AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__pyro_reg_100.orf -o056_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	RPH01583	215	Pyrococcus_OT3

Motif number 1

ATAGAGCAAGAGATTTATGGACAAAAGTAAA	1	16	0	AGTTTATGGA	    0.910551	-200
AAAAATTGTGAACATTATAAAATAGGAGTAC	1	48	0	AAATTATAAA	    0.855028	-168
ATATAATACTAAGATTTTCGAAAAAAATTGT	1	70	0	AAATTTTCGA	    0.993723	-146
AAATTTTAGAAAATTTTTCTATATAATACTA	1	90	0	AATTTTTCTA	    0.902676	-126
TAAGATCTTAAAAATTTTAGAAAATTTTTCT	1	101	0	AAATTTTAGA	    0.990167	-115
TTATCGAATAAAATTTTAAGATCTTAAAAAT	1	117	0	AATTTTAAGA	    0.943476	-99
ATTTTCGAGAAATATCTTGGATTATCGAATA	1	138	0	AAATCTTGGA	     0.97368	-78
CTAGGTATATAAAATTTTCGAGAAATATCTT	1	151	0	AAATTTTCGA	    0.993724	-65
GTGGGTGATGAATATTAAGGAAGGAAATA  	1	197	1	AAATTAAGGA	    0.963293	-19
          ** ********

Masking position 5
Map Score:   13.2454

Number of sites scoring better than the average of aligned sites = 355
Number in coding regions = 283
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

ACACTTTACTTTTGTCCATAAATCTCTTGC	1	12	1	TTTGTCCATA	    0.940342	-204
GTTCACAATTTTTTTCGAAAATCTTAGTAT	1	66	1	TTTTTCGAAA	    0.968681	-150
TTTTAGAAAATTTTTCTATATAATACTAAG	1	88	0	TTTTTCTATA	    0.982783	-128
GATCTTAAAAATTTTAGAAAATTTTTCTAT	1	99	0	ATTTTAGAAA	    0.917126	-117
TCTTAAAATTTTATTCGATAATCCAAGATA	1	127	1	TTATTCGATA	    0.972499	-89
ATCCAAGATATTTCTCGAAAATTTTATATA	1	147	1	TTTCTCGAAA	    0.723468	-69
TTTCTCGAAAATTTTATATACCTAGGTTCA	1	157	1	ATTTTATATA	    0.872328	-59
          **********

Masking position 8
Map Score:   9.10463

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 176
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

  TACACTTTACTTTTGTCCATAAATCTCT	1	9	1	ACTTTTGTCC	    0.945885	-207
CTCTTGCTCTATTGTACTCCTATTTTATAA	1	35	1	ATTGTACTCC	    0.957353	-181
AATGTTCACAATTTTTTTCGAAAATCTTAG	1	63	1	ATTTTTTTCG	    0.987878	-153
AGATCTTAAAATTTTATTCGATAATCCAAG	1	124	1	ATTTTATTCG	    0.982721	-92
ATAATCCAAGATATTTCTCGAAAATTTTAT	1	144	1	ATATTTCTCG	    0.955954	-72
         TATTTCCTTCCTTAATATTCA	1	205	0	ATTTCCTTCC	    0.945885	-11
          **********

Masking position 8
Map Score:   3.95037

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 156
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

          **********

No masking
Map Score:   3.08538e-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:   3.08538e-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:   3.08538e-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