AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i314_mixed28_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	trpE	215	anthranilate synthase

Motif number 1

GAAATACACAAGAGTGTGTATAAAGCAATTAG	1	29	1	AGAGTGTGTA	    0.987819	-187
TAAAGCAATTAGAATGAGTTGAGTTAGAGAAT	1	49	1	AGAATGAGTA	    0.997484	-167
AGGGTAGCAGAGAATGAGTTTAGTTGAGCTGA	1	81	1	AGAATGAGTA	    0.997484	-135
ATGAGAAGATGGCATGAGAGGATAAAATACTA	1	168	0	GGCATGAGAA	    0.991749	-48
TATGGCAAGGAGAATGAGAAGATGGCATGAGA	1	181	0	AGAATGAGAA	    0.997484	-35
CTTGCCATAAGGAGTGAGAGCA          	1	204	1	GGAGTGAGAA	    0.996344	-12
          *********  *

Masking position 5
Map Score:   13.7774

Number of sites scoring better than the average of aligned sites = 69
Number in coding regions = 49
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

TTCTAAGCTGTTCTTATCGTA         	1	2	0	TTCTTATCGT	    0.974521	-214
ACTCAACTCATTCTAATTGCTTTATACACA	1	43	0	TTCTAATTGC	    0.955348	-173
AAAGAAAGACTTCTTTTGGGTAGAATAAAC	1	121	0	TTCTTTTGGG	    0.994879	-95
AAAGAAGTCTTTCTTTTGGGTTTATTTGTT	1	135	1	TTCTTTTGGG	    0.994879	-81
 TGCTCTCACTCCTTATGGCAAGGAGAATG	1	197	0	TCCTTATGGC	    0.989977	-19
          **********

Masking position 4
Map Score:   6.54901

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 174
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

CCTATTCTCTAACTCAACTCATTCTAATTG	1	54	0	AACTCAACTC	    0.980786	-162
TTCTCTGCTACCCTATTCTCTAACTCAACT	1	65	0	CCCTATTCTC	     0.97729	-151
GTCTCAGCTCAACTAAACTCATTCTCTGCT	1	86	0	AACTAAACTC	    0.983955	-130
GGTAGAATAAACATAATGTCTCAGCTCAAC	1	103	0	ACATAATGTC	    0.933881	-113
ACTATATAACAAATAAACCCAAAAGAAAGA	1	142	0	AAATAAACCC	    0.934744	-74
TCCTCTCATGCCATCTTCTCATTCTCCTTG	1	178	1	CCATCTTCTC	    0.957792	-38
          **********

Masking position 4
Map Score:   3.69081

Number of sites scoring better than the average of aligned sites = 388
Number in coding regions = 315
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 4

TTAGAGAATAGGGTAGCAGAGAATGAGTTT	1	72	1	GGGTAGCAGA	     0.99516	-144
GACTTCTTTTGGGTAGAATAAACATAATGT	1	114	0	GGGTAGAATA	    0.993716	-102
TGGCATGAGAGGATAAAATACTATATAACA	1	161	0	GGATAAAATA	     0.93587	-55
CACTCCTTATGGCAAGGAGAATGAGAAGAT	1	190	0	GGCAAGGAGA	    0.977885	-26
          **********

Masking position 5
Map Score:   1.47428

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 86
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 5

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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:   3.08538e-14

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