AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i098_Phosphate_regulatory_cassete_synecho_reg_300.orf -o098_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY20606	122	Synechocystis

Motif number 1

AAAATGAAATCAGGATGAAATTTAGAGCTCA	1	28	0	CAGATGAAAT	    0.988613	-95
TCTGGCAAAGCAAAATGAAATCAGGATGAAA	1	39	0	CAAATGAAAT	    0.994838	-84
TTTGCTTTGCCAGACTGGAATTAGAGAAGGA	1	56	1	CAACTGGAAT	    0.997871	-67
GAATTGATTACCCACGGGAATGCTTACCTCC	1	90	0	CCACGGGAAT	    0.989597	-33
CCCATATATCCAGAATTGATTACCCACGGGA	1	102	0	CAAATTGATT	    0.961965	-21
          ** ********

Masking position 9
Map Score:   5.84247

Number of sites scoring better than the average of aligned sites = 287
Number in coding regions = 263
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

TCATTTATAAAGTCTTGTAA          	1	1	0	AGTCTTGTAA	    0.989665	-122
CTCTAATTCCAGTCTGGCAAAGCAAAATGA	1	52	0	AGTCTGGCAA	    0.997359	-71
TGGGTAATCAATTCTGGATATATGGG    	1	107	1	ATTCTGGATA	    0.980472	-16
          **********

Masking position 1
Map Score:   1.91156

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 77
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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