AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_synecho_ctra_100.orf -o279_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	RCY05296	114	Synechocystis

Motif number 1

GCGGTTTAGCCGACGGAACTTTAGGGAAAT	1	23	0	CGACGGAACT	    0.998624	-92
TCGGCTAAACCGCCCGATCTCCCAAGTTTG	1	40	1	CGCCCGATCT	    0.996613	-75
GACCAAAGCGCCACCAAACTTGGGAGATCG	1	54	0	CCACCAAACT	    0.987023	-61
GGGATCAACTGGACCGAAGTGCTCCGGAAC	1	88	1	GGACCGAAGT	    0.988408	-27
GACCGAAGTGCTCCGGAACACTCATA    	1	99	1	CTCCGGAACA	    0.983698	-16
          **********

Masking position 7
Map Score:   7.17768

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 217
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

CATAATTTCCCTAAAGTTCCGTCGGCTAAA	1	19	1	CTAAAGTTCC	    0.993493	-96
GTTCCGTCGGCTAAACCGCCCGATCTCCCA	1	34	1	CTAAACCGCC	    0.997156	-81
TCCCAATTGACCAAAGCGCCACCAAACTTG	1	62	0	CCAAAGCGCC	    0.999313	-53
ATCAACTGGACCGAAGTGCTCCGGAACACT	1	91	1	CCGAAGTGCT	    0.992844	-24
          **********

Masking position 5
Map Score:   7.07993

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 191
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

TTTCCCTAAAGTTCCGTCGGCTAAACCGCC	1	24	1	GTTCCGTCGG	      0.9869	-91
AAACTTGGGAGATCGGGCGGTTTAGCCGAC	1	39	0	GATCGGGCGG	    0.991111	-76
GTGGCGCTTTGGTCAATTGGGATCAACTGG	1	70	1	GGTCAATTGG	    0.991305	-45
GGTCAATTGGGATCAACTGGACCGAAGTGC	1	80	1	GATCAACTGG	    0.991305	-35
GAGTGTTCCGGAGCACTTCGGTCCAGTTGA	1	92	0	GAGCACTTCG	    0.954339	-23
          **********

Masking position 4
Map Score:   2.32838

Number of sites scoring better than the average of aligned sites = 789
Number in coding regions = 709
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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 6

          **********

No masking
Map Score:   -1.60993e-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