AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i309_synecho_ctra_100.orf -o309_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	RCY27002	202	Synechocystis

Motif number 1

ATCATTCGATCAATTGTGGGCTAGAT      	1	5	0	CAATGTGGGT	    0.998179	-198
CTCGTCGGACCAGTACTGGGCTCAATCCAGGG	1	42	1	CAGTCTGGGT	    0.998822	-161
GTACTGGGCTCAATCCAGGGGTGAAGGTAAAT	1	54	1	CAATCAGGGT	    0.995411	-149
TAAGCAACAACAGTAGTGGCATTGTCCGTTAT	1	170	1	CAGTGTGGCT	    0.996848	-33
          **** ***** *

Masking position 4
Map Score:   5.47712

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 54
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

TCGATCAATTGTGGGCTAGAT         	1	2	0	GTGGGCTAGA	    0.944354	-201
GAGCCCAGTACTGGTCCGACGAGCTTCGAT	1	35	0	CTGGTCCGAC	    0.975708	-168
CGGACCAGTACTGGGCTCAATCCAGGGGTG	1	47	1	CTGGGCTCAA	    0.977484	-156
GGGCTCAATCCAGGGGTGAAGGTAAATTTC	1	59	1	CAGGGGTGAA	    0.951262	-144
GGATATGGGGACAGGCTGGCCCGGGCCGGC	1	115	1	ACAGGCTGGC	    0.944116	-88
ACAGGCTGGCCCGGGCCGGCGCAATTTTTT	1	125	1	CCGGGCCGGC	    0.926359	-78
          **********

Masking position 4
Map Score:   2.41996

Number of sites scoring better than the average of aligned sites = 2987
Number in coding regions = 2795
Number in noncoding regions = 192
Number of orfs with sites within 600 bp upstream = 218
Fraction of orfs with sites within 600 bp upstream = 0.0350145


Motif number 3

GGTAAATTTCCAGAATTCCTTCAGATTCCC	1	79	1	CAGAATTCCT	    0.980228	-124
AGAATTCCTTCAGATTCCCTAATATGGATA	1	90	1	CAGATTCCCT	    0.988203	-113
CAGCCTGTCCCCATATCCATATTAGGGAAT	1	103	0	CCATATCCAT	    0.954744	-100
TTTTGTTAATCCAAATCTCTAAGCAACAAC	1	151	1	CCAAATCTCT	    0.981568	-52
          **********

Masking position 6
Map Score:   0.837072

Number of sites scoring better than the average of aligned sites = 630
Number in coding regions = 554
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

          **********

No masking
Map Score:   3.22176e-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:   3.22176e-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:   3.22176e-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