AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i341_bsub_mtub_100.orf -o341_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	ykpA	180	similar to ABC transporter (ATP-binding protein)

Motif number 1

TACACACTCTCATGGAGGAACACG      	1	5	0	CATGGAGGAA	    0.990073	-176
AATGCATCCGCCTGGAAAATTACACACTCT	1	25	0	CCTGGAAAAT	    0.939134	-156
TACAATTAAAGAGAGAGAATGCATCCGCCT	1	42	0	GAGAGAGAAT	    0.988037	-139
CCTGATAAAACAGAGAGAAAACACTTATAC	1	93	0	CAGAGAGAAA	    0.988037	-88
TGAATGCAGGGCAAGAGAAATGATTCCCTG	1	119	0	GCAAGAGAAA	    0.961691	-62
TGATAGACATGATGGAGGATAATAA     	1	166	1	GATGGAGGAT	    0.990073	-15
          **********

Masking position 6
Map Score:   6.55828

Number of sites scoring better than the average of aligned sites = 980
Number in coding regions = 847
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 146
Fraction of orfs with sites within 600 bp upstream = 0.02345


Motif number 2

 CGTGTTCCTCCATGAGAGTGTGTAATTTT	1	10	1	CCATGAGAGT	    0.991351	-171
AGCTGTGTTACAATTAAAGAGAGAGAATGC	1	50	0	CAATTAAAGA	     0.96304	-131
TAAAAGTATACCATGAATGCAGGGCAAGAG	1	132	0	CCATGAATGC	    0.972948	-49
TGTCTATCATCAATAAAAGTATACCATGAA	1	145	0	CAATAAAAGT	    0.978979	-36
          **********

Masking position 6
Map Score:   1.42485

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 168
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          **********

No masking
Map Score:   -3.81261e-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 4

          **********

No masking
Map Score:   -3.81261e-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 5

          **********

No masking
Map Score:   -3.81261e-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