AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_pyro_reg_300.orf -o012_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	RPH00972	82	Pyrococcus_OT3
#2	RPH01394	71	Pyrococcus_OT3

Motif number 1

AAATTTTCAGAAAGGTTAATAAGATTAAGGA	1	26	0	AAAGGTTAAA	    0.995879	-57
AACCTTTCTGAAAATTTAAAAAAGTGAGGAT	1	40	1	AAAATTTAAA	    0.977218	-43
TGAAACTTTGAATGGTGAAAAGG        	2	3	0	AATGGTGAAA	    0.970663	-69
TTCACCATTCAAAGTTTCAAATAAGGTTTTT	2	15	1	AAAGTTTCAA	    0.990181	-57
TTTTAGAATTACAGTTTAATATAAAAACCTT	2	37	0	ACAGTTTAAA	    0.990181	-35
          ********* *

Masking position 6
Map Score:   5.90373

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 126
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

CAGAAAGGTTAATAAGATTAAGGATGAAGG	1	20	0	AATAAGATTA	    0.967935	-63
CTGAAAATTTAAAAAAGTGAGGATGAACTC	1	47	1	AAAAAAGTGA	    0.908312	-36
ATGAACTCTCAATGGGGTTTTAAA      	1	69	1	AATGGGGTTT	    0.966704	-14
CAAAGTTTCAAATAAGGTTTTTATATTAAA	2	24	1	AATAAGGTTT	    0.990961	-48
GTAATTCTAAAATTAGGTGATCTGAC    	2	56	1	AATTAGGTGA	    0.985362	-16
          **********

Masking position 8
Map Score:   3.37634

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 259
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 3

TTTTTAAATTTTCAGAAAGGTTAATAAGAT	1	32	0	TTCAGAAAGG	    0.981928	-51
TGAGGATGAACTCTCAATGGGGTTTTAAA 	1	64	1	CTCTCAATGG	    0.995781	-19
TTATTTGAAACTTTGAATGGTGAAAAGG  	2	9	0	CTTTGAATGG	    0.993098	-63
          **********

Masking position 6
Map Score:   1.16515

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 42
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 4

 CGGAAGCTCCCTTCATCCTTAATCTTATT	1	10	1	CCTTCATCCT	    0.997417	-73
CCCCATTGAGAGTTCATCCTCACTTTTTTA	1	56	0	AGTTCATCCT	    0.995552	-27
          **********

Masking position 6
Map Score:   0.278564

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 16
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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