AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_mgen_reg_300.orf -o043_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

GGTTATTCCAAAATACTTTGCATTGTTTTG	1	37	0	AAATACTTTG	    0.984778	-76
ACCAGATAATAACTGCTTTTCCTCAAAAGA	1	64	1	AACTGCTTTT	    0.936846	-49
TTTTCACTGTAACTTCTTTTGAGGAAAAGC	1	78	0	AACTTCTTTT	    0.978377	-35
TACAGTGAAAAAATGATTTTAAGTTG    	1	97	1	AAATGATTTT	    0.756052	-16
          AAACACTTTTGCAGTTGATT	2	11	0	AAACACTTTT	    0.940501	-10
          **********

Masking position 7
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

         CTTTGGGATAGTGCTTCAGTC	1	2	1	TTTGGGATAG	    0.986331	-111
TTTGCATTGTTTTGCTAATGACTGAAGCAC	1	21	0	TTTGCTAATG	    0.934021	-92
TGCAAAGTATTTTGGAATAACCAGATAATA	1	45	1	TTTGGAATAA	    0.957654	-68
TGTAACTTCTTTTGAGGAAAAGCAGTTATT	1	71	0	TTTGAGGAAA	    0.915365	-42
GAAAAAATGATTTTAAGTTG          	1	103	1	TTTTAAGTTG	    0.913363	-10
   AAACACTTTTGCAGTTGATT       	2	4	0	TTTGCAGTTG	    0.990602	-17
          **********

Masking position 3
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	    0.986581	-97
TTGAGGAAAAGCAGTTATTATCTGGTTATT	1	60	0	GCAGTTATTA	    0.995835	-53
AAACACTTTTGCAGTTGATT          	2	1	0	GCAGTTGATT	    0.984786	-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