AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_synecho_reg_100.orf -o194_synecho_100.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	RCY03330	108	Synechocystis

Motif number 1

GGCAAACCTTTCTGGGGTAG          	1	1	0	TCTGGGGTAG	    0.988886	-108
TATCGCCAATTATCGGCAAACCTTTCTGGG	1	15	0	TATCGGCAAA	    0.983511	-94
TGTGCTACGCTATCGCCAATTATCGGCAAA	1	25	0	TATCGCCAAT	    0.959688	-84
TAGCACAATATATGGGGAAGGTGGCTGTCA	1	48	1	TATGGGGAAG	    0.997514	-61
ACCAAGGGCCTGTGGGCAGGGGAATTGACA	1	73	0	TGTGGGCAGG	    0.990211	-36
          **********

Masking position 3
Map Score:   6.02807

Number of sites scoring better than the average of aligned sites = 659
Number in coding regions = 568
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 2

GAATTGACAGCCACCTTCCCCATATATTGT	1	52	0	CCACCTTCCC	    0.998605	-57
GGCTGTCAATTCCCCTGCCCACAGGCCCTT	1	70	1	TCCCCTGCCC	    0.999034	-39
          **********

Masking position 6
Map Score:   0.686308

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 112
Number in noncoding regions = 22
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:   1.37435e-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:   1.37435e-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:   1.37435e-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