AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i314_mixed28_aful_reg_100.orf -o314_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	RAG50267	46	Archaeoglobus_fulgidus
#2	RAG23554	37	Archaeoglobus_fulgidus
#3	RAG23596	126	Archaeoglobus_fulgidus
#4	RAG49167	48	Archaeoglobus_fulgidus

Motif number 1

          GTAAAGTTTTTTTGATTCAAAT	1	1	1	GTAAATTTTT	    0.933865	-46
GAAGGCATCAGAAAAAGTTGATTTGAATCAAA	1	21	0	GAAAAGTTAT	    0.992987	-26
         CGAAACCTTTATTTGACATGCTG	2	2	1	GAAACTTTTT	     0.95047	-36
ATTCTCACCTGAAAAGGTTTTAAAGCTGACGA	3	23	0	GAAAAGTTTA	     0.98321	-104
CTTTTCAGGTGAGAATTTTTAAACATAAACAA	3	39	1	GAGAATTTAA	     0.91628	-88
AGAAGTTATAGATAATGTTGTTTATGTTTAAA	3	56	0	GATAAGTTTT	    0.971567	-71
TCGCTATCGTGAAGAAGTTATAGATAATGTTG	3	68	0	GAAGAGTTTA	    0.958816	-59
ACGATAGCGAGAAAAAGTTAATATTCTTTCAG	3	90	1	GAAAAGTTAT	    0.990867	-37
CAAAACCTCGGAAAAGTGTAATAAATAACTAA	4	25	0	GAAAATGTAT	    0.948945	-24
          ***** *** **

Masking position 9
Map Score:   14.1849

Number of sites scoring better than the average of aligned sites = 422
Number in coding regions = 341
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

AATGAAGGCATCAGAAAAAGTTGATTTGAAT	1	25	0	TAGAAAAAGT	    0.953078	-22
CTCAGCATGTCAAATAAAGGTTTCG      	2	5	0	CAATAAAGGT	    0.925342	-33
CTTTATTTGACATGCTGAGGTGGTGGGGAAC	2	17	1	CTGCTGAGGT	    0.959235	-21
AAAATTCTCACCTGAAAAGGTTTTAAAGCTG	3	27	0	CTGAAAAGGT	    0.992749	-100
TTCTCGCTATCGTGAAGAAGTTATAGATAAT	3	72	0	CTGAAGAAGT	    0.987516	-55
TTCACGATAGCGAGAAAAAGTTAATATTCTT	3	87	1	CAGAAAAAGT	    0.994532	-40
TAATAAATAACTAACTAAAGTAAGCTCG   	4	8	0	CAACTAAAGT	    0.926614	-41
  GGCAAAACCTCGGAAAAGTGTAATAAATA	4	30	0	CCGGAAAAGT	    0.973623	-19
          * *********

Masking position 8
Map Score:   9.32807

Number of sites scoring better than the average of aligned sites = 571
Number in coding regions = 533
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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