AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_moxr_hypothetical_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 
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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	moxR	138	moxR

Motif number 1

CGACGCCGCGGTGGTGCCCGGCAAATCACA	1	17	0	GTGGTGCCCG	    0.997517	-122
CCTGGATTCCGTCGACGCCGCGGTGGTGCC	1	29	0	GTCGACGCCG	    0.996464	-110
GCGGGGCAGCGACGCGCCCGCGTTCAACTA	1	69	0	GACGCGCCCG	     0.99765	-70
CGACATGACCAACGTCGCGGGGCAGCGACG	1	85	0	AACGTCGCGG	    0.975717	-54
CGCGACGTTGGTCATGTCGGCAGTCGTGTC	1	96	1	GTCATGTCGG	    0.989331	-43
CATGTCGGCAGTCGTGTCCGATTGAGCTGT	1	108	1	GTCGTGTCCG	    0.999129	-31
          **********

Masking position 8
Map Score:   11.9424

Number of sites scoring better than the average of aligned sites = 8342
Number in coding regions = 7831
Number in noncoding regions = 511
Number of orfs with sites within 600 bp upstream = 392
Fraction of orfs with sites within 600 bp upstream = 0.0629618


Motif number 2

CCGTCGACGCCGCGGTGGTGCCCGGCAAAT	1	21	0	CGCGGTGGTG	     0.99392	-118
GCGACGCGCCCGCGTTCAACTATTCCAGGC	1	61	0	CGCGTTCAAC	    0.939257	-78
TGAACGCGGGCGCGTCGCTGCCCCGCGACG	1	73	1	CGCGTCGCTG	    0.982449	-66
GCTGCCCCGCGACGTTGGTCATGTCGGCAG	1	89	1	GACGTTGGTC	    0.964577	-50
TGGTCATGTCGGCAGTCGTGTCCGATTGAG	1	104	1	GGCAGTCGTG	    0.978664	-35
TGTCCGATTGAGCTGTGGAGGATTTTG   	1	122	1	AGCTGTGGAG	    0.957321	-17
          **********

Masking position 3
Map Score:   3.61907

Number of sites scoring better than the average of aligned sites = 20886
Number in coding regions = 19723
Number in noncoding regions = 1163
Number of orfs with sites within 600 bp upstream = 729
Fraction of orfs with sites within 600 bp upstream = 0.11709


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