AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i322_mixed7_mthe_reg_300.orf -o322_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 RTH00954 31 M.thermo #2 RTH00250 30 M.thermo #3 RTH00057 21 M.thermo #4 RTH01659 205 M.thermo #5 RTH01211 72 M.thermo #6 RTH00503 300 M.thermo Motif number 1 GAGGGGTCCCGATCCATTTGA 3 2 0 GGCCCTCCTG 0.996916 -20 CGAAATGGAGGTCAACCTCCTCCCCCTGGAGGAGGCCA 5 25 0 GTCCTTCCTG 0.986491 -48 AAGGAACTGGGAGGCCCTCCCGAAATGGAGGTCAACC 5 46 0 GGCCCCCGTG 0.999358 -27 CATCTCAATGGTTCTCATGGCCCTCCTGTGGGGCGTTA 6 15 0 GTCATCCCTG 0.972006 -286 GAGACGTCTCGGGCACCTTGCCGTTGTGGTGGATGTGA 6 66 0 GGCCTCCGTG 0.999225 -235 TATTGAGGGGGGTTCTCTATCCGGTATGTGCTTTACTC 6 209 0 GGTCTCCGTG 0.994054 -92 GGTCTCCCTCCCGGTGTGCAGCAGGTGA 6 283 0 GGCCCCCGTG 0.999358 -18 ** *** *** ** Masking position 17 Map Score: 13.1997 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 79 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 TCAAATGGATCGGGACCCCTC 3 11 1 CGGGACCCCC 0.991714 -11 TGTTCATATTCATGACCACACAGCACCCCAA 4 25 1 CATGACCACC 0.968214 -181 GAGGATAGCACTGGCCTCCTCCAGGGGGAGG 5 14 1 CTGGCCTCCC 0.76392 -59 AAGGAACTGGGAGGCCCTCCCGAAATGGAGG 5 52 0 GAGGCCCTCC 0.938626 -21 CTGATAACGCCCCACAGGAGGGC 6 3 1 GATAACGCCC 0.831461 -298 GATGATTAAACATGACCTCACATCCACCACA 6 49 1 CATGACCTCC 0.990117 -252 GCAAGGTGCCCGAGACGTCTCCATATACTGT 6 83 1 CGAGACGTCC 0.887979 -218 CTTTACTTCTCAGGCGCTCTCTATCTCTTTT 6 179 0 CAGGCGCTCC 0.954539 -122 ATACCGGATAGAGAACCCCCCTCAATAACTC 6 220 1 GAGAACCCCC 0.917022 -81 ********* * Masking position 9 Map Score: 8.10018 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 920 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 TGTGTGGTCATGAATATGAACAGCCAGTTAT 4 16 0 TAATATGAAC 0.96351 -190 GTTAACCAGTTAAATATGAATTTTTTGAATT 4 137 1 TAATATGAAT 0.838696 -69 ACAGCTGGATTTAACATAAATTCAAAAAATT 4 155 0 TAACATAAAT 0.838696 -51 ATCTCAATGGTTCTCATGGCCCTCCTGTGGG 6 21 0 TCTCATGGCC 0.839822 -280 TTGAGATGATTAAACATGACCTCACATCCAC 6 45 1 TAACATGACC 0.975236 -256 GTGGAGTGGATTATTATGCACAGTCTGAGGA 6 120 0 TATTATGCAC 0.886921 -181 TTAAATAATCTCCACATGAACATGGTAGTGG 6 147 0 TCACATGAAC 0.985175 -154 AAACTTAAGATGCACATACACTGAGTTATTG 6 242 0 TCACATACAC 0.924999 -59 CAGGTGATATTGATCATAAACTTAAGATGCA 6 259 0 TATCATAAAC 0.932665 -42 * ********* Masking position 6 Map Score: 6.08116 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 440 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GAGGGGTCCCGATCCATTTGA 3 7 0 GGTCCGATCC 0.993066 -15 CCGAAATGGAGGTCAACCTCCTCCCCCTGGA 5 33 0 GGTCACCTCC 0.991378 -40 AAGGAACTGGGAGGCCCTCCCGAAATGGAG 5 53 0 GGAGCCCTCC 0.55359 -20 ATTGAGGGGGGTTCTCTATCCGGTATGTGCT 6 215 0 GTTCCTATCC 0.954328 -86 GGTCTCCCTCCCGGTGTGCAG 6 290 0 GGTCCCCTCC 0.998187 -11 **** ****** Masking position 9 Map Score: 4.8104 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 175 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TAGGATAAGGGAGTATTTAAATCTTGACAT 4 62 0 GAGTATTTAA 0.771488 -144 TCCTATTATAGAGTATTCCATACTGGCGGT 4 87 1 GAGTATTCCA 0.971217 -119 GATGAGGATAGCACTGGCCTCCT 5 4 1 GAGGATAGCA 0.987023 -69 CCTCCCCCTGGAGGAGGCCAGTGCTATCCT 5 15 0 GAGGAGGCCA 0.963195 -58 TGCACAGTCTGAGGAAATCAAACAGTATAT 6 105 0 GAGGAAATCA 0.971684 -196 GAGAAGTAAAGAGTAAAGCACATACCGGAT 6 199 1 GAGTAAAGCA 0.971229 -102 ********** Masking position 5 Map Score: 2.38725 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 490 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 CCCGCATAACTGGCTGTTCATATTCATG 4 8 1 AACTGGCGTT 0.855131 -198 TTAAATCTTGACATGGTGGTTTGGGGTGCTG 4 45 0 ACATGGTGTT 0.974659 -161 GAGTATTCCATACTGGCGGTGTATGTAACTC 4 97 1 TACTGGCGTG 0.964845 -109 CGTCTCGGGCACCTTGCCGTTGTGGTGGATG 6 69 0 ACCTTGCGTT 0.97336 -232 CTCCACATGAACATGGTAGTGGAGTGGATTA 6 138 0 ACATGGTGTG 0.976476 -163 ******* *** Masking position 4 Map Score: 1.31272 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 258 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 7 AGATCATAAATCTAGGAAGGTGGGTT 2 7 1 TAAATCTAGG 0.982115 -24 AGGGAGTATTTAAATCTTGACATGGTGGTT 4 55 0 TAAATCTTGA 0.952478 -151 TATGTAACTCTAAATCATGGTTAACCAGTT 4 118 1 TAAATCATGG 0.968888 -88 GAATTTATGTTAAATCCAGCTGTTTTTACG 4 163 1 TAAATCCAGC 0.961658 -43 ********** Masking position 5 Map Score: 0.566027 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ATGACCACACAGCACCCCAAACCACCATGT 4 36 1 AGCACCCCAA 0.968329 -170 TAGAGTTACATACACCGCCAGTATGGAATA 4 100 0 TACACCGCCA 0.895789 -106 CTTAATCTTTAACACCGTAAAAACAGCTGG 4 178 0 AACACCGTAA 0.946273 -28 TATATCACCTTAATCTTTAACAC 4 193 0 ATCACCTTAA 0.942247 -13 GTCATGTTTAATCATCTCAATGGTTCTCAT 6 35 0 ATCATCTCAA 0.901886 -266 TGACCTCACATCCACCACAACGGCAAGGTG 6 61 1 TCCACCACAA 0.895926 -240 TCAGTGTATGTGCATCTTAAGTTTATGATC 6 249 1 TGCATCTTAA 0.840939 -52 ********** Masking position 4 Map Score: 0.390273 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 407 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ********** No masking Map Score: -1.39734e-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: -1.39734e-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: -1.39734e-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