AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i343_weak4_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	Rv0692	164	hypothetical protein Rv0692

Motif number 1

GCATCGAGTGCCGAAATGGAAGGGCGAATG	1	13	0	CCGAAATGGA	    0.967095	-152
TGGACACAATATGGCATCGAGTGCCGAAAT	1	26	0	ATGGCATCGA	    0.938142	-139
CCATATTGTGTCCAGATCGACGGATCGCTG	1	42	1	TCCAGATCGA	    0.825647	-123
CCAGCAGGTCTCGACAGCGATCCGTCGATC	1	56	0	TCGACAGCGA	    0.963084	-109
CGAAAGGCAATCCAGATGGACTACGAAACC	1	86	1	TCCAGATGGA	    0.893165	-79
CAGATGGACTACGAAACCGATACCGACACC	1	98	1	ACGAAACCGA	    0.981196	-67
GAAACCGATACCGACACCGAGCTTGTCACC	1	110	1	CCGACACCGA	    0.989794	-55
GACACCGAGCTTGTCACCGAGACCCTGGTT	1	122	1	TTGTCACCGA	    0.958554	-43
          **********

Masking position 6
Map Score:   13.3929

Number of sites scoring better than the average of aligned sites = 7700
Number in coding regions = 7327
Number in noncoding regions = 373
Number of orfs with sites within 600 bp upstream = 293
Fraction of orfs with sites within 600 bp upstream = 0.0470607


Motif number 2

CAATATGGCATCGAGTGCCGAAATGGAAGG	1	20	0	TCGAGTGCCG	    0.977146	-145
TCCGTCGATCTGGACACAATATGGCATCGA	1	36	0	TGGACACAAT	    0.930928	-129
TGTGTCCAGATCGACGGATCGCTGTCGAGA	1	48	1	TCGACGGATC	    0.955743	-117
CGGATCGCTGTCGAGACCTGCTGGCGAAAG	1	62	1	TCGAGACCTG	    0.980671	-103
GTAGTCCATCTGGATTGCCTTTCGCCAGCA	1	80	0	TGGATTGCCT	     0.88861	-85
GAGCTTGTCACCGAGACCCTGGTTGAAGAG	1	128	1	CCGAGACCCT	    0.962344	-37
ATTCCGTCGATGGACACCTCTTCAACCAGG	1	145	0	TGGACACCTC	    0.976164	-20
GAGGTGTCCATCGACGGAAT          	1	155	1	TCGACGGAAT	     0.94786	-10
          **********

Masking position 4
Map Score:   5.20805

Number of sites scoring better than the average of aligned sites = 7544
Number in coding regions = 7035
Number in noncoding regions = 509
Number of orfs with sites within 600 bp upstream = 424
Fraction of orfs with sites within 600 bp upstream = 0.0681015


Motif number 3

          **********

No masking
Map Score:   4.35863e-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 4

          **********

No masking
Map Score:   4.35863e-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:   4.35863e-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