AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i032_Pyruvate_Synthase_pyro_reg_300.orf -o032_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	RPH01532	194	Pyrococcus_OT3

Motif number 1

AATTAACCTTTTTATCCAAATCATCTTCCAT	1	43	1	TTTTCCAAAT	    0.988395	-152
TATTTGAAAGTTTATCAAAATTTTCGAGCAT	1	76	0	TTTTCAAAAT	    0.971757	-119
CGTTGTTTCTTTTTTGAACATTAATGTCCAT	1	122	1	TTTTGAACAT	    0.934364	-73
GATGTTTACATTTGTCAACATTTAAAGCTTT	1	158	0	TTTTCAACAT	    0.994526	-37
          *** *******

Masking position 5
Map Score:   5.54451

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 25
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

 TTCTACCACCATCCTAAGATTCTGGGTTCGTTA	1	10	1	CTCCTAATCT	    0.996925	-185
TCCAAATCATCTTCCATAAATGCTCGAAAATTTT	1	57	1	CTCCAAATCT	     0.99878	-138
TTTTGATAAACTTTCAAATATCCTCCCATTTTGC	1	87	1	CTTCAAATCT	    0.995173	-108
CATTAATGTCCATCTACAAAAGCTTTAAATGTTG	1	140	1	CTCTAAAACT	    0.987892	-55
          * **** * ** **

Masking position 8
Map Score:   2.80603

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 38
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

CCCAGAATCTTAGGATGGTGGTAGAA    	1	7	0	TAGGATGGTG	    0.976615	-188
AGCATTTATGGAAGATGATTTGGATAAAAA	1	51	0	GAAGATGATT	    0.949496	-144
ACGAGCAAAATGGGAGGATATTTGAAAGTT	1	95	0	TGGGAGGATA	    0.987222	-100
ACATCAGAGTGGGGATGATAA         	1	184	1	GGGGATGATA	    0.995108	-11
          **********

Masking position 5
Map Score:   0.997031

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 311
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

CCATAAATGCTCGAAAATTTTGATAAACTT	1	70	1	TCGAAAATTT	    0.969202	-125
GGGAGGATATTTGAAAGTTTATCAAAATTT	1	84	0	TTGAAAGTTT	     0.98778	-111
TTTGTCAACATTTAAAGCTTTTGTAGATGG	1	149	0	TTTAAAGCTT	    0.968407	-46
TCATCCCCACTCTGATGTTTACATTTGTCA	1	172	0	TCTGATGTTT	    0.949406	-23
          **********

Masking position 5
Map Score:   0.440867

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 201
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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