AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i295_mixed10_mgen_reg_100.orf -o295_mgen_100.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG03425	36	Mycoplasma
#2	RMG04443	58	Mycoplasma

Motif number 1

AATTAACAATAAAAATTAGACTTTTAATTA	1	11	1	AAAAATTAGA	    0.990385	-26
      AGCTAATAATTAAAAGTCTAATTT	1	23	0	AATAATTAAA	    0.939998	-14
AAAAGTCTTATAAAATTAAATAATCGAATT	2	12	0	TAAAATTAAA	    0.935785	-47
GCTATATATTAATAATTAAACATTTTAAAA	2	38	0	AATAATTAAA	    0.939998	-21
          **********

Masking position 5
Map Score:   10.3406

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 68
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

        AATTAACAATAAAAATTAGACTTT	1	3	1	TTAAAATAAA	    0.991001	-34
 AGCTAATAATTAAAAGTCTAATTTTTATTGT	1	16	0	TTAAAGTCAA	    0.964724	-21
CTTATAAAATTAAATAATCGAATTA       	2	4	0	TAAAAATCAA	      0.9926	-55
ATTAAACATTTTAAAAGTCTTATAAAATTAAA	2	22	0	TTAAAGTCTA	    0.982647	-37
 AGCTATATATTAATAATTAAACATTTTAAAA	2	38	0	TTAAAATTAA	    0.989068	-21
          **** **** **

Masking position 6
Map Score:   10.108

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 15
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

          **********

No masking
Map Score:   9.48026e-14

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:   9.48026e-14

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:   9.48026e-14

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