AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_pyro_reg_100.orf -o316_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	RPH01790	122	Pyrococcus_OT3

Motif number 1

CACCGGGCCTGGCGAGGAGGTGAAGGAG  	1	9	0	GGCGAGGAGG	    0.998932	-114
CTCCTCGCCAGGCCCGGTGGGTTCCCTTTC	1	20	1	GGCCCGGTGG	    0.996768	-103
CACTTAGCACGGCTCGGGGGTGTCCGAAAG	1	45	0	GGCTCGGGGG	    0.996768	-78
          **********

Masking position 6
Map Score:   6.23369

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 12
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 2

GCCTGGCGAGGAGGTGAAGGAG         	1	2	0	GAGGTGAGGA	    0.984988	-121
GGAACCCACCGGGCCTGGCGAGGAGGTGAAG	1	14	0	GGGCCTGCGA	    0.995406	-109
GCACGGCTCGGGGGTGTCCGAAAGGGAACCC	1	38	0	GGGGTGCCGA	    0.997473	-85
GGACACCCCCGAGCCGTGCTAAGTGATCATG	1	50	1	GAGCCGGCTA	    0.991564	-73
          ****** ****

Masking position 11
Map Score:   0.839235

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 86
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

TAAAGATTTTTAAAGGTACTTTATAACCCA	1	87	0	TAAAGGTACT	    0.985177	-36
GAATCTTAAGTAAAGATTTTTAAAGGTACT	1	97	0	TAAAGATTTT	    0.975889	-26
AAATCTTTACTTAAGATTCCAAGTG     	1	108	1	TTAAGATTCC	     0.98508	-15
          **********

Masking position 4
Map Score:   0.12119

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 97
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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