AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_synecho_ctra_100.orf -o119_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	RCY38580	145	Synechocystis

Motif number 1

TAAACGGTACTTTAAATAAGAATTATTTGC	1	29	0	TTTAAATAAG	      0.9489	-117
AAAGCAAGTATTTAAACGGTACTTTAAATA	1	41	0	TTTAAACGGT	     0.99664	-105
AAATACTTGCTTTAAACAGTTTAGATCTGA	1	58	1	TTTAAACAGT	    0.994809	-88
AGGTCTGAGTTTTAAACGGGATCAGTCCTC	1	91	1	TTTAAACGGG	    0.997825	-55
          **********

Masking position 5
Map Score:   7.30763

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 48
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

CAGTTTAGATCTGAATCAGGTCTGAGTTTT	1	74	1	CTGAATCAGG	    0.995122	-72
GAGTTTTAAACGGGATCAGTCCTCCCACTA	1	97	1	CGGGATCAGT	    0.989269	-49
          AGGAACCAGGGGCAAAAAAG	1	136	0	AGGAACCAGG	    0.995363	-10
          **********

Masking position 5
Map Score:   1.97122

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 111
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 3

TTTAAACAGTTTAGATCTGAATCAGGTCTG	1	68	1	TTAGATCTGA	    0.527098	-78
TAGATCTGAATCAGGTCTGAGTTTTAAACG	1	79	1	TCAGGTCTGA	    0.513292	-67
AACAATAGTGGGAGGACTGATCCCGTTTAA	1	102	0	GGAGGACTGA	    0.972404	-44
          **********

Masking position 3
Map Score:   1.75149

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 19
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

AAGAATTATTTGCAAGAGTTAAGGTTAACA	1	12	0	TGCAAGAGTT	    0.985277	-134
CGGTACTTTAAATAAGAATTATTTGCAAGA	1	25	0	AATAAGAATT	    0.946458	-121
AACTGTTTAAAGCAAGTATTTAAACGGTAC	1	49	0	AGCAAGTATT	    0.990093	-97
GCAAAAAAGCAGCAACAATAGTGGGAGGAC	1	115	0	AGCAACAATA	    0.977233	-31
          **********

Masking position 5
Map Score:   1.3804

Number of sites scoring better than the average of aligned sites = 382
Number in coding regions = 317
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 5

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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 7

          **********

No masking
Map Score:   2.43208e-15

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