AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i335_2_7_7_40_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ctsR 300 transcriptional regulator #2 sms 91 DNA repair protein homolog #3 yacL 115 similar to hypothetical proteins Motif number 1 ACAGGGGGAAACCCCCGACTACCATCGGCG 1 20 0 ACCCCCGACT 0.976799 -281 AAGCAAGCTTAAACCCAGCTCAATGAGCTG 1 67 1 AAACCCAGCT 0.991881 -234 AAAATACAAAAAACCCAGCTCATTGAGCTG 1 82 0 AAACCCAGCT 0.991881 -219 TGATACCAATAAACCAAAATACAAAAAACC 1 97 0 AAACCAAAAT 0.854605 -204 TCAACCCCCTCCTTTACTGACTT 1 288 0 ACCCCCTCCT 0.984621 -13 GAATAAACAAAAACCAACATTAATATACCC 3 35 0 AAACCAACAT 0.929793 -81 ACCCCCACCTCCTTTTTTAA 3 106 0 ACCCCCACCT 0.996161 -10 ********** Masking position 1 Map Score: 8.77697 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 165 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 CAAAGTCAGTAAAGGAGGGGGTTGA 1 286 1 AAAGGAGGGG 0.995937 -15 TAGAAGACGGAAATGAGGCATACAGCATGT 2 13 1 AAATGAGGCA 0.979708 -79 CTTGATATGAAAGTGAGGCATACACTTACA 2 40 0 AAGTGAGGCA 0.981174 -52 GAAATAGAACAAGGGAGAGGTCTTACACTA 2 69 1 AAGGGAGAGG 0.980658 -23 AAATGTTAAAAAAGGAGGTGGGGGT 3 101 1 AAAGGAGGTG 0.988994 -15 ********** Masking position 6 Map Score: 5.22699 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 105 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 CAATAAACCAAAATACAAAAAACCCAGCTCAT 1 89 0 AAAACAAAAA 0.632112 -212 AGTTAAGTGGAATTTTATGATACCAATAAACC 1 112 0 AATTTAGATA 0.921582 -189 AATTCGGTATAAAGTTATTATATTATACAGTT 1 140 0 AAATTATATA 0.884486 -161 ATTTGACTTTAATCTTACTATAAGCCGTTTCT 1 249 0 AATTTATATA 0.935469 -52 AAATATAGTCAAAGTCAGTAAAGGAGGGGGTT 1 277 1 AAATCATAAA 0.924307 -24 GCCTCACTTTCATATCAAGAAATAGAACAAGG 2 51 1 CATTCAGAAA 0.800912 -41 AACAAAAACCAACATTAATATACCCGTATTCA 3 28 0 AACTTATATA 0.817507 -88 GCATCCTACGAATATCAGAATAAACAAAAACC 3 50 0 AATTCAAATA 0.958796 -66 TTAACATTTTAATTTCACAAAGTCTTATGCAT 3 78 0 AATTCAAAAG 0.829195 -38 GTGAAATTAAAATGTTAAAAAAGGAGGTGGGG 3 92 1 AATTTAAAAA 0.935854 -24 *** *** **** Masking position 7 Map Score: 4.071 Number of sites scoring better than the average of aligned sites = 912 Number in coding regions = 705 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 4 AGCTGGGTTTAAGCTTGCTTGGCGGCGTCC 1 57 0 AAGCTTGCTT 0.847562 -244 CCAGCTCATTGAGCTGGGTTTAAGCTTGCT 1 68 0 GAGCTGGGTT 0.996093 -233 CCAGCTCAATGAGCTGGGTTTTTTGTATTT 1 81 1 GAGCTGGGTT 0.996093 -220 CGGGTATATTAATGTTGGTTTTTGTTTATT 3 34 1 AATGTTGGTT 0.880539 -82 GTTAAAAAAGGAGGTGGGGGT 3 105 1 GAGGTGGGGG 0.975393 -11 ********** Masking position 5 Map Score: 2.47951 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 176 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CTGATTGCTGATTTAAAATTCGGTATAAAGT 1 157 0 ATTTAAAATC 0.668698 -144 ATCCTTCATTATTTCCATTTTCCCGGTCCAC 1 193 0 ATTTCCATTT 0.959238 -108 TTTCTCGAGAATTTTCAACTTTCTCGCTCTA 1 223 0 ATTTTCAATT 0.916997 -78 ACTATATTTGACTTTAATCTTACTATAAGCC 1 255 0 ACTTTAATTT 0.936233 -46 TGTATGCCTCATTTCCGTCTTCTATA 2 6 0 ATTTCCGTTT 0.846116 -86 TGAGGCATACACTTACATGCTGTATGCCTCA 2 26 0 ACTTACATCT 0.745677 -66 TGTATGCCTCACTTTCATATCAAGAAATAGA 2 46 1 ACTTTCATTC 0.959666 -46 GAATACGGGTATATTAATGTTGGTTTTTGTT 3 29 1 ATATTAATTT 0.73726 -87 CTTTTTTAACATTTTAATTTCACAAAGTCTT 3 84 0 ATTTTAATTC 0.936234 -32 ******** ** Masking position 4 Map Score: 2.54634 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 767 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 6 TCCCCCTGTGAGAGTAGGACGCCGCCAAGC 1 41 1 AGAGTAGGAC 0.941811 -260 CTTTAATCTTACTATAAGCCGTTTCTCGAG 1 245 0 ACTATAAGCC 0.949428 -56 ACACTTACATGCTGTATGCCTCATTTCCGT 2 19 0 GCTGTATGCC 0.977598 -73 ACAGCATGTAAGTGTATGCCTCACTTTCAT 2 34 1 AGTGTATGCC 0.992885 -58 ATATAGTGTAAGACCTCTCCCTTG 2 78 0 AGTGTAAGAC 0.98446 -14 ********** Masking position 5 Map Score: 2.73484 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 145 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ********** No masking Map Score: 2.58227e-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 8 ********** No masking Map Score: 2.58227e-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: 2.58227e-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