AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_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	ribH	32	riboflavin synthase (beta subunit)
#2	ypuE	258	ypuE

Motif number 1

CCCTTCGATCCGAAAGGTGATGTTTT     	2	6	0	CGAAGGTGAT	    0.982455	-253
CCTTTCGGATCGAAGGGTGATGTTTTGTTTT	2	20	1	CGAGGGTGAT	    0.995525	-239
GTATCTTCGGGGCAGGGTGGAAATCCCGACC	2	131	1	GGCGGGTGGA	    0.993445	-128
GTGGAAATCCCGACCGGCGGTAGTAAAGCAC	2	147	1	CGACGGCGGT	    0.990842	-112
TGTGCATAAGCACGCGGTGGATTCAGTTTAA	2	202	1	CACCGGTGGA	    0.968531	-57
GTGAAAGTCTGGATGGGAGAAGG        	2	246	1	GGAGGGAGAA	    0.972485	-13
          *** *******

Masking position 6
Map Score:   5.29542

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 226
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

       TCACAAATATCACAAAAAAGGAT	1	4	1	CAAATATCAC	    0.988462	-29
          AAAACATCACCTTTCGGATC	2	1	1	AAAACATCAC	    0.996425	-258
TGAGAAAAACAAAACATCACCCTTCGATCC	2	26	0	AAAACATCAC	    0.996425	-233
          **********

Masking position 6
Map Score:   4.20329

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 37
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

AAATATCACAAAAAAGGATGGGAATCAT   	1	15	1	AAAAAGGATG	    0.995497	-18
TGCGTACTTTAAAAAGGATCGCTATAATAAC	2	75	1	AAAAAGGATG	    0.995497	-184
TATAATAACCAATAAGGACAAATGAATAAAG	2	97	1	AATAAGGACA	    0.970276	-162
AGGACAAATGAATAAAGATTGTATCTTCGGG	2	111	1	AATAAAGATG	    0.982347	-148
          ********* *

Masking position 5
Map Score:   3.29969

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 81
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

TATTTCATTGCGTACTTTAAAAAGGATCGC	2	67	1	CGTACTTTAA	    0.972702	-192
TACCGCCGGTCGGGATTTCCACCCTGCCCC	2	139	0	CGGGATTTCC	    0.975737	-120
CTAAAGCAAATGTGCTTTACTACCGCCGGT	2	159	0	TGTGCTTTAC	     0.94321	-100
ACACGGGTCACGGGCTCTAAAGCAAATGTG	2	175	0	CGGGCTCTAA	    0.987876	-84
TTCTCCCATCCAGACTTTCACTGTCGGCTT	2	237	0	CAGACTTTCA	    0.943208	-22
          **********

Masking position 6
Map Score:   0.922508

Number of sites scoring better than the average of aligned sites = 960
Number in coding regions = 864
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 5

          **********

No masking
Map Score:   8.97716e-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:   8.97716e-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:   8.97716e-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