AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i251_chemotaxis_hpyl_reg_100.orf -o251_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 
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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP01329	56	AE000511
#2	RHP01332	22	AE000511
#3	RHP01335	28	AE000511
#4	RHP01336	120	AE000511
#5	RHP00471	290	AE000511

Motif number 1

TATTTTACAATTTTATAAAAAGAA       	1	4	0	TTTTATAAAA	    0.866332	-53
   AGAGTGATTTTAAAAGCATGAGAATGGC	3	8	1	TTTTAAAAGA	    0.979918	-21
      CACATTTTGAAAATTTTCTTTAAAA	4	5	1	TTTTGAAAAT	     0.87966	-116
TGAAAATTTTCTTTAAAAAAACCGCTAATTG	4	18	1	CTTTAAAAAA	    0.947844	-103
TTACAAAATCGTTTAAAAACTAACAATTAGC	4	41	0	GTTTAAAAAT	    0.965878	-80
TCCTTTTTTGGCTTACAAAATCGTTTAAAAA	4	53	0	GCTTACAAAT	     0.86003	-68
AAGACAAGGATTTTACAAGTAA         	5	2	0	TTTTACAAGA	    0.968323	-289
TCATTGGATGGTTTGAAAAAAGAAAGACAAG	5	25	0	GTTTGAAAAA	      0.9648	-266
TATGATAATCGTTTAAAAGTAATAAAATAAC	5	76	0	GTTTAAAAGA	    0.984962	-215
AACTGAATTTTTTTACAAATAAGAACGCTCA	5	114	1	TTTTACAAAA	    0.973745	-177
CGCTTTGGCTGTTTAAAAAGAGCCTAATTTA	5	244	1	GTTTAAAAAA	    0.987515	-47
TTAAATGCAATCTTAAAAGGAGAAGCACT  	5	272	1	TCTTAAAAGA	    0.944124	-19
          ********* *

Masking position 7
Map Score:   19.908

Number of sites scoring better than the average of aligned sites = 950
Number in coding regions = 740
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 149
Fraction of orfs with sites within 600 bp upstream = 0.0239319


Motif number 2

TATAAAATTGTAAAATACTCTTATCTCAAACG	1	18	1	TAAAATCTCT	    0.969361	-39
         TTAAAACCCCTTTTTAGCGTTTG	1	44	0	TAAAACCCTT	    0.948729	-13
CTCATGCTTTTAAAATCACTCT          	3	1	0	TAAAATACTT	    0.978049	-28
  CACATTTTGAAAATTTTCTTTAAAAAAACC	4	9	1	GAAAATTTCT	    0.657002	-112
TTGTTAGTTTTTAAACGATTTTGTAAGCCAAA	4	46	1	TTAAACATTT	    0.758935	-75
CAAAAAAGGATACAATACCCTTAAGGATTTTA	4	74	1	TACAATCCCT	    0.962357	-47
TGCCTTACTATAAAATAAATATAAAATCCTTA	4	95	0	TAAAATAATT	    0.852493	-26
   TTACTTGTAAAATCCTTGTCTTTCTTTTT	5	8	1	TAAAATCTTT	    0.958161	-283
TTTCAAACCATCCAATGACCCTTTATCGCACT	5	38	1	TCCAATACCT	    0.854063	-253
TTAAAAGTAATAAAATAACTCTTTGAGTGCGA	5	63	0	TAAAATACTT	    0.978049	-228
TTTATTACTTTTAAACGATTATCATAGCAAAC	5	81	1	TTAAACATTT	    0.758955	-210
TACCTTGACCGACAATAATCATTGGCTAAATG	5	155	0	GACAATATCT	    0.859827	-136
ATGTTTTGATTAAAATTACCTTGACCGACAAT	5	171	0	TAAAATACCT	    0.984015	-120
          ****** *** *

Masking position 5
Map Score:   13.9472

Number of sites scoring better than the average of aligned sites = 908
Number in coding regions = 761
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 3

   TTAAAACCCCTTTTTAGCGTTTGAGATA	1	39	0	CCCTTTTTGC	    0.996515	-18
     AATTCTTCTTTATGGCTATTCT    	2	7	0	TTCTTTATGC	    0.944426	-16
GGTATTGTATCCTTTTTTGGCTTACAAAATC	4	62	0	CCTTTTTTGC	    0.982076	-59
CATCCAATGACCCTTTATCGCACTCAAAGAG	5	46	1	CCCTTTATGC	    0.995017	-245
TCATTGAACGCTCCATTTAGCCAATGATTAT	5	142	1	CTCCATTTGC	    0.945653	-149
          ******** **

Masking position 6
Map Score:   3.67224

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 190
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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