AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_Metabolism__mgen_reg_300.orf -o038_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
#3	RMG02322	24	Mycoplasma

Motif number 1

CAAAACAATGCAAAGTATTTTGGAATAACC	1	37	1	CAAAGTATTT	    0.983916	-76
TCTTTTGAGGAAAAGCAGTTATTATCTGGT	1	64	0	AAAAGCAGTT	    0.941099	-49
GCTTTTCCTCAAAAGAAGTTACAGTGAAAA	1	78	1	AAAAGAAGTT	    0.978609	-35
    CAACTTAAAATCATTTTTTCACTGTA	1	97	0	AAAATCATTT	    0.765577	-16
AATCAACTGCAAAAGTGTTT          	2	11	1	AAAAGTGTTT	    0.943113	-10
          **********

Masking position 4
Map Score:   8.35462

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	1	0	CTATCCAAAG	    0.979574	-112
CTTTGCATTGTTTTGCTAATGACTGAAGCAC	1	21	0	TTTTCTAATG	    0.891971	-92
TATTATCTGGTTATTCCAAAATACTTTGCAT	1	44	0	TTATCCAAAA	    0.977944	-69
ATAATAACTGCTTTTCCTCAAAAGAAGTTAC	1	69	1	CTTTCCTCAA	    0.909207	-44
CTTAAAATCATTTTTTCACTGTAACTTCTTT	1	89	0	TTTTTCACTG	    0.957493	-24
        AGTTATTCCAATGCCTAATAAGG	3	12	0	TTATCCAATG	    0.994146	-13
          **** ******

Masking position 4
Map Score:   5.32041

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 155
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

ATTGTTTTGCTAATGACTGAAGCACTATCC	1	16	0	TAATGACTGA	    0.982956	-97
AATAACCAGATAATAACTGCTTTTCCTCAA	1	60	1	TAATAACTGC	    0.994692	-53
          AATCAACTGCAAAAGTGTTT	2	1	1	AATCAACTGC	    0.980659	-20
          **********

Masking position 6
Map Score:   0.523859

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:   -9.70439e-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:   -9.70439e-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:   -9.70439e-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