AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_aful_reg_100.orf -o099_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG48533	126	Archaeoglobus_fulgidus

Motif number 1

     ATACCATCGTGAAAATCTAAATATTT	1	6	1	ATCTGAAAAT	    0.963815	-121
TAGTTAGTAAATGTTGTATATACCATCCCTT	1	50	0	ATGTGTATAT	    0.994416	-77
TACTAACTATATGATGTATATTTTAATGCGA	1	72	1	ATGTGTATAT	    0.997768	-55
TTAATGCGACAAGATGTATATCTCTCAGATA	1	94	1	AAGTGTATAT	    0.995018	-33
          *** *******

Masking position 5
Map Score:   6.59302

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 22
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AAAATCTAAATATTTATGCGTTTTCCCTAA	1	22	1	TATTTATGCG	    0.994662	-105
ATGATGTATATTTTAATGCGACAAGATGTA	1	82	1	TTTTAATGCG	     0.99467	-45
          **********

Masking position 6
Map Score:   0.585025

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 8
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

CCCTAAGGGATGGTATATACAACATTTACT	1	46	1	TGGTATATAC	    0.989083	-81
CTTGTCGCATTAAAATATACATCATATAGT	1	77	0	TAAAATATAC	    0.976182	-50
GTATTATCTGAGAGATATACATCTTGTCGC	1	99	0	AGAGATATAC	    0.989083	-28
          **********

Masking position 5
Map Score:   0.575827

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 24
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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