AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_pyro_reg_100.orf -o299_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00249	136	Pyrococcus_OT3

Motif number 1

CGATCTAGGCTAGTATTCAATCATTTAAAA	1	22	1	TAGTATTCAA	    0.977988	-115
CATATGAAAATAATTTTAAATGATTGAATA	1	35	0	TAATTTTAAA	    0.984112	-102
TCATATGTTTTAGTTTTCAACCAAGAGTGT	1	58	1	TAGTTTTCAA	    0.993359	-79
TGTGAGGGCAAAATTGTCCAGAAAATTTTA	1	85	1	AAATTGTCCA	    0.951842	-52
ATTGTCCAGAAAATTTTAAATTCCCTTCAC	1	97	1	AAATTTTAAA	    0.977389	-40
          **********

Masking position 4
Map Score:   6.04166

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 133
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

AACTAAAACATATGAAAATAATTTTAAATGA	1	42	0	TATGAAAAAA	    0.944993	-95
CAACCAAGAGTGTGAGGGCAAAATTGTCCAG	1	75	1	TGTGAGGGAA	    0.995939	-62
AGGGCAAAATTGTCCAGAAAATTTTAAATTC	1	89	1	TGTCCAGAAA	    0.977712	-48
AAGGATGTCATGTGAAGGGAATTTAAAATTT	1	107	0	TGTGAAGGAA	    0.997608	-30
          ******** **

Masking position 3
Map Score:   1.70428

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 207
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TGCCCTCACACTCTTGGTTGAAAACTAAAA	1	65	0	CTCTTGGTTG	    0.997293	-72
ACATGACATCCTTTTGGTAGCT        	1	125	1	CTTTTGGTAG	     0.99509	-12
          **********

Masking position 5
Map Score:   0.802485

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 6
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   -9.70439e-14

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:   -9.70439e-14

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:   -9.70439e-14

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