AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i077_mgen_mpneu_300.orf -o077_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 =  	0.36
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG02346	48	Mycoplasma
#2	RMP00559	44	Mycoplasma_pneumoniae

Motif number 1

CAAAATTGGAAAATTATTTATCTTAATTTT	1	23	0	AAATTATTTA	    0.951713	-26
ATAATTTTCCAATTTTGTTTTCA       	1	36	1	AATTTTGTTT	    0.977233	-13
aatagaattaaaattcgttaat        	2	3	0	aaattcgtta	    0.990114	-42
aacgaattttaattctattattaaaaaatt	2	14	1	aattctatta	    0.962571	-31
gcttctgtttaaattttttaataatagaat	2	25	0	aaatttttta	    0.990799	-20
          **********

Masking position 4
Map Score:   7.36223

Number of sites scoring better than the average of aligned sites = 195
Number in coding regions = 172
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

      TACTTATTGCTTAAAATTAAGATA	1	5	1	TATTGCTTAA	    0.961684	-44
TGGAAAATTATTTATCTTAATTTTAAGCAA	1	17	0	TTTATCTTAA	    0.888554	-32
AATTTTCCAATTTTGTTTTCA         	1	38	1	TTTTGTTTTC	    0.946325	-11
ctgtttaaattttttaataatagaattaaa	2	21	0	tttttaataa	    0.873365	-24
        gcttctgtttaaattttttaat	2	33	0	ttctgtttaa	    0.978589	-12
          **********

Masking position 8
Map Score:   2.66368

Number of sites scoring better than the average of aligned sites = 739
Number in coding regions = 663
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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:   5.21701e-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