AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_mgen_mpneu_100.orf -o002_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	RMG00101	91	Mycoplasma
#2	RMP00093	55	Mycoplasma_pneumoniae

Motif number 1

GATGCTTGATAACATTGCTTTGAACATGATT	1	23	1	AACATTCTTT	    0.984083	-69
CATTGCTTTGAACATGATTTTTAATTATTTA	1	35	1	AACATGTTTT	    0.960798	-57
ATGATTTTTAATTATTTATTATTAAATAATG	1	48	1	ATTATTATTA	    0.953249	-44
GTTTTATTAAAACATTATTTAATAATAAATA	1	60	0	AACATTTTTA	    0.980099	-32
     ATTGCAATATTGTTTTATTAAAACAT	1	76	0	AATATTTTTT	    0.990578	-16
tatttttttatttattaatttcgtgg     	2	6	0	tttattattt	    0.906797	-50
atgcatctttattatttttttatttattaat	2	18	0	attatttttt	    0.988664	-38
          ****** ****

Masking position 4
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

AATAATAAATAATTAAAAATCATGTTCAAA	1	41	0	AATTAAAAAT	    0.968411	-51
AATTATTTATTATTAAATAATGTTTTAATA	1	57	1	TATTAAATAA	    0.955237	-35
AATAATGTTTTAATAAAACAATATTGCAAT	1	72	1	TAATAAAACA	    0.954549	-20
cgaaattaataaataaaaaaataataaaga	2	14	1	aaataaaaaa	    0.982779	-42
aataaaaaaataataaagatgcatatctat	2	25	1	taataaagat	    0.971261	-31
 ctttgatcgaaatagatatgcatctttat	2	37	0	aaatagatat	    0.936054	-19
          **********

Masking position 5
Map Score:   6.36406

Number of sites scoring better than the average of aligned sites = 497
Number in coding regions = 392
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 3

          **********

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 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