AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_synecho_reg_300.orf -o194_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	RCY03330	108	Synechocystis

Motif number 1

          CTACCCCAGAAAGGTTTGCC	1	1	1	CTACCCCAGA	    0.988657	-108
CCCAGAAAGGTTTGCCGATAATTGGCGATA	1	15	1	TTTGCCGATA	    0.983528	-94
TTTGCCGATAATTGGCGATAGCGTAGCACA	1	25	1	ATTGGCGATA	     0.95941	-84
TGACAGCCACCTTCCCCATATATTGTGCTA	1	48	0	CTTCCCCATA	    0.997482	-61
TGTCAATTCCCCTGCCCACAGGCCCTTGGT	1	73	1	CCTGCCCACA	    0.990201	-36
          **********

Masking position 8
Map Score:   6.02807

Number of sites scoring better than the average of aligned sites = 659
Number in coding regions = 568
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 2

ACAATATATGGGGAAGGTGGCTGTCAATTC	1	52	1	GGGAAGGTGG	    0.998729	-57
AAGGGCCTGTGGGCAGGGGAATTGACAGCC	1	70	0	GGGCAGGGGA	    0.999115	-39
          **********

Masking position 5
Map Score:   0.686308

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 112
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

          **********

No masking
Map Score:   1.37435e-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:   1.37435e-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:   1.37435e-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