AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i249_min_operon_pyro_reg_100.orf -o249_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	RPH00492	170	Pyrococcus_OT3
#2	RPH01473	161	Pyrococcus_OT3

Motif number 1

TAATATCGAAACGTTAAATTTTTAAATGAATTG	1	25	0	ATTAATTTTT	    0.944847	-146
AGTAGCTTGAATATTTATTTCTTTTGGAATCAG	1	77	0	ATTTATTCTT	     0.94133	-94
TATTCAAGCTACTTTAACGTCCTTAAAGACGAG	1	97	1	ATTAAGTCCT	    0.980732	-74
TAACTTTCTAATGTTAAGTTCCGAAAACTATTT	2	39	0	ATTAATTCCG	    0.980732	-123
AAGAGCTCAAAGAATAACTTTCTAATGTTAAGT	2	53	0	AATAATTTCT	    0.930623	-109
TTCATTCCTAAAGTTAAATATCTTTCTACTTTC	2	99	0	ATTAATATCT	    0.930463	-63
CCTTCTAAGCAAATTTCATTCCTAAAGTTAAAT	2	113	0	ATTTCTTCCT	    0.975431	-49
TCACCCCTAGAGATTACGTTCCTTCTAAGCAAA	2	133	0	ATTACTTCCT	     0.99086	-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

TATCGAAACGTTAAATTTTTAAATGAATTGA	1	24	0	TTAATTTTTA	    0.889105	-147
AGCTTGAATATTTATTTCTTTTGGAATCAGT	1	76	0	TTTATTCTTT	    0.870672	-95
TCAAGCTACTTTAACGTCCTTAAAGACGAGT	1	100	1	TTAAGTCCTT	    0.938378	-71
CTTTCTAATGTTAAGTTCCGAAAACTATTTT	2	38	0	TTAATTCCGA	    0.949395	-124
AGCTCAAAGAATAACTTTCTAATGTTAAGTT	2	52	0	ATAATTTCTA	    0.865642	-110
TAAATATCTTTCTACTTTCTATTTCATTAGA	2	87	0	TCTATTTCTA	    0.833585	-75
ATTCCTAAAGTTAAATATCTTTCTACTTTCT	2	98	0	TTAATATCTT	     0.83947	-64
TCTAAGCAAATTTCATTCCTAAAGTTAAATA	2	112	0	TTTCTTCCTA	     0.95368	-50
CCCCTAGAGATTACGTTCCTTCTAAGCAAAT	2	132	0	TTACTTCCTT	    0.969566	-30
          **** ******

Masking position 7
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

TTCGCAACTATCTCAATTCATTTAAAAATT	1	12	1	TCTCAATTCA	    0.954011	-159
CTGAACACCTTCTCAAATTAATATCGAAAC	1	46	0	TCTCAAATTA	    0.961746	-125
ATTTAACTCGTCTTTAAGGACGTTAAAGTA	1	106	0	TCTTTAAGGA	     0.81431	-65
CGAGTTAAATTGTCATATCATCCGATTATC	1	126	1	TGTCATATCA	    0.826225	-45
ATCATCCGATTATCAAAGCAGAACCAAGGA	1	142	1	TATCAAAGCA	    0.949151	-29
TTAGAGAAGAGCTCAAAGAATAACTTTCTA	2	62	0	GCTCAAAGAA	    0.903347	-100
TTTGAGCTCTTCTCTAATGAAATAGAAAGT	2	75	1	TCTCTAATGA	    0.967021	-87
          **********

Masking position 10
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

TTCGATATTAATTTGAGAAGGTGTTCAGAC	1	48	1	ATTTGAGAAG	    0.891928	-123
GTTCAGACTGATTCCAAAAGAAATAAATAT	1	70	1	ATTCCAAAAG	    0.977249	-101
ATATCATCCGATTATCAAAGCAGAACCAAG	1	140	1	ATTATCAAAG	    0.965358	-31
GTTCGGTGTAATAATCAAAGCC        	2	3	0	ATAATCAAAG	     0.87874	-159
TTTCTATTTCATTAGAGAAGAGCTCAAAGA	2	73	0	ATTAGAGAAG	    0.968838	-89
AGCAAATTTCATTCCTAAAGTTAAATATCT	2	109	0	ATTCCTAAAG	    0.947196	-53
          **********

Masking position 8
Map Score:   3.18017

Number of sites scoring better than the average of aligned sites = 252
Number in coding regions = 234
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


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


Motif number 7

          **********

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