AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i345_synecho_ctra_100.orf -o345_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY09050	106	Synechocystis

Motif number 1

TTGATCCTCTAGCCATGTTTTTATTGATAC	1	14	0	AGCCATGTTT	    0.932882	-93
ATGGCTAGAGGATCAAGTTTGGTCTACTCC	1	28	1	GATCAAGTTT	    0.959317	-79
GGTCTACTCCAGCCATGTTTAAGCAGAAAT	1	48	1	AGCCATGTTT	    0.932882	-59
 AAAAAATTTGGTCATGATTATTTTTATCT	1	88	0	GGTCATGATT	    0.868852	-19
          **********

Masking position 5
Map Score:   8.13488

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 159
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

CCAAACTTGATCCTCTAGCCATGTTTTTAT	1	20	0	TCCTCTAGCC	     0.99598	-87
AAGTTTGGTCTACTCCAGCCATGTTTAAGC	1	42	1	TACTCCAGCC	     0.99598	-65
          **********

Masking position 4
Map Score:   1.77864

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 16
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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