AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i115_Glycine_Transport_bbur_reg_100.orf -o115_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	RBB00590	153	3615

Motif number 1

    AATTCTAGTTTAATTGGTATAAATTGTA	1	7	1	AGTTTTTGGT	    0.962666	-147
ATCTTTTGTTAATACAATTTATACCAATTAAA	1	19	0	AATACTTTAT	    0.927169	-135
GATCCTTTAAAGGATCTTTTGTTAATACAATT	1	32	0	AGGATTTTGT	    0.995789	-122
GATCCTTTAAAGGATCTTTTGTTTTTTTATTT	1	48	1	AGGATTTTGT	    0.995789	-106
TAATAATTTTAGTATAATTTATAATGATGTGT	1	96	1	AGTATTTTAT	     0.99449	-58
ATAAGCCTGCATTATGCTTTATAACACATCAT	1	119	0	ATTATTTTAT	    0.971687	-35
          *****  *****

Masking position 8
Map Score:   6.87461

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 88
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TTATACCAATTAAACTAGAATT        	1	3	0	TAAACTAGAA	    0.972847	-151
TGGTATAAATTGTATTAACAAAAGATCCTT	1	25	1	TGTATTAACA	    0.945998	-129
TTTGCCGATCTGAAATAAAAAAACAAAAGA	1	62	0	TGAAATAAAA	    0.971113	-92
CATTATAAATTATACTAAAATTATTAAATT	1	92	0	TATACTAAAA	    0.983789	-62
          **********

Masking position 6
Map Score:   1.02829

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 157
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

          **********

No masking
Map Score:   -8.99385e-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 4

          **********

No masking
Map Score:   -8.99385e-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:   -8.99385e-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