AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_synecho_ctra_100.orf -o303_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	RCY50877	115	Synechocystis
#2	RCY38476	116	Synechocystis

Motif number 1

TTGACCAACTGCTTTGACTCCGCCTCTGAA	1	44	0	GCTTTGACTC	    0.997944	-72
ACTGAACGAAGCTTTGACCAACTGCTTTGA	1	57	0	GCTTTGACCA	    0.989898	-59
     TAACTGGTTTTGCTCTCCCCCATTG	2	6	1	GGTTTTGCTC	    0.976921	-111
TCCCCCATTGGTTTTGACTACTTTTCCCGA	2	26	1	GTTTTGACTA	    0.987626	-91
GTGTTTTTACGGTTTGATTCGGGAATCTTT	2	67	1	GGTTTGATTC	    0.989341	-50
          **********

Masking position 5
Map Score:   6.93177

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 259
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

          CACCTCGGGTTTGTAACAGTTT	1	1	1	CACCCGGGTT	    0.988667	-115
GCTTTGACTCCGCCTCTGAACTAGTGTAACGA	1	32	0	CGCCCTGAAT	    0.996227	-84
TTTTGCTCTCCCCCATTGGTTTTGACTACTTT	2	18	1	CCCCTTGGTT	    0.993078	-99
TTTTCCCGATCGCCGTTGAAGTGTTTTTACGG	2	47	1	CGCCTTGAAT	    0.994177	-70
          **** ***** *

Masking position 12
Map Score:   0.609698

Number of sites scoring better than the average of aligned sites = 312
Number in coding regions = 282
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

GTTACACTAGTTCAGAGGCGGAGTCAAAGCA	1	34	1	TTCAGGGCGG	    0.996166	-82
TTGTTATTTATCTAAGTGCGGATAATACTGA	1	82	0	TCTAATGCGG	    0.977437	-34
AGTAGTCAAAACCAATGGGGGAGAGCAAAAC	2	17	0	ACCAAGGGGG	    0.990104	-100
GTAAAAACACTTCAACGGCGATCGGGAAAAG	2	46	0	TTCAAGGCGA	    0.991098	-71
          ***** *****

Masking position 4
Map Score:   0.553205

Number of sites scoring better than the average of aligned sites = 729
Number in coding regions = 674
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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