AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i130_ecoli_mtub_100.orf -o130_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	Rv3779	89	hypothetical protein Rv3779

Motif number 1

         GCCAGCCACCTTAGAACTCGG	1	2	1	CCAGCCACCT	    0.996226	-88
CTGGGACGTCTAGGACACCCGAGTTCTAAG	1	20	0	TAGGACACCC	     0.98517	-70
CCTAGACGTCCCAGCCCGCCCGGGCTTCCC	1	36	1	CCAGCCCGCC	    0.998895	-54
TGACATGGCTCAGGGAAGCCCGGGCGGGCT	1	48	0	CAGGGAAGCC	    0.993077	-42
GCCATGTCACCCGGCCAGCCATACTAATCG	1	69	1	CCGGCCAGCC	    0.999779	-21
          **********

Masking position 4
Map Score:   10.7613

Number of sites scoring better than the average of aligned sites = 1437
Number in coding regions = 1373
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

CTAGGACACCCGAGTTCTAAGGTGGCTGGC  	1	9	0	CGAGTTAAGG	    0.996363	-81
CAGGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	CGGGCGCTGG	    0.957415	-54
TATGGCTGGCCGGGTGACATGGCTCAGGGAAG	1	60	0	CGGGTCATGG	    0.998734	-30
         TCGATTAGTATGGCTGGCCGGGT	1	77	0	CGATTTATGG	    0.989935	-13
          *****  *****

Masking position 2
Map Score:   3.6567

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 174
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

       GCCAGCCACCTTAGAACTCGGGT	1	4	1	AGCCACCTTA	    0.994977	-86
GGGACGTCTAGGACACCCGAGTTCTAAGGT	1	18	0	GGACACCCGA	    0.986868	-72
CGGGTGTCCTAGACGTCCCAGCCCGCCCGG	1	29	1	AGACGTCCCA	    0.991225	-61
GGCTTCCCTGAGCCATGTCACCCGGCCAGC	1	58	1	AGCCATGTCA	    0.965689	-32
TCACCCGGCCAGCCATACTAATCGA     	1	75	1	AGCCATACTA	    0.990507	-15
          **********

Masking position 10
Map Score:   6.17498

Number of sites scoring better than the average of aligned sites = 641
Number in coding regions = 592
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


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