AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i253_chemotaxis2_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	motA	300	motility protein A

Motif number 1

TAAAAAAGTGTAAAGGATGAAGGGAAGTAGCGCT  	1	9	0	TAAGGAGGAA	    0.998474	-292
TTACACTTTTTTAAGGAGGGATGGAACATGTTTATA	1	32	1	TAAGGATGAA	    0.995497	-269
GAATACCATCTGAAGGACAGCTTGCAAGCAAGCTGC	1	98	1	TAAGGATGCA	    0.990024	-203
CATGAAATATTCAAGGAAGAGGCATAGAAGGGAGAA	1	188	0	TAAGGAGATA	    0.968521	-113
GCCCGGAACTTTAGGGACATTGTGAATTTGTTCATG	1	220	0	TAGGGAGGAA	    0.995788	-81
AAGCTAGTAAAAAAGGATTTGGTGAAAACT      	1	281	1	AAAGGAGGAA	    0.993843	-20
          * *****    * ***

Masking position 7
Map Score:   7.63302

Number of sites scoring better than the average of aligned sites = 163
Number in coding regions = 140
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

GGATGGAACATGTTTATATACAGTGAATAT	1	50	1	TGTTTATATA	    0.865448	-251
ATACAGTGAATATGTATTTCTACTATTATA	1	67	1	TATGTATTTC	    0.910856	-234
GCAAGCAAGCTGCTAATTTCAGTAGACCCC	1	121	1	TGCTAATTTC	    0.964195	-180
AGCCCGTTTTTGTTTATTTCTCCCTTCTAT	1	171	1	TGTTTATTTC	    0.989646	-130
GCCTCTTCCTTGAATATTTCATGAACAAAT	1	201	1	TGAATATTTC	    0.876267	-100
TTAGGGACATTGTGAATTTGTTCATGAAAT	1	216	0	TGTGAATTTG	    0.933332	-85
GCTTGTCTATGGTTAATATCGGTTTTGGTG	1	255	0	GGTTAATATC	    0.907871	-46
          **********

Masking position 6
Map Score:   3.46279

Number of sites scoring better than the average of aligned sites = 671
Number in coding regions = 576
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 3

AGTAGACCCCCGGGCTTTTCAATTTTGGAGAG	1	141	1	CGGGCTTCAA	    0.997276	-160
TAAACAAAAACGGGCTCTCCAAAATTGAAAAG	1	155	0	CGGGCTCCAA	     0.99898	-146
CCTAAAGTTCCGGGCACCAAAACCGATATTAA	1	241	1	CGGGCACAAA	    0.995216	-60
          *******  ***

Masking position 11
Map Score:   1.08321

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 7
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

AAATTAGCAGCTTGCTTGCAAGCTGTCCTT	1	110	0	CTTGCTTGCA	    0.956581	-191
AGTAGACCCCCGGGCTTTTCAATTTTGGAG	1	141	1	CGGGCTTTTC	    0.993563	-160
TAAACAAAAACGGGCTCTCCAAAATTGAAA	1	157	0	CGGGCTCTCC	     0.99285	-144
TCCTTTTTTACTAGCTTGTCTATGGTTAAT	1	268	0	CTAGCTTGTC	    0.982636	-33
          **********

Masking position 6
Map Score:   0.617625

Number of sites scoring better than the average of aligned sites = 381
Number in coding regions = 343
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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