AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i304_bsub_mtub_300.orf -o304_bsub_mtub_300.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	fadE7	35	fadE7
#2	Rv3272	100	hypothetical protein Rv3272

Motif number 1

          GCCGCGAGGCTACCGGGCCG	1	1	1	GCCGCGAGGC	    0.501073	-35
ACTCAATACTGCCCCGGCCCGGTAGCCTCG	1	15	0	GCCCCGGCCC	    0.612558	-21
GGCAAGACATGCCGGGCGGTCGCCGCGGCG	2	26	1	GCCGGGCGGT	    0.530934	-75
CCGGGCGGTCGCCGCGGCGTCGCGAACCCG	2	37	1	GCCGCGGCGT	    0.612991	-64
CAGGGAGGATGCCGCACGCCAGGGAAGGTC	2	74	1	GCCGCACGCC	    0.530957	-27
          **********

Masking position 3
Map Score:   12.8329

Number of sites scoring better than the average of aligned sites = 195
Number in coding regions = 180
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

       GCCGCGAGGCTACCGGGCCGGGG	1	4	1	GCGAGGCTAC	    0.983259	-32
CGAGGCTACCGGGCCGGGGCAGTATTGAGT	1	15	1	GGGCCGGGGC	    0.764858	-21
AAGACATGCCGGGCGGTCGCCGCGGCGTCG	2	29	1	GGGCGGTCGC	    0.766668	-72
ATACGGGTTCGCGACGCCGCGGCGACCGCC	2	40	0	GCGACGCCGC	    0.508705	-61
GTATGGTTCAGGGAGGATGCCGCACGCCAG	2	66	1	GGGAGGATGC	    0.991411	-35
CGCACGCCAGGGAAGGTCACCACCG     	2	86	1	GGAAGGTCAC	    0.967243	-15
          **********

Masking position 6
Map Score:   12.6897

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 364
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

ATACTGCCCCGGCCCGGTAGCCTCGCGGC 	1	10	0	GGCCCGGTAG	    0.761462	-26
CCGCGGCGACCGCCCGGCATGTCTTGCCTC	2	24	0	CGCCCGGCAT	    0.759688	-77
GCCGGGCGGTCGCCGCGGCGTCGCGAACCC	2	36	1	CGCCGCGGCG	    0.499972	-65
AACCCGTATGGTTCAGGGAGGATGCCGCAC	2	61	1	GTTCAGGGAG	    0.917804	-40
GGATGCCGCACGCCAGGGAAGGTCACCACC	2	80	1	CGCCAGGGAA	    0.761331	-21
          **********

Masking position 4
Map Score:   4.78779

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 476
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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 6

          **********

No masking
Map Score:   -2.03625e-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