AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i103_bsub_mtub_100.orf -o103_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	ideR	132	ideR

Motif number 1

CAGACGGTATGCCCGCCGCGCCAGCGGCGG	1	35	1	GCCCGCCGCG	    0.996538	-98
GCAGCGGTATGCCCGCCGCTGGCGCGGCGG	1	47	0	GCCCGCCGCT	    0.996088	-86
GCGGCGGGCATACCGCTGCGGTGGGGCGGC	1	58	1	TACCGCTGCG	     0.99343	-75
GAAAATGGTTGCCCGCCGCCCCACCGCAGC	1	72	0	GCCCGCCGCC	     0.93481	-61
AGTCTACTTGGCCAGCTGCGAAAATGGTTG	1	91	0	GCCAGCTGCG	    0.824789	-42
CACCCTCCATTGCAGCTGAGTCTACTTGGC	1	109	0	TGCAGCTGAG	    0.836364	-24
          **********

Masking position 5
Map Score:   21.8191

Number of sites scoring better than the average of aligned sites = 233
Number in coding regions = 218
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

CCGTCTGCTACCTGGCTCAGGATGTCCAGC	1	12	0	CCTGGCTCAG	    0.969796	-121
TATGCCCGCCGCTGGCGCGGCGGGCATACC	1	40	0	GCTGGCGCGG	    0.979381	-93
ATACCGCTGCGGTGGGGCGGCGGGCAACCA	1	67	1	GGTGGGGCGG	    0.997357	-66
CATTTTCGCAGCTGGCCAAGTAGACTCAGC	1	95	1	GCTGGCCAAG	    0.779277	-38
          **********

Masking position 3
Map Score:   7.06657

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 219
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

CTACCTGGCTCAGGATGTCCAGCT      	1	5	0	CAGGATGTCC	    0.995582	-128
AGGTAGCAGACGGTATGCCCGCCGCGCCAG	1	29	1	CGGTATGCCC	     0.97443	-104
CCCACCGCAGCGGTATGCCCGCCGCTGGCG	1	53	0	CGGTATGCCC	     0.97443	-80
AGCTGCGAAAATGGTTGCCCGCCGCCCCAC	1	78	0	ATGGTTGCCC	    0.988962	-55
          **********

Masking position 6
Map Score:   9.05764

Number of sites scoring better than the average of aligned sites = 128
Number in coding regions = 124
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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 6

          **********

No masking
Map Score:   5.21701e-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