AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00930_mjan_reg_100.orf -o00930_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MJ0140	138	conserved hypothetical protein

Motif number 1

TGTCAAGTTAAGTTTTTATTAAATATTGATAAAA	1	22	0	AGTTATTAAT	       0.982	-117
TTAACTTGACAGTCCCTATAATAAGTTTTAAAAT	1	45	1	AGTTATAAAA	    0.989092	-94
AGTTAGAACAAGTGAATTTTAAAACTTATTATAG	1	60	0	AGTTTTTAAA	    0.988913	-79
TATTAGATATAGTGAATATTATATTAGAGTTAGA	1	87	0	AGTTATTAAT	    0.994579	-52
ATAGTTAGAAAGTATTTATTAGATATAGTGAATA	1	103	0	AGTTATTAAT	    0.997611	-36
          ***   ***** **

Masking position 7
Map Score:   10.1929

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 41
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

TAAATATTGATAAAAAATAATAAACT     	1	6	0	TAAAAAAAAT	    0.939547	-133
TAAGTTTTTATTAAATATTGATAAAAAATAA	1	17	0	TTAAATATGA	    0.897796	-122
CAATATTTAATAAAAACTTAACTTGACAGTC	1	28	1	TAAAAACTAA	    0.898423	-111
CAAGTGAATTTTAAAACTTATTATAGGGACT	1	55	0	TTAAAACTAT	    0.974406	-84
TATATTAGAGTTAGAACAAGTGAATTTTAAA	1	71	0	TTAGAACAGT	    0.966585	-68
GTTCTAACTCTAATATAATATTCACTATATC	1	85	1	TAATATATAT	    0.825278	-54
AAAGTATTTATTAGATATAGTGAATATTATA	1	98	0	TTAGATAAGT	    0.948442	-41
CCTCCCATAGTTAGAAAGTATTTATTAGATA	1	112	0	TTAGAAATAT	    0.979665	-27
          ******* ***

Masking position 5
Map Score:   7.19178

Number of sites scoring better than the average of aligned sites = 1368
Number in coding regions = 1073
Number in noncoding regions = 295
Number of orfs with sites within 600 bp upstream = 262
Fraction of orfs with sites within 600 bp upstream = 0.0420816


Motif number 3

          **********

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 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