AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_synecho_reg_100.orf -o198_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	RCY30474	106	Synechocystis

Motif number 1

GGGGGGAAAGTTGTCGCTCTGTGACCTCCG	1	21	0	TTGTCGCTCT	    0.987834	-86
GAGCGACAACTTTCCCCCCGTATCCAGGGC	1	32	1	TTTCCCCCCG	    0.996421	-75
CTCTCCGGTATTTCTGCCCTGGATACGGGG	1	47	0	TTTCTGCCCT	    0.987853	-60
GGGGCATCCCCTTCCCCTCTCCGGTATTTC	1	63	0	CTTCCCCTCT	    0.997032	-44
GGGGAAGGGGATGCCCCTATAATTATGGCT	1	76	1	ATGCCCCTAT	    0.978896	-31
          **********

Masking position 2
Map Score:   6.24774

Number of sites scoring better than the average of aligned sites = 1657
Number in coding regions = 1420
Number in noncoding regions = 237
Number of orfs with sites within 600 bp upstream = 234
Fraction of orfs with sites within 600 bp upstream = 0.0375843


Motif number 2

       CTTTTGCCAACGGAGGTCACAGAGC	1	4	1	TTGCAACGGG	    0.998677	-103
TATTTCTGCCCTGGATACGGGGGGAAAGTTGT	1	37	0	CTGATACGGG	    0.997709	-70
ATAATTATGGCTGTCAACTGTGT         	1	94	1	CTGCAACTGG	    0.998791	-13
          *** ****** *

Masking position 7
Map Score:   2.16547

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 130
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

          **********

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 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