AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i348_bsub_mtub_100.orf -o348_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	yviE	46	yviE
#2	flgM	80	anti-sigma factor repressor of sigma-D-dependent transcription
#3	yvyF	73	alternate gene name: yviB; similar to flagellar protein
#4	comFB	59	late competence gene
#5	comFA	105	late competence protein

Motif number 1

TAGGAGTTCGCTTTTTTTATAGTTCAGGAG	1	19	1	CTTTTTTTAT	    0.985338	-28
    ATGATTCTGTTTTTATGCCGATATAA	3	7	1	CTGTTTTTAT	    0.974395	-67
TTTTTTTCTCCTTATTAGATAATATGCCTG	3	53	0	CTTATTAGAT	    0.895005	-21
          CTTTTTTTCTCCTTATTAGA	3	64	0	CTTTTTTTCT	    0.946949	-10
        CCATTATTTGAAAACGTGGTAC	4	3	1	ATTATTTGAA	    0.854103	-57
TAGAGCGGAGATTTTTTTATATTCTTATTT	5	28	1	ATTTTTTTAT	     0.93891	-78
TTTTTATATTCTTATTTTAATAGTTGGACA	5	41	1	CTTATTTTAA	    0.963117	-65
TTCAGGCATACTGTTTCGAAAGGAGGCGTG	5	82	1	CTGTTTCGAA	    0.877368	-24
          **********

Masking position 5
Map Score:   7.96382

Number of sites scoring better than the average of aligned sites = 2067
Number in coding regions = 1558
Number in noncoding regions = 509
Number of orfs with sites within 600 bp upstream = 476
Fraction of orfs with sites within 600 bp upstream = 0.0764536


Motif number 2

 GCGGCTCTTAGGAGTTCGCTTTTTTTATAG	1	10	1	AGGAGTCGCT	    0.984801	-37
          AGGATTCCTCTCGCTTTCCGT	2	70	0	AGGATTCTCT	     0.98127	-11
AAATTGACACAGGCATATTATCTAATAAGGA	3	44	1	AGGCATTTAT	    0.963773	-30
ATATTCATTCAGGCATACTGTTTCGAAAGGA	5	75	1	AGGCATCTGT	    0.991504	-31
TTTCGAAAGGAGGCGTGCTAT          	5	95	1	AGGCGTCTAT	    0.995366	-11
          ****** ****

Masking position 6
Map Score:   2.90131

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 118
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

GTCAATTTCTAGTGATTATATCGGCATAAAA	3	21	0	ATGATTATAT	    0.905864	-53
GCTCCTCATCATCGGTTATATGAGTATACTG	4	32	0	ACGGTTATAT	    0.979926	-28
CCGCTCTAAAAACGGAGATTTGGCC      	5	5	0	ACGGAGATTT	    0.990849	-101
CCGTTTTTAGAGCGGAGATTTTTTTATATTC	5	21	1	ACGGAGATTT	    0.990852	-85
AGTATGCCTGAATGAATATTTTCTGTCCAAC	5	63	0	ATGAATATTT	    0.951621	-43
          * *********

Masking position 8
Map Score:   2.47462

Number of sites scoring better than the average of aligned sites = 376
Number in coding regions = 343
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

CTTTTATCGACTGCGTTTTCAGTTAGTTTAG	2	15	0	CTCGTTTTCA	    0.996485	-66
      ATGATTCTGTTTTTATGCCGATATA	3	5	1	TTTGTTTTTA	    0.920707	-69
GTATACTGTACCACGTTTTCAAATAATGG  	4	9	0	CCCGTTTTCA	    0.994023	-51
  GGCCAAATCTCCGTTTTTAGAGCGGAGAT	5	9	1	CTCGTTTTTA	    0.994574	-97
          ** ********

Masking position 6
Map Score:   3.08422

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 82
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

CACTCTACCTCCTGAACTATAAAAAAAGCG	1	27	0	CCTGAACTAT	    0.989813	-20
       TTCCCTAAACTAACTGAAAACGC	2	4	1	CCTAAACTAA	    0.984331	-77
AAACAGTATGCCTGAATGAATATTTTCTGT	5	68	0	CCTGAATGAA	    0.981413	-38
          **********

Masking position 5
Map Score:   0.097356

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 41
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   -6.29951e-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 7

          **********

No masking
Map Score:   -6.29951e-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:   -6.29951e-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