AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -ilacI_aful_opreg_100.orf -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	AF1055	111	flagellin (flaB1-2)

Motif number 1

TTTCTAAGTTGAAATTTCCTTTACGTAATT	1	11	0	GAAATTTCCT	    0.998156	-101
CTTATATGTTGAAATTACCTTTTTCTAAGT	1	32	0	GAAATTACCT	    0.996758	-80
CAATATATAAGAATTTTCTTATATGTTGAA	1	49	0	GAATTTTCTT	    0.991184	-63
          **********

Masking position 3
Map Score:   5.30107

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 34
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

AATTACCTTTTTCTAAGTTGAAATTTCCTT	1	20	0	TTCTAAGTTG	    0.993596	-92
AAGAATTTTCTTATATGTTGAAATTACCTT	1	41	0	TTATATGTTG	    0.996394	-71
AAGAAAATTCTTATATATTGCTAATCGCTG	1	59	1	TTATATATTG	    0.985968	-53
          **********

Masking position 5
Map Score:   4.47139

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 5
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

CTAAGTTGAAATTTCCTTTACGTAATT   	1	8	0	ATTTCCTTTA	    0.987966	-104
ATATGTTGAAATTACCTTTTTCTAAGTTGA	1	29	0	ATTACCTTTT	    0.993043	-83
ATATATAAGAATTTTCTTATATGTTGAAAT	1	47	0	ATTTTCTTAT	    0.935065	-65
       CCCATCACCTCTCACCTCATCCT	1	99	0	ATCACCTCTC	    0.976666	-13
          **********

Masking position 7
Map Score:   2.03645

Number of sites scoring better than the average of aligned sites = 313
Number in coding regions = 279
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

          **********

No masking
Map Score:   -1.17788e-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 5

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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