AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i249_min_operon_pyro_reg_300.orf -o249_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	RPH00492	170	Pyrococcus_OT3
#2	RPH01473	161	Pyrococcus_OT3

Motif number 1

TAATATCGAAACGTTAAATTTTTAAATGAATTG	1	25	0	ATTAATTTTT	    0.939936	-146
AGTAGCTTGAATATTTATTTCTTTTGGAATCAG	1	77	0	ATTTATTCTT	    0.936127	-94
TATTCAAGCTACTTTAACGTCCTTAAAGACGAG	1	97	1	ATTAAGTCCT	    0.978944	-74
TAACTTTCTAATGTTAAGTTCCGAAAACTATTT	2	39	0	ATTAATTCCG	    0.978944	-123
AAGAGCTCAAAGAATAACTTTCTAATGTTAAGT	2	53	0	AATAATTTCT	    0.924553	-109
TTCATTCCTAAAGTTAAATATCTTTCTACTTTC	2	99	0	ATTAATATCT	    0.924408	-63
CCTTCTAAGCAAATTTCATTCCTAAAGTTAAAT	2	113	0	ATTTCTTCCT	    0.973168	-49
TCACCCCTAGAGATTACGTTCCTTCTAAGCAAA	2	133	0	ATTACTTCCT	    0.990004	-29
          *  **** *****

Masking position 1
Map Score:   7.15138

Number of sites scoring better than the average of aligned sites = 548
Number in coding regions = 498
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

TCAATTCATTTAAAAATTTAACGTTTCGATA	1	24	1	TAAAAATTAA	    0.898572	-147
ACTGATTCCAAAAGAAATAAATATTCAAGCT	1	76	1	AAAGAATAAA	    0.881584	-95
ACTCGTCTTTAAGGACGTTAAAGTAGCTTGA	1	100	0	AAGGACTTAA	    0.943945	-71
AAAATAGTTTTCGGAACTTAACATTAGAAAG	2	38	1	TCGGAATTAA	    0.954016	-124
AACTTAACATTAGAAAGTTATTCTTTGAGCT	2	52	1	TAGAAATTAT	    0.876919	-110
TCTAATGAAATAGAAAGTAGAAAGATATTTA	2	87	1	TAGAAATAGA	    0.847077	-75
AGAAAGTAGAAAGATATTTAACTTTAGGAAT	2	98	1	AAGATATTAA	    0.852569	-64
TATTTAACTTTAGGAATGAAATTTGCTTAGA	2	112	1	TAGGAAGAAA	    0.957927	-50
ATTTGCTTAGAAGGAACGTAATCTCTAGGGG	2	132	1	AAGGAAGTAA	    0.972399	-30
          ****** ****

Masking position 5
Map Score:   4.85371

Number of sites scoring better than the average of aligned sites = 1162
Number in coding regions = 1044
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 3

AATTTTTAAATGAATTGAGATAGTTGCGAA	1	12	0	TGAATTGAGA	    0.963382	-159
GTTTCGATATTAATTTGAGAAGGTGTTCAG	1	46	1	TAATTTGAGA	    0.969585	-125
TACTTTAACGTCCTTAAAGACGAGTTAAAT	1	106	1	TCCTTAAAGA	    0.843279	-65
GATAATCGGATGATATGACAATTTAACTCG	1	126	0	TGATATGACA	    0.857726	-45
TCCTTGGTTCTGCTTTGATAATCGGATGAT	1	142	0	TGCTTTGATA	    0.959469	-29
TAGAAAGTTATTCTTTGAGCTCTTCTCTAA	2	62	1	TTCTTTGAGC	    0.922205	-100
ACTTTCTATTTCATTAGAGAAGAGCTCAAA	2	75	0	TCATTAGAGA	    0.973548	-87
          **********

Masking position 8
Map Score:   2.05598

Number of sites scoring better than the average of aligned sites = 452
Number in coding regions = 419
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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