AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_mthe_reg_300.orf -o064_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01080 300 M.thermo #2 RTH02062 231 M.thermo #3 RTH02127 159 M.thermo #4 RTH01004 66 M.thermo #5 RTH01088 218 M.thermo #6 RTH00663 79 M.thermo #7 RTH00777 35 M.thermo #8 RTH00316 57 M.thermo #9 RTH00321 44 M.thermo #10 RTH01047 56 M.thermo #11 RTH02145 30 M.thermo #12 RTH00013 16 M.thermo #13 RTH00133 56 M.thermo #14 RTH01743 127 M.thermo #15 RTH00602 189 M.thermo #16 RTH00576 116 M.thermo #17 RTH00954 31 M.thermo #18 RTH00250 30 M.thermo #19 RTH00057 21 M.thermo #20 RTH01659 205 M.thermo #21 RTH01211 72 M.thermo #22 RTH00503 300 M.thermo Motif number 1 TCTTTGCCTGTAATGCCGGGGTGATAAACTG 2 76 0 TATGCCGGGG 0.956372 -156 AGGTTACCTATAATCCAGGGGAGAGTGTGAC 2 211 1 TATCCAGGGG 0.88974 -21 TATTCTGCACTACTGCAGATGTAACCCTGCA 3 38 1 TCTGCAGATG 0.862822 -122 ATGTTTCTGTAGCTGCAGGGTTACATCTGCA 3 51 0 ACTGCAGGGT 0.897206 -109 GGGGTTCAAATCCCCCCGGGTCCGCTTTTTT 5 26 0 TCCCCCGGGT 0.887258 -193 GATGTATCCGCCGGGGACAGGGTCAT 8 6 1 ACCGCCGGGG 0.906215 -52 GTAGAACCTATGGCGCCGGTTCTTTATATCT 9 23 0 TGCGCCGGTT 0.566622 -22 AACTGGAGGGGGTTGC 12 1 1 ACTGGAGGGG 0.906696 -16 AGGGGTGAGGTGGTGGAGGGGT 13 2 0 TGTGGAGGGG 0.866821 -55 ACTGATTTTTTTCTCCCGGAGCCATCCAGAA 13 33 1 TCTCCCGGAG 0.884373 -24 GAATGATAGATCCTGCAGATGAACGGATAAA 15 118 1 TCTGCAGATG 0.862822 -72 TACATTAAGCTCCTGCAGGGTTTATCCGTTC 15 138 0 TCTGCAGGGT 0.9701 -52 GAGTATTCCATACTGGCGGTGTATGTAACTC 20 97 1 TCTGGCGGTG 0.949603 -109 AGCACTGGCCTCCTCCAGGGGGAGGAGGTTG 21 20 1 TCTCCAGGGG 0.985811 -53 CCTCCCGGTGTGCAGCAGGTGATATTGATCA 22 274 0 TCAGCAGGTG 0.870274 -27 GGTCTCCCTCCCGGTGTGCAGCAGGT 22 285 0 CCTCCCGGTG 0.852371 -16 * ********* Masking position 8 Map Score: 15.9828 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 1080 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 CAAATGGTAGTCATATCCATGGGATGAATTC 1 126 1 TCATTCCATG 0.994614 -175 AGTTTATCTCCATGAAACTTTATA 3 4 1 TTATTCCATG 0.953751 -156 GATGAAATCATCATTTCCATGCAGTAAGATA 14 77 0 TCATTCCATG 0.994614 -51 GTTTATCCGTTCATCTGCAGGATCTATCATT 15 119 0 TCATTGCAGG 0.918344 -71 ATCCCATGATTCATATCCATGGATTGATTAA 16 37 0 TCATTCCATG 0.994614 -80 AACTGGCTGTTCATATTCATGACCACACAGC 20 18 1 TCATTTCATG 0.980536 -188 TCATGTTTAATCATCTCAATGGTTCTCATGG 22 33 0 TCATTCAATG 0.953751 -268 CACTCCACTACCATGTTCATGTGGAGATTAT 22 143 1 CCATTTCATG 0.930462 -158 **** ****** Masking position 3 Map Score: 12.1371 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 90 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 TTGGTCCATTAGATGCCCCCTAATCCAAATTA 1 64 1 AGGCCCCCTA 0.967875 -237 AGGCTAGACTACGGGCCCCCTACACACATCTC 5 91 1 ACGCCCCCTA 0.991202 -128 CCCCTCCACCACCTCACCCCTACTGATTTTTT 13 12 1 ACCACCCCTA 0.985993 -45 TCGGTCAGGGACCGGACTCCAAACCTATTATA 15 47 1 ACGACTCCAA 0.924697 -143 ATTACGTCACCTCAAATGTCTGTGG 16 102 0 ACCACCTCAA 0.892613 -15 TCAAATGGATCGGGACCCCTC 19 10 1 TCGACCCCTC 0.940663 -12 TCATGACCACACAGCACCCCAAACCACCATGT 20 34 1 ACCACCCCAA 0.979626 -172 TGAGGATAGCACTGGCCTCCTCCAGGGGGAGG 21 13 1 ACGCCTCCTC 0.954755 -60 AGATGATTAAACATGACCTCACATCCACCACA 22 48 1 ACGACCTCAC 0.930089 -253 TACCGGATAGAGAACCCCCCTCAATAACTCAG 22 221 1 AGCCCCCCTC 0.9567 -80 ** ******** Masking position 7 Map Score: 8.42278 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 260 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TTTATATTAATCTGTGGTCATTCCTTAATTTGGATT 1 85 0 TGGCATTCCT 0.982839 -216 TGGTTGATGGTTGGAATTCATCCCATGGATATGACT 1 134 0 TGACATCCCT 0.979771 -167 TGGTTAGTTTTATGGAGCCATTCCCTTTTAAGAATT 1 250 0 TGACATTCCT 0.97287 -51 GTAACCGGAATCATGGGCCATCCCCTGGGCACAGCC 2 22 0 TTGCATCCCT 0.986099 -210 CTTAATGGTTATTCCTCCCTTTTTATGATCC 4 46 0 TTACCTCCCT 0.950313 -21 TCAGTGTCATTGTTGGGGCATTCCGTGGAGCATTTC 10 17 1 TTGCATTCCT 0.978013 -40 TGTTTATTAACCATTCCCTTTGATGTACA 14 4 1 TTACATTCCT 0.965392 -124 GGAACCATGATGCAAATCCATCCCATGATTCATATC 16 51 0 TAACATCCCT 0.916488 -66 CCTTATCCTATTATAGAGTATTCCATACTGGCGGTG 20 82 1 TTGTATTCCT 0.795353 -124 AAGGAACTGGGAGGCCCTCCCGAAATGGAGGTC 21 50 0 TGGCCTCCCA 0.84562 -23 * * * ****** * Masking position 11 Map Score: 8.39878 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 72 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TAATGGACCAAAATTTTTAAATAATAAGTTTA 1 43 0 AAATTTTAAT 0.932601 -258 CTACCATTTGCAATTTTTATATTAATCTGTGG 1 104 0 CAATTTTATT 0.924039 -197 AACCATCAACCAATGTTTAAGTGAAAGCATAT 1 158 1 CAATTTTAAT 0.933778 -143 GCATATAAATAAATGTTTATATTACTGGAATT 1 184 1 AAATTTTATT 0.922619 -117 GGAATTCTTCAAATTATTAAATGATCCGGTGT 1 210 1 AAATATTAAT 0.595473 -91 ATGGTACTTACAATATTTATTTACCATCAGCG 2 162 1 CAATTTTATT 0.915602 -70 CCTATGGCAACAATATTTATCGCTGATGGTAA 2 182 0 CAATTTTATG 0.793411 -50 GTTGATGAGAAAATATTTAAATGGTTAACTTT 5 128 0 AAATTTTAAT 0.932462 -91 ATGTAATAATATATCTTTATATTGTAAGAAGA 6 42 0 ATATTTTATT 0.709172 -38 ATCCGTCAACTCTTTATTTCTGGTGATTC 11 8 1 AACTTTTATT 0.653233 -23 TATGTACAGTAAAGTTTTAAATAGTTCTTTAA 14 42 1 AAAGTTTAAT 0.813841 -86 ATGCAGTAAGATATCTTTAAAGAACTATTTAA 14 58 0 ATATTTTAAG 0.471709 -70 ACCACCATGTCAAGATTTAAATACTCCCTTAT 20 56 1 CAAGTTTAAT 0.816675 -150 **** ***** * Masking position 9 Map Score: 8.17602 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 15 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GAATGGTTAGTTTTATGGAGCCATTCCCTT 1 259 0 TTTTATGGAG 0.893233 -42 CCCTAACTTTTTCACTGGAGG 1 290 1 TTCACTGGAG 0.953455 -11 CTTTATAAAGTTTCATGGAGATAAACT 3 8 0 TTTCATGGAG 0.848996 -152 CTTGAGTGATGTTTCTGTAGCTGCAGGGTT 3 60 0 GTTTCTGTAG 0.875582 -100 CTTGACTGATGTTTCTGTAGCTACAGGGTT 3 95 0 GTTTCTGTAG 0.875582 -65 TGTTGGGGCATTCCGTGGAGCATTTCAGGG 10 27 1 TTCCGTGGAG 0.80937 -30 CGTTTCTGGATGGCTCCGGGA 13 46 0 GTTTCTGGAT 0.780541 -11 TCTATCATTCTTCACTGGAGATTAACTTAT 15 98 0 TTCACTGGAG 0.953455 -92 GTTAACTCAGGTCACTGGAGAG 17 3 0 GTCACTGGAG 0.970296 -29 AAATCAAACAGTATATGGAGACGTCTCGGG 22 91 0 GTATATGGAG 0.766962 -210 ********** Masking position 6 Map Score: 5.73955 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 378 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ACATTGGTTGATGGTTGGAATTCATCCCAT 1 144 0 ATGGTTGGAA 0.955175 -157 AAATGTTTATATTACTGGAATTCTTCAAAT 1 194 1 ATTACTGGAA 0.925497 -107 TGATAAACTGATAACTGGAAAAACACATGT 2 56 0 ATAACTGGAA 0.925497 -176 ATCACCTCATGGCTGGAACTGGTCCCTA 14 110 0 ATGGCTGGAA 0.991088 -18 GTTATGCAACATGGCTGGAACCATGATGCA 16 73 0 ATGGCTGGAA 0.991088 -44 ********** Masking position 6 Map Score: 3.94786 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 CAGGGGATGGCCCATGATTCCGGTTACATG 2 31 1 CCCATGATTC 0.981157 -201 TGTCTGCTGTCCCCTGAGTCTGGTCTTCGG 5 167 0 CCCCTGAGTC 0.915121 -52 ACCAGTTCCAGCCATGAGGTGAT 14 115 1 GCCATGAGGT 0.887757 -13 GCAAATCCATCCCATGATTCATATCCATGG 16 46 0 CCCATGATTC 0.981157 -71 CATGGCTGGAACCATGATGCAAATCCATCC 16 64 0 ACCATGATGC 0.965405 -53 CATGGTTCCAGCCATGTTGCATAACCACAG 16 78 1 GCCATGTTGC 0.89946 -39 TAACTGGTTAACCATGATTTAGAGTTACAT 20 119 0 ACCATGATTT 0.863097 -87 ********** Masking position 5 Map Score: 3.24188 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 126 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 TAAGAATTTAGGGGGCACACCGGATCATTTA 1 227 0 GGGGGACACC 0.971562 -74 TCATAAAAAGGGAGGAATAACCATTAAG 4 49 1 GGAGGATAAC 0.879334 -18 GGTTCAACAAGGAGGATGACCCTGTCCCCGG 8 21 0 GGAGGTGACC 0.991391 -37 TCCAGGGGGAGGAGGTTGACCTCCATTTCGG 21 33 1 GGAGGTGACC 0.991391 -40 CTCCATTTCGGGAGGGCCTCCCAGTTCCTT 21 53 1 GGAGGCCTCC 0.498698 -20 CTGCACACCGGGAGGGAGACC 22 290 1 GGAGGAGACC 0.993671 -11 ***** ***** Masking position 5 Map Score: 4.24619 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 160 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 TATAAGTGTGTATTAAACTTATTATTTAAAAA 1 30 1 TTTAAATTAT 0.885758 -271 TTACTGGAATTCTTCAAATTATTAAATGATCC 1 205 1 TTTCAATTAT 0.819753 -96 GTCCGTAAGTTGTGGAATTTATCTTGACTGAT 3 115 0 TTGGAATTAT 0.918247 -45 GGTTAATGCGTTTTGAGATTATGTGAACACC 7 10 0 TTTGAGTTAT 0.942399 -26 CCGATTATAAGTTAGAACTTATAAGTTATAAG 15 19 0 GTAGAATTAT 0.668089 -171 CTCGATGACTGGTTAAATTTATTTTACATTAA 15 161 0 GTTAAATTAT 0.791226 -29 AATATGAATTTTTTGAATTTATGTTAAATCCA 20 149 1 TTTGAATTAT 0.952004 -57 ACCATGTTCATGTGGAGATTATTTAAGAAAAG 22 152 1 TTGGAGTTAT 0.902578 -149 TGTATGTGCATCTTAAGTTTATGATCAATATC 22 253 1 TTTAAGTTAT 0.864778 -48 * ***** **** Masking position 6 Map Score: 1.51519 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 35 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 CCATGAGAAAAAAAATCAGATTCTATACTG 2 136 0 AAAAATCAGA 0.904508 -96 GCAGCTACAGAAACATCACTCAAGATTGTA 3 66 1 AAACATCACT 0.905252 -94 GTAGCTACAGAAACATCAGTCAAGATAAAT 3 101 1 AAACATCAGT 0.971132 -59 TAAAAAGCAGTTAATAAAAAA 5 2 1 AAAAAGCAGT 0.933505 -217 TCCGGGAGAAAAAAATCAGTAGGGGTGAGG 13 23 0 AAAAATCAGT 0.968908 -34 ********** Masking position 5 Map Score: 0.674384 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 10 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 ********** No masking Map Score: 2.16959e-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: 2.16959e-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 14 ********** No masking Map Score: 2.16959e-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