AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_synecho_ctra_100.orf -o107_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	RCY20248	131	Synechocystis

Motif number 1

GTTGCTTACTCAACCCTCAAATTTCCCCAT	1	33	1	CAACCCTCAA	     0.98663	-99
CCCTCAAATTTCCCCATCAAACCTTGGTGG	1	46	1	TCCCCATCAA	    0.998466	-86
TGGTGGCCAATCCCCACCAAGGTTTGATGG	1	59	0	TCCCCACCAA	    0.996601	-73
TGGGGATTGGCCACCATCAATTTTCGTGAA	1	73	1	CCACCATCAA	    0.998466	-59
TGAACTTCCATTACAATCAAGCCTGTTATC	1	99	1	TTACAATCAA	    0.966749	-33
          **********

Masking position 9
Map Score:   9.97918

Number of sites scoring better than the average of aligned sites = 689
Number in coding regions = 635
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

     GGGTCTGTGGGCCAAAATTCTAGTT	1	6	1	TGTGGGCCAA	     0.99753	-126
CACCAAGGTTTGATGGGGAAATTTGAGGGT	1	45	0	TGATGGGGAA	    0.983808	-87
CGAAAATTGATGGTGGCCAATCCCCACCAA	1	69	0	TGGTGGCCAA	    0.998196	-63
CAATCAAGCCTGTTATCCAACGGGTGAAAG	1	112	1	TGTTATCCAA	    0.979637	-20
          **********

Masking position 9
Map Score:   4.31733

Number of sites scoring better than the average of aligned sites = 742
Number in coding regions = 706
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

          **********

No masking
Map Score:   8.05918e-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:   8.05918e-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:   8.05918e-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