AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_aful_mthe_300.orf -o179_aful_mthe_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	RAG46815	38	Archaeoglobus_fulgidus
#2	RAG26652	64	Archaeoglobus_fulgidus
#3	RTH01987	83	M.thermo

Motif number 1

        GCAAAAAGTTATATTTCAAGTTT	1	3	1	AAAAAGTTTA	    0.976221	-36
CGTAAGAAGGCAAAGGTTTTAAGAGTTATCT	2	17	1	CAAAGGTTTA	     0.99304	-48
AGAGTTATCTCAGAAGTTCTACGCCTGAGGT	2	38	1	CAGAAGTTTA	    0.981394	-27
AGTTCTACGCCTGAGGTGATATC        	2	52	1	CTGAGGTGTA	    0.962998	-13
TATTTCTCCTACAAGGTTAGAGTATTCAAAC	3	43	1	ACAAGGTTGA	    0.972496	-41
AATCTTTATAAAGATGTTTGAATACTCTAAC	3	58	0	AAGATGTTGA	    0.968696	-26
          ******** **

Masking position 7
Map Score:   5.4034

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 229
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

TCAAGTTTCTGTGAGGTGGACAC       	1	26	1	GTGAGGTGGA	    0.989215	-13
          GTGTGGCGTAAGAAGGCAAA	2	1	1	GTGTGGCGTA	    0.991583	-64
  GATATCACCTCAGGCGTAGAACTTCTGA	2	47	0	CTCAGGCGTA	     0.98033	-18
GCAAGTTCTCATATGGTGAATACCG     	3	6	0	ATATGGTGAA	     0.96954	-78
TGTAGGAGAAATAAGGGGAAGCAAGTTCTC	3	26	0	ATAAGGGGAA	    0.974578	-58
          **********

Masking position 2
Map Score:   2.81152

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 292
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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