AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_synecho_ctra_100.orf -o033_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	RCY19932	300	Synechocystis

Motif number 1

TAGAAAAAGTTAGGAAAAATTA        	1	3	0	TAGGAAAAAT	     0.98478	-298
ACCCGCAACTTAGAAAAAGTTAGGAAAAAT	1	13	0	TAGAAAAAGT	    0.964286	-288
ATCTAAACCATAGAAAAAAACCTGGGTGTG	1	79	0	TAGAAAAAAA	     0.98849	-222
GAATTTCCTTTCGGAAAAAACGCCATAACT	1	195	0	TCGGAAAAAA	    0.990107	-106
CTCCGTAAAGTCGAAAAAAATAATATTGTC	1	254	0	TCGAAAAAAA	    0.989329	-47
          **********

Masking position 5
Map Score:   8.26702

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 88
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

CCACTGGCCTACCCGCAACTTAGAAAAAGTTAG	1	20	0	ACCCAACTAG	    0.983209	-281
GGTAAAGCGAATCTAAACCATAGAAAAAAACCT	1	86	0	ACTAACCTAG	    0.849553	-215
GGTTTAGATTCGCTTTACCTTTGCTTTAAGCTC	1	100	1	CCTTACCTTG	    0.952436	-201
CAAGAAAAACCGCTTCAACAGAGCTTAAAGCAA	1	120	0	CCTCAACGAG	    0.977092	-181
TCGGAAAAAACGCCATAACTTCAAATTCTGTTA	1	182	0	CCCTAACTCA	    0.970261	-119
GGCTAGTTTACCCCACACCTGAATTTCCTTTCG	1	212	0	CCCCACCGAA	    0.982535	-89
ACCGAGGGTTCTCCGTAAAGTCGAAAAAAATAA	1	261	0	CCCTAAATCG	    0.817508	-40
TGACTATCGGCTCCTTAACCGAGGGTTCTCCGT	1	278	0	CCCTAACGAG	    0.965556	-23
          * ** **** ***

Masking position 7
Map Score:   5.52561

Number of sites scoring better than the average of aligned sites = 1594
Number in coding regions = 1411
Number in noncoding regions = 183
Number of orfs with sites within 600 bp upstream = 170
Fraction of orfs with sites within 600 bp upstream = 0.0273049


Motif number 3

ACAAAAGTTAGACTGGCGGCGATCGCCACT	1	48	0	GACTGGCGGC	    0.995286	-253
TCTTTAGAGTGACTTTGAGCTTGTAACCAA	1	150	0	GACTTTGAGC	    0.984075	-151
ATATTGTCAGGATTATGGGCTAGTTTACCC	1	232	0	GATTATGGGC	    0.988808	-69
         TGACTATCGGCTCCTTAACCG	1	290	0	GACTATCGGC	    0.988974	-11
          **********

Masking position 4
Map Score:   4.16292

Number of sites scoring better than the average of aligned sites = 97
Number in coding regions = 88
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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