AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i212_translation_transcription_mthe_reg_300.orf -o212_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 RTH00775 222 M.thermo #2 RTH01794 51 M.thermo #3 RTH00390 52 M.thermo #4 RTH01426 28 M.thermo #5 RTH00392 20 M.thermo #6 RTH01100 231 M.thermo #7 RTH00041 184 M.thermo Motif number 1 TGATTTTTTAGTGGAACACGGGTGCATTCCT 3 18 0 GTGGAAACGG 0.963897 -35 ATGCCTGCAGGAGGAGTCTGGT 4 17 1 GAGGAGCTGG 0.976074 -12 GTGGACAGATGTGCAGTATGGTTTTGTAGTA 6 91 1 GTGCAGATGG 0.983279 -141 TTACCTTACAGTGATCTATGGTTAGATCTGA 6 181 0 GTGATCATGG 0.922153 -51 TTACCTTGAAGAGGTGAATGG 6 221 1 GAGGTGATGG 0.993164 -11 ATAATTAAGAGTGGTGGATGGGCTGTGCCAT 7 63 1 GTGGTGATGG 0.997014 -122 AGGTCACAGGGTGGTGGGCGGCAGATCCTTT 7 98 1 GTGGTGGCGG 0.987976 -87 ****** **** Masking position 3 Map Score: 7.87547 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 208 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 TAGGAGAGCAATCTAACCATTTTAAAGCCT 1 16 0 ATCTAACCAT 0.984324 -207 ATCTAATCACCTCGTAAGTG 1 213 0 ATCTAATCAC 0.890292 -10 TGACCCCAATATCTAGCTATATAGGATAAG 2 22 1 ATCTAGCTAT 0.972271 -30 ATGCCTCCGAATCTTACTACAAAACCATAC 6 106 0 ATCTTACTAC 0.93846 -126 ATATAATCAGATCTAACCATAGATCACTGT 6 175 1 ATCTAACCAT 0.984324 -57 ATGATTGAGGATCTTAATATAGGTCCTCAA 7 127 0 ATCTTAATAT 0.872046 -58 TGAATTCATTATCTAGATATGATTGAGGAT 7 145 0 ATCTAGATAT 0.922074 -40 ********** Masking position 9 Map Score: 7.08462 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TACCTGATCTTCAGAGAATAGGAGAGCAATCT 1 32 0 TCAGGAATGG 0.862839 -191 TCTCTGAAGATCAGGTACTCTGCAATGAAACT 1 47 1 TCAGTACTTG 0.919618 -176 TGTTGATCCATCAGTTTCATTGCAGAGTACCT 1 59 0 TCAGTTCATG 0.882578 -164 CCAGGTGGTGTCACATACAAAGGTATAAATAG 1 121 1 TCACTACAAG 0.923159 -102 GCTTACTTTTTCACTTACGAGGTGATTAGAT 1 202 1 TCACTACGGG 0.975655 -21 TCACTTAAGGGGTAATTCTA 5 1 1 TCACTAAGGG 0.927421 -20 AGATACCACACCAGATAAAGGG 6 1 0 CCAGTAAAGG 0.856827 -231 TGCGGCTGGCTCTCATGCATGGTAATCAGAGG 6 48 1 TCTCTGCAGG 0.942526 -184 TGCATGGTAATCAGAGGCATGGTAATCAGTGG 6 63 1 TCAGGGCAGG 0.988645 -169 GTAGTAAGATTCGGAGGCATGGAGTAATCGAT 6 116 1 TCGGGGCAGG 0.947802 -116 GGTTTCACCTGCAGTGATGGATAATC 7 5 1 TCACTGCATG 0.970491 -180 **** **** ** Masking position 2 Map Score: 8.52686 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 1007 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 ATTGATGAGGAATGCACCCGTGTTCC 3 7 1 GAGGAATGCA 0.972825 -46 AAATAGATGCCTGCAGGAGGAGTCT 4 6 1 GATGCCTGCA 0.974061 -23 GGCTGGCTCTCATGCATGGTAATCAGAGGC 6 51 1 CATGCATGGT 0.926584 -181 ATGGTAATCAGAGGCATGGTAATCAGTGGA 6 66 1 GAGGCATGGT 0.992001 -166 GTAAGATTCGGAGGCATGGAGTAATCGATC 6 119 1 GAGGCATGGA 0.995697 -113 ATCTGTGAACGTCGCATGCAAAAGCATATA 6 146 1 GTCGCATGCA 0.955149 -86 ********** Masking position 7 Map Score: 4.71597 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 159 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GATCAACACGGATTAGCAGTTTAAGGTTCA 1 83 1 GATTAGCAGT 0.948386 -140 TAGATATTGGGGTCATGATTTATATA 2 7 0 GGTCATGATT 0.77543 -45 AGCTATATAGGATAAGGAGGACGAAA 2 36 1 GATAAGGAGG 0.932909 -16 ATTGATGAGGAATGCACCCGTGT 3 4 1 GATGAGGAAT 0.870497 -49 TCTCATGCATGGTAATCAGAGGCATGGTAA 6 58 1 GGTAATCAGA 0.784021 -174 TCAGAGGCATGGTAATCAGTGGACAGATGT 6 73 1 GGTAATCAGT 0.962684 -159 TCAGTGGACAGATGTGCAGTATGGTTTTGT 6 88 1 GATGTGCAGT 0.799972 -144 TTTGTAGTAAGATTCGGAGGCATGGAGTAA 6 113 1 GATTCGGAGG 0.661447 -119 ATCACTGTAAGGTAAGCATTGTTTTTACCT 6 197 1 GGTAAGCATT 0.931188 -35 TGCAGTGATGGATAATCATTAACTATTGTT 7 20 1 GATAATCATT 0.911258 -165 CCTATATTAAGATCCTCAATCATATCTAGA 7 134 1 GATCCTCAAT 0.690669 -51 ATCATATCTAGATAATGAATTCAATTTTCA 7 152 1 GATAATGAAT 0.881218 -33 ********** Masking position 8 Map Score: 5.05595 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 495 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GATATGCTGCAGAATGATTTTT 3 41 0 TATGCTGCAG 0.974603 -12 GATAGGCCAGTGTGCGGCTGGCTCTCATGC 6 36 1 TGTGCGGCTG 0.993848 -196 CACAGGGTGGTGGGCGGCAGATCCTTTGAG 7 102 1 TGGGCGGCAG 0.995795 -83 ********** Masking position 1 Map Score: 0.0686756 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: -1.79524e-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 8 ********** No masking Map Score: -1.79524e-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 9 ********** No masking Map Score: -1.79524e-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