AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i045_Trehalose_Utilization_bsub_reg_300.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	treP	192	phosphotransferase system (PTS) trehalose-specific enzyme IIBC component
#2	treA	70	trehalose-6-phosphate hydrolase

Motif number 1

GTCTGTTTCATATATTCCAGACTAGGATGA	1	74	1	TATATTCCAG	    0.955708	-119
ATGAAAGCGCTATAAAAAAGTGTTGACTAC	1	100	1	TATAAAAAAG	    0.979922	-93
TGACTACCTGTATATACAGGAATACAATAT	1	123	1	TATATACAGG	    0.989291	-70
TTATAAGTTGTATATACAAGTTATAAAAAC	1	155	1	TATATACAAG	    0.993688	-38
ATATACAAGTTATAAAAACGGATACGGAGG	1	166	1	TATAAAAACG	    0.966251	-27
          **********

Masking position 4
Map Score:   5.14661

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 100
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

     AGAGGCTCACCCTGCTTTTTAATGTCA	1	6	1	CTCACCCCTT	    0.974031	-187
TTTTTTATAGCGCTTTCATCCTAGTCTGGAAT	1	87	0	CGCTTTCCCT	    0.972635	-106
CCAACCCCTCCGTATCCGTTTTTATAACTTGT	1	170	0	CGTATCCTTT	    0.984217	-23
CAACACGTCCCGCTCCCCACTTG         	2	2	0	CGCTCCCCTT	    0.997794	-69
ACGTGTTGAACGTTCCCTTTTCCCGTTTTCAA	2	26	1	CGTTCCCTTC	    0.985272	-45
TCCCTTTTCCCGTTTTCAATTTAAATATGGTG	2	39	1	CGTTTTCTTT	    0.975195	-32
          *******  ***

Masking position 7
Map Score:   3.65644

Number of sites scoring better than the average of aligned sites = 993
Number in coding regions = 893
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 3

GCGCTATAAAAAAGTGTTGACTACCTGTAT	1	106	1	AAAGTGTTGA	    0.973656	-87
AACGGATACGGAGGGGTTGGC         	1	182	1	GAGGGGTTGG	    0.992982	-11
TGGGGAGCGGGACGTGTTGAACGTTCCCTT	2	15	1	GACGTGTTGA	    0.988336	-56
CAATTTAAATATGGTGGTGGAAACAG    	2	55	1	ATGGTGGTGG	    0.973119	-16
          **********

Masking position 8
Map Score:   0.689565

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 101
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

TTCCTGTATATACAGGTAGTCAACACTTTT	1	115	0	TACAGGTAGT	    0.985586	-78
ACAATATGATTATAAGTTGTATATACAAGT	1	146	1	TATAAGTTGT	    0.981342	-47
AAGTTGTATATACAAGTTATAAAAACGGAT	1	159	1	TACAAGTTAT	    0.981345	-34
          **********

Masking position 4
Map Score:   0.0871167

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 9
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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 7

          **********

No masking
Map Score:   -1.75204e-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