AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__mjan_reg_100.orf -o056_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 RMJ04589 300 M_jannaschii_chromosome #2 RMJ13440 183 M_jannaschii_chromosome #3 RMJ06792 300 M_jannaschii_chromosome #4 RMJ13997 135 M_jannaschii_chromosome #5 RMJ05932 226 M_jannaschii_chromosome #6 RMJ04294 123 M_jannaschii_chromosome #7 RMJ00596 205 M_jannaschii_chromosome #8 RMJ11884 235 M_jannaschii_chromosome Motif number 1 TACGAAAAACTATGAAAATTTTCTTTTAATC 1 31 0 TATGAAAATT 0.915248 -270 TAAATTTAGTTATGAAAAATTGAACACCCTC 1 69 1 TATGAAAATT 0.915248 -232 TGTCATATCCTATCAAAAATATGCAAATCAA 1 195 1 TATCAAAATA 0.927726 -106 AAAATATGCAAATCAAAAATTTCAGGTATCA 1 210 1 AATCAAAATT 0.893925 -91 TAAATCTTACTATAAAAAGGATTG 1 287 1 TATAAAAAGA 0.912903 -14 AAAGACTAAAAATAAAAAATAGAATTAAAGA 2 17 0 AATAAAAATA 0.836186 -167 AAAAGTTTGATATAAAAAAGTGTTGGTATTT 2 68 0 TATAAAAAGT 0.945164 -116 TTTGAAGAACTTTAAAAAGTTTGATATAAAA 2 82 0 TTTAAAAATT 0.923087 -102 AAATCCTTAGTATAAAAATTTTTATATATGA 2 117 1 TATAAAAATT 0.954598 -67 GATGATGAGCAATAAAAAGCTGACTTAATAT 3 23 0 AATAAAAACT 0.800404 -278 TAAAAAAGTTTATAAAAAATCTTTCATGAAT 3 107 0 TATAAAAATC 0.727254 -194 GTGTAAGTGATATAAAAAAGTTTATAAAAAA 3 119 0 TATAAAAAGT 0.945164 -182 GTATAGTGCCTTTCAAAACTTATTGAGATAA 3 157 1 TTTCAAAATT 0.923367 -144 ATATAGTGCCTTTCAAAATTAATAAACTTAT 3 238 0 TTTCAAAATA 0.87991 -63 TAACTTAACCTTTCAAAATGATAGATTAAAG 4 28 0 TTTCAAAAGA 0.857277 -108 GATGGGATGTTATAAAAATTTTACCTAATCA 4 79 0 TATAAAAATT 0.954598 -57 ATAACAGAAAATTAAAAAGTTTTGGTGGGAT 4 114 1 ATTAAAAATT 0.827333 -22 AATTCTGGAATTTCAAAAGTTAAAGTTATCG 5 45 0 TTTCAAAATT 0.923367 -182 TGTTGAAAAAATTGAAAAAGAATGTGAAGAA 5 171 1 ATTGAAAAGA 0.550933 -56 TATTGTTTAATATGAAAATCTAAATATAAGA 6 25 0 TATGAAAACT 0.837638 -99 TTATAACTAAAATAAAAAGTAAGTGAATAAA 6 72 0 AATAAAAATA 0.836186 -52 CATTAATCATATTCAAAAGGTGAAATA 6 107 1 ATTCAAAAGT 0.797715 -17 AAATCGATACTATAAAAACCATATAATAATA 7 146 0 TATAAAAACA 0.859315 -60 ATATAGTGTCTTTCAAAAACATTTTGAAGTA 8 184 0 TTTCAAAACA 0.777796 -52 AAAGACACTATATAAAAAAGTTTTTGGTGCT 8 202 1 TATAAAAAGT 0.945164 -34 ******** ** Masking position 3 Map Score: 35.9742 Number of sites scoring better than the average of aligned sites = 1199 Number in coding regions = 815 Number in noncoding regions = 384 Number of orfs with sites within 600 bp upstream = 349 Fraction of orfs with sites within 600 bp upstream = 0.0560553 Motif number 2 AAAAACTATGAAAATTTTCTTTTAATCTTA 1 28 0 AAAATTTTCT 0.57679 -273 TTATGATACCTGAAATTTTTGATTTGCATA 1 214 0 TGAAATTTTT 0.543304 -87 ATTAAATACCAACACTTTTTTATATCAAAC 2 65 1 AACACTTTTT 0.852034 -119 TTTTTTATATCAAACTTTTTAAAGTTCTTC 2 80 1 CAAACTTTTT 0.782196 -104 TCCTTAGTATAAAAATTTTTATATATGATT 2 120 1 AAAAATTTTT 0.489413 -64 CTTTACCCTTAACATTTTTTGGTGATTGG 2 165 1 AACATTTTTT 0.808684 -19 TTATTCATGAAAGATTTTTTATAAACTTTT 3 105 1 AAGATTTTTT 0.808684 -196 AGATTTTTTATAAACTTTTTTATATCACTT 3 116 1 TAAACTTTTT 0.938184 -185 AGTGCCTTTCAAAACTTATTGAGATAATAA 3 161 1 AAAACTTATT 0.930236 -140 TCAAAATTAATAAACTTATTATTAAACTTT 3 227 0 TAAACTTATT 0.909303 -74 TCTGATTAGGTAAAATTTTTATAACATCCC 4 77 1 TAAAATTTTT 0.722032 -59 AATCCCACCAAAACTTTTTAATTTTCTGT 4 117 0 AAAACTTTTT 0.896341 -19 TTGAAATTCCAGAATTTATTGATAAAAATA 5 60 1 AGAATTTATT 0.817173 -167 AGCTCCTTTTTGAATTTATTTTTATCAATA 5 76 0 TGAATTTATT 0.728481 -151 TTTCTCTCCCAAGATTTTTTTCTTGATGAA 5 113 0 AAGATTTTTT 0.808684 -114 TTTCTGAATTTGAATTTTTTTCTAAATTCT 5 198 0 TGAATTTTTT 0.804562 -29 TACAGAAAACAAAACTTATTTATTCACTTA 6 54 1 AAAACTTATT 0.930236 -70 ATTTATGTTTTAAATTTATTTCACTATAAT 7 82 1 TAAATTTATT 0.882638 -124 ATTAATACGGTATATTTATTGTTTCTATTT 8 39 0 TATATTTATT 0.605691 -197 TTTATTGTCAAATATTTATTAATAAACTTT 8 111 0 AATATTTATT 0.696147 -125 AAGGCATTTAAATATTTATTGTCAAATATT 8 125 0 AATATTTATT 0.696147 -111 GTGTCTTTCAAAAACATTTTGAAGTAACCA 8 180 0 AAAACATTTT 0.511765 -56 GACAGCACCAAAAACTTTTTTATATAGTGT 8 206 0 AAAACTTTTT 0.896341 -30 ********** Masking position 7 Map Score: 25.377 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 697 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 3 AAAATTAAGTTAAGATTAAAAGAAAATTTTCATAGTT 1 18 1 TATTAAAAAT 0.65956 -283 AAAATTTTCATAGTTTTTCGTAAAGTTGTTAAATTTA 1 40 1 TATTTGTATT 0.649096 -261 AGCCTTGTCATATCCTATCAAAAATATGCAAATCAAA 1 190 1 TATATAAAAT 0.659508 -111 CTTTTTATAGTAAGATTTAAAAATAATAAAATAGATA 1 269 0 TATTTAAAAT 0.951312 -32 ACTAAGGATTTAGCATTTGAAGAACTTTAAAAAGTTT 2 91 0 TATTTAAATT 0.947565 -93 AATTTTTATATATGATTTCAATTTTATCATTACTTTA 2 133 1 TATTTAATAT 0.772362 -51 ACTTTACCCTTAACATTTTTTGGTGATTGG 2 164 1 TATTTTTGAT 0.525811 -20 ATTATCTCAATAAGTTTTGAAAGGCACTATACTTTTA 3 152 0 TATTTAAGAC 0.661035 -149 AACTTATTATTAAACTTTGAACGCCTTCCTTTAGGAG 3 208 0 TATTTAAGTT 0.956366 -93 CGCTATAACTTAACCTTTCAAAATGATAGATTAAAGT 4 27 0 TATTTAAAAT 0.951149 -109 GGTTAAGTTATAGCGTTTTAATGATATATCTGATTAG 4 49 1 TATTTAAGAT 0.960661 -87 TCTGATTAGGTAAAATTTTTATAACATCCCATCATAA 4 77 1 TATTTTAAAT 0.689782 -59 TTTTATTTTTTGGTGGTAATTATGGCTACA 5 4 1 TATTTGTGAT 0.714157 -223 GGAAAAGGTGTAGATGTTGAAAAAATTGAAAAAGAAT 5 157 1 TAGTTAAATT 0.583452 -70 TATTTCACCTTTTGAATATGATTAATGTAGAT 6 102 0 CATTTAAAAT 0.619537 -22 AACCAACATTTATGTTTTAAATTTATTTCACTATAAT 7 75 1 TATTTAATTT 0.758214 -131 TTTATTTCACTATAATTTAGTTGTGTTCTAATGGTAT 7 96 1 TATTTGTGTT 0.69795 -110 AATAATAACATAGAATTTAAATACCATTAGAACACAA 7 116 0 TATTTAAAAT 0.951338 -90 AATTCTATGTTATTATTATATGGTTTTTATAGTATCG 7 136 1 TATTAATGTT 0.471896 -70 AATACTATTTTAAGGTTTTCGGTTTAATT 7 187 0 TATTTAAGTT 0.957573 -19 TCCCTCTTATTAACGTTTAATAGAAATAGAAACAATA 8 16 1 TATTTATGAT 0.906971 -220 TTGAAGACAGTATAGTTTAAAGATATTTTTAAGTATT 8 66 0 TATTTAAATT 0.947588 -170 TATTTATTAATAAACTTTAATTAATTTTGAAGACAGT 8 92 0 TATTTATATT 0.878307 -144 ATTTGACAATAAATATTTAAATGCCTTCCTTTGGAAG 8 128 1 AATTTAAGTT 0.558081 -108 AAGTAACCAGTAGCTTATGAACACCTTCCAAAGGAAG 8 152 0 TATATAAATT 0.641545 -84 ** *** ** * ** Masking position 2 Map Score: 25.54 Number of sites scoring better than the average of aligned sites = 1172 Number in coding regions = 901 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 4 GAAACCAAAAATTAAGTTAAGATTA 1 2 1 AAAAAATTAA 0.968815 -299 TTCTAAAGATAAAGGACATAATAAATGTCTTTCG 1 103 0 AAAAAAATAA 0.922113 -198 ATATTTGCAAAAACCAATAATTTAGATGCCAATT 1 136 1 AAAATATTTA 0.836248 -165 ATTAATTAACAAAAGAAAAATTAAGCCTTGTCAT 1 167 1 AAAAAATTAA 0.968815 -134 TAAAAATAATAAAATAGATATTTAGTAGAACTCA 1 255 0 AAAAAATTTA 0.914907 -46 GACTAAAAATAAAAAATAGAATTAAAGAAAGAAA 2 11 0 AAAAAAATTA 0.80563 -173 TTAAGATTAGTAATTAAATATTAAATACCAACAC 2 46 1 TAAAAATTAA 0.83821 -138 GATAAAATTGAAATCATATATAAAAATTTTTATA 2 127 0 AAAAAATAAA 0.915806 -57 TGTTAAGGGTAAAGTAATGATAAAATTGAAATCA 2 145 0 AAAATATAAA 0.836249 -39 GTTATTCTTATAAAGACTAATTAAATGGTGAGAT 3 276 1 TAAATATTAA 0.716829 -25 TAACCTTTCAAAATGATAGATTAAAGTTCATTTA 4 20 0 AAAAAATTAA 0.968815 -116 GTAGATGTTGAAAAAATTGAAAAAGAATGTGAAG 5 166 1 AAAATAAAAA 0.660569 -61 GATTATAACTAAAATAAAAAGTAAGTGAATAAAT 6 71 0 AAAAAAGTAA 0.842099 -53 GATACTATAAAAACCATATAATAATAACATAGAA 7 138 0 AAAAAAATAA 0.92211 -68 ATAGAAATAGAAACAATAAATATACCGTATTAAT 8 35 1 AAAAAATATA 0.79203 -201 TATTTATTGTCAAATATTTATTAATAAACTTTAA 8 109 0 CAAATATTAA 0.679813 -127 *** * * ***** Masking position 6 Map Score: 17.3074 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 575 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 5 AATTAATTGGCATCTAAATTATTGGTTTTT 1 144 0 CATCTAAATT 0.778758 -157 ATTTAGATGCCAATTAATTAACAAAAGAAA 1 155 1 CAATTAATTA 0.874773 -146 ATGGTGAGTTCTACTAAATATCTATTTTAT 1 251 1 CTACTAAATA 0.812296 -50 TAGTAATTAAATATTAAATACCAACACTTT 2 53 1 ATATTAAATA 0.707788 -131 AATCTCACCATTTAATTAGTCTTTATAA 3 283 0 CATTTAATTA 0.846313 -18 TTAATATGAAAATCTAAATATAAGAAAATA 6 20 0 AATCTAAATA 0.882402 -104 CATTATCCTAAAATTAAATAGTATGGTGAA 7 15 0 AAATTAAATA 0.868183 -191 CATTAGAACACAACTAAATTATAGTGAAAT 7 99 0 CAACTAAATT 0.80988 -107 AATAACATAGAATTTAAATACCATTAGAAC 7 120 0 AATTTAAATA 0.806866 -86 ACTGTCTTCAAAATTAATTAAAGTTTATTA 8 92 1 AAATTAATTA 0.756214 -144 CAAAGGAAGGCATTTAAATATTTATTGTCA 8 131 0 CATTTAAATA 0.925504 -105 ********** Masking position 6 Map Score: 6.82436 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 340 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 6 TTCATAACTAAATTTAACAACTTTACGAAA 1 55 0 AATTTAACAA 0.711807 -246 TAAAAAATAGAATTAAAGAAAGAAA 2 6 0 AATTAAAGAA 0.751036 -178 CCTAAATTATTATTCATGAAAGATTTTTTA 3 96 1 TATTCATGAA 0.836496 -205 TAATAAAAGGTATTAATGAACGCCTCCTAA 3 185 1 TATTAATGAA 0.762365 -116 TGCCTTTCAAAATTAATAAACTTATTATTA 3 233 0 AATTAATAAA 0.818373 -68 AAGTTCATTTAATTCATCAA 4 1 0 AATTCATCAA 0.886167 -135 GATAAAAATAAATTCAAAAAGGAGCTTGAA 5 80 1 AATTCAAAAA 0.853635 -147 GAATGTGAAGAATTTAGAAAAAAATTCAAA 5 190 1 AATTTAGAAA 0.783363 -37 AAAAAATTCAAATTCAGAAATTGAATTTT 5 208 1 AATTCAGAAA 0.902447 -19 TAGATTTTCATATTAAACAATACAGAAAAC 6 34 1 TATTAAACAA 0.773769 -90 TTATAAACGATATTTAGCAATTACACGGAG 7 47 0 TATTTAGCAA 0.771779 -159 TTTAATTTGATATTCAGAAATCGATACTAT 7 164 0 TATTCAGAAA 0.888707 -42 AATTAAAGTTTATTAATAAATATTTGACAA 8 107 1 TATTAATAAA 0.795476 -129 ********** Masking position 6 Map Score: 8.52154 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 470 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 AAACTTTTTAAAGTTCTTCAAATGCTAAAT 2 91 1 AAGTTCTTCA 0.946317 -93 ATATGATTTCAATTTTATCATTACTTTACC 2 142 1 AATTTTATCA 0.87287 -42 GAAAGGTTCATCATATTAAGTCA 3 4 1 AGGTTCATCA 0.943619 -297 AGCCCCCGTAAGGTTCATCATCCTAAATTA 3 75 1 AGGTTCATCA 0.943619 -226 AATCTCACCATTTAATTAGT 3 291 0 AATCTCACCA 0.780776 -10 AAAGTTCATTTAATTCATCAA 4 2 0 TAATTCATCA 0.708547 -134 GGAGCTTGAAAATTTCATCAAGAAAAAAAT 5 100 1 AATTTCATCA 0.97544 -127 ATTCTTTTTCAATTTTTTCAACATCTACAC 5 164 0 AATTTTTTCA 0.756628 -63 ATTTTTTTCTAAATTCTTCACATTCTTTTT 5 185 0 AAATTCTTCA 0.886668 -42 AAATTTCACCATACTATTTAA 7 2 1 AATTTCACCA 0.944684 -204 ********** Masking position 5 Map Score: 7.51613 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 418 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TCTTTCGATAGAGGGTGTTCAATTTTTCAT 1 80 0 GAGGGTGTTC 0.977204 -221 CCTTCCTTTAGGAGGCGTTCATTAATACCT 3 192 0 GGAGGCGTTC 0.969678 -109 CCTCCTAAAGGAAGGCGTTCAAAGTTTAAT 3 207 1 GAAGGCGTTC 0.784475 -94 CCTTCCAAAGGAAGGCATTTAAATATTTAT 8 136 0 GAAGGCATTT 0.879074 -100 CCTTCCTTTGGAAGGTGTTCATAAGCTACT 8 151 1 GAAGGTGTTC 0.976948 -85 ********** Masking position 8 Map Score: 4.82928 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 8 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TATTTAGTAGAACTCACCATATAATAATTAT 1 240 0 AACCACCATA 0.924839 -61 TAAGTTTTGAAAGGCACTATACTTTTAGAGT 3 148 0 AAGCACTATA 0.987098 -153 TTAATTTTGAAAGGCACTATATATCTACAGT 3 247 1 AAGCACTATA 0.987098 -54 ATATATCATTAAAACGCTATAACTTAACCTT 4 47 0 AAACGCTATA 0.795672 -89 AAATTTCACCATACTATTTAATT 7 3 1 ATTCACCATA 0.842752 -203 TTTTAAATTTATTTCACTATAATTTAGTTGT 7 89 1 ATTCACTATA 0.904438 -117 ATTAATTTTGAAGACAGTATAGTTTAAAGAT 8 79 0 AAGCAGTATA 0.926801 -157 ATGTTTTTGAAAGACACTATATAAAAAAGTT 8 193 1 AAGCACTATA 0.987098 -43 *** ******* Masking position 9 Map Score: 6.10297 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 41 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 TTGCAAATATTCTAAAGATAAAGGACATAA 1 116 0 TCTAAAGATA 0.931176 -185 TATAGTAAGATTTAAAAATAATAAAATAGA 1 271 0 TTTAAAAATA 0.882559 -30 AATCTTAAAGACTAAAAATAAAAAATAGAA 2 24 0 ACTAAAAATA 0.538862 -160 TCACTTACACTCTAAAAGTATAGTGCCTTT 3 140 1 TCTAAAAGTA 0.777604 -161 GCGTTCAAAGTTTAATAATAAGTTTATTAA 3 221 1 TTTAATAATA 0.882418 -80 GTTATAGCGTTTTAATGATATATCTGATTA 4 55 1 TTTAATGATA 0.909632 -81 AATTCCAGAATTTATTGATAAAAATAAATT 5 64 1 TTTATTGATA 0.693151 -163 AATATGAAAATCTAAATATAAGAAAATAGA 6 18 0 TCTAAATATA 0.675615 -106 TTAGTTGTGTTCTAATGGTATTTAAATTCT 7 112 1 TCTAATGGTA 0.824318 -94 ATAAAAACCATATAATAATAACATAGAATT 7 136 0 TATAATAATA 0.604622 -70 GACAGTATAGTTTAAAGATATTTTTAAGTA 8 68 0 TTTAAAGATA 0.909777 -168 TTGTCAAATATTTATTAATAAACTTTAATT 8 107 0 TTTATTAATA 0.627349 -129 ********** Masking position 4 Map Score: 7.68993 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 373 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 11 GATTTGCATATTTTTGATAGGATATGACAA 1 194 0 TTTTTGATAG 0.845889 -107 CCCTTAACATTTTTTGGTGATTGG 2 170 1 TTTTTGGTGA 0.952653 -14 TTTTCTGTTATTTATGATGGGATGTTATAA 4 95 0 TTTATGATGG 0.897468 -41 AAATTAAAAAGTTTTGGTGGGATT 4 122 1 GTTTTGGTGG 0.974615 -14 TTTTATTTTTTGGTGGTAATTATGGC 5 7 1 TTTTTGGTGG 0.990566 -220 TATAAAAAAGTTTTTGGTGCTGTCTATGAT 8 212 1 TTTTTGGTGC 0.967555 -24 ********** Masking position 5 Map Score: 4.07693 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 107 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 12 ********** No masking Map Score: 9.54559e-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 13 ********** No masking Map Score: 9.54559e-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 14 ********** No masking Map Score: 9.54559e-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