AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i309_aful_mthe_100.orf -o309_aful_mthe_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	RAG23596	126	Archaeoglobus_fulgidus

Motif number 1

TCAGCTTTAAAACCTTTTCAGGTGAGAATT	1	26	1	AACCTTTTCA	    0.994993	-101
TTTATGTTTAAAAATTCTCACCTGAAAAGG	1	38	0	AAAATTCTCA	    0.963732	-89
AAACATAAACAACATTATCTATAACTTCTT	1	59	1	AACATTATCT	    0.984901	-68
CATTATCTATAACTTCTTCACGATAGCGAG	1	71	1	AACTTCTTCA	    0.990697	-56
AAAGAATATTAACTTTTTCTCGCTATCGTG	1	89	0	AACTTTTTCT	    0.993969	-38
          **********

Masking position 5
Map Score:   7.46811

Number of sites scoring better than the average of aligned sites = 338
Number in coding regions = 301
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

          GATGTTAAATTGTCGTCAGCTT	1	1	1	GTGTTAATTG	    0.983538	-126
CACCTGAAAAGGTTTTAAAGCTGACGACAATT	1	18	0	GTTTTAAGCT	    0.990867	-109
TATAGATAATGTTGTTTATGTTTAAAAATTCT	1	50	0	GTGTTATGTT	    0.993966	-77
TTCTTTCAGAGTTTTTGAAGTTCA        	1	113	1	GTTTTAAGTT	    0.996265	-14
          * **** *****

Masking position 6
Map Score:   2.47909

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 112
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

          **********

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 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