AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_mgen_mpneu_300.orf -o002_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	RMG00101	91	Mycoplasma
#2	RMP00093	55	Mycoplasma_pneumoniae

Motif number 1

AATCATGTTCAAAGCAATGTTATCAAGCATC	1	23	0	AAAGAATGTT	    0.984332	-69
TAAATAATTAAAAATCATGTTCAAAGCAATG	1	35	0	AAAACATGTT	      0.9609	-57
CATTATTTAATAATAAATAATTAAAAATCAT	1	48	0	TAATAATAAT	     0.95396	-44
TATTTATTATTAAATAATGTTTTAATAAAAC	1	60	1	TAAAAATGTT	      0.9803	-32
ATGTTTTAATAAAACAATATTGCAAT     	1	76	1	AAAAAATATT	    0.990704	-16
     ccacgaaattaataaataaaaaaata	2	6	1	aaataataaa	    0.908146	-50
attaataaataaaaaaataataaagatgcat	2	18	1	aaaaaataat	    0.988842	-38
          **** ******

Masking position 7
Map Score:   10.5706

Number of sites scoring better than the average of aligned sites = 306
Number in coding regions = 275
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

TTGAACATGATTTTTAATTATTTATTATTA	1	42	1	TTTTTAATTA	    0.918186	-50
TTTTAATTATTTATTATTAAATAATGTTTT	1	53	1	TTATTATTAA	    0.673374	-39
TTGCAATATTGTTTTATTAAAACATTATTT	1	71	0	GTTTTATTAA	    0.982597	-21
ctttattatttttttatttattaatttcgt	2	13	0	tttttattta	    0.987468	-43
tagatatgcatctttattatttttttattt	2	24	0	tctttattat	    0.955314	-32
          **********

Masking position 5
Map Score:   6.6303

Number of sites scoring better than the average of aligned sites = 293
Number in coding regions = 243
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

GTTATCAAGCATCGTTATGCGCACG     	1	6	0	ATCGTTATGC	    0.996208	-86
tttgatcgaaatagatatgcatctttatta	2	35	0	atagatatgc	    0.994118	-21
          **********

Masking position 6
Map Score:   0.392231

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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