AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mgen_mpneu_100.orf -o303_mgen_mpneu_100.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	RMG03030	66	Mycoplasma
#2	RMP00236	54	Mycoplasma_pneumoniae

Motif number 1

AACAATATTTTTCTATTTAAT          	1	1	0	TTCTATTAAT	    0.988694	-66
TATAATAATTTTATTAACAATATTTTTCTAT	1	16	0	TTATTAAAAT	    0.950147	-51
ATCTTAAAACATATAATAATTTTATTAACAA	1	27	0	ATATAATATT	    0.938725	-40
GTTTTAAGATTTCTATTAATTCAAGTAAT  	1	48	1	TTCTATTATT	     0.98536	-19
ttaaattcatttataatcaatcttcgcagta	2	11	0	ttataataat	    0.990034	-44
aaataaccagttatattaaattcatttataa	2	26	0	ttatattaat	    0.989924	-29
atataactggttatttaaatcctt       	2	41	1	ttatttaatc	    0.854384	-14
          ******* ***

Masking position 9
Map Score:   10.1095

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 148
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

ATTAACAATATTTTTCTATTTAAT      	1	5	0	TTTTTCTATT	    0.945548	-62
AAACATATAATAATTTTATTAACAATATTT	1	22	0	TAATTTTATT	    0.887453	-45
TATGTTTTAAGATTTCTATTAATTCAAGTA	1	45	1	GATTTCTATT	    0.990649	-22
atattaaattcatttataatcaatcttcgc	2	15	0	catttataat	    0.960108	-40
tttaaataaccagttatattaaattcattt	2	30	0	cagttatatt	    0.978288	-25
       aaggatttaaataaccagttata	2	42	0	gatttaaata	    0.593394	-13
          **********

Masking position 5
Map Score:   3.7124

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 186
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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