AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i343_bsub_mtub_100.orf -o343_bsub_mtub_100.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 gbsA 198 glycine betaine aldehyde dehydrogenase #2 ywiA 133 similar to hypothetical proteins #3 Rv0692 164 hypothetical protein Rv0692 Motif number 1 ACTGACCCTCTTTTCCTTTAGAAA 1 1 1 ACACCCTTTT 0.969758 -198 TTTCTTTTTGACTTTTCCTCATGTTTCGTTAAGA 1 70 0 ACTCCCATGT 0.958039 -129 TTAAACTGTCAAAGTCCCATTTTGATTTTTCTTT 1 97 0 AATCCTTTTG 0.978718 -102 TTTGACAGTTTAAAAACCATATGTTAGATTAAGG 1 118 1 TAACCTATGT 0.632156 -81 TAGTAGAATGACTATGCCCTTTTGGGAGATCC 2 9 0 ACTCCTTTTG 0.990805 -125 TAGTCATTCTACTATGCCCTTTTTAAGTAAATTA 2 29 1 ACTCCTTTTT 0.99004 -105 CTTTTTAAGTAAATTACAATTTTTAACTAAAATC 2 47 1 AATCATTTTT 0.787507 -87 TTTTAACTAAAATCTACCTCTTGGATATACATAC 2 67 1 AATCCCTTGG 0.958871 -67 GGATATACATACACAACCGTTTTTCATTTGAATC 2 89 1 ACACCTTTTT 0.97806 -45 ATTTCGGCACTCGATGCCATATTGTGTCCAGATC 3 26 1 TCTCCTATTG 0.931338 -139 ** * ** ***** Masking position 12 Map Score: 9.65411 Number of sites scoring better than the average of aligned sites = 1230 Number in coding regions = 1029 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 2 ATAAGCCTCCTTGACGTAAATAAAGT 1 183 0 CTCCTTGACG 0.953279 -16 CATTTCGGCACTCGATGCCATATTGTGTCC 3 25 1 CTCGATGCCA 0.961944 -140 AGATCGACGGATCGCTGTCGAGACCTGCTG 3 55 1 ATCGCTGTCG 0.984584 -110 CGGTGTCGGTATCGGTTTCGTAGTCCATCT 3 99 0 ATCGGTTTCG 0.963618 -66 CGGTGACAAGCTCGGTGTCGGTATCGGTTT 3 111 0 CTCGGTGTCG 0.99803 -54 CAACCAGGGTCTCGGTGACAAGCTCGGTGT 3 123 0 CTCGGTGACA 0.9917 -42 ********** Masking position 6 Map Score: 6.48781 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 280 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 CCTCTTTTCCTTTAGAAAATTAAATTCGTTA 1 17 1 TTTAGAAATT 0.766638 -182 AAGAAATAACTTAACGAATTTAATTTTCTAA 1 28 0 TTAACAATTT 0.9328 -171 TTTCGTTAAGATAAAGAACATAAAGAAATAA 1 50 0 ATAAAAACAT 0.732213 -149 CTTTGACAGTTTAAAAACCATATGTTAGATT 1 117 1 TTAAAACCAT 0.896266 -82 TTTAATGTTTTTAACAACCTTAATCTAACAT 1 138 0 TTAACACCTT 0.976202 -61 AAATTTTTATTTAACAAACTTTATTTACGTC 1 166 1 TTAACAACTT 0.986383 -33 TATGCCCTTTTTAAGTAAATTACAATTTTTA 2 41 1 TTAAGAAATT 0.948272 -93 ATTACAATTTTTAACTAAAATCTACCTCTTG 2 59 1 TTAACAAAAT 0.956261 -75 ***** ***** Masking position 7 Map Score: 4.48669 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 213 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 TAGTAGAATGACTATGCCCTTTTGGGAGAT 2 13 0 ACTATGCCCT 0.996702 -121 TAGTCATTCTACTATGCCCTTTTTAAGTAA 2 29 1 ACTATGCCCT 0.996702 -105 AATACCATCCCCTATACATATGA 2 121 0 ACCATCCCCT 0.989558 -13 ATTTCGGCACTCGATGCCATATTGTGTCCA 3 26 1 TCGATGCCAT 0.961986 -139 ********** Masking position 5 Map Score: 4.36548 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 29 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GGATCTCCCAAAAGGGCATAGTCATTC 2 8 1 CCAAAAGGGC 0.928387 -126 ATTCGCCCTTCCATTTCGGCACTCGATGCC 3 14 1 CCATTTCGGC 0.964588 -151 CATATTGTGTCCAGATCGACGGATCGCTGT 3 43 1 CCAGATCGAC 0.993644 -122 GGATCGCTGTCGAGACCTGCTGGCGAAAGG 3 63 1 CGAGACCTGC 0.955893 -102 GAAAGGCAATCCAGATGGACTACGAAACCG 3 87 1 CCAGATGGAC 0.988057 -78 ACTACGAAACCGATACCGACACCGAGCTTG 3 105 1 CGATACCGAC 0.975403 -60 ********** Masking position 3 Map Score: 3.80413 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 511 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 AAATTAAATTCGTTAAGTTATTTCTTTATG 1 33 1 CGTTAAGTTA 0.928327 -166 AGATAAAGAACATAAAGAAATAACTTAACG 1 43 0 CATAAAGAAA 0.974895 -156 CCTCATGTTTCGTTAAGATAAAGAACATAA 1 58 0 CGTTAAGATA 0.977071 -141 GAGGAAAAGTCAAAAAGAAAAATCAAAATG 1 84 1 CAAAAAGAAA 0.921893 -115 GCCTCCTTGACGTAAATAAAGTTTGTTAAA 1 175 0 CGTAAATAAA 0.943713 -24 ********** Masking position 5 Map Score: 1.89482 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 357 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ********** No masking Map Score: -6.86222e-14 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: -6.86222e-14 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: -6.86222e-14 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