AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_mjan_pyro_300.orf -o038_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	RPH00721	54	Pyrococcus_OT3
#2	RPH00717	92	Pyrococcus_OT3

Motif number 1

TTTGACTATTATAGTCAAAAC         	2	2	0	ATAGTCAAAA	    0.997699	-91
TTTGACTATAATAGTCAAAAACTTAATAAA	2	13	1	ATAGTCAAAA	    0.997699	-80
GCTCACTCACATTGTCGAAAATTTTATTAA	2	35	0	ATTGTCGAAA	      0.9931	-58
GTAATGTTGTAGAGTCTAAAAATCTTCAAG	2	64	0	AGAGTCTAAA	    0.993117	-29
          **********

Masking position 5
Map Score:   9.17926

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 18
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

CACCAACCTTAAAATTGTTTAGTTCAAAGTAT	1	28	0	AAATTGTTAG	    0.992367	-27
AAACAATTTTAAGGTTGGTGAGAGT       	1	40	1	AAGTTGGTAG	     0.99821	-15
CATTGTCGAAAATTTTATTAAGTTTTTGACTA	2	24	0	AATTTATTAG	    0.982965	-69
AATTTTCGACAATGTGAGTGAGCTTGAAGATT	2	42	1	AAGTGAGTAG	     0.99111	-51
AAAGATCAGTAATGTTGTAGAGTCTAAAAATC	2	70	0	AAGTTGTAAG	    0.993671	-23
          ** ****** **

Masking position 5
Map Score:   6.12752

Number of sites scoring better than the average of aligned sites = 148
Number in coding regions = 139
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 3

          **********

No masking
Map Score:   2.15595e-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 4

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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