AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_mgen_mpneu_300.orf -o179_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	RMG04443	58	Mycoplasma
#2	RMP00361	287	Mycoplasma_pneumoniae

Motif number 1

TTTTAAAAGTCTTATAAAATTAAATAATCGAATT	1	12	0	CTTAAAATAA	    0.977128	-47
tctctagaatcttataaaatcagaatagcgtaat	2	13	0	cttaaaacaa	    0.996392	-275
ctatcaaaatctttaaaaaacagattcgtgataa	2	148	1	cttaaaacaa	    0.996392	-140
acccaccaatcaccgaaaaccaaattaaggcgat	2	181	1	cacaaaacaa	    0.981859	-107
gggtcgtaagctttctgaaacacaagtcaaggaa	2	227	1	ctttgaacaa	    0.961408	-61
ttatgcgctccattaaaaaccagaagtaattaat	2	262	1	cataaaacaa	    0.993289	-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

GTCTTATAAAATTAAATAATCGAATTA   	1	8	0	ATTAAATAAT	    0.716494	-51
ATGTTTAATTATTAATATATAGCT      	1	45	1	ATTAATATAT	    0.938152	-14
gaggattaagattaagatatagatatgaat	2	45	1	attaagatat	    0.922356	-243
gcgcaagatcattcatatctatatcttaat	2	55	0	attcatatct	    0.928417	-233
ttttatttctatcaaaatctttaaaaaaca	2	140	1	atcaaaatct	    0.928501	-148
tatgcgctccattaaaaaccagaagtaatt	2	263	1	attaaaaacc	    0.908849	-25
        ttattaattacttctggttttt	2	276	0	attaattact	    0.764762	-12
          **********

Masking position 5
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

ACATTTTAAAAGTCTTATAAAATTAAATAA	1	19	0	AGTCTTATAA	    0.970122	-40
tcctctctagaatcttataaaatcagaata	2	20	0	aatcttataa	    0.982255	-268
tctatatcttaatcttaatcctctctagaa	2	38	0	aatcttaatc	    0.927797	-250
tttctatcaaaatctttaaaaaacagattc	2	145	1	aatctttaaa	    0.956345	-143
          **********

Masking position 5
Map Score:   0.680682

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 24
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

acctaaggcaagcgcaagatcattcatatc	2	66	0	agcgcaagat	     0.98856	-222
gaaataaaatagccaataatgacaccgact	2	119	0	agccaataat	    0.973239	-169
tttttaatggagcgcataatttccttgact	2	251	0	agcgcataat	    0.994548	-37
          **********

Masking position 6
Map Score:   0.0113902

Number of sites scoring better than the average of aligned sites = 3
Number in coding regions = 3
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


Motif number 7

          **********

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