AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i100_Ion_Transporter_mgen_reg_300.orf -o100_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

Purged sequences:
RMG03444	167	Mycoplasma

Input sequences:
#1	RMG01751	167	Mycoplasma

Motif number 1

CAAAAAATTCGTTGGGTAATAGTCTCACCT	1	54	1	GTTGGGTAAT	    0.981999	-114
AAACTCACCACTTGGTTAAAAAAAATTGGC	1	86	0	CTTGGTTAAA	    0.995725	-82
GACAAAACCAGATGGTAAAACTCACCACTT	1	103	0	GATGGTAAAA	    0.989387	-65
        ACCTTGGTAAAATTATATTTGA	1	156	0	CTTGGTAAAA	    0.995725	-12
          **********

Masking position 3
Map Score:   5.20802

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 46
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

         AAATAACAGCAAACTTCCAAACAA	1	2	1	AAAACAAAAC	    0.995167	-166
CAAACTTCCAAACAAGATGCAATAGATATAAAA	1	20	1	AAAAGACAAT	    0.987359	-148
CAATAGATATAAAAACAAAAAATTCGTTGGGTA	1	39	1	AAAACAAAAT	    0.992546	-129
TTTTAATGACAAGAAGACAAAACCAGATGGTAA	1	115	0	AAAAGAAAAC	    0.995168	-53
          ** ****  ****

Masking position 7
Map Score:   2.7483

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 36
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

AAATTCGTTGGGTAATAGTCTCACCTCAGCC	1	58	1	GGTAATATCT	    0.987357	-110
CTCACCACTTGGTTAAAAAAAATTGGCTGAG	1	82	0	GGTTAAAAAA	    0.952383	-86
AAAACCAGATGGTAAAACTCACCACTTGGTT	1	99	0	GGTAAAATCA	    0.994958	-69
     ACCTTGGTAAAATTATATTTGATAGC	1	152	0	GGTAAAATAT	    0.992229	-16
          ******* ***

Masking position 5
Map Score:   2.64416

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 37
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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 6

          **********

No masking
Map Score:   -1.11255e-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