AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i045_Trehalose_Utilization_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	treP	192	phosphotransferase system (PTS) trehalose-specific enzyme IIBC component
#2	treA	70	trehalose-6-phosphate hydrolase

Motif number 1

TCATCCTAGTCTGGAATATATGAAACAGAC	1	74	0	CTGGAATATA	    0.952155	-119
GTAGTCAACACTTTTTTATAGCGCTTTCAT	1	100	0	CTTTTTTATA	    0.978268	-93
ATATTGTATTCCTGTATATACAGGTAGTCA	1	123	0	CCTGTATATA	    0.988401	-70
GTTTTTATAACTTGTATATACAACTTATAA	1	155	0	CTTGTATATA	    0.993161	-38
CCTCCGTATCCGTTTTTATAACTTGTATAT	1	166	0	CGTTTTTATA	    0.963512	-27
          **********

Masking position 7
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

TGACATTAAAAAGCAGGGTGAGCCTCT     	1	6	0	AAGGGGTGAG	    0.974085	-187
ATTCCAGACTAGGATGAAAGCGCTATAAAAAA	1	87	1	AGGGAAAGCG	    0.972693	-106
ACAAGTTATAAAAACGGATACGGAGGGGTTGG	1	170	1	AAAGGATACG	    0.984251	-23
         CAAGTGGGGAGCGGGACGTGTTG	2	2	1	AAGGGGAGCG	    0.997799	-69
TTGAAAACGGGAAAAGGGAACGTTCAACACGT	2	26	0	GAAGGGAACG	    0.985303	-45
CACCATATTTAAATTGAAAACGGGAAAAGGGA	2	39	0	AAAGAAAACG	    0.975248	-32
          ***  *******

Masking position 6
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

CGCTATAAAAAAGTGTTGACTACCTGTATA	1	107	1	AAGTGTTGAC	    0.983211	-86
ACGGATACGGAGGGGTTGGC          	1	183	1	AGGGGTTGGC	    0.993148	-10
GGGGAGCGGGACGTGTTGAACGTTCCCTTT	2	16	1	ACGTGTTGAA	    0.982491	-55
AATTTAAATATGGTGGTGGAAACAG     	2	56	1	TGGTGGTGGA	    0.973742	-15
          **********

Masking position 7
Map Score:   0.689565

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 130
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TTCCTGTATATACAGGTAGTCAACACTTTT	1	115	0	TACAGGTAGT	    0.986725	-78
ACAATATGATTATAAGTTGTATATACAAGT	1	146	1	TATAAGTTGT	    0.982811	-47
AAGTTGTATATACAAGTTATAAAAACGGAT	1	159	1	TACAAGTTAT	    0.982814	-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