AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i310_mixed24_synecho_reg_300.orf -o310_synecho_300.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	RCY36605	100	Synechocystis

Motif number 1

ATCGTTGAGCCCTTTCTCTCACC        	1	3	0	CCTTTCTTCA	    0.980531	-98
AGAGAAAGGGCTCAACGATCAACACTGTCCC	1	15	1	CTCAACGTCA	    0.965711	-86
GGCAGAACCGCCCATCAACCATTAAAACAGG	1	44	0	CCCATCACCA	    0.995786	-57
GGTTGATGGGCGGTTCTGCCAAATTTTTGTC	1	55	1	CGGTTCTCCA	    0.987929	-46
AATTTTTGTCGCCAACTTCCACTTCTCTTCT	1	76	1	GCCAACTCCA	    0.989642	-25
ACTTCCACTTCTCTTCTGCCT          	1	90	1	CTCTTCTCCT	    0.988394	-11
          ******* ***

Masking position 6
Map Score:   5.44022

Number of sites scoring better than the average of aligned sites = 2075
Number in coding regions = 1869
Number in noncoding regions = 206
Number of orfs with sites within 600 bp upstream = 221
Fraction of orfs with sites within 600 bp upstream = 0.0354963


Motif number 2

          **********

No masking
Map Score:   -1.04149e-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 3

          **********

No masking
Map Score:   -1.04149e-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:   -1.04149e-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