AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_aful_reg_100.orf -o122_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	RAG31144	182	Archaeoglobus_fulgidus

Motif number 1

TGGGACACTTCCTACAAATCACCGAATCGT	1	12	1	CCTACAAATC	      0.9697	-171
GGCAGAACTCCCAAAAAATTTAAATCACGA	1	38	0	CCAAAAAATT	    0.985346	-145
TAAAACTTAACCAAAAACGAAGTCAGGCAG	1	63	0	CCAAAAACGA	    0.943206	-120
TAACTTTAAACCTAAAACTTAACCAAAAAC	1	75	0	CCTAAAACTT	    0.993443	-108
CAAGCTGATTCAGAAAACTTTATCAAATCC	1	105	1	CAGAAAACTT	    0.949026	-78
TCATGATTTTCCTAAAAATCGGATTTGATA	1	125	0	CCTAAAAATC	    0.990477	-58
TTAGGAAAATCATGAAAAGTTGTAAAGCTA	1	140	1	CATGAAAAGT	    0.876331	-43
          **********

Masking position 6
Map Score:   9.19732

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 275
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

CCAAAAAATTTAAATCACGATTCGGTGATT	1	28	0	TAAATCACGA	    0.980901	-155
TTTTAGGTTTAAAGTTACAAGCTGATTCAG	1	88	1	AAAGTTACAA	    0.970294	-95
GATTTTTAGGAAAATCATGAAAAGTTGTAA	1	135	1	AAAATCATGA	    0.970294	-48
GAAAAGTTGTAAAGCTACGAAAATTGAAGC	1	153	1	AAAGCTACGA	    0.987034	-30
          **********

Masking position 7
Map Score:   1.55218

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 103
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACCGAATCGTGATTTAAATTTTTTGGGAGT	1	32	1	GATTTAAATT	    0.911494	-151
AGTTCTGCCTGACTTCGTTTTTGGTTAAGT	1	59	1	GACTTCGTTT	    0.965587	-124
CTTCGTTTTTGGTTAAGTTTTAGGTTTAAA	1	71	1	GGTTAAGTTT	    0.942824	-112
TTAAGTTTTAGGTTTAAAGTTACAAGCTGA	1	83	1	GGTTTAAAGT	    0.969459	-100
 TGTGAGCACGGCTTCAATTTTCGTAGCTT	1	164	0	GGCTTCAATT	    0.988192	-19
          **********

Masking position 4
Map Score:   2.44508

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 97
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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