AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__mthe_reg_300.orf -o056_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 RTH00661 61 M.thermo #2 RTH01407 25 M.thermo #3 RTH01538 300 M.thermo #4 RTH01353 75 M.thermo #5 RTH00151 64 M.thermo #6 RTH00311 135 M.thermo #7 RTH01312 127 M.thermo #8 RTH02147 135 M.thermo #9 RTH02014 144 M.thermo #10 RTH00569 142 M.thermo Motif number 1 TGCCCCATGGACCACTTGCTGGAACCTTTATGAAC 3 244 1 ACCCTGGGAC 0.972522 -57 AGGCCGCAGGCCCTCAGGAGGGATCG 6 2 0 CCCCGGGGAC 0.992935 -134 CCCGGCCACATCCACCTGAGGGAACTTGCAGAGGC 6 98 1 TCCCTGGGAC 0.980651 -38 ACCCTCCTTAACAGCCTCTGCAAGTT 6 120 0 CCCCTTCAGC 0.898453 -16 ATCACCTCATGGCTGGAACTGGTCCCTA 7 4 1 ACCCTGTGGA 0.845572 -124 CATAACATCCCCCGCCGGTGCTGCATGGTGGACAT 8 17 0 CCCCGGCTGA 0.977954 -119 CCTTATGAGACCCACGGGTCCTGTCATCATAACAT 8 44 0 CCCCGGCTGC 0.993679 -92 AAGAATAGATTCCACTGGGAGGGTCAAATATGAGG 9 38 0 TCCCGGGGGC 0.994856 -107 GTCACTCCCCCATGTTGAGGAGGTATGTCTG 9 124 0 CCCCTGGAGA 0.967877 -21 CTTGATTCCCCGTGGTCTGGCATTTTATCTG 10 122 0 TCCCTGCTGC 0.982587 -21 *** * ** *** * Masking position 5 Map Score: 9.87045 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 567 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 TCCATGAAAAACATCATCAGTCATCTTGGG 1 13 0 ACATCATCAG 0.948367 -49 ACATATGGGGACATCAGAAGGTTAAAGAGG 3 197 1 ACATCAGAAG 0.948367 -104 TTTCTCGAAGTCATCATCTGTCAGGCCGCA 6 29 0 TCATCATCTG 0.957679 -107 AATGATGATTTCATCAGTAGGGACCAGTTC 7 26 0 TCATCAGTAG 0.923828 -102 ACTGATGAAATCATCATTTCCATGCAGTAA 7 38 1 TCATCATTTC 0.838077 -90 ACATATATGTACATCAAAGGGAATGGTTAA 7 102 1 ACATCAAAGG 0.785972 -26 ACGGGTCCTGTCATCATAACATCCCCCGCC 8 36 0 TCATCATAAC 0.906165 -100 AACAACACAAACATCAACTCACCCTATACT 8 86 0 ACATCAACTC 0.835341 -50 CATGGCACGGTCATCAGATGCATTGCAGCC 9 89 1 TCATCAGATG 0.957679 -56 ********** Masking position 6 Map Score: 6.22068 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 337 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 GATGATGTTTTTCATGGACCAGATAGAACA 1 25 1 TTCATGGACC 0.911135 -37 TATTAATCAAGTGAGGGACC 3 1 0 GTGAGGGACC 0.930967 -300 AAGACAGTTATCCAGTGAACATATGGGGAC 3 179 1 TCCAGTGAAC 0.648255 -122 CACAGACTGCCCCATGGACCACTTGCTGGA 3 237 1 CCCATGGACC 0.892837 -64 CATGGACCACTTGCTGGAACCTTTATGAAC 3 249 1 TTGCTGGAAC 0.868518 -52 GCAGGCCCTCAGGAGGGATCG 6 2 0 AGGAGGGATC 0.793867 -134 AGGTGGATGTGGCCGGGAACTATGTCAGTG 6 85 0 GGCCGGGAAC 0.975033 -51 CCACATCCACCTGAGGGAACTTGCAGAGGC 6 103 1 CTGAGGGAAC 0.918398 -33 ATCACCTCATGGCTGGAACTGGTCCCTAC 7 10 1 TGGCTGGAAC 0.939313 -118 TGATTTCATCAGTAGGGACCAGTTCCAGCC 7 21 0 AGTAGGGACC 0.756643 -107 GATATCTTACTGCATGGAAATGATGATTTC 7 44 0 TGCATGGAAA 0.657953 -84 AGCGTATGCGGGCATGGCACGGTCATCAGA 9 77 1 GGCATGGCAC 0.818673 -68 ATTACCTGGCACCCGGGAACCCGGGTTATA 10 24 1 ACCCGGGAAC 0.927576 -119 ********** Masking position 7 Map Score: 5.99944 Number of sites scoring better than the average of aligned sites = 1947 Number in coding regions = 1852 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 CGGGGCGTGATATTATTAATCAAGTGAGGGACC 3 9 0 TATTATACAT 0.843634 -292 AATAACTTATTAGTTTTCAGGAGCTCACCAAGTCT 3 52 0 TAGTTTAGAT 0.93284 -249 ATTTAAATCTTATTATCAAAGTATTTATAGGGCCG 3 94 1 TATTATAGTT 0.922683 -207 CCATAAATTTTATTTTAAATGAGCTGTTAATTAGA 4 49 1 TATTTTAGAT 0.981237 -27 TGAAAGTATATATTTTATAGGAAATATGTCATTAA 5 16 1 TATTTTAGAT 0.981237 -49 AATCTGTCATTATTATTAATGACATATTTCCTATA 5 31 0 TATTATAGAT 0.970237 -34 TGCAGTAAGATATCTTTAAAGAACTATTTAAAACT 7 60 1 TATCTTAGAT 0.967334 -68 TTATAAGTTATATCTTATAAGTTATAACCCGGGTT 10 41 0 TATCTTAGTT 0.915547 -102 ****** * ** * Masking position 9 Map Score: 4.73541 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 20 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TATGAACCCTTCAATTATTCTGCTAAAGGA 3 272 1 TCAATTATTC 0.839938 -29 CTTCTATCCTCCTTTAGCAGAA 3 289 0 TCTATCCTCC 0.973113 -12 CACCCTATACTCAATACTCCTTATGAGACC 8 67 0 TCAATACTCC 0.984051 -69 CACCCTGTACTCAATACTCCAGCAAAACAA 8 111 0 TCAATACTCC 0.984051 -25 CCCAGTGGAATCTATTCTTCAATAGCGTAT 9 54 1 TCTATTCTTC 0.950277 -91 ********** Masking position 5 Map Score: 2.48597 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTAAATATATAGTAATAACTTATTAGTTTTC 3 69 0 AGTAATACTT 0.952009 -232 ATTACTATATATTTAAATCTTATTATCAAAG 3 84 1 ATTTAAACTT 0.959248 -217 TTAAAGAACTATTTAAAACTTTACTGTACAT 7 75 1 ATTTAAACTT 0.959247 -53 CGGGAACCCGGGTTATAACTTATAAGATATA 10 37 1 GGTTATACTT 0.931193 -106 GTATGTTATAAGTTATATCTTATAAGTTATA 10 50 0 AGTTATACTT 0.973693 -93 GTGGGCTACAATTAAAAGCTTTTACACACAG 10 80 0 ATTAAAACTT 0.926556 -63 ******* *** Masking position 5 Map Score: 3.12265 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 13 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 TTGATTAATAATATCACGCCCCGTCTATAAAA 3 21 1 ATACACGCCC 0.961503 -280 AAGTCATCATCTGTCAGGCCGCAGGCCCTCAG 6 20 0 CTGCAGGCCC 0.98692 -116 TCCTGTCATCATAACATCCCCCGCCGGTGCTG 8 29 0 ATACATCCCC 0.943983 -107 GGATGTTATGATGACAGGACCCGTGGGTCTCA 8 42 1 ATGCAGGACC 0.969542 -94 CATCAGATGCATTGCAGCCCTCGACAGACATA 9 100 1 ATTCAGCCCC 0.990903 -45 AAAGCTTTTAATTGTAGCCCACAGAAATTTAA 10 89 1 ATTTAGCCCC 0.933903 -54 AGCAGATAAAATGCCAGACCACGGGGAATCAA 10 120 1 ATGCAGACCC 0.984062 -23 *** ****** * Masking position 6 Map Score: 3.82779 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 237 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 CCGTCTATAAAAGACTTGGTGAGCTCCTGAAA 3 41 1 AAGATGGTGA 0.910126 -260 AAGTATTTATAGGGCCGGGTGAAAATATAGAT 3 112 1 AGGGGGGTGA 0.99595 -189 TGTACATCAAAGGGAATGGTTAATAAACA 7 109 1 AGGGTGGTTA 0.927826 -19 AGGAGTATTGAGTATAGGGTGAGTTGATGTTT 8 76 1 AGTAGGGTGA 0.981429 -60 TGGAGTATTGAGTACAGGGTGATGGG 8 120 1 AGTAGGGTGA 0.981429 -16 CCTCCTCAACATGGGGGAGTGAC 9 132 1 ATGGGAGTGA 0.879377 -13 **** ****** Masking position 10 Map Score: 0.948186 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 262 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 ********** No masking Map Score: 3.38462e-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 10 ********** No masking Map Score: 3.38462e-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 11 ********** No masking Map Score: 3.38462e-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