AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_mgen_mpneu_100.orf -o179_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	RMG04443	58	Mycoplasma
#2	RMP00361	287	Mycoplasma_pneumoniae

Motif number 1

TTTTAAAAGTCTTATAAAATTAAATAATCGAATT	1	12	0	CTTAAAATAA	    0.979479	-47
tctctagaatcttataaaatcagaatagcgtaat	2	13	0	cttaaaacaa	     0.99677	-275
ctatcaaaatctttaaaaaacagattcgtgataa	2	148	1	cttaaaacaa	     0.99677	-140
acccaccaatcaccgaaaaccaaattaaggcgat	2	181	1	cacaaaacaa	    0.983732	-107
gggtcgtaagctttctgaaacacaagtcaaggaa	2	227	1	ctttgaacaa	    0.965319	-61
ttatgcgctccattaaaaaccagaagtaattaat	2	262	1	cataaaacaa	     0.99399	-26
          ***  **** ** *

Masking position 8
Map Score:   7.87904

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 34
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 2

   TAATTCGATTATTTAATTTTATAAGAC	1	8	1	ATTATTTAAT	    0.716787	-51
      AGCTATATATTAATAATTAAACAT	1	45	0	ATATATTAAT	    0.935782	-14
attcatatctatatcttaatcttaatcctc	2	45	0	atatcttaat	    0.916825	-243
attaagatatagatatgaatgatcttgcgc	2	55	1	agatatgaat	    0.923208	-233
tgttttttaaagattttgatagaaataaaa	2	140	0	agattttgat	    0.923286	-148
aattacttctggtttttaatggagcgcata	2	263	0	ggtttttaat	    0.902354	-25
aaaaaccagaagtaattaataa        	2	276	1	agtaattaat	     0.76885	-12
          **********

Masking position 9
Map Score:   2.85585

Number of sites scoring better than the average of aligned sites = 293
Number in coding regions = 253
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

TATTTAATTTTATAAGACTTTTAAAATGTTT	1	20	1	TTAAGACTTT	    0.965385	-39
ATATTAATAATTAAACATTTTAAAAGTCTTA	1	32	0	TAAACATTTT	     0.96146	-27
attctgattttataagattctagagaggatt	2	21	1	ttaagattct	    0.965285	-267
gatatagatatgaatgatcttgcgcttgcct	2	60	1	taatgatctt	    0.922931	-228
aatctgttttttaaagattttgatagaaata	2	143	0	taaagatttt	    0.988747	-145
          * *********

Masking position 7
Map Score:   0.842723

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 106
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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 6

          **********

No masking
Map Score:   -2.60469e-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