTTCCTTTGGAAGGCGTTCAAAAGTTCAT 1 38 0 GAAGGCGTTC 0.644084 -81 CCTTCCAAAGGAAGACGTTCGTTAGTGCAA 1 53 1 GAAGACGTTC 0.926311 -66 CCCCCTTTATGAAAGCGTTCAAAATTCA 12 9 0 GAAAGCGTTC 0.640291 -170 ********** Masking position 3 Map Score: 1.26263 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 4 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 TGAAGCCAGTGGTGCGGCCTCCGGGATTTG 7 16 1 GGTGCGGCCT 0.997136 -285 GAGCGGCCTTGGTGTAGCCTGGTAACACAC 7 73 0 GGTGTAGCCT 0.979473 -228 TGCTTGCAATGGAGCGGCCTTGGTGTAGCC 7 84 0 GGAGCGGCCT 0.995003 -217 ********** Masking position 10 Map Score: 0.913553 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 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 11 TGTCTTTCAAAAAATAAAAATTTATTAAT 1 10 1 AAAAATAAAA 0.798878 -109 GAAATATAATAAAAAGTAAGTATA 3 5 1 TATAATAAAA 0.850556 -37 AAAAAGTAAGTATAATAAAAATAGGGATAG 3 21 1 TATAATAAAA 0.850556 -21 TGTAATATTTAAAAATAAAAAAAGAAAGTA 4 17 0 AAAAATAAAA 0.798878 -135 CTTCCCAAACTCCAACAAACATAATATGTG 5 104 0 TCCAACAAAC 0.665911 -97 CATTGCAAGCAACAATAACATACTCAGAAC 7 103 1 AACAATAACA 0.874859 -198 AAATATTTAATACAATAAAACCGAAAAGTA 7 142 0 TACAATAAAA 0.952767 -159 TCTAACATAATCTAATAAAACAAATCAAAG 7 227 0 TCTAATAAAA 0.824011 -74 AATAATCACCAGTAAAATTCTACCAGT 7 284 0 ACCAGTAAAA 0.740177 -17 TATAAATATTTACAACAAAAAATAAAAAGT 10 18 0 TACAACAAAA 0.874859 -80 TAAAGATAATAACAATAACAACCAGATGTT 10 56 0 AACAATAACA 0.874859 -42 AATACTAAGGACCAATAAACACCCCCTTTA 12 30 0 ACCAATAAAC 0.851879 -149 ********** Masking position 4 Map Score: 8.1535 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 726 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 12 AAATCCCGGAGGCCGCACCACTGGCTTCAA 7 15 0 GGCCGCACCA 0.996624 -286 TGTGTTACCAGGCTACACCAAGGCCGCTCC 7 74 1 GGCTACACCA 0.977538 -227 GCTACACCAAGGCCGCTCCATTGCAAGCAA 7 85 1 GGCCGCTCCA 0.994543 -216 ********** Masking position 10 Map Score: 0.913553 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 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 13 AGGCGTTCAAAAGTTCATTAATAAATTTTT 1 26 0 AAGTTCATTA 0.823958 -93 ATTCCTGCGAAAGTTCTATAATATTGAGGT 8 17 0 AAGTTCTATA 0.972527 -189 AAAAACTGCGAAGTTCTATATTAATTCATT 8 100 1 AAGTTCTATA 0.972527 -106 TAACAACCAGATGTTCTATAAATTATAAAT 10 41 0 ATGTTCTATA 0.897259 -57 GTATTATTTTAAATTCTTTTTATAGAGTCT 12 75 0 AAATTCTTTT 0.774524 -104 GTAATTTATTAAATTCTATTTTAATTTTAG 12 104 0 AAATTCTATT 0.865057 -75 ********** Masking position 5 Map Score: 2.23342 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 168 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 14 ********** No masking Map Score: -3.15948e-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 15 ********** No masking Map Score: -3.15948e-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