AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00271_aful_reg_100.orf -o00271_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	AF1452	117	signal-transducing histidine kinase
#2	AF1453	37	methionyl-tRNA synthetase (metS)
#3	AF2113	44	A. fulgidus predicted coding region AF2113

Motif number 1

AATTTTTGTTTTGGTTACCTGTAAAGCGTATTTG	1	16	1	TTGTACTGAA	    0.992269	-102
GTAAAGCGTATTTGCTGGCGGCAGTTTTTTGGAA	1	36	1	TTGCGGGGAG	    0.976502	-82
ATTTGGCCGATTATTCAGATGCAATCCATTCCAA	1	64	0	TTTTAGTGAA	    0.988145	-54
GAGGGAAAAGGTTGCGAGGGGTAAATAACGTTTT	2	13	0	GTGCAGGGAA	    0.991502	-25
          TTTGTCAGGTGCAAAATTTTTTAA	3	1	1	TTGTAGTGAA	    0.995958	-44
GGTGCAAAATTTTTTAACAGGAAAATAACTCAAT	3	18	1	TTTTACGGAA	    0.985184	-27
          ** ** ** ** **

Masking position 2
Map Score:   5.05212

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 118
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

ACGCTTTACAGGTAACCAAAACAAAAATTA	1	15	0	GGTAACCAAA	    0.975696	-103
TGCCTATCTTTGTAAATAAAAGCATTTGGC	1	91	0	TGTAAATAAA	    0.984817	-27
GGTTGCGAGGGGTAAATAACGTTTTAC   	2	8	0	GGTAAATAAC	     0.99249	-30
GTTATTTTCCTGTTAAAAAATTTTGCACCT	3	17	0	TGTTAAAAAA	    0.890367	-28
TTTTTTAACAGGAAAATAACTCAATTAT  	3	27	1	GGAAAATAAC	    0.980286	-18
          **********

Masking position 5
Map Score:   4.76409

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 57
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

GGCCGATTATTCAGATGCAATCCATTCCAA	1	64	0	TCAGATGCAA	    0.996869	-54
      TTTGTCAGGTGCAAAATTTTTTAA	3	5	1	TCAGGTGCAA	    0.998084	-40
          **********

Masking position 6
Map Score:   1.61308

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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