AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i341_weak2_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ykpA	180	similar to ABC transporter (ATP-binding protein)

Motif number 1

      CGTGTTCCTCCATGAGAGTGTGTA	1	5	1	TTCCTCCATG	    0.988847	-176
AGAGTGTGTAATTTTCCAGGCGGATGCATT	1	25	1	ATTTTCCAGG	    0.932049	-156
AGGCGGATGCATTCTCTCTCTTTAATTGTA	1	42	1	ATTCTCTCTC	    0.986563	-139
GTATAAGTGTTTTCTCTCTGTTTTATCAGG	1	93	1	TTTCTCTCTG	    0.986563	-88
CAGGGAATCATTTCTCTTGCCCTGCATTCA	1	119	1	TTTCTCTTGC	    0.957111	-62
     TTATTATCCTCCATCATGTCTATCA	1	166	0	ATCCTCCATC	    0.988847	-15
          **********

Masking position 5
Map Score:   6.55828

Number of sites scoring better than the average of aligned sites = 980
Number in coding regions = 847
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 146
Fraction of orfs with sites within 600 bp upstream = 0.02345


Motif number 2

 CGTGTTCCTCCATGAGAGTGTGTAATTTT	1	10	1	CCATGAGAGT	    0.991401	-171
AGCTGTGTTACAATTAAAGAGAGAGAATGC	1	50	0	CAATTAAAGA	    0.963245	-131
TAAAAGTATACCATGAATGCAGGGCAAGAG	1	132	0	CCATGAATGC	    0.972964	-49
TGTCTATCATCAATAAAAGTATACCATGAA	1	145	0	CAATAAAAGT	      0.9791	-36
          **********

Masking position 6
Map Score:   1.42485

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 168
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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