AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i333_1_5_3_1_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	tenA	248	transcriptional regulator

Motif number 1

ACGAATACATATTGAATTGTTCTGCACCTC	1	43	0	ATTGAATTGT	    0.824222	-206
AAGGGCTGAGATAAAAGTGTGACTTTTAGA	1	97	1	ATAAAAGTGT	    0.939617	-152
AGACCTGCGTAGGGAAGTGGAGCGGTATTT	1	149	1	AGGGAAGTGG	    0.996117	-100
GAAAAGTGGTTTGGAATTGGCATAGTAAAA	1	185	0	TTGGAATTGG	    0.956179	-64
TTTCCCGCAAGGAAAAGTGGTTTGGAATTG	1	196	0	GGAAAAGTGG	     0.98737	-53
TTTTCCTTGCGGGAAAGTGGTTTTTTTATT	1	210	1	GGGAAAGTGG	    0.994355	-39
          **********

Masking position 5
Map Score:   5.32504

Number of sites scoring better than the average of aligned sites = 612
Number in coding regions = 519
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 2

GTGTTAATATAGAGGTGCAGAACAATTCAA	1	32	1	AGAGGTGCAG	    0.991637	-217
GGACACCCCTAGTGGTTAAACGAATACATA	1	62	0	AGTGGTTAAA	    0.927904	-187
CATAACTTGAACAGGTTCAGACCTGCGTAG	1	131	1	ACAGGTTCAG	    0.970408	-118
TGCGTAGGGAAGTGGAGCGGTATTTGTGTT	1	154	1	AGTGGAGCGG	     0.98331	-95
CGCAAGGAAAAGTGGTTTGGAATTGGCATA	1	191	0	AGTGGTTTGG	    0.992239	-58
CTTGCGGGAAAGTGGTTTTTTTATTTTCAG	1	215	1	AGTGGTTTTT	     0.89982	-34
          **********

Masking position 1
Map Score:   4.3591

Number of sites scoring better than the average of aligned sites = 381
Number in coding regions = 338
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

CTCTATATTAACACGAATCCTTATTTGGTC	1	16	0	ACACGAATCC	    0.996544	-233
CCTAGTGGTTAAACGAATACATATTGAATT	1	55	0	AAACGAATAC	    0.992113	-194
TAGTAAAATAACACAAATACCGCTCCACTT	1	163	0	ACACAAATAC	    0.992113	-86
          **********

Masking position 6
Map Score:   2.98958

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 = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TCTCAGCCCTTATGAAGGACACCCCTAGTG	1	78	0	TATGAAGGAC	    0.992954	-171
CTGTTCAAGTTATGAGGGTCTAAAAGTCAC	1	115	0	TATGAGGGTC	    0.995208	-134
TCCACTTCCCTACGCAGGTCTGAACCTGTT	1	140	0	TACGCAGGTC	    0.993873	-109
          **********

Masking position 2
Map Score:   1.85355

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 19
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

CTGCACCTCTATATTAACACGAATCCTTAT	1	22	0	ATATTAACAC	    0.962408	-227
TGAGGGTCTAAAAGTCACACTTTTATCTCA	1	103	0	AAAGTCACAC	    0.982653	-146
TTGGCATAGTAAAATAACACAAATACCGCT	1	169	0	AAAATAACAC	     0.99137	-80
TCTGAAAATAAAAAAACCACTTTCCCGCAA	1	216	0	AAAAAACCAC	    0.963866	-33
          **********

Masking position 3
Map Score:   1.81526

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 99
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 6

TATTGAATTGTTCTGCACCTCTATATTAAC	1	34	0	TTCTGCACCT	    0.965642	-215
ACACTTTTATCTCAGCCCTTATGAAGGACA	1	87	0	CTCAGCCCTT	     0.99074	-162
AAGTGTGACTTTTAGACCCTCATAACTTGA	1	111	1	TTTAGACCCT	    0.978685	-138
CTTGAACAGGTTCAGACCTGCGTAGGGAAG	1	136	1	TTCAGACCTG	    0.985751	-113
          **********

Masking position 2
Map Score:   0.399286

Number of sites scoring better than the average of aligned sites = 448
Number in coding regions = 385
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 7

          **********

No masking
Map Score:   -4.23894e-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 8

          **********

No masking
Map Score:   -4.23894e-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 9

          **********

No masking
Map Score:   -4.23894e-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