AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_bbur_reg_100.orf -o002_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	RBB00142	87	3615

Motif number 1

     GTTTTTAGCTTATTTTACATTGACTAT	1	6	1	TATTATTTTA	    0.942419	-82
TTTATTTTATTGAAATATTGTAATATAGTCAA	1	30	0	TGATATTGTA	    0.527874	-58
TTAGCCATTGTGGTTTATTTTATTGAAATATT	1	43	0	TGTTATTTTA	    0.993883	-45
ATTTCCCACCTGTTATATTTTATTAGCCATTG	1	65	0	TGATATTTTA	    0.948645	-23
          **  ********

Masking position 6
Map Score:   7.36366

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 36
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

     GTTTTTAGCTTATTTTACATTGACT	1	6	1	TAGCTTATTT	    0.975055	-82
TATTGTAATATAGTCAATGTAAAATAAGCT	1	17	0	TAGTCAATGT	    0.994702	-71
TATATTTTATTAGCCATTGTGGTTTATTTT	1	54	0	TAGCCATTGT	    0.996578	-34
          **********

Masking position 2
Map Score:   2.13028

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 12
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

TTTTTAGCTTATTTTACATTGACTATATTA	1	12	1	ATTTTACATT	    0.950626	-76
TACATTGACTATATTACAATATTTCAATAA	1	26	1	ATATTACAAT	    0.950626	-62
CCCACCTGTTATATTTTATTAGCCATTGTG	1	63	0	ATATTTTATT	    0.973227	-25
          **********

Masking position 8
Map Score:   2.52209

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 58
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


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