AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i048_Polysaccharide_Biosynthesis_2_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	yvyH	245	similar to UDP-N-acetylglucosamine 2-epimerase

Motif number 1

AGTTTAACCATAAATTTTTTCGATCATAAGGAAG	1	22	0	TAATTTTCAT	    0.967589	-224
AAATTTATGGTTAAACTATTCTCTATTTACCCTT	1	39	1	TAACATTCCT	    0.964914	-207
TATTCTCTATTTACCCTTTTCAATATGTTTTTAC	1	55	1	TACCTTTCAT	     0.97902	-191
CAATATGTTTTTACACATTTTTATGATATCGGAT	1	75	1	TACCTTTTAT	    0.984958	-171
TGATATCGGATAAACCATTTTTAAACAAGCTTTA	1	98	1	TAACTTTTAA	    0.903911	-148
ATATTAAAACTTATATCATTTTATTTGAATCAAG	1	138	1	TATTATTTAT	    0.936725	-108
ATGCATCATTTTAAATCATTTCATTCTTGATTCA	1	163	0	TAATATTTAT	    0.971452	-83
TGATTTAAAATGATGCATTTTCATGTAGAATATG	1	179	1	TATCTTTTAT	    0.966764	-67
ATATGTAGTATGAATTTATTTACTATAGCAGAAA	1	208	1	TAATATTTCT	    0.960366	-38
     ATTTGTCACCTGGTTTTCTGCTATAGTAA	1	227	0	TACTGTTTCT	    0.914525	-19
          * ** * **** **

Masking position 9
Map Score:   12.1462

Number of sites scoring better than the average of aligned sites = 838
Number in coding regions = 686
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 171
Fraction of orfs with sites within 600 bp upstream = 0.0274655


Motif number 2

CATTTTTATGATATCGGATAAACCATTTTTAA	1	90	1	ATTCGATAAA	     0.95908	-156
AAGTTTTAATATTAAGGATAAAGCTTGTTTAA	1	118	0	ATAAGATAAA	    0.970654	-128
TTCTTGATTCAAATAAAATGATATAAGTTTTA	1	142	0	AATAAATGAT	    0.794914	-104
TTTTATTTGAATCAAGAATGAAATGATTTAAA	1	156	1	ATAAGATGAA	    0.985489	-90
GAATGAAATGATTTAAAATGATGCATTTTCAT	1	171	1	ATTAAATGAT	     0.94911	-75
CATGTAGAATATGTAGTATGAATTTATTTACT	1	200	1	ATTAGATGAA	    0.993682	-46
AATTTATTTACTATAGCAGAAAACCAGGTGAC	1	220	1	CTTAGAGAAA	    0.878225	-26
          ** *** *****

Masking position 8
Map Score:   3.81483

Number of sites scoring better than the average of aligned sites = 493
Number in coding regions = 348
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 157
Fraction of orfs with sites within 600 bp upstream = 0.0252168


Motif number 3

TATGATCGAAAAAATTTATGGTTAAACTATT	1	28	1	AAAATTTATG	    0.975436	-218
AAAATGTGTAAAAACATATTGAAAAGGGTAA	1	65	0	AAAACATATG	    0.970959	-181
TATTAAGGATAAAGCTTGTTTAAAAATGGTT	1	110	0	AAAGCTTGTT	    0.923059	-136
CCTTAATATTAAAACTTATATCATTTTATTT	1	133	1	AAAACTTATT	    0.975419	-113
ATTTTCATGTAGAATATGTAGTATGAATTTA	1	195	1	AGAATATGTG	    0.936013	-51
ATATGTAGTATGAATTTATTTACTATAGCAG	1	208	1	TGAATTTATT	    0.837782	-38
          ********* *

Masking position 7
Map Score:   1.10824

Number of sites scoring better than the average of aligned sites = 417
Number in coding regions = 323
Number in noncoding regions = 94
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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