AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i331_synecho_ctra_300.orf -o331_synecho_ctra_300.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	RCY48931	211	Synechocystis

Motif number 1

TGCTAAAATAAACAATAGTTAATCGAGGT  	1	9	0	AACAATGTTA	    0.987206	-203
AATTAGCACTGGCATTAATTAGTAGCGATGA	1	49	0	GGCATTATTA	    0.980319	-163
GGATGGAAACGACGTTTATTATGGTCAGTTT	1	109	0	GACGTTATTA	    0.980319	-103
TGGCTTGACTGACAATGGTTAGATTAATTTA	1	142	0	GACAATGTTA	    0.994281	-70
GCCCTAGGATAACATTCGTTATAAAGTGGAA	1	177	1	AACATTGTTA	    0.991037	-35
          ****** ****

Masking position 6
Map Score:   6.22882

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 92
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TAATTAAGCAGTGATATTGCTATTATTTTG	1	75	1	GTGATATTGC	    0.974127	-137
GTTTATTATGGTCAGTTTGCGCCAAAATAA	1	97	0	GTCAGTTTGC	    0.995858	-115
TGTCAGTCAAGCCATTCTGCCCTAGGATAA	1	159	1	GCCATTCTGC	    0.980478	-53
AGTGGAATCCGTGAGGTTGCA         	1	201	1	GTGAGGTTGC	    0.995177	-11
          **********

Masking position 4
Map Score:   3.84343

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 134
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

CGAGAGGATTGCTAAAATAAACAATAGTTA	1	19	0	GCTAAAATAA	    0.993038	-193
CAATATCACTGCTTAATTAGCACTGGCATT	1	64	0	GCTTAATTAG	    0.931647	-148
GTCAGTTTGCGCCAAAATAATAGCAATATC	1	87	0	GCCAAAATAA	    0.993547	-125
GCGCAAACTGACCATAATAAACGTCGTTTC	1	105	1	ACCATAATAA	     0.89968	-107
GTTTCCATCCGGTAAATTAATCTAACCATT	1	130	1	GGTAAATTAA	    0.965837	-82
          **********

Masking position 6
Map Score:   3.61791

Number of sites scoring better than the average of aligned sites = 624
Number in coding regions = 524
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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