AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i089_Sugar_Transport_1_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	yurJ	181	similar to multiple sugar ABC transporter (ATP-binding protein)

Motif number 1

TAACCTATTATTTATATTATAATGTATTATG	1	26	1	TTTTATTATA	    0.993735	-156
AAAATGTAAATTTGTATTATAACGTCATAAT	1	51	0	TTTTATTATA	    0.993941	-131
AAATTTACATTTTTTATTTTAGAAATATAGC	1	69	1	TTTTATTTTA	    0.980379	-113
TCGATTCCCATTTTTGCTATATTTCTAAAAT	1	84	0	TTTTGCTATA	    0.987633	-98
CAACTTGGTCTTTCTGTTATTTTTAGAGTAA	1	115	0	TTTTGTTATT	    0.981798	-67
          *** *******

Masking position 5
Map Score:   8.55287

Number of sites scoring better than the average of aligned sites = 88
Number in coding regions = 28
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 2

GGTAGCCTCCTTTTAACCTATTATTTATAT	1	13	1	TTTTAACCTA	     0.95837	-169
ATTATTTATATTATAATGTATTATGACGTT	1	32	1	TTATAATGTA	    0.972949	-150
TAAATTTGTATTATAACGTCATAATACATT	1	46	0	TTATAACGTC	    0.985337	-136
AATTTACATTTTTTATTTTAGAAATATAGC	1	70	1	TTTTATTTTA	    0.827855	-112
TTTCTGTTATTTTTAGAGTAATCGATTCCC	1	106	0	TTTTAGAGTA	    0.922877	-76
TTTTGACCCGTTATTTCGTCACTGGAAACA	1	144	0	TTATTTCGTC	    0.920445	-38
          **********

Masking position 4
Map Score:   2.34526

Number of sites scoring better than the average of aligned sites = 523
Number in coding regions = 412
Number in noncoding regions = 111
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 3

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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