AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_mjan_pyro_100.orf -o227_mjan_pyro_100.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	    0.989353	-119
AAGAATTTACCTTCTTTAGGTATTTAAAGC	1	25	1	CTTCTTTAGG	    0.981661	-104
TATTTAAAGCTTGCTTTTGGCTTGAGGTTT	1	45	1	TTGCTTTTGG	    0.996234	-84
TATTAGGATGTCGGTTTTGGCAACTATGAA	1	73	0	TCGGTTTTGG	    0.984789	-56
CATCCAGGAATTTTATTAGGATGTCGGTTT	1	86	0	TTTTATTAGG	    0.959053	-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

         TCTTCATCACCAAAAAGAATT	1	2	1	CTTCATCACC	    0.991076	-127
ACCAAAAAGAATTTACCTTCTTTAGGTATT	1	19	1	ATTTACCTTC	    0.978932	-110
TCACCTCCTTAATCTCCATCCAGGAATTTT	1	102	0	AATCTCCATC	    0.966567	-27
     TCACCCTTCACCTCCTTAATCTCCA	1	114	0	CTTCACCTCC	    0.997741	-15
          **********

Masking position 3
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

CCTAAAGAAGGTAAATTCTTTTTGGTGATG	1	15	0	GTAAATTCTT	    0.936497	-114
AAAGCAAGCTTTAAATACCTAAAGAAGGTA	1	32	0	TTAAATACCT	    0.990112	-97
TTTTGGCAACTATGAAACCTCAAGCCAAAA	1	59	0	TATGAAACCT	    0.901983	-70
GACATCCTAATAAAATTCCTGGATGGAGAT	1	91	1	TAAAATTCCT	    0.990019	-38
          **********

Masking position 5
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