AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i347_weak8_pyro_reg_100.orf -o347_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	RPH00141	201	Pyrococcus_OT3

Motif number 1

ATTACCTGTAGGGTCCCGCGGTAGCCTAGCC	1	88	1	GGGTCCGCGG	    0.999789	-114
AGCCTAGCCTGGGAGTGGCGGCGGACTGTAG	1	110	1	GGGAGTGCGG	    0.997783	-92
ATTTGAACCGGGGACCTGCGGATCTACAGTC	1	133	0	GGGACCGCGG	    0.999792	-69
AGAATTCTGGTGGTCCCGCGGCCCGGATTTG	1	159	0	TGGTCCGCGG	    0.999172	-43
          ****** ****

Masking position 8
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

TAAAGTTTTCGCGAGGAGTTTTAAACAAGG	1	28	0	GCGAGGAGTT	    0.921132	-174
GCTAGGCTACCGCGGGACCCTACAGGTAAT	1	88	0	CGCGGGACCC	    0.993254	-114
GGTAGCCTAGCCTGGGAGTGGCGGCGGACT	1	107	1	CCTGGGAGTG	    0.975153	-95
CTGGGAGTGGCGGCGGACTGTAGATCCGCA	1	118	1	CGGCGGACTG	    0.991625	-84
CGGATTTGAACCGGGGACCTGCGGATCTAC	1	137	0	CCGGGGACCT	    0.997012	-65
TGGTCCCGCGGCCCGGATTTGAACCGGGGA	1	150	0	GCCCGGATTT	    0.921132	-52
AAATCCGGGCCGCGGGACCACCAGAATTCT	1	160	1	CGCGGGACCA	    0.990146	-42
          **********

Masking position 7
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	     0.97331	-194
TTTAAAACTCCTCGCGAAAACTTTATAAAC	1	33	1	CTCGCGAAAA	    0.990716	-169
CCAAAATCATCTCACTAAATGTGGGTTTAT	1	57	0	CTCACTAAAT	    0.973294	-145
CCTACAGGTAATCCCAAAATCATCTCACTA	1	70	0	ATCCCAAAAT	    0.971974	-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