AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00252_mgen_reg_100.orf -o00252_mgen_100.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	MG035	28	histidyl-tRNA synthetase
#2	MG109	59	serine/threonine protein kinase, putative
#3	MG292	57	alanyl-tRNA synthetase (alaS)
#4	MG294	117	conserved hypothetical protein

Motif number 1

    GTGTCATTAATTATAATTTCGAAATT	1	13	0	TTAATTATAA	    0.630019	-16
GGTGATATTGTTGAAAATAAGTATCAAATT	2	16	1	TTGAAAATAA	    0.968678	-44
TTTACCAGTGATAAAAATAACTATAGTTCT	3	19	0	ATAAAAATAA	    0.977901	-39
TAAATTGCATTTAAAATTAAGCA       	3	45	1	TTAAAATTAA	    0.544635	-13
ACTTTTAAAAAGAAAAATAATGTTTACTAG	4	26	0	AGAAAAATAA	    0.941802	-92
ATTTTTCTTTTTAAAAGTAAGTGAAGAACG	4	38	1	TTAAAAGTAA	    0.867278	-80
AAATATACATCTAATAATAAAAGTGGATGG	4	76	0	CTAATAATAA	    0.934036	-42
GTGGGATAAATTAAATATACATCTAATAAT	4	88	0	TTAAATATAC	    0.911155	-30
          **********

Masking position 4
Map Score:   10.1942

Number of sites scoring better than the average of aligned sites = 395
Number in coding regions = 340
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 2

 GTGTCATTAATTATAATTTCGAAATTAT 	1	10	0	ATTATAATTT	    0.656021	-19
TTTCAATTTGATACTTATTTTCAACAATAT	2	20	0	ATACTTATTT	    0.925118	-40
CCCCTATTTAAAAGCTTTTCAATTTGATAC	2	36	0	AAAGCTTTTC	    0.710537	-24
       CCCACCCCTATTTAAAAGCTTTT	2	47	0	ACCCCTATTT	    0.933701	-13
TAAAAGAACTATAGTTATTTTTATCACTGG	3	15	1	ATAGTTATTT	    0.941643	-43
CTTAATTTTAAATGCAATTTACCAGTGATA	3	36	0	AATGCAATTT	    0.885088	-22
GTTTACTAGAAAAACTATTTTTTC      	4	5	0	AAAACTATTT	    0.938805	-113
TTTTCTAGTAAACATTATTTTTCTTTTTAA	4	22	1	AACATTATTT	    0.938753	-96
ATGGAAGTGAAACGTTCTTCACTTACTTTT	4	50	0	AACGTTCTTC	    0.869377	-68
TATTTAATTTATCCCACTTTATCATTA   	4	101	1	ATCCCACTTT	    0.873699	-17
          **********

Masking position 8
Map Score:   4.80387

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 624
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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