AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_aquae_reg_300.orf -o257_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	RAA00931	213	Aquifex_aeolicus

Motif number 1

CCTCCTATACTTTAATATACTTTTGTTAAA	1	19	1	TTTAATATAC	    0.897887	-195
TATACTTTTGTTAAATTTTCTTAACAAGAG	1	34	1	TTAAATTTTC	    0.985158	-180
TATCCGATTTTTCAATTTTCGAAGCCTTAT	1	72	1	TTCAATTTTC	    0.978375	-142
TTTTTTGCACTTAAATAATCTTCAAGTACT	1	108	0	TTAAATAATC	    0.981782	-106
TGCAAAAAACTTAAATTACCTCTTGACAAA	1	129	1	TTAAATTACC	    0.982102	-85
ACACCAGAAATTATATTAACATCCTCGGAT	1	159	0	TTATATTAAC	    0.930422	-55
          **********

Masking position 5
Map Score:   7.37624

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 74
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

CTTTAATATACTTTTGTTAAATTTTCTTAA	1	28	1	CTTTTGTTAA	    0.990677	-186
TATTAGTCTGCTCTTGTTAAGAAAATTTAA	1	44	0	CTCTTGTTAA	    0.996558	-170
CTTAAATTACCTCTTGACAAAATCCGAGGA	1	138	1	CTCTTGACAA	    0.992759	-76
          **********

Masking position 9
Map Score:   3.08994

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 14
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

  GGCAAGCACCTCCTATACTTTAATATACTT	1	9	1	CCTCCTTATT	    0.981854	-205
TATACTTTAATATACTTTTGTTAAATTTTCTT	1	24	1	TATACTTTTT	    0.913762	-190
CGGATATTAGTCTGCTCTTGTTAAGAAAATTT	1	46	0	TCTGCTTTTT	    0.961082	-168
AGCAGACTAATATCCGATTTTTCAATTTTCGA	1	62	1	TATCCGTTTT	    0.978588	-152
ATTATATTAACATCCTCGGATTTTGTCAAGAG	1	148	0	CATCCTGGTT	    0.852251	-66
CCGTCCACCTCCTCCGTGGTTTACCTGTTTAC	1	191	0	CCTCCGGGTT	    0.990199	-23
          ****** ** **

Masking position 3
Map Score:   2.17111

Number of sites scoring better than the average of aligned sites = 433
Number in coding regions = 376
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 4

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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