AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i017_Glycolysis___PPS_mgen_reg_300.orf -o017_mgen_300.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	RMG00209	112	Mycoplasma
#2	RMG02317	20	Mycoplasma

Motif number 1

CAAAACAATGCAAAGTATTTTGGAATAACC	1	37	1	CAAAGTATTT	    0.983799	-76
TCTTTTGAGGAAAAGCAGTTATTATCTGGT	1	64	0	AAAAGCAGTT	    0.941611	-49
GCTTTTCCTCAAAAGAAGTTACAGTGAAAA	1	78	1	AAAAGAAGTT	    0.978626	-35
    CAACTTAAAATCATTTTTTCACTGTA	1	97	0	AAAATCATTT	    0.766757	-16
AATCAACTGCAAAAGTGTTT          	2	11	1	AAAAGTGTTT	    0.943416	-10
          **********

Masking position 4
Map Score:   9.0199

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 144
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

GACTGAAGCACTATCCCAAAG         	1	2	0	CTATCCCAAA	    0.986719	-111
GTGCTTCAGTCATTAGCAAAACAATGCAAA	1	21	1	CATTAGCAAA	    0.935792	-92
TATTATCTGGTTATTCCAAAATACTTTGCA	1	45	0	TTATTCCAAA	    0.958825	-68
AATAACTGCTTTTCCTCAAAAGAAGTTACA	1	71	1	TTTCCTCAAA	     0.91679	-42
          CAACTTAAAATCATTTTTTC	1	103	0	CAACTTAAAA	     0.91566	-10
       AATCAACTGCAAAAGTGTTT   	2	4	1	CAACTGCAAA	    0.990872	-17
          **********

Masking position 8
Map Score:   3.99109

Number of sites scoring better than the average of aligned sites = 463
Number in coding regions = 416
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

GGATAGTGCTTCAGTCATTAGCAAAACAAT	1	16	1	TCAGTCATTA	    0.985305	-97
TTGAGGAAAAGCAGTTATTATCTGGTTATT	1	60	0	GCAGTTATTA	    0.995433	-53
AAACACTTTTGCAGTTGATT          	2	1	0	GCAGTTGATT	    0.983332	-20
          **********

Masking position 3
Map Score:   0.922323

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 38
Number in noncoding regions = 5
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:   7.34864e-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:   7.34864e-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 6

          **********

No masking
Map Score:   7.34864e-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