AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i130_bsub_mtub_300.orf -o130_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	Rv3779	89	hypothetical protein Rv3779

Motif number 1

CCGAGTTCTAAGGTGGCTGGC         	1	2	0	AGGTGGCTGG	    0.996226	-88
CTTAGAACTCGGGTGTCCTAGACGTCCCAG	1	20	1	GGGTGTCCTA	     0.98517	-70
GGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	GGCGGGCTGG	    0.998895	-54
AGCCCGCCCGGGCTTCCCTGAGCCATGTCA	1	48	1	GGCTTCCCTG	    0.993077	-42
CGATTAGTATGGCTGGCCGGGTGACATGGC	1	69	0	GGCTGGCCGG	    0.999779	-21
          **********

Masking position 7
Map Score:   10.7613

Number of sites scoring better than the average of aligned sites = 639
Number in coding regions = 593
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

CTAGGACACCCGAGTTCTAAGGTGGCTGGC  	1	9	0	CGAGTTAAGG	    0.996262	-81
CAGGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	CGGGCGCTGG	    0.958574	-54
TATGGCTGGCCGGGTGACATGGCTCAGGGAAG	1	60	0	CGGGTCATGG	    0.998708	-30
         TCGATTAGTATGGCTGGCCGGGT	1	77	0	CGATTTATGG	    0.989925	-13
          *****  *****

Masking position 2
Map Score:   3.6567

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 74
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

       GCCAGCCACCTTAGAACTCGGGT	1	4	1	AGCCACCTTA	    0.994722	-86
GGGACGTCTAGGACACCCGAGTTCTAAGGT	1	18	0	GGACACCCGA	    0.986204	-72
CGGGTGTCCTAGACGTCCCAGCCCGCCCGG	1	29	1	AGACGTCCCA	    0.990882	-61
GGCTTCCCTGAGCCATGTCACCCGGCCAGC	1	58	1	AGCCATGTCA	    0.966388	-32
TCACCCGGCCAGCCATACTAATCGA     	1	75	1	AGCCATACTA	    0.990025	-15
          **********

Masking position 10
Map Score:   6.17498

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 369
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   -4.67335e-15

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:   -4.67335e-15

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:   -4.67335e-15

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