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

Motif number 1

  AGCGCTACTTCCCTTCATCCTTTACACTTTTTTA	1	9	1	TTCCTCCTTA	    0.998424	-292
TATAAACATGTTCCATCCCTCCTTAAAAAAGTGTAA	1	32	0	TTCATCCTTA	     0.99535	-269
GCAGCTTGCTTGCAAGCTGTCCTTCAGATGGTATTC	1	98	0	TGCATCCTTA	    0.989702	-203
TTCTCCCTTCTATGCCTCTTCCTTGAATATTTCATG	1	188	1	TATCTCCTTA	     0.96752	-113
CATGAACAAATTCACAATGTCCCTAAAGTTCCGGGC	1	220	1	TTCCTCCCTA	    0.995653	-81
      AGTTTTCACCAAATCCTTTTTTACTAGCTT	1	281	0	TTCCTCCTTT	    0.993642	-20
          *** *    ***** *

Masking position 10
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

ATATTCACTGTATATAAACATGTTCCATCC	1	50	0	TATATAAACA	    0.865046	-251
TATAATAGTAGAAATACATATTCACTGTAT	1	67	0	GAAATACATA	    0.910579	-234
GGGGTCTACTGAAATTAGCAGCTTGCTTGC	1	121	0	GAAATTAGCA	    0.964075	-180
ATAGAAGGGAGAAATAAACAAAAACGGGCT	1	171	0	GAAATAAACA	     0.98961	-130
ATTTGTTCATGAAATATTCAAGGAAGAGGC	1	201	0	GAAATATTCA	    0.875902	-100
ATTTCATGAACAAATTCACAATGTCCCTAA	1	216	1	CAAATTCACA	    0.933116	-85
CACCAAAACCGATATTAACCATAGACAAGC	1	255	1	GATATTAACC	     0.90758	-46
          **********

Masking position 4
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	    0.997388	-160
TAAACAAAAACGGGCTCTCCAAAATTGAAAAG	1	155	0	CGGGCTCCAA	     0.99902	-146
CCTAAAGTTCCGGGCACCAAAACCGATATTAA	1	241	1	CGGGCACAAA	    0.995413	-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	    0.954442	-191
AGTAGACCCCCGGGCTTTTCAATTTTGGAG	1	141	1	CGGGCTTTTC	    0.993233	-160
TAAACAAAAACGGGCTCTCCAAAATTGAAA	1	157	0	CGGGCTCTCC	     0.99249	-144
TCCTTTTTTACTAGCTTGTCTATGGTTAAT	1	268	0	CTAGCTTGTC	    0.981756	-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