AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00520_mgen_reg_300.orf -o00520_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MG109	59	serine/threonine protein kinase, putative
#2	MG115	24	conserved hypothetical protein
#3	MG452	52	conserved hypothetical protein

Motif number 1

CAATTTGATACTTATTTTCAACAATATCACC	1	16	0	CTATTTTCAA	    0.990602	-44
AAATAAGTATCAAATTGAAAAGCTTTTAAAT	1	30	1	CAATTGAAAA	    0.963051	-30
    CCCACCCCTATTTAAAAGCTTTTCAAT	1	43	0	CTATTTAAAA	     0.99655	-17
AAATTAACAACATAATTTAAACAA       	3	4	0	CTAATTTAAA	    0.985862	-49
TTATCTTAAACTTATTTAAAATTAACAACAT	3	22	0	CTATTTAAAA	    0.996533	-31
 TATCTCCAGCTTATCTTAAACTTATTTAAA	3	33	0	CTATCTTAAA	    0.990261	-20
          * *********

Masking position 4
Map Score:   13.9628

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 19
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

 AGATAGGTGATATTGTTGAAAATAAGTAT	1	10	1	ATATTGTTGA	    0.945766	-50
TCAAATTGAAAAGCTTTTAAATAGGGGTGG	1	39	1	AAGCTTTTAA	    0.965192	-21
TGTTTAAATTATGTTGTTAATTTTAAATAA	3	12	1	ATGTTGTTAA	    0.975839	-41
AATTTTAAATAAGTTTAAGATAAGCTGGAG	3	30	1	AAGTTTAAGA	    0.941125	-23
AGTTTAAGATAAGCTGGAGATA        	3	41	1	AAGCTGGAGA	    0.982943	-12
          **********

Masking position 5
Map Score:   2.17413

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 357
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

          **********

No masking
Map Score:   -2.59896e-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 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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