AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_bsub_mtub_300.orf -o301_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yqhZ 263 similar to transcription termination #2 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #3 spoIIIAC 22 spoIIIAC #4 spoIIIAA 75 spoIIIAA #5 yqhV 144 alternate gene name: yqgE #6 efp 24 elongation factor P #7 yqhS 86 similar to 3-dehydroquinate dehydratase #8 yqhR 226 yqhR #9 pepQ 33 pepQ Motif number 1 TTCAAAGCATGAAGAAAGCCGGCTTACATAGCCG 1 73 1 GAAGAAAGGT 0.962382 -191 TCACGTTCATGAAGAAACTCGGCTATGTAAGCCG 1 92 0 GAAGAAACGT 0.833523 -172 GTAATAGGGTAAAAAAACCTTGATTTCAATATGC 1 164 1 AAAAAAACGT 0.940875 -100 ATGCGGATACGAAAAAAATATGTTATGATCTCTT 1 194 1 GAAAAAAAGT 0.948914 -70 GAATGAGGGAAAAAAGCCCGCTAAACAAGCGG 2 9 1 GAAAAAAGGT 0.990334 -147 TGACAGCAACGCAAAAAGCCCGCTTGTTTAGCGG 2 28 0 GCAAAAAGGT 0.928537 -128 AGTAACCTATAAAAAAAGAAATTTCATACATAGG 2 121 1 AAAAAAAGTT 0.931187 -35 CCAATCGGTAGAAAGGAGGAGGCTCTG 4 59 1 GAAAGGAGGT 0.956989 -17 AAAGGAAAAAAGAAGTCTGTTCCCAAATGGG 5 8 1 AAAAGAAGGT 0.978275 -137 TTTTGGGCACAAAAAAAGCCTGCTCCCATTTGGG 5 32 0 AAAAAAAGGT 0.987851 -113 ATTTCCGTATAAAAGAAAGATTCTGTTTTTGGGC 5 58 0 AAAAGAAATT 0.57671 -87 ATATCATATAAAAAAATGGGAGGTTGGGAGAGTG 5 119 1 AAAAAATGGT 0.966066 -26 TTTCTCATGTAAAAAATGTTCACTTCTCGTGAAC 7 40 0 AAAAAATGAT 0.652184 -47 ACAATAGAGTGAAAGGAAATGGTTAGCAATCCTA 8 33 0 GAAAGGAAGT 0.801342 -194 CGCAGCTGCCAAAAAGTGTGAGCTTTTTTATTGA 8 166 1 AAAAAGTGGT 0.917576 -61 AAGTGTGCCCAAAAAATGAAATGTCAATAAAAAA 8 189 0 AAAAAATGTT 0.82572 -38 ******** * * Masking position 3 Map Score: 19.7628 Number of sites scoring better than the average of aligned sites = 1834 Number in coding regions = 1425 Number in noncoding regions = 409 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 2 AAGCATGAAGAAAGCCGGCTTACATAGCCG 1 77 1 AAAGCCGGCT 0.994147 -187 GTTCATGAAGAAACTCGGCTATGTAAGCCG 1 92 0 AAACTCGGCT 0.970257 -172 ATGAGGGAAAAAAGCCCGCTAAACAAGCGG 2 13 1 AAAGCCCGCT 0.996932 -143 AGCAACGCAAAAAGCCCGCTTGTTTAGCGG 2 28 0 AAAGCCCGCT 0.996932 -128 GTTGAATTCACAAGTCCGCTCCTGTAAGAT 2 69 1 CAAGTCCGCT 0.97954 -87 GGCTTGTCATAAAGTCTGCCTCACATCATA 4 16 1 AAAGTCTGCC 0.979796 -60 GGGCACAAAAAAAGCCTGCTCCCATTTGGG 5 32 0 AAAGCCTGCT 0.993685 -113 ATTGTACAGGAAACACCGCTAAACCTCTAG 8 62 1 AAACACCGCT 0.949925 -165 ACCTCCAGTTAAAGTGTGCCCAAAAAATGA 8 204 0 AAAGTGTGCC 0.875719 -23 ********** Masking position 3 Map Score: 18.5574 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 278 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 GCTTAACACGAAACCAAGGGGAGGGCGGCCC 1 14 1 AAACCAAGGG 0.989778 -250 ACGTGTAAAAAAACCAAAGGGCCGCCCTCCC 1 32 0 AAACCAAGGG 0.989778 -232 TTCATGCTTTGAAATAAAGGGTAACGTGTAA 1 55 0 GAAATAAGGG 0.924169 -209 AAGGTGTGTGAAAATATTCGGTAATAGGGTA 1 144 1 AAAATATCGG 0.853793 -120 TTGTGGCTTAACGACAAGCGGATAAAGAGGA 1 227 1 ACGACAACGG 0.915416 -37 AAAAGCCCGCTAAACAAGCGGGCTTTTTGCG 2 22 1 TAAACAACGG 0.944392 -134 CATTTTAAAGAAGCCAATCGGTAGAAAGGAG 4 46 1 AAGCCAACGG 0.974496 -30 CATATCATATAAAAAAATGGGAGGTTGGGAG 5 118 1 AAAAAAAGGG 0.947807 -27 GTAAAATTTGAAAATAACGGGTATAATGCAT 8 134 0 AAAATAAGGG 0.978671 -93 ******* *** Masking position 6 Map Score: 9.22938 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 345 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 CACGAAACCAAGGGGAGGGCGGCCCTTTGG 1 20 1 AGGGGAGGGC 0.946861 -244 AGAGGATCAAAGGAGAAAGAAA 1 252 1 AGGAGAAAGA 0.810265 -12 TTCATCTTACAGGAGCGGACTTGTGAATTC 2 72 0 AGGAGCGGAC 0.981871 -84 ACGTGAGGGGAGCAAAAATAAA 3 8 1 GGGAGCAAAA 0.845405 -15 ATCGGTAGAAAGGAGGAGGCTCTG 4 62 1 AGGAGGAGGC 0.975697 -14 GCTCCCATTTGGGAACAGACTTCTTTTTTC 5 15 0 GGGAACAGAC 0.907297 -130 GTTCCCAAATGGGAGCAGGCTTTTTTTGTG 5 29 1 GGGAGCAGGC 0.995559 -116 ATGGGAGGTTGGGAGAGTGCT 5 134 1 GGGAGAGTGC 0.942732 -11 ********** Masking position 3 Map Score: 5.4401 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 863 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 CGAAACCAAGGGGAGGGCGGCCCTTTGGTT 1 22 1 GGGAGGGCGG 0.947064 -242 AGAGAGGCTTGTCATAAAGTC 4 2 1 GAGAGGCTTG 0.957904 -74 AATGTATGATGTGAGGCAGACTTTATGACA 4 20 0 GTGAGGCAGA 0.870874 -56 ATAAAAAAATGGGAGGTTGGGAGAGTGCT 5 126 1 GGGAGGTTGG 0.988154 -19 TAAAGAAATAGGCAGGTTGATAAT 8 5 0 GGCAGGTTGA 0.966829 -222 CCTGTCAATCTAGAGGTTTAGCGGTGTTTC 8 71 0 TAGAGGTTTA 0.608508 -156 CCTCTAGATTGACAGGCTGAAAAAATTGCC 8 85 1 GACAGGCTGA 0.966829 -142 ********** Masking position 4 Map Score: 1.33741 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 368 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 TTTTCACACACCTTAATATGATTATTCGGA 1 128 0 CCTTAATATG 0.847138 -136 TGAAAATATTCGGTAATAGGGTAAAAAAAC 1 152 1 CGGTAATAGG 0.96524 -112 GTGAATTCAACTCTAATATGACAGCAACGC 2 50 0 CTCTAATATG 0.950107 -106 AAGTCCGCTCCTGTAAGATGAACATAGTAT 2 80 1 CTGTAAGATG 0.942098 -76 CGATTGGCTTCTTTAAAATGTATGATGTGA 4 36 0 CTTTAAAATG 0.924768 -40 TTTTATCATACTGGAAAAGGATTATACA 7 9 0 CTGGAAAAGG 0.957517 -78 GAGAAACCCTCGCGAAAAGGAGAGATTGT 7 68 1 CGCGAAAAGG 0.927685 -19 ********** Masking position 5 Map Score: 1.26523 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 247 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CGCTTGTTTAGCGGGCTTTTTTCCCTCATT 2 12 0 GCGGGCTTTT 0.983669 -144 CGCTAAACAAGCGGGCTTTTTGCGTTGCTG 2 29 1 GCGGGCTTTT 0.983669 -127 TGAACATAGTATGTACTTTTAGTAGTAACC 2 98 1 ATGTACTTTT 0.723803 -58 TTCACTTCTCGTGAACATTTTATCATACTG 7 26 0 GTGAACATTT 0.958229 -61 TTCACGAGAAGTGAACATTTTTTACATGAG 7 41 1 GTGAACATTT 0.958229 -46 GCCAAAAAGTGTGAGCTTTTTTATTGACAT 8 173 1 GTGAGCTTTT 0.985357 -54 ********** Masking position 8 Map Score: 4.97077 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 158 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 ********** No masking Map Score: -8.50219e-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 9 ********** No masking Map Score: -8.50219e-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: -8.50219e-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