AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_mjan_reg_300.orf -o146_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 RMJ08206 98 M_jannaschii_chromosome #2 RMJ10471 175 M_jannaschii_chromosome #3 RMJ03238 201 M_jannaschii_chromosome #4 RMJ02105 108 M_jannaschii_chromosome #5 RMJ11183 138 M_jannaschii_chromosome #6 RMJ11456 35 M_jannaschii_chromosome #7 RMJ00462 107 M_jannaschii_chromosome #8 RMJ11437 192 M_jannaschii_chromosome #9 RMJ13747 52 M_jannaschii_chromosome #10 RMJ00104 143 M_jannaschii_chromosome Motif number 1 TATTCAGAAACCATAGGGCTTCGCCCTATT 1 26 1 CCATAGGGCT 0.978029 -73 CTGGGTATCCCAATAGGGCGAAGCCCTATG 1 37 0 CAATAGGGCG 0.993434 -62 TACATTGTATCCATAGGGGAAACCCCCTAT 2 21 1 CCATAGGGGA 0.990847 -155 AGGTTCATCCCAATAGGGGGTTTCCCCTAT 2 33 0 CAATAGGGGG 0.997289 -143 GGGAGTATCCCAATAGAGGGGCGAAGCCCC 2 133 1 CAATAGAGGG 0.990631 -43 TGTATAAGACCCATAGAGGGGCTTCGCCCC 2 150 0 CCATAGAGGG 0.995454 -26 TTGACAAAGCATAGGAGGAGACCTCCTA 4 9 1 GCATAGGAGG 0.898931 -100 GGTGGTATAGCAATAGGAGGTCTCCTCCTA 4 22 0 CAATAGGAGG 0.978971 -87 AACTTGGAAACCATAGAGGGAAACCCTCTA 5 29 1 CCATAGAGGG 0.995454 -110 GGGTGTATCCCAATAGAGGGTTTCCCTCTA 5 42 0 CAATAGAGGG 0.990631 -97 ATTGGGATACCCAGAGCGGGGCTTCACTAC 7 42 0 CCAGAGCGGG 0.936371 -66 CTGGGTATCCCAATAGGGCGAAGCCCTATG 7 58 1 CAATAGGGCG 0.993434 -50 TTATTATACACCATAGGGCTTCGCCCTATT 7 69 0 CCATAGGGCT 0.978029 -39 TTAAAAGTTCCCATAGGTGATAAA 8 5 0 CCATAGGTGA 0.885944 -188 ********** Masking position 5 Map Score: 40.425 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 32 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 TATCCCAATAGGGCGAAGCCCTATGGTTTCT 1 31 0 GGGGAAGCCC 0.774762 -68 GCAATGCATCCTGGGTATCCCAATAGGGCGA 1 46 0 CTGGTATCCC 0.973911 -53 CATCCCAATAGGGGGTTTCCCCTATGGATAC 2 27 0 GGGGTTTCCC 0.981211 -149 GTAAGATTTGGGGAGTATCCCAATAGAGGGG 2 123 1 GGGGTATCCC 0.829797 -53 CCCAATAGAGGGGCGAAGCCCCTCTATGGGT 2 141 1 GGGGAAGCCC 0.774762 -35 TATCCCAATAGAGGGTTTCCCTCTATGGTTT 5 36 0 GAGGTTTCCC 0.971263 -103 GGAGGTGTTAGGGTGTATCCCAATAGAGGGT 5 51 0 GGGGTATCCC 0.985957 -88 GGGCTGAACGTAGTGAAGCCCCGCTCTGGGT 7 33 1 TAGGAAGCCC 0.910144 -75 AAGCCCCGCTCTGGGTATCCCAATAGGGCGA 7 48 1 CTGGTATCCC 0.973911 -60 TATCCCAATAGGGCGAAGCCCTATGGTGTAT 7 63 1 GGGGAAGCCC 0.774762 -45 *** ******* Masking position 9 Map Score: 29.1215 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 10 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CCGAGCGTAAGCGAGGAGGTGTTAGGTTTTGG 2 79 0 GCGGAGGTGT 0.99956 -97 CCTCGCTTACGCTCGGAGGTGTAAATTAGTAA 2 95 1 GCGGAGGTGT 0.99956 -81 TCCGAGCGAAGCGAGGAGGTGTTAGTTTTTGA 3 142 0 GCGGAGGTGT 0.99956 -60 TCCTCGCTTCGCTCGGAAGTGTAAATTTACAA 3 157 1 GCGGAAGTGT 0.997161 -45 CCGAGCGTAAGCGAGGAGGTGTTAGGGTGTAT 5 64 0 GCGGAGGTGT 0.99956 -75 CCTCGCTTACGCTCGGAGGTGTAAATTAATTT 5 80 1 GCGGAGGTGT 0.99956 -59 ** ******** Masking position 7 Map Score: 26.1262 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 0 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AATGAAAAGCTACATTGTATCCA 2 4 1 GAAAAGCTAC 0.962003 -172 AAGCTTTTACTAAAAGGTTCATCCCAATAG 2 47 0 TAAAAGGTTC 0.955908 -129 AACCTTTTAGTAAAAGCTTCACCAAAACCT 2 58 1 TAAAAGCTTC 0.983015 -118 CAACTTTTTCTAAAAGTTTCGTTTATAGTC 3 61 0 TAAAAGTTTC 0.97671 -141 TTAGATTGATTAAAAGTTCCCATAGGTGAT 8 14 0 TAAAAGTTCC 0.955908 -179 AAAATAAGACGAAAAGTTTATATATTAGAT 8 38 0 GAAAAGTTTA 0.750199 -155 GGGAAATATATAAAAGTTACCCACAAAAAA 8 64 0 TAAAAGTTAC 0.973612 -129 ACCAAAAAGCTAAAAGCTATTAAAAACATA 10 59 0 TAAAAGCTAT 0.853035 -85 ********** Masking position 5 Map Score: 8.79953 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 102 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 TAAGCGAGGAGGTGTTAGGTTTTGGTGAAGCTT 2 71 0 GGTGTTATTT 0.984263 -105 TACGCTCGGAGGTGTAAATTAGTAAGATTTGGG 2 102 1 GGTGTAATAT 0.984263 -74 GAAGCGAGGAGGTGTTAGTTTTTGATGAAATGG 3 134 0 GGTGTTATTT 0.984263 -68 TAAGCGAGGAGGTGTTAGGGTGTATCCCAATAG 5 56 0 GGTGTTAGTT 0.97254 -83 TACGCTCGGAGGTGTAAATTAATTTTGATTAAT 5 87 1 GGTGTAATAT 0.984263 -52 GAAAAAGTATGGTGAATATTTATGGAACTCGTT 6 11 1 GGTGAATTTT 0.868115 -25 GAAGCCCTATGGTGTATAATAATTCATTGCTGG 7 77 1 GGTGTATTAT 0.958151 -31 TGACAGATTAGGTTTAACAGTATATAAACATTA 10 97 0 GGTTTAAGTT 0.863845 -47 ******* ** * Masking position 3 Map Score: 7.08395 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 24 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CGAAGCCCTATGGTTTCTGAATAATTCTTTCATCATGG 1 11 0 TTCTATAATT 0.665224 -88 CTCTAAGAGTTTTCGTTCAACTTTTTCTAAAAGTTTCG 3 70 0 TTTCATTTTT 0.925906 -132 AGTTAGGGCTTTCAGCCCTAATTAATGTCCATTATTTA 4 61 1 TCCCATTATT 0.949056 -48 TTTATCTCACCTAATTTTATTAAATAATGGAC 4 87 0 TCCTATTTTA 0.700379 -22 TTTCCCTCTATGGTTTCCAAGTTTTTTCATTATTTCCC 5 14 0 TTCCATTTTC 0.913201 -125 CTTCACTACGTTCAGCCCCACTTTCTTTTATTTCCCTG 7 13 0 TCCCATTTTT 0.969322 -95 TATATAAACTTTTCGTCTTATTTTTTGTGGGTAACTTT 8 44 1 TTCTATTTTT 0.963668 -149 TGGCGGAATATGTTTTCCTAATTTATTTGGTAGATATC 8 144 1 TTCCATTTTT 0.980563 -49 TTCTATTTAACTTTCTCTAAAAGATTGG 9 1 1 TTTTATTTTT 0.867903 -52 CATTTTGATTTTTTGTCTAATTTAGTTTTACGCTTCAA 10 12 1 TTCTATTATT 0.939899 -132 AATTTAGTTTTACGCTTCAAATTAATATTTATGTTTTT 10 30 1 TTTCATTATT 0.880495 -114 * *** * *** * * Masking position 10 Map Score: 6.35988 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 389 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 ATCCATATCCTCACCCAGATTTTTATTTTA 3 17 0 TCACCCAGAT 0.981536 -185 AAGCATCACCCAGATTTTATCAGTT 3 187 0 TCACCCAGAT 0.981536 -15 TATTACCCACCTCAAATTTTTC 5 127 0 TTACCCACCT 0.949689 -12 CTTTCTTTTATTTCCCTGAT 7 1 0 TTTCCCTGAT 0.925241 -107 CCCTATTGGGATACCCAGAGCGGGGCTTCA 7 46 0 ATACCCAGAG 0.889594 -62 TATATAAAAGTTACCCACAAAAAATAAGAC 8 58 0 TTACCCACAA 0.946995 -135 CTTTTATATATTTCCCAGAGGATAATGTTA 8 78 1 TTTCCCAGAG 0.96555 -115 TAATTCATATTCTCCCTCCAATCTTTTAGA 9 26 0 TCTCCCTCCA 0.693528 -27 ********** Masking position 5 Map Score: 5.07921 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 54 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GCTTCTTTGCAGAAGCAATGCATCCTGGGT 1 61 0 AGAAGCAATG 0.959017 -38 GCTTCTGCAAAGAAGCAATGCCTCTTAAAA 1 75 1 AGAAGCAATG 0.959017 -24 ACCTCCGAGCGTAAGCGAGGAGGTGTTAGG 2 85 0 GTAAGCGAGG 0.987887 -91 CACTTCCGAGCGAAGCGAGGAGGTGTTAGT 3 148 0 CGAAGCGAGG 0.99008 -54 ACCTCCGAGCGTAAGCGAGGAGGTGTTAGG 5 70 0 GTAAGCGAGG 0.987887 -69 ********** Masking position 4 Map Score: 3.89174 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 6 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 CCATGATGAAAGAATTATTCAGA 1 4 1 TGATGAAAGA 0.942889 -95 AGGGGGAAATAATGAAAAAACTTGGAAAC 5 10 1 TAATGAAAAA 0.958851 -129 GGCGATAATATAATGATTGATTATGAAAAA 8 114 1 TAATGATTGA 0.863204 -79 TAATGATTGATTATGAAAAATGGCGGAATA 8 124 1 TTATGAAAAA 0.876194 -69 TCATTATCATTAATGACAGATTAGGTTTAA 10 113 0 TAATGACAGA 0.955553 -31 TCATTAATGATAATGATAAATTATTTG 10 127 1 TAATGATAAA 0.942085 -17 ********** Masking position 6 Map Score: 1.59814 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 183 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 AATGAAAAGCTACATTGTATCCAT 2 5 1 AAAAGCTACA 0.799619 -171 AAGCTTCACCAAAACCTAACACCTCCTCGC 2 71 1 AAAACCTAAC 0.893031 -105 AAATATTAAAATAAAAATCTGGGTGAG 3 8 1 AAAATAAAAA 0.768173 -194 CCATTTCATCAAAAACTAACACCTCCTCGC 3 134 1 AAAAACTAAC 0.75374 -68 TAATCAATCTAATATATAAACTTTTCGTCT 8 32 1 AATATATAAA 0.768169 -161 TCCTCTGGGAAATATATAAAAGTTACCCAC 8 70 0 AATATATAAA 0.768169 -123 AATTAGACAAAAAATCAAAATGG 10 4 0 AAAATCAAAA 0.866847 -140 AAAGCTATTAAAAACATAAATATTAATTTG 10 47 0 AAAACATAAA 0.896834 -97 TTAGCAACCAAAAAGCTAAAAGCTATTAAA 10 65 0 AAAAGCTAAA 0.944688 -79 ********** Masking position 4 Map Score: 1.7154 Number of sites scoring better than the average of aligned sites = 968 Number in coding regions = 787 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 11 ACCCCCTATTGGGATGAACCTTTTAGTAAA 2 42 1 GGGATGAACC 0.986899 -134 ACATTAATTAGGGCTGAAAGCCCTAACTTA 4 59 0 GGGCTGAAAG 0.970237 -50 ACCCTCTATTGGGATACACCCTAACACCTC 5 51 1 GGGATACACC 0.953033 -88 AAAGAAAGTGGGGCTGAACGTAGTGAAGCC 7 23 1 GGGCTGAACG 0.994155 -85 ACCCAGAGCGGGGCTTCACTACGTTCAGCC 7 34 0 GGGCTTCACT 0.944276 -74 ********** Masking position 5 Map Score: 1.05798 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 12 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 GCATTGCTTCTTTGCAGAAGCAATGCATCC 1 66 0 TTTGCAGAAG 0.78012 -33 GGATGAACCTTTTAGTAAAAGCTTCACCAA 2 53 1 TTTAGTAAAA 0.914687 -123 GGTGTTAGGTTTTGGTGAAGCTTTTACTAA 2 64 0 TTTGGTGAAG 0.93926 -112 AAACGAAACTTTTAGAAAAAGTTGAACGAA 3 67 1 TTTAGAAAAA 0.915559 -135 GGTGTTAGTTTTTGATGAAATGGAGAGCTA 3 127 0 TTTGATGAAA 0.868633 -75 ATGTCCATTATTTAATAAAATTAGGTGAGA 4 85 1 TTTAATAAAA 0.736601 -24 GATTAATTTGTTTGGAAAAATTTGAGGTGG 5 113 1 TTTGGAAAAA 0.945 -26 CCTCCAATCTTTTAGAGAAAGTTAAATAGA 9 12 0 TTTAGAGAAA 0.945 -41 ********** Masking position 8 Map Score: 4.42195 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 346 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 13 ********** No masking Map Score: -3.45081e-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: -3.45081e-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: -3.45081e-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