AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_pyro_reg_300.orf -o149_pyro_300.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

CCTCCTCAACCATTGGTTTAAAACGCTATT	1	18	1	CATTGGTTTA	    0.982748	-207
AAGGAAGTAAAATAGCGTTTTAAACCAATG	1	28	0	AATAGCGTTT	    0.881099	-197
TAGAAATCTTAAAAGGGTTTTTTAAAGCTT	1	87	1	AAAAGGGTTT	    0.900003	-138
ATTTTCAATTCTAAGCTTTAAAAAACCCTT	1	99	0	CTAAGCTTTA	    0.947234	-126
AGTGTTCAACCTTTGGTTTAATATCTTTGG	1	132	1	CTTTGGTTTA	    0.977661	-93
GGTTTAATATCTTTGGTTTTGGTGATACAC	1	146	1	CTTTGGTTTT	    0.982752	-79
TTGTGCCCCAAAATGCTTTTAAATATTCAC	1	178	1	AAATGCTTTT	    0.647563	-47
          **********

Masking position 8
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	    0.988741	-210
AAAAGTGTTCAACCTTTGGTTTAATATCTT	1	129	1	AACCTTTGGT	      0.9968	-96
TTTGGTTTAATATCTTTGGTTTTGGTGATA	1	143	1	TATCTTTGGT	    0.987814	-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

TGGTTTAAAACGCTATTTTACTTCCTTATT	1	31	1	CGCTATTTTA	    0.987361	-194
AAGATTTCTACGCTATCTTCTCTCTGAAGA	1	67	0	CGCTATCTTC	     0.97436	-158
AAGATAGCGTAGAAATCTTAAAAGGGTTTT	1	78	1	AGAAATCTTA	    0.912578	-147
CCAAAGGTTGAACACTTTTATTTTCAATTC	1	118	0	AACACTTTTA	    0.912628	-107
ACCTCCACGTAGCTCTTTTAGTGAATATTT	1	198	0	AGCTCTTTTA	    0.987365	-27
          **********

Masking position 6
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

AAAACGCTATTTTACTTCCTTATTTTTTCT	1	37	1	TTTACTTCCT	    0.957021	-188
CTTCCTTATTTTTTCTTCTTCAGAGAGAAG	1	51	1	TTTTCTTCTT	    0.935049	-174
CTTTTAAGATTTCTACGCTATCTTCTCTCT	1	72	0	TTCTACGCTA	     0.90935	-153
CACTTTTATTTTCAATTCTAAGCTTTAAAA	1	106	0	TTCAATTCTA	    0.966935	-119
      TTCCTTCACCTCCACGTAGCTCTT	1	211	0	TTCACCTCCA	    0.987274	-14
          **********

Masking position 2
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