AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_bbur_reg_100.orf -o012_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00573	139	3615

Motif number 1

TTTTATGATAAAATCTATTA          	1	1	0	AAATCTATTA	    0.893753	-139
AAAAAATTAGAAATTAAATACTTTTATGAT	1	22	0	AAATTAAATA	    0.922139	-118
AGCAATTTTAAAAAAAATTAGAAATTAAAT	1	33	0	AAAAAAATTA	    0.914919	-107
TCAGAACAACATATTAAATAGCAATTTTAA	1	52	0	ATATTAAATA	     0.97219	-88
TTCTGATCTGATATTTATTATAATTTATAA	1	76	1	ATATTTATTA	     0.93322	-64
TCCCACTGTGTTATAAATTATAATAAATAT	1	86	0	TTATAAATTA	    0.722761	-54
TTAATAATTTAAATAAATTCCCACTGTGTT	1	104	0	AAATAAATTC	    0.889841	-36
TTTATTTAAATTATTAATTAATAGAGGTTT	1	117	1	TTATTAATTA	    0.617659	-23
          **********

Masking position 7
Map Score:   12.9764

Number of sites scoring better than the average of aligned sites = 1337
Number in coding regions = 723
Number in noncoding regions = 614
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 2

TAAATACTTTTATGATAAAATCTATTA   	1	8	0	TATGATAAAA	    0.792837	-132
TAAAAGTATTTAATTTCTAATTTTTTTTAA	1	26	1	TAATTTCTAA	    0.920908	-114
ATTTCTAATTTTTTTTAAAATTGCTATTTA	1	38	1	TTTTTTAAAA	    0.572216	-102
TTAAAATTGCTATTTAATATGTTGTTCTGA	1	52	1	TATTTAATAT	    0.931477	-88
TTATAAATTATAATAAATATCAGATCAGAA	1	76	0	TAATAAATAT	    0.877062	-64
ATATTTATTATAATTTATAACACAGTGGGA	1	86	1	TAATTTATAA	    0.902412	-54
TATTAATTAATAATTTAAATAAATTCCCAC	1	110	0	TAATTTAAAT	    0.969087	-30
          **********

Masking position 9
Map Score:   6.2855

Number of sites scoring better than the average of aligned sites = 1426
Number in coding regions = 778
Number in noncoding regions = 648
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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