AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_hypothetical4_synecho_reg_100.orf -o279_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	RCY05296	114	Synechocystis

Motif number 1

GCGGTTTAGCCGACGGAACTTTAGGGAAAT	1	23	0	CGACGGAACT	    0.998597	-92
TCGGCTAAACCGCCCGATCTCCCAAGTTTG	1	40	1	CGCCCGATCT	    0.996567	-75
GACCAAAGCGCCACCAAACTTGGGAGATCG	1	54	0	CCACCAAACT	    0.986767	-61
GGGATCAACTGGACCGAAGTGCTCCGGAAC	1	88	1	GGACCGAAGT	    0.988182	-27
GACCGAAGTGCTCCGGAACACTCATA    	1	99	1	CTCCGGAACA	    0.983377	-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

TTTAGCCGACGGAACTTTAGGGAAATTATG	1	19	0	GGAACTTTAG	    0.993163	-96
TGGGAGATCGGGCGGTTTAGCCGACGGAAC	1	34	0	GGCGGTTTAG	    0.997011	-81
CAAGTTTGGTGGCGCTTTGGTCAATTGGGA	1	62	1	GGCGCTTTGG	    0.999277	-53
AGTGTTCCGGAGCACTTCGGTCCAGTTGAT	1	91	0	AGCACTTCGG	    0.992481	-24
          **********

Masking position 6
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	    0.987528	-91
AAACTTGGGAGATCGGGCGGTTTAGCCGAC	1	39	0	GATCGGGCGG	    0.991538	-76
GTGGCGCTTTGGTCAATTGGGATCAACTGG	1	70	1	GGTCAATTGG	    0.991724	-45
GGTCAATTGGGATCAACTGGACCGAAGTGC	1	80	1	GATCAACTGG	    0.991724	-35
GAGTGTTCCGGAGCACTTCGGTCCAGTTGA	1	92	0	GAGCACTTCG	    0.956459	-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