AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i329_not_clear4_pyro_reg_300.orf -o329_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	RPH00798	50	Pyrococcus_OT3
#2	RPH00797	116	Pyrococcus_OT3

Motif number 1

CTGGAGAAATTATCCAATGAAGGAAGTTAA	1	22	0	TATCCAATGA	    0.997381	-29
TTGGATAATTTCTCCAGTGATGAAAA    	1	35	1	TCTCCAGTGA	    0.993092	-16
CCCACTCCCAGTTCCAATGAATTTGTTAAG	2	20	1	GTTCCAATGA	    0.985616	-97
ATGGATATTTTATCCCGTAAGGAACTTAAC	2	44	0	TATCCCGTAA	    0.978931	-73
CCTGGGATTCTATTCTATGAAACAATATTT	2	87	0	TATTCTATGA	    0.966822	-30
          **********

Masking position 3
Map Score:   5.82137

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 131
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

AGAAATTATCCAATGAAGGAAGTTAAAAAG	1	18	0	CAATGAAGGA	    0.948706	-33
GATAATTTCTCCAGTGATGAAAA       	1	38	1	CCAGTGATGA	    0.993607	-13
GATATTTTATCCCGTAAGGAACTTAACAAA	2	41	0	CCCGTAAGGA	    0.987764	-76
TTAAGAGTTGCTAGTATGGATATTTTATCC	2	59	0	CTAGTATGGA	    0.972546	-58
GAATAGAATCCCAGGGGTGAGAAAA     	2	102	1	CCAGGGGTGA	    0.990812	-15
          **********

Masking position 10
Map Score:   3.84955

Number of sites scoring better than the average of aligned sites = 517
Number in coding regions = 485
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

TTTTTAACTTCCTTCATTGGATAATTTCTC	1	19	1	CCTTCATTGG	    0.995769	-32
       TTTTCATCACTGGAGAAATTATC	1	38	0	TCATCACTGG	    0.989952	-13
GAACTTAACAAATTCATTGGAACTGGGAGT	2	23	0	AATTCATTGG	    0.987977	-94
          **********

Masking position 6
Map Score:   1.48185

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 68
Number in noncoding regions = 4
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:   -2.10731e-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 5

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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