AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i155_Hydrogenase_2_aful_reg_100.orf -o155_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	RAG48483	139	Archaeoglobus_fulgidus

Motif number 1

TTGAAAAAAGTTAATAAATTAATATGTTAA	1	18	0	TTAATAAATT	     0.92035	-122
CAATTTTTAGTTGAAAAAAGTTAATAAATT	1	28	0	TTGAAAAAAG	    0.928984	-112
CTTTTTTCAACTAAAAATTGCACAATTTTT	1	38	1	CTAAAAATTG	    0.979645	-102
AATAGATGCATGAAAAATTGTGCAATTTTT	1	50	0	TGAAAAATTG	    0.990638	-90
ATTGTAAAAGTTAATAGATGCATGAAAAAT	1	62	0	TTAATAGATG	    0.964802	-78
ATTACATACATGAAAAATTGTAAAAGTTAA	1	78	0	TGAAAAATTG	    0.990638	-62
ATGTAATTATTTATAAAATGATTTAAAGCT	1	101	1	TTATAAAATG	    0.977015	-39
          **********

Masking position 6
Map Score:   9.92246

Number of sites scoring better than the average of aligned sites = 326
Number in coding regions = 229
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 2

TAGTTAACATATTAATTTATTAACTTTTTT	1	15	1	ATTAATTTAT	    0.861246	-125
TATTAACTTTTTTCAACTAAAAATTGCACA	1	32	1	TTTCAACTAA	    0.923897	-108
TTGCACAATTTTTCATGCATCTATTAACTT	1	55	1	TTTCATGCAT	    0.943352	-85
TTTTACAATTTTTCATGTATGTAATTATTT	1	83	1	TTTCATGTAT	    0.942706	-57
GAATTCCAGCTTTAAATCATTTTATAAATA	1	108	0	TTTAAATCAT	    0.957392	-32
          **********

Masking position 5
Map Score:   3.37468

Number of sites scoring better than the average of aligned sites = 197
Number in coding regions = 171
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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