AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_pyro_reg_100.orf -o149_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	RPH01313	224	Pyrococcus_OT3

Motif number 1

AATAGCGTTTTAAACCAATGGTTGAGGAGG	1	18	0	TAAACCAATG	    0.979949	-207
CATTGGTTTAAAACGCTATTTTACTTCCTT	1	28	1	AAACGCTATT	    0.878254	-197
AAGCTTTAAAAAACCCTTTTAAGATTTCTA	1	87	0	AAACCCTTTT	    0.894872	-138
AAGGGTTTTTTAAAGCTTAGAATTGAAAAT	1	99	1	TAAAGCTTAG	    0.940304	-126
CCAAAGATATTAAACCAAAGGTTGAACACT	1	132	0	TAAACCAAAG	    0.974056	-93
GTGTATCACCAAAACCAAAGATATTAAACC	1	146	0	AAAACCAAAG	    0.979953	-79
GTGAATATTTAAAAGCATTTTGGGGCACAA	1	178	0	AAAAGCATTT	    0.659729	-47
          **********

Masking position 3
Map Score:   7.37715

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 292
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 2

AAACCTCCTCAACCATTGGTTTAAAACGCT	1	15	1	AACCATTGGT	    0.988751	-210
AAAAGTGTTCAACCTTTGGTTTAATATCTT	1	129	1	AACCTTTGGT	    0.996791	-96
TTTGGTTTAATATCTTTGGTTTTGGTGATA	1	143	1	TATCTTTGGT	    0.987757	-82
          **********

Masking position 2
Map Score:   3.75548

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 17
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

AATAAGGAAGTAAAATAGCGTTTTAAACCA	1	31	0	TAAAATAGCG	    0.988497	-194
TCTTCAGAGAGAAGATAGCGTAGAAATCTT	1	67	1	GAAGATAGCG	    0.976637	-158
AAAACCCTTTTAAGATTTCTACGCTATCTT	1	78	0	TAAGATTTCT	    0.919875	-147
GAATTGAAAATAAAAGTGTTCAACCTTTGG	1	118	1	TAAAAGTGTT	    0.919931	-107
AAATATTCACTAAAAGAGCTACGTGGAGGT	1	198	1	TAAAAGAGCT	    0.988501	-27
          **********

Masking position 5
Map Score:   2.22574

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 339
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

AGAAAAAATAAGGAAGTAAAATAGCGTTTT	1	37	0	AGGAAGTAAA	    0.957408	-188
CTTCTCTCTGAAGAAGAAAAAATAAGGAAG	1	51	0	AAGAAGAAAA	    0.935619	-174
AGAGAGAAGATAGCGTAGAAATCTTAAAAG	1	72	1	TAGCGTAGAA	    0.910125	-153
TTTTAAAGCTTAGAATTGAAAATAAAAGTG	1	106	1	TAGAATTGAA	    0.967229	-119
AAGAGCTACGTGGAGGTGAAGGAA      	1	211	1	TGGAGGTGAA	    0.987392	-14
          **********

Masking position 9
Map Score:   0.816793

Number of sites scoring better than the average of aligned sites = 783
Number in coding regions = 700
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 5

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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 7

          **********

No masking
Map Score:   7.34864e-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