AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_bsub_mtub_100.orf -o288_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	moxR	138	moxR

Motif number 1

TGTGATTTGCCGGGCACCACCGCGGCGTCG	1	17	1	CGGGCACCAC	     0.99732	-122
GGCACCACCGCGGCGTCGACGGAATCCAGG	1	29	1	CGGCGTCGAC	    0.996176	-110
TAGTTGAACGCGGGCGCGTCGCTGCCCCGC	1	69	1	CGGGCGCGTC	    0.997462	-70
CGTCGCTGCCCCGCGACGTTGGTCATGTCG	1	85	1	CCGCGACGTT	    0.973785	-54
GACACGACTGCCGACATGACCAACGTCGCG	1	96	0	CCGACATGAC	    0.988469	-43
ACAGCTCAATCGGACACGACTGCCGACATG	1	108	0	CGGACACGAC	    0.999058	-31
          **********

Masking position 3
Map Score:   11.9424

Number of sites scoring better than the average of aligned sites = 420
Number in coding regions = 392
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

ATTTGCCGGGCACCACCGCGGCGTCGACGG	1	21	1	CACCACCGCG	     0.99409	-118
GCCTGGAATAGTTGAACGCGGGCGCGTCGC	1	61	1	GTTGAACGCG	    0.936508	-78
CGTCGCGGGGCAGCGACGCGCCCGCGTTCA	1	73	0	CAGCGACGCG	    0.981652	-66
CTGCCGACATGACCAACGTCGCGGGGCAGC	1	89	0	GACCAACGTC	    0.963277	-50
CTCAATCGGACACGACTGCCGACATGACCA	1	104	0	CACGACTGCC	    0.978106	-35
   CAAAATCCTCCACAGCTCAATCGGACA	1	122	0	CTCCACAGCT	    0.955347	-17
          **********

Masking position 8
Map Score:   3.61907

Number of sites scoring better than the average of aligned sites = 1362
Number in coding regions = 1261
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 3

          **********

No masking
Map Score:   -9.70439e-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 4

          **********

No masking
Map Score:   -9.70439e-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 5

          **********

No masking
Map Score:   -9.70439e-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