AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_mthe_reg_300.orf -o225_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 RTH02127 159 M.thermo #2 RTH01004 66 M.thermo #3 RTH01932 194 M.thermo Motif number 1 AGTTTATCTCCATGAAACTTTATAAAGTATTCTG 1 10 1 CCTGAACTAA 0.995157 -150 GCAGATGTAACCCTGCAGCTACAGAAACATCACTC 1 52 1 CCTGAGCTAA 0.995986 -108 AAGATTGTAACCCTGTAGCTACAGAAACATCAGTC 1 87 1 CCTGAGCTAA 0.995986 -73 TTTTTATGATCCGGTGAACTTCAGAGTATATTATT 2 23 0 CCGTAACTAA 0.985442 -44 CGGTCCATGGACCGGAAACTCCACCCTCGAGGCAG 3 112 1 ACGGAACTAC 0.908289 -83 TCGAGGCAGTCATGGCAGCTATTAAGGTTGATCAG 3 138 1 CAGGAGCTTA 0.944355 -57 ACTTATATCTCACTTCAACTTGAAATATAAGG 3 173 1 CATTAACTAA 0.938619 -22 ** ** **** * * Masking position 7 Map Score: 6.42119 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 268 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 2 AGCTACAGAAACATCACTCAAGATTGTAAC 1 68 1 ACATCACTCA 0.995483 -92 AGCTACAGAAACATCAGTCAAGATAAATTC 1 103 1 ACATCAGTCA 0.987995 -57 TACGGACTTCACATTTATCACGGAATTCAA 1 140 1 ACATTTATCA 0.945039 -20 TAAATATTGAACATCTCACATTTATTAGTG 3 33 1 ACATCTCACA 0.979078 -162 GACAGCCATGACAGTACTCATCCGTGGTTT 3 78 0 ACAGTACTCA 0.977635 -117 ********** Masking position 3 Map Score: 5.28093 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 98 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 ACAGAAACATCACTCAAGATTGTAACCCTG 1 72 1 CACTCAAGAT 0.98026 -88 ACAGAAACATCAGTCAAGATAAATTCCACA 1 107 1 CAGTCAAGAT 0.992546 -53 ACCGCCGGGACAGCCATGACAGTACTCATC 3 86 0 CAGCCATGAC 0.991791 -109 ACCCTCGAGGCAGTCATGGCAGCTATTAAG 3 134 1 CAGTCATGGC 0.991791 -61 ********** Masking position 6 Map Score: 3.15834 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 35 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 CTACTGCAGATGTAACCCTGCAGCTACAGA 1 47 1 TGTAACCCTG 0.997138 -113 CACTCAAGATTGTAACCCTGTAGCTACAGA 1 82 1 TGTAACCCTG 0.997138 -78 AGATTGGTAGATTGACCCTGA 3 2 0 ATTGACCCTG 0.983842 -193 ********** Masking position 5 Map Score: 2.72871 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TAAAGTTTCATGGAGATAAACT 1 3 0 TGGAGATAAA 0.970165 -157 TCTGCACTACTGCAGATGTAACCCTGCAGC 1 41 1 TGCAGATGTA 0.956114 -119 ACTAATAAATGTGAGATGTTCAATATTTAA 3 32 0 GTGAGATGTT 0.925473 -163 TTATTAGTGTTGGAAATGAAATTAAAACCA 3 54 1 TGGAAATGAA 0.9452 -141 TCAAGTTGAAGTGAGATATAAGTCTGATCA 3 166 0 GTGAGATATA 0.969707 -29 TCACTTCAACTTGAAATATAAGG 3 182 1 TTGAAATATA 0.928798 -13 ********** Masking position 6 Map Score: 2.77616 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 394 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 TTGAGTGATGTTTCTGTAGCTGCAGGGTTA 1 59 0 TTTCTGTAGC 0.99677 -101 TTGACTGATGTTTCTGTAGCTACAGGGTTA 1 94 0 TTTCTGTAGC 0.99677 -66 ********** Masking position 5 Map Score: 1.33838 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 CTTAATGGTTATTCCTCCCTTTTTATGATC 2 47 0 ATTCCTCCCT 0.99268 -20 CCATGACAGTACTCATCCGTGGTTTTAATT 3 73 0 ACTCATCCGT 0.985181 -122 TGGACCGGAAACTCCACCCTCGAGGCAGTC 3 119 1 ACTCCACCCT 0.995253 -76 ********** Masking position 1 Map Score: 0.677549 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 43 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TGATAAATGTGAAGTCCGTAAGTTGTGGAAT 1 129 0 GAATCCGTAA 0.969658 -31 TTGAATTCCGTGATAAATGTGAA 1 147 0 GAATCCGTGA 0.992185 -13 CCGGTCCATGGACCGCCGGGACAGCCATGAC 3 96 0 GACGCCGGGA 0.995938 -99 TAGCTGCCATGACTGCCTCGAGGGTGGAGTT 3 128 0 GACGCCTCGA 0.984678 -67 *** ******* Masking position 2 Map Score: 0.207248 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 95 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: -8.57325e-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 10 ********** No masking Map Score: -8.57325e-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 11 ********** No masking Map Score: -8.57325e-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