AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i094_Ribose_Transport_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	yufN	300	similar to ABC transporter (lipoprotein)
#2	yufO	75	similar to ABC transporter (ATP-binding protein)

Motif number 1

ACTTATGACTTAGTTTTTCGGGATCAACTAAC	1	14	0	TAGTTTTCGG	    0.985766	-287
AAACGATGTCACGGTTTTCCGCCCGGAACGCC	1	57	1	ACGTTTTCGC	    0.959236	-244
AAGGATGCGGAAGGCGTTCCGGGCGGAAAACC	1	69	0	AAGCGTTCGG	    0.991997	-232
TAGAATCGATAAAATTTTCTGATAATAACAAA	1	177	0	AAATTTTCGA	    0.961519	-124
CGATTCTAAGAAATTGTTCAGGACAGCCCATC	1	201	1	AAATGTTCGG	    0.994899	-100
ATTTGGTTCAAAGCTGATCCGGCCAGTCATGT	1	233	0	AAGTGATCGG	    0.988184	-68
GCTTTGAACCAAATTTTTCTGGGGGGTTATAT	1	251	1	AAATTTTCGG	    0.993847	-50
          *** ***** **

Masking position 8
Map Score:   9.38414

Number of sites scoring better than the average of aligned sites = 352
Number in coding regions = 317
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

TGAAGTAAGACTTATGACTTAGTTTTTCGG	1	25	0	CTTATGACTT	    0.922648	-276
CCGCATCCTTCTCTTCCCCGCCTTTCGAAG	1	91	1	CTCTTCCCCG	    0.984023	-210
GACAGTTCTATTCTTCCCTGAATAAGCGTG	1	134	0	TTCTTCCCTG	    0.963043	-167
GACAGCCCATCACATGACTGGCCGGATCAG	1	222	1	CACATGACTG	    0.931936	-79
GCTCGACCTCCTTATCCCTGCGATTC    	2	7	0	CTTATCCCTG	    0.995022	-69
AGGTCGAGCCCTTATCCCTTGTTTTTCTTT	2	28	1	CTTATCCCTT	    0.985409	-48
          **********

Masking position 5
Map Score:   4.81482

Number of sites scoring better than the average of aligned sites = 490
Number in coding regions = 429
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 3

GCGGGGAAGAGAAGGATGCGGAAGGCGTTCC	1	81	0	GAAGATGCGG	    0.943865	-220
TATTTCCTTCGAAAGGCGGGGAAGAGAAGGA	1	96	0	GAAAGCGGGG	     0.99502	-205
CTTCCCTGAATAAGCGTGGTGTGAGTATTTC	1	121	0	TAAGGTGGTG	    0.833442	-180
ATTCAGGGAAGAATAGAACTGTCTCAGCGCA	1	141	1	GAATGAACTG	    0.878958	-160
AATAACAAATGGAATGCGCTGAGACAGTTCT	1	155	0	GGAAGCGCTG	    0.964596	-146
          GAATCGCAGGGATAAGGAGGT	2	1	1	GAATGCAGGG	    0.976666	-75
CAAAATAAAAGAAAAACAAGGGATAAGGGCT	2	34	0	GAAAACAAGG	    0.818046	-42
TATTTTGAAATAAAGGAGCGGTCAATCA   	2	58	1	TAAAGAGCGG	    0.953011	-18
          **** ******

Masking position 3
Map Score:   2.29102

Number of sites scoring better than the average of aligned sites = 2254
Number in coding regions = 1965
Number in noncoding regions = 289
Number of orfs with sites within 600 bp upstream = 231
Fraction of orfs with sites within 600 bp upstream = 0.0371025


Motif number 4

          **********

No masking
Map Score:   4.64285e-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:   4.64285e-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:   4.64285e-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