AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i235_sensory_cassete1_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ygiX	151	putative 2-component transcriptional regulator
#2	HI1708	62	transcriptional regulatory protein (ygiX)
#3	HI1709	114	conserved hypothetical protein

Motif number 1

CTGTTTCCGAGCATTTAACAAGATAGTCCTTA	1	32	1	GCTTTAAAAG	    0.976404	-120
TTTATTTTTTTCCCTTAAGAAGTTGTTAAGGA	1	58	0	TCCTTAAAAG	    0.988739	-94
          TCATTTCTGAAAATGCGAGCAT	2	1	1	TCTTTCTAAA	    0.949893	-62
CTCGCTGTTTTTGTTTATAAAGTGCGGTCAAT	2	36	1	TTTTTATAAG	    0.940637	-27
     TAAAGTCTTTTCAAAAAAGTATAGTCC	3	6	1	TCTTTCAAAA	    0.951464	-109
GTCCTCTTAATCTTTTATTAAGATTTATTTGT	3	34	1	TCTTTATAAG	    0.990383	-81
TGAAATTAACTAACTTAAAAAGGAAACGTT  	3	95	1	TACTTAAAAG	    0.932875	-20
          ** ***** ***

Masking position 10
Map Score:   6.59554

Number of sites scoring better than the average of aligned sites = 123
Number in coding regions = 98
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

 GTTTATTACTCCCTTTAATGTCTGTTTCC	1	10	1	TCCCTTTAAT	    0.874296	-142
AATGTCTGTTTCCGAGCATTTAACAAGATA	1	27	1	TCCGAGCATT	    0.986989	-125
CCGTATTTGCTGCCAGTAAACCGTGTTGTA	1	113	0	TGCCAGTAAA	    0.882614	-39
   TTTTTCATCCCTGCGATAACCGTATTT	1	135	0	TCCCTGCGAT	    0.966396	-17
TTTCTGAAAATGCGAGCATTAGCTCGCTGT	2	14	1	TGCGAGCATT	     0.98298	-49
GTTTATAAAGTGCGGTCAATTTTTT     	2	48	1	TGCGGTCAAT	    0.942246	-15
AATACACACATCCAAGCAATGGAGCTTGAA	3	69	1	TCCAAGCAAT	    0.977724	-46
          **********

Masking position 1
Map Score:   4.31255

Number of sites scoring better than the average of aligned sites = 1587
Number in coding regions = 1465
Number in noncoding regions = 122
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 3

TTCTTAAGGGAAAAAAATAAAATTTAGTGC	1	69	1	AAAAAAATAA	    0.980453	-83
          AAAAAATTGACCGCACTTTA	2	53	0	AAAAAATTGA	    0.957606	-10
AAGTCTTTTCAAAAAAGTATAGTCCTCTTA	3	13	1	AAAAAAGTAT	      0.9275	-102
AAATCTTAATAAAAGATTAAGAGGACTATA	3	30	0	AAAAGATTAA	    0.957606	-85
GTGTGTATTAAAACAAATAAATCTTAATAA	3	48	0	AAACAAATAA	     0.95762	-67
          **********

Masking position 6
Map Score:   2.79289

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 71
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

GGACTATCTTGTTAAATGCTCGGAAACAGA	1	31	0	GTTAAATGCT	    0.906118	-121
GCATTTAACAAGATAGTCCTTAACAACTTC	1	42	1	AGATAGTCCT	    0.975541	-110
AAAAAATAAAATTTAGTGCTGTACAGAGCG	1	80	1	ATTTAGTGCT	    0.984679	-72
AAAAACAGCGAGCTAATGCTCGCATTTTCA	2	18	0	AGCTAATGCT	    0.935578	-45
GTTTTTGTTTATAAAGTGCGGTCAATTTTT	2	42	1	ATAAAGTGCG	    0.947508	-21
TTTCAAAAAAGTATAGTCCTCTTAATCTTT	3	19	1	GTATAGTCCT	    0.975559	-96
          **********

Masking position 5
Map Score:   2.45989

Number of sites scoring better than the average of aligned sites = 269
Number in coding regions = 223
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


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


Motif number 7

          **********

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