AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_aful_reg_300.orf -o179_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	RAG46815	38	Archaeoglobus_fulgidus
#2	RAG26652	64	Archaeoglobus_fulgidus

Motif number 1

        GCAAAAAGTTATATTTCAAGTTT	1	3	1	AAAAAGTTTA	    0.978978	-36
CGTAAGAAGGCAAAGGTTTTAAGAGTTATCT	2	17	1	CAAAGGTTTA	    0.993809	-48
AGAGTTATCTCAGAAGTTCTACGCCTGAGGT	2	38	1	CAGAAGTTTA	    0.925294	-27
AGTTCTACGCCTGAGGTGATATC        	2	52	1	CTGAGGTGTA	    0.993668	-13
          ******** **

Masking position 7
Map Score:   5.39823

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 51
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

       GTGTCCACCTCACAGAAACTTGA	1	26	0	TCCACCTCAC	     0.99754	-13
TTTGCCTTCTTACGCCACAC          	2	1	0	TACGCCACAC	    0.998665	-64
TCAGAAGTTCTACGCCTGAGGTGATATC  	2	47	1	TACGCCTGAG	    0.997427	-18
          **********

Masking position 9
Map Score:   3.54156

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 34
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

        GTGTGGCGTAAGAAGGCAAAGG	2	3	1	GTGGCGTAAG	    0.992219	-62
GTGGCGTAAGAAGGCAAAGGTTTTAAGAGT	2	13	1	AAGGCAAAGG	    0.989282	-52
GATATCACCTCAGGCGTAGAACTTCTGAGA	2	45	0	CAGGCGTAGA	    0.995818	-20
          **********

Masking position 8
Map Score:   0.0919171

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 311
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

          **********

No masking
Map Score:   -6.15168e-14

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:   -6.15168e-14

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:   -6.15168e-14

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