AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i327_bsub_mtub_100.orf -o327_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	lepA	133	GTP-binding protein

Motif number 1

    GTACGTGAAAGAGAAAAGCAACCCAG	1	7	1	GAAAGAGAAA	    0.997934	-127
ACCCAGATATGATAGGGAACTTTTCTCTTT	1	31	1	GATAGGGAAC	     0.99477	-103
TGTAAAACAAGAAAGAGAAAAGTTCCCTAT	1	42	0	GAAAGAGAAA	    0.997934	-92
          **********

Masking position 4
Map Score:   5.10395

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 87
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

GTACGTGAAAGAGAAAAGCAACCCAGATAT	1	11	1	GAGAAAAGCA	    0.994558	-123
AAACAAGAAAGAGAAAAGTTCCCTATCATA	1	38	0	GAGAAAAGTT	    0.991604	-96
CAATCCTATTGATATAATCTAAGCTAGTGT	1	83	1	GATATAATCT	    0.960882	-51
          **********

Masking position 6
Map Score:   0.608161

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 221
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

GAAAAGTTCCCTATCATATCTGGGTTGCTT	1	26	0	CTATCATATC	    0.975675	-108
TGAATCTTTACAATCCTATTGATATAATCT	1	73	1	CAATCCTATT	    0.995661	-61
   AATCTATCACTCCTACTATTAAACGCA	1	117	0	CACTCCTACT	    0.993871	-17
          **********

Masking position 8
Map Score:   0.650889

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 27
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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