AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_aquae_reg_100.orf -o076_aquae_100.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	RAA00033	89	Aquifex_aeolicus
#2	RAA00044	263	Aquifex_aeolicus

Motif number 1

  AACTTCTTTTTTCTCCTCTTCATCGGAT	1	9	1	TTTTCTCCTC	    0.943089	-81
GCTAACTAGATCTTCCTTTACCTCTATAAG	1	47	1	TCTTCCTTTA	    0.965263	-43
        GATTTTCTATTGTATACTCAAT	1	78	0	TTTTCTATTG	    0.890987	-12
AAGCTATAATTTTTCAATTATGGGCAAGCT	2	25	1	TTTTCAATTA	    0.883604	-239
CAGCAAATAAAATTCCCTTATTAAGGGATA	2	111	1	AATTCCCTTA	     0.79797	-153
TTCTTTTAATTTATCCCTTAATAAGGGAAT	2	122	0	TTATCCCTTA	    0.936317	-142
TATAAACACGTATTCTTTTAATTTATCCCT	2	134	0	TATTCTTTTA	     0.94166	-130
AGCTTTTTTCTTTTCCTTTCCAAGTTTTTA	2	171	0	TTTTCCTTTC	    0.972176	-93
AGAAAAAAGCTTTTCCATTAAGAATCTTGA	2	190	1	TTTTCCATTA	    0.980025	-74
GTAGATTATTTCTTCTTCTAAATCAAGATT	2	224	0	TCTTCTTCTA	    0.916064	-40
GAAGAAGAAATAATCTACTCAAAGCTTAAG	2	236	1	TAATCTACTC	     0.64106	-28
          **********

Masking position 4
Map Score:   10.8756

Number of sites scoring better than the average of aligned sites = 1835
Number in coding regions = 1692
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 2

AAGATCTAGTTAGCTTAATTATATCCGATG	1	31	0	TAGCTTAATT	    0.983216	-59
TGAAAAATTATAGCTTAAAATAACCTAATT	2	11	0	TAGCTTAAAA	    0.917359	-253
CTTGAAAATTTAGCATTATAAACCAAAAAG	2	58	0	TAGCATTATA	    0.894654	-206
CTAAATTTTCAAGCATATTTAGGGTAATTA	2	75	1	AAGCATATTT	    0.937565	-189
CTTAATGGAAAAGCTTTTTTCTTTTCCTTT	2	182	0	AAGCTTTTTT	    0.937616	-82
AAGCTTTGAGTAGATTATTTCTTCTTCTAA	2	233	0	TAGATTATTT	    0.853708	-31
AATCTACTCAAAGCTTAAGAACATAAA   	2	247	1	AAGCTTAAGA	    0.926659	-17
          **********

Masking position 2
Map Score:   4.43997

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 167
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

TTCATCGGATATAATTAAGCTAACTAGATC	1	29	1	ATAATTAAGC	    0.876173	-61
ATACTCAATTCTTATAGAGGTAAAGGAAGA	1	57	0	CTTATAGAGG	    0.902816	-33
AAAATTTAGCATTATAAACCAAAAAGAACA	2	54	0	ATTATAAACC	    0.881427	-210
ATAAAATTCCCTTATTAAGGGATAAATTAA	2	117	1	CTTATTAAGG	    0.976069	-147
TACCTTCAAGATTCTTAATGGAAAAGCTTT	2	195	0	ATTCTTAATG	    0.913702	-69
ATTATTTCTTCTTCTAAATCAAGATTACCT	2	220	0	CTTCTAAATC	    0.943334	-44
     TTTATGTTCTTAAGCTTTGAGTAGA	2	249	0	GTTCTTAAGC	      0.9602	-15
          **********

Masking position 8
Map Score:   1.81948

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 394
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 4

          **********

No masking
Map Score:   -1.17788e-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 5

          **********

No masking
Map Score:   -1.17788e-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 6

          **********

No masking
Map Score:   -1.17788e-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