AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_aful_reg_300.orf -o122_aful_300.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	    0.973583	-171
GGCAGAACTCCCAAAAAATTTAAATCACGA	1	38	0	CCAAAAAATT	    0.987251	-145
TAAAACTTAACCAAAAACGAAGTCAGGCAG	1	63	0	CCAAAAACGA	    0.950311	-120
TAACTTTAAACCTAAAACTTAACCAAAAAC	1	75	0	CCTAAAACTT	    0.994301	-108
CAAGCTGATTCAGAAAACTTTATCAAATCC	1	105	1	CAGAAAACTT	    0.955438	-78
TCATGATTTTCCTAAAAATCGGATTTGATA	1	125	0	CCTAAAAATC	     0.99172	-58
TTAGGAAAATCATGAAAAGTTGTAAAGCTA	1	140	1	CATGAAAAGT	    0.890835	-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	    0.979954	-155
TTTTAGGTTTAAAGTTACAAGCTGATTCAG	1	88	1	AAAGTTACAA	    0.968837	-95
GATTTTTAGGAAAATCATGAAAAGTTGTAA	1	135	1	AAAATCATGA	    0.968837	-48
GAAAAGTTGTAAAGCTACGAAAATTGAAGC	1	153	1	AAAGCTACGA	    0.986386	-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

ACTCCCAAAAAATTTAAATCACGATTCGGT	1	32	0	AATTTAAATC	    0.878153	-151
ACTTAACCAAAAACGAAGTCAGGCAGAACT	1	59	0	AAACGAAGTC	    0.954509	-124
TCAGCTTGTAACTTTAAACCTAAAACTTAA	1	83	0	ACTTTAAACC	    0.970156	-100
AAGCTACGAAAATTGAAGCCGTGCTCACA 	1	164	1	AATTGAAGCC	    0.992822	-19
          **********

Masking position 6
Map Score:   1.00138

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 100
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


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