AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i347_weak8_pyro_reg_300.orf -o347_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	RPH00141	201	Pyrococcus_OT3

Motif number 1

GGCTAGGCTACCGCGGGACCCTACAGGTAAT	1	88	0	CCGCGGACCC	    0.999816	-114
CTACAGTCCGCCGCCACTCCCAGGCTAGGCT	1	110	0	CCGCACTCCC	     0.99808	-92
GACTGTAGATCCGCAGGTCCCCGGTTCAAAT	1	133	1	CCGCGGTCCC	     0.99982	-69
CAAATCCGGGCCGCGGGACCACCAGAATTCT	1	159	1	CCGCGGACCA	    0.999283	-43
          **** ******

Masking position 4
Map Score:   11.9796

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

CCTTGTTTAAAACTCCTCGCGAAAACTTTA	1	28	1	AACTCCTCGC	    0.922326	-174
ATTACCTGTAGGGTCCCGCGGTAGCCTAGC	1	88	1	GGGTCCCGCG	    0.993362	-114
AGTCCGCCGCCACTCCCAGGCTAGGCTACC	1	107	0	CACTCCCAGG	     0.97555	-95
TGCGGATCTACAGTCCGCCGCCACTCCCAG	1	118	0	CAGTCCGCCG	    0.991761	-84
GTAGATCCGCAGGTCCCCGGTTCAAATCCG	1	137	1	AGGTCCCCGG	    0.997061	-65
TCCCCGGTTCAAATCCGGGCCGCGGGACCA	1	150	1	AAATCCGGGC	    0.922326	-52
AGAATTCTGGTGGTCCCGCGGCCCGGATTT	1	160	0	TGGTCCCGCG	    0.990306	-42
          **********

Masking position 4
Map Score:   6.81948

Number of sites scoring better than the average of aligned sites = 231
Number in coding regions = 191
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

TTAAACAAGGATAGCGAAATTTGCTTT   	1	8	0	ATAGCGAAAT	    0.973128	-194
TTTAAAACTCCTCGCGAAAACTTTATAAAC	1	33	1	CTCGCGAAAA	    0.990619	-169
CCAAAATCATCTCACTAAATGTGGGTTTAT	1	57	0	CTCACTAAAT	    0.973018	-145
CCTACAGGTAATCCCAAAATCATCTCACTA	1	70	0	ATCCCAAAAT	    0.971689	-132
          **********

Masking position 7
Map Score:   0.879554

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 63
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   6.63809e-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 5

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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