AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i238_sensory_cassete4_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	yclJ	212	similar to two-component response regulator [YclK]

Motif number 1

GTATAGGTATTTTTATTGATAAGACCGCCT	1	23	1	TTTTATTGAT	    0.974412	-190
ATTGTTCATATTTTTTTCATACCTTTGGAC	1	88	0	TTTTTTTCAT	    0.992077	-125
ATTGTTAGTTTTTATTTCATCAACTAGAAA	1	121	0	TTTATTTCAT	    0.974397	-92
GTTTTGATGCTTTTTTATATAATAGCACCA	1	179	0	TTTTTTATAT	     0.93333	-34
TATCCTCCGGTTGTTTTGATGCTTTTTTAT	1	191	0	TTGTTTTGAT	    0.982591	-22
          **********

Masking position 6
Map Score:   5.60374

Number of sites scoring better than the average of aligned sites = 448
Number in coding regions = 325
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 2

TCCTCCGTATAGGTATTTTTATTGATAAGA	1	17	1	AGGTATTTTT	    0.924031	-196
CATATTTTTTTCATACCTTTGGACTACTAT	1	82	0	TCATACCTTT	    0.907981	-131
AATAGATTGTTCATATTTTTTTCATACCTT	1	93	0	TCATATTTTT	    0.934344	-120
GTTTCACAATTGTTAGTTTTTATTTCATCA	1	129	0	TGTTAGTTTT	    0.940682	-84
CATTTTAAACAGAAGGTTTTGCGTTTCACA	1	151	0	AGAAGGTTTT	    0.849882	-62
CTGTTTAAAATGGTGCTATTATATAAAAAA	1	169	1	TGGTGCTATT	    0.940462	-44
CCGGTTGTTTTGATGCTTTTTTATATAATA	1	185	0	TGATGCTTTT	    0.989195	-28
          **********

Masking position 9
Map Score:   2.62495

Number of sites scoring better than the average of aligned sites = 2015
Number in coding regions = 1680
Number in noncoding regions = 335
Number of orfs with sites within 600 bp upstream = 281
Fraction of orfs with sites within 600 bp upstream = 0.0451333


Motif number 3

AAAAATACCTATACGGAGGAACATAA    	1	7	0	ATACGGAGGA	    0.983309	-206
ATTAATAGTAGTCCAAAGGTATGAAAAAAA	1	78	1	GTCCAAAGGT	    0.957153	-135
CACCATTTTAAACAGAAGGTTTTGCGTTTC	1	154	0	AACAGAAGGT	    0.974385	-59
GCATCAAAACAACCGGAGGATATA      	1	199	1	AACCGGAGGA	    0.995743	-14
          **********

Masking position 7
Map Score:   0.947543

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 293
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

CTTGCTGATAAATTAATAGTAGTCCAAAGG	1	67	1	AATTAATAGT	    0.975591	-146
ATCAACTAGAAATAGATTGTTCATATTTTT	1	103	0	AATAGATTGT	     0.97376	-110
TGCGTTTCACAATTGTTAGTTTTTATTTCA	1	132	0	AATTGTTAGT	    0.983499	-81
          **********

Masking position 2
Map Score:   0.267211

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 38
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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