AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_aquae_reg_300.orf -o183_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01395	37	Aquifex_aeolicus
#2	RAA01396	163	Aquifex_aeolicus
#3	RAA01090	65	Aquifex_aeolicus

Motif number 1

ACCGCTGAGCTACGCCGGCTGAGTATATTA	2	81	0	TACGCCGGCT	    0.995457	-83
TCAGCGGTAGAGCGCGGGCTTCGTAAGCCT	2	103	1	AGCGCGGGCT	    0.641308	-61
CGAACCCACGACCTCAGGCTTACGAAGCCC	2	118	0	ACCTCAGGCT	    0.990613	-46
TTCGAATCCCACCGCCGGCTCTCAAACACC	2	144	1	ACCGCCGGCT	    0.996799	-20
          **********

Masking position 10
Map Score:   7.65587

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 10
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

GAAATTTTTCAGTGATTTAAATATA     	1	6	0	AGTGATTTAA	    0.984296	-32
          AATAATTTAATACTTTAAAT	2	1	1	AATAATTTAA	    0.992063	-163
AAATTCGGGAAATAATTTAAAGTATTAAAT	2	15	0	AATAATTTAA	    0.992063	-149
GGCTGAGTATATTAATTTAAACATTCATAA	2	65	0	ATTAATTTAA	    0.984431	-99
          **********

Masking position 5
Map Score:   6.37245

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 10
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TACCGCTGAGCTACGCCGGCTGAGTATATT	2	82	0	CTACGCCGGC	      0.9949	-82
CTCAGCGGTAGAGCGCGGGCTTCGTAAGCC	2	102	1	GAGCGCGGGC	    0.882727	-62
TCGAACCCACGACCTCAGGCTTACGAAGCC	2	119	0	GACCTCAGGC	    0.985835	-45
GTTCGAATCCCACCGCCGGCTCTCAAACAC	2	143	1	CACCGCCGGC	    0.992608	-21
          **********

Masking position 6
Map Score:   5.50746

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 11
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

TATTTAAATCACTGAAAAATTTCTGGAGGT	1	13	1	ACTGAAAAAT	    0.995668	-25
CTTTTCAACACCTGAAAAATTCGGGAAATA	2	31	0	CCTGAAAAAT	     0.99495	-133
TCTTATAAGAACTGGAAAATAAGGT     	3	51	1	ACTGGAAAAT	    0.994867	-15
          **********

Masking position 6
Map Score:   4.2241

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 9
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 5

ATCACTGAAAAATTTCTGGAGGTAGCCA  	1	20	1	AATTTCTGGA	    0.981819	-18
AACACCTGAAAAATTCGGGAAATAATTTAA	2	25	0	AAATTCGGGA	     0.98766	-139
GTTGAAAAGGAAATTATGAATGTTTAAATT	2	52	1	AAATTATGAA	    0.956902	-112
TTTATTAATAACATTCTAAAACTCTTATAA	3	29	1	ACATTCTAAA	    0.928692	-37
          **********

Masking position 5
Map Score:   0.393959

Number of sites scoring better than the average of aligned sites = 280
Number in coding regions = 271
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 6

          **********

No masking
Map Score:   5.92755e-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:   5.92755e-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 8

          **********

No masking
Map Score:   5.92755e-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