AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_mjan_pyro_300.orf -o227_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00468	128	Pyrococcus_OT3

Motif number 1

AGAAGGTAAATTCTTTTTGGTGATGAAGA 	1	10	0	TTCTTTTTGG	    0.989261	-119
AAGAATTTACCTTCTTTAGGTATTTAAAGC	1	25	1	CTTCTTTAGG	    0.981506	-104
TATTTAAAGCTTGCTTTTGGCTTGAGGTTT	1	45	1	TTGCTTTTGG	    0.996201	-84
TATTAGGATGTCGGTTTTGGCAACTATGAA	1	73	0	TCGGTTTTGG	    0.984659	-56
CATCCAGGAATTTTATTAGGATGTCGGTTT	1	86	0	TTTTATTAGG	    0.958712	-43
          **********

Masking position 6
Map Score:   5.42561

Number of sites scoring better than the average of aligned sites = 250
Number in coding regions = 229
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

AATTCTTTTTGGTGATGAAGA         	1	2	0	GGTGATGAAG	    0.990922	-127
AATACCTAAAGAAGGTAAATTCTTTTTGGT	1	19	0	GAAGGTAAAT	    0.978572	-110
AAAATTCCTGGATGGAGATTAAGGAGGTGA	1	102	1	GATGGAGATT	    0.966004	-27
TGGAGATTAAGGAGGTGAAGGGTGA     	1	114	1	GGAGGTGAAG	    0.997702	-15
          **********

Masking position 8
Map Score:   2.77301

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 210
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

CATCACCAAAAAGAATTTACCTTCTTTAGG	1	15	1	AAGAATTTAC	    0.936182	-114
TACCTTCTTTAGGTATTTAAAGCTTGCTTT	1	32	1	AGGTATTTAA	     0.99006	-97
TTTTGGCTTGAGGTTTCATAGTTGCCAAAA	1	59	1	AGGTTTCATA	    0.901512	-70
ATCTCCATCCAGGAATTTTATTAGGATGTC	1	91	0	AGGAATTTTA	    0.989967	-38
          **********

Masking position 6
Map Score:   0.441311

Number of sites scoring better than the average of aligned sites = 569
Number in coding regions = 510
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

          **********

No masking
Map Score:   -1.89414e-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:   -1.89414e-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:   -1.89414e-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