AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_mjan_pyro_300.orf -o129_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	RPH00900	127	Pyrococcus_OT3

Motif number 1

GGTGATACCTTTAAAAAGCTTAGAAAAAACA	1	50	0	TTAAAAACTT	    0.996383	-78
AAACATTCTGTTAAGTAACTTCACTTATCCG	1	80	0	TTAAGTACTT	    0.989204	-48
GATTGTTAACTTAAAAACATTCTGTTAAGTA	1	94	0	TTAAAAAATT	    0.985781	-34
TGTTTTTAAGTTAACAATCTTGAGGATTAGT	1	106	1	TTAACAACTT	    0.995699	-22
          ******* ***

Masking position 7
Map Score:   5.63339

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 129
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

CGAAGAGAGCTCTAGGGATAACT       	1	4	0	TCTAGGGATA	    0.824968	-124
AGAAAAAACATCACGCGAGATGGAAGCGAA	1	30	0	TCACGCGAGA	    0.518388	-98
TTTAAAGGTATCACCGGATAAGTGAAGTTA	1	66	1	TCACCGGATA	    0.701274	-62
          **********

Masking position 8
Map Score:   1.59773

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 4
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

ACGCGAGATGGAAGCGAAGAGAGCTCTAGG	1	18	0	GAAGCGAAGA	    0.985955	-110
ATACCTTTAAAAAGCTTAGAAAAAACATCA	1	47	0	AAAGCTTAGA	    0.930286	-81
TATCACCGGATAAGTGAAGTTACTTAACAG	1	74	1	TAAGTGAAGT	    0.987245	-54
TTAAAAACATTCTGTTAAGTAACTTCACTT	1	85	0	TCTGTTAAGT	    0.907466	-43
AGAATGTTTTTAAGTTAACAATCTTGAGGA	1	102	1	TAAGTTAACA	    0.966875	-26
          **********

Masking position 8
Map Score:   1.39429

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 377
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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:   1.87173e-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