AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_mgen_mpneu_100.orf -o232_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	RMG02914	110	Mycoplasma
#2	RMP00301	60	Mycoplasma_pneumoniae

Motif number 1

   AACAACTTTTTTACGATAATGATTTTG	1	8	1	TTTTTACGAT	    0.988432	-103
ATGATTAATTTTGTCTGGCTGAGTTACAAC	1	49	0	TTGTCTGGCT	    0.975458	-62
TACTATTTTATTGTTACGATGATTAATTTT	1	67	0	TTGTTACGAT	    0.994828	-44
cacttagcgcttttttggatt         	2	2	0	ttttttggat	    0.988626	-59
attacatcgattgttagtatt         	2	50	1	ttgttagtat	    0.981736	-11
          **********

Masking position 4
Map Score:   7.19579

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 47
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ACAACTTTTTTACGATAATGATTTTGAAATT	1	12	1	TAGATAATGA	    0.976389	-99
ATTTTATTGTTACGATGATTAATTTTGTCTG	1	62	0	TAGATGATTA	    0.991046	-49
AATAGTACCTTCTGATGTTAAGTCTTTTTGT	1	90	1	TCGATGTTAA	    0.973268	-21
gcgctaagtgtcatataataatagaatgatt	2	22	1	tctataataa	    0.930055	-39
catataataatagaatgattacatcgattgt	2	33	1	taaatgatta	    0.965338	-28
          ** ********

Masking position 6
Map Score:   2.04205

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 60
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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