AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_mjan_reg_100.orf -o071_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 RMJ05709 83 M_jannaschii_chromosome #2 RMJ12675 131 M_jannaschii_chromosome #3 RMJ05070 300 M_jannaschii_chromosome #4 RMJ14264 70 M_jannaschii_chromosome #5 RMJ02456 300 M_jannaschii_chromosome #6 RMJ04788 300 M_jannaschii_chromosome #7 RMJ09060 71 M_jannaschii_chromosome #8 RMJ14877 185 M_jannaschii_chromosome #9 RMJ02772 29 M_jannaschii_chromosome #10 RMJ03862 33 M_jannaschii_chromosome #11 RMJ14786 89 M_jannaschii_chromosome #12 RMJ06121 273 M_jannaschii_chromosome Motif number 1 TAATTAAAGTATTTAAAAATATCTATTAGG 1 30 0 ATTTAAAAAT 0.811839 -54 TTTTTAAATACTTTAATTATGAATTTTTAT 1 41 1 CTTTAATTAT 0.886852 -43 TAATTATGAATTTTTATAATAAACTTGGAG 1 54 1 TTTTTATAAT 0.894567 -30 ATGTAAAATTATTTAATTATTTTTTGTACT 2 12 1 ATTTAATTAT 0.948799 -120 ACTATAAAAATCTTAAAAATTTAGTACAAA 2 34 0 TCTTAAAAAT 0.49629 -98 TTATTATCCTTTATAATTATGTCTTATATT 2 73 1 TTATAATTAT 0.675226 -59 ACTATACCAAATTTAAATATGTACAAAAAT 3 143 1 ATTTAAATAT 0.921793 -158 TTTAAGTATTTTTTAAATTTTTGTACATAT 3 159 0 TTTTAAATTT 0.775396 -142 ATATTTGCATATTTAAGTATTTTTTAAATT 3 170 0 ATTTAAGTAT 0.639266 -131 AATATGCAAATATTTATTATAATACTATAA 3 187 1 TATTTATTAT 0.698216 -114 ATACTATAAGATATAAATATAATTGGAGTT 3 208 1 ATATAAATAT 0.462313 -93 ATTTTGGATTTCTTAATTATTTTTAACTCC 3 232 0 TCTTAATTAT 0.779985 -69 TTATACTATTATTTTATTTTATCCTACCTT 4 15 1 ATTTTATTTT 0.702758 -56 ATCCTACCTTTTTTAAATAGCAATTCTTTT 4 35 1 TTTTAAATAG 0.691937 -36 ATAGCAATTCTTTTTATTAAATGTGATAAT 4 51 1 TTTTTATTAA 0.60944 -20 TTTCTGTAGTTTTTTATAATATCATCTTTG 5 58 1 TTTTTATAAT 0.894567 -243 ATTTTATTATTTTTTATTATCATTATTGTA 5 209 0 TTTTTATTAT 0.953295 -92 GCAGAGGTAAATTTTATTATTTTTTATTAT 5 219 0 ATTTTATTAT 0.926718 -82 CGAAAGTCCTATTTAAATATCACAGGTGAT 5 248 1 ATTTAAATAT 0.921793 -53 TGCAATGACACTTTTATAATTTACTGACAT 5 281 0 CTTTTATAAT 0.698109 -20 TACAAATATTAATTAATTATACAATTTGAA 6 173 1 AATTAATTAT 0.676746 -128 ATTTTTGTTAATTTAAAAATTCAAATTGTA 6 192 0 ATTTAAAAAT 0.811839 -109 CATTCACATTATTTTATTTTTGTTAATTTA 6 207 0 ATTTTATTTT 0.702758 -94 TTTTATCTTATATTAATAATATTCCAACAA 6 260 0 TATTAATAAT 0.582075 -41 TGACACCTAAATTTTATATTTTATCTTATA 6 278 0 ATTTTATATT 0.499061 -23 TTTTATTTTTTTAATTATCATTAAATCA 9 12 0 TTTTAATTAT 0.966754 -18 ATTTCTTTAATTTTTTAACCTTTT 10 5 1 CTTTAATTTT 0.58678 -29 GAGGGACAGATTTTAAATAAAAGAACAATA 12 21 1 TTTTAAATAA 0.592074 -253 AATGTTTGTTTTTTTAAAATTAACACTAAT 12 113 0 TTTTTAAAAT 0.703713 -161 AAACAAACATTTTTTATTATTTTTTGCAGT 12 132 1 TTTTTATTAT 0.953295 -142 CAACGATAACTTTTAATTAGGATTGAGATA 12 174 0 TTTTAATTAG 0.774174 -100 TGGAAAATCTTTTTAAAAATACCAACATTG 12 202 1 TTTTAAAAAT 0.887684 -72 AAAAGATGCATTTTTAATATATTTTTAATA 12 242 1 TTTTTAATAT 0.913004 -32 TTTTAATATATTTTTAATATATTATCTTTC 12 253 1 TTTTTAATAT 0.913004 -21 ********** Masking position 6 Map Score: 32.9158 Number of sites scoring better than the average of aligned sites = 2284 Number in coding regions = 1585 Number in noncoding regions = 699 Number of orfs with sites within 600 bp upstream = 491 Fraction of orfs with sites within 600 bp upstream = 0.0788628 Motif number 2 TTAGTACAAAAAATAATTAAATAATTTTACATC 2 11 0 AAATATAATA 0.68033 -121 CTTTTACTATAAAAATCTTAAAAATTTAGTACA 2 36 0 AAAAATAAAA 0.814697 -96 AGACATAATTATAAAGGATAATAATCACCTTTT 2 64 0 ATAAAAAATA 0.928023 -68 CATCCTAACATTAAAATATAAGACATAATTATA 2 84 0 TTAAAAAAGA 0.864682 -48 AAATATGTACAAAAATTTAAAAAATACTTAAAT 3 157 1 AAAAATAAAA 0.814697 -144 ATATTTATTATAATACTATAAGATATAAATATA 3 196 1 TAATAAAAGA 0.725422 -105 AAAAGGTAGGATAAAATAAAATAATAGTATAAG 4 14 0 ATAAAAAATA 0.928023 -57 ACCTAATGTTTTAAACTACAAAAAAGTTCTATT 5 132 1 TTAAAAAAAA 0.862465 -169 AATAATGATAATAAAAAATAATAAAATTTACCT 5 212 1 ATAAAAAATA 0.928023 -89 TTAAAAAATAATAACTATTATTT 6 1 1 TTAAAAAATA 0.90281 -300 AATATATAACTTAAATAAAAATAATAGTTATTA 6 19 0 TTAAAAAATA 0.902812 -282 TATTTAAGTTATATATTAGAAAATCTAATAACT 6 35 1 ATATAAAAAA 0.739866 -266 AAATGACTATAAATATGAGAATAGTCAGAAATT 6 70 1 AAATAAAATA 0.842041 -231 TTTAAATTAACAAAAATAAAATAATGTGAATGA 6 205 1 CAAAAAAATA 0.688802 -96 AAAACCGGATTTAAACGTTAATATCATTCACAT 6 228 0 TTAAATAATA 0.787624 -73 TTAATATAAGATAAAATATAAAATTTAGGTGTC 6 274 1 ATAAAAAAAA 0.896947 -27 TAATGATAATTAAAAAAATAAAA 9 17 1 TAAAAAAAAA 0.888069 -13 CCAAAAGGTTAAAAAATTAAAGAAAT 10 4 0 AAAAATAAGA 0.817522 -30 ACTGTATTTCTAAAAACACAATAAAAAACATAA 11 16 1 TAAAAAAATA 0.921589 -74 AAACACAATAAAAAACATAAATACCTAATTATC 11 29 1 AAAAATAATA 0.866895 -61 TCAATTCAATAAAAACAATAAGAGTGTTATTGG 11 60 1 AAAAAAAAGA 0.918179 -30 AGATTTTAAATAAAAGAACAATAGTTTCTTTTG 12 28 1 TAAAAAAATA 0.921589 -246 ATGCCCAACGATATAACAAAAGAAACTATTGTT 12 44 0 ATATAAAAGA 0.743472 -230 TACTACTGCAAAAAATAATAAAAAATGTTTGTT 12 133 0 AAAAAAAAAA 0.916753 -141 TGAAAGATAATATATTAAAAATATATTAAA 12 254 0 TAATATAAAA 0.508391 -20 ***** * **** Masking position 5 Map Score: 33.6718 Number of sites scoring better than the average of aligned sites = 2111 Number in coding regions = 1447 Number in noncoding regions = 664 Number of orfs with sites within 600 bp upstream = 415 Fraction of orfs with sites within 600 bp upstream = 0.066656 Motif number 3 TAAAATTCAAATAGGACTTTCTGTAGTTTT 5 41 1 ATAGGACTTT 0.988461 -260 ATCATCTTTGATAGAACGTTCGTAGACTAA 5 78 1 ATAGAACGTT 0.961573 -223 AAAGTTCCAAATAGAACTTTTTTGTAGTTT 5 144 0 ATAGAACTTT 0.967486 -157 TCATTATTGTATAGGACGTAATTGTATATG 5 190 0 ATAGGACGTA 0.957487 -111 TGATATTTAAATAGGACTTTCGCAGAGGTA 5 240 0 ATAGGACTTT 0.988461 -61 TCAAGACACCATAGGACTTCGCCCTATTGG 8 86 1 ATAGGACTTC 0.975743 -100 ********** Masking position 6 Map Score: 7.71485 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 10 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AAAATATCTATTAGGTGATAATTTGTTATAT 1 14 0 TTAGTGATAA 0.843361 -70 TATAAATATAATTGGAGTTAAAAATAATTAA 3 219 1 ATTGAGTTAA 0.83722 -82 ATGTTTAAAGTTTCAAGATAAATTGGGGAGT 3 276 1 TTTAAGATAA 0.630499 -25 TCTTTTTATTAAATGTGATAAT 4 59 1 AAAGTGATAA 0.790345 -12 ATGGATGTACAAAGGTGTTAAAGTTCCAAAT 5 162 0 AAAGTGTTAA 0.682549 -139 CGTCCTATACAATAATGATAATAAAAAATAA 5 202 1 AATATGATAA 0.803219 -99 AACTTTGGTTATTAATGTTAATTTCTGACTA 6 91 0 ATTATGTTAA 0.888328 -210 ACATTATTTTATTTTTGTTAATTTAAAAATT 6 201 0 ATTTTGTTAA 0.775813 -100 AATATTATTAATATAAGATAAAATATAAAAT 6 267 1 ATAAAGATAA 0.630474 -34 GTGATTTAATGATAATTAAAAAAAT 9 5 1 TTTATGATAA 0.853592 -25 TTTTTAACCTTTTGGTGATAAT 10 22 1 TTTGTGATAA 0.927958 -12 TAAGAGTGTTATTGGTGATAAA 11 78 1 ATTGTGATAA 0.968566 -12 ATCTAAATCAATTTTTGATAATATGTATAAA 12 80 0 ATTTTGATAA 0.858505 -194 ATTTAGATAAATTAGTGTTAATTTTAAAAAA 12 103 1 ATTGTGTTAA 0.946161 -171 *** ******* Masking position 10 Map Score: 11.6959 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 306 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 CTTTTACTATAAAAATCTTAAAAATTTAGTA 2 38 0 AAAATCTTAA 0.844602 -94 AGCCCTCAACCACAAGCGAAATTAAAGTATG 3 77 1 CAAAGCGAAA 0.916695 -224 TTAAGAAATCCAAAATCTTAAAGGGAAAGTA 3 246 1 CAAATCTTAA 0.976691 -55 AGCAATTATACAAAAGCTAAAACTTTGGTTA 6 111 0 CAAAGCTAAA 0.976432 -190 AATACTATTTCAGAAGCTAAAATTATCTTTT 7 38 1 CAAAGCTAAA 0.976432 -34 GATTACTTGAGACAATCTTAAGAGACATTAA 8 21 1 GAAATCTTAA 0.88957 -165 AAAGGTTGATCAAAATCTTAATTTAAATGGG 8 120 0 CAAATCTTAA 0.976691 -66 ATTATCACCAAAAGGTTAAAAAATTAAAG 10 15 0 CAAAGGTTAA 0.916668 -19 ** ******** Masking position 5 Map Score: 6.31066 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 65 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TTTAAGATTTTTATAGTAAAAGGTGATTATTA 2 47 1 TTATGTAAAG 0.935508 -85 ATATAAGACATAATTATAAAGGATAATAATCA 2 70 0 TAATATAAAG 0.860367 -62 ATATTTATTATAATACTATAAGATATAAATAT 3 196 1 TAATCTATAG 0.785201 -105 TAAAATAAAATAATAGTATAAGCTC 4 4 0 TAATGTATAG 0.961772 -67 TAGCAATTCTTTTTATTAAATGTGATAAT 4 52 1 TTTTTTAAAG 0.519182 -19 CAATGATAAATTTTAGTCTACGAACGTTCTAT 5 88 0 TTTTGTCTAG 0.679078 -213 GTATAGGACGTAATTGTATATGGATGTACAAA 5 180 0 TAATGTATAG 0.961772 -121 TTTATTATCATTATTGTATAGGACGTAATTGT 5 195 0 TTATGTATAG 0.950258 -106 TCACCTGTGATATTTAAATAGGACTTTCGCAG 5 245 0 TATTAAATAG 0.720345 -56 GTTGGAATATTATTAATATAAGATAAAATATA 6 262 1 TATTATATAG 0.860368 -39 TTGTCTCAAGTAATCGAATATGTCT 8 4 0 TAATGAATAG 0.913174 -182 CGAACAACCTTTTTAGAAAAGGTTGATCAAAA 8 136 0 TTTTGAAAAG 0.821574 -50 CACTCCAACTTTTTAGTAAAAGCTGCCCGAAC 8 163 0 TTTTGTAAAG 0.916768 -23 CTGCAAAAAATAATAAAAAATGTTTGTTTTTT 12 129 0 TAATAAAAAG 0.720345 -145 **** ***** * Masking position 10 Map Score: 9.55251 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 154 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TTATTTAATTATTTTTTGTACTAAATTTTT 2 20 1 ATTTTTTGTA 0.849937 -112 TTTTTAAGATTTTTATAGTAAAAGGTGATT 2 45 1 TTTTATAGTA 0.808482 -87 GTATTTTTTAAATTTTTGTACATATTTAAA 3 154 0 AATTTTTGTA 0.536353 -147 TATACTATTATTTTATTTTATCCTACCTTT 4 16 1 TTTTATTTTA 0.535781 -55 AATAGCAATTCTTTTTATTAAATGTGATAA 4 50 1 CTTTTTATTA 0.627527 -21 CATTAGGTCACTTTTTTGTGCAATGATAAA 5 110 0 CTTTTTTGTG 0.900864 -191 CCAAATAGAACTTTTTTGTAGTTTAAAACA 5 138 0 CTTTTTTGTA 0.966402 -163 TTTTTATTATCATTATTGTATAGGACGTAA 5 199 0 CATTATTGTA 0.835283 -102 ACTAAAAGCCCTTTAATGTATCCGTTCTGG 8 56 1 CTTTAATGTA 0.72544 -130 CCCGAACAACCTTTTTAGAAAAGGTTGATC 8 140 0 CTTTTTAGAA 0.731151 -46 CCACTCCAACTTTTTAGTAAAAGCTGCCC 8 167 0 CTTTTTAGTA 0.930145 -19 TATTTATGTTTTTTATTGTGTTTTTAGAAA 11 22 0 TTTTATTGTG 0.742392 -68 CTCTTATTGTTTTTATTGAATTGATAATTA 11 54 0 TTTTATTGAA 0.650726 -36 ********** Masking position 4 Map Score: 5.15585 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 575 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 GTATTTAAAAATATCTATTAGGTGATAATT 1 22 0 ATATCTATTA 0.891005 -62 AATATAAGACATAATTATAAAGGATAATAA 2 73 0 ATAATTATAA 0.824905 -59 AAATATGCAAATATTTATTATAATACTATA 3 186 1 ATATTTATTA 0.690407 -115 ACTATAAGATATAAATATAATTGGAGTTAA 3 210 1 ATAAATATAA 0.824625 -91 TTGTGCAATGATAAATTTTAGTCTACGAAC 5 95 0 ATAAATTTTA 0.581428 -206 TTAAAAAATAATAACTATTATTTTTATTTA 6 11 1 ATAACTATTA 0.953539 -290 AGAAAATCTAATAACTATAAATGACTATAA 6 52 1 ATAACTATAA 0.945259 -249 ATAACTATAAATGACTATAAATATGAGAAT 6 62 1 ATGACTATAA 0.764843 -239 TTCAAAACGTATAAGTATTACTACCAAATA 7 12 1 ATAAGTATTA 0.896482 -60 ATTTTTGATAATATGTATAAAATTATGCCC 12 71 0 ATATGTATAA 0.743747 -203 TTTTCCAACGATAACTTTTAATTAGGATTG 12 179 0 ATAACTTTTA 0.835858 -95 ********** Masking position 1 Map Score: 7.2111 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 205 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 9 GATGTAAAATTATTTAATTATTTTTTG 2 8 1 AATTATTTAA 0.749406 -124 TAAAAATCTTAAAAATTTAGTACAAAAAAT 2 30 0 AAAAATTTAG 0.262434 -102 ATTTTGGGGGATTGATTTAA 2 122 1 ATTGATTTAA 0.897643 -10 AAAGTGACCTAATGTTTTAAACTACAAAAA 5 126 1 AATGTTTTAA 0.923506 -175 ATTAATAACCAAAGTTTTAGCTTTTGTATA 6 106 1 AAAGTTTTAG 0.784018 -195 CATGGGCATAAATGAGTTAGGGCTATATTC 6 143 1 AATGAGTTAG 0.735541 -158 TTTTATTTTTTTAATTATCATTAA 9 16 0 ATTTTTTTAA 0.684773 -14 ATTTCTTTAATTTTTTAACCTTTTGGTG 10 9 1 AATTTTTTAA 0.749406 -25 TAACACTCTTATTGTTTTTATTGAATTGAT 11 59 0 ATTGTTTTTA 0.503912 -31 ATTATCAAAAATTGATTTAGATAAATTAGT 12 89 1 ATTGATTTAG 0.921684 -185 TTGCAGTAGTAATGTTTTATATCTCAATCC 12 155 1 AATGTTTTAT 0.714808 -119 AAATACCAACATTGATTTAGAATTAAAAGA 12 218 1 ATTGATTTAG 0.921684 -56 ********** Masking position 1 Map Score: 2.57898 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 607 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 10 ACCTAATAGATATTTTTAAATACTTTAATT 1 29 1 TATTTTTAAA 0.862086 -55 ATGTGTAACTTATATATAAACTTTTCGGTA 3 105 1 TATATATAAA 0.854738 -196 CAAATTTAAATATGTACAAAAATTTAAAAA 3 150 1 TATGTACAAA 0.899952 -151 AAAGGGAAAGTATGTTTAAAGTTTCAAGAT 3 265 1 TATGTTTAAA 0.948547 -36 ATTGTATATGGATGTACAAAGGTGTTAAAG 5 170 0 GATGTACAAA 0.85529 -131 AATCACCTGTGATATTTAAATAGGACTTTC 5 249 0 GATATTTAAA 0.779731 -52 TTTTTGATAATATGTATAAAATTATGCCCA 12 70 0 TATGTATAAA 0.944094 -204 TCAATGTTGGTATTTTTAAAAAGATTTTCC 12 203 0 TATTTTTAAA 0.862086 -71 ********** Masking position 8 Map Score: 4.17894 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 72 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ********** No masking Map Score: -5.24137e-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 12 ********** No masking Map Score: -5.24137e-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 13 ********** No masking Map Score: -5.24137e-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