AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i076_Lipopolysaccharide_Biosynthesis_1_aquae_reg_300.orf -o076_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	RAA00033	89	Aquifex_aeolicus
#2	RAA00044	263	Aquifex_aeolicus

Motif number 1

  AACTTCTTTTTTCTCCTCTTCATCGGAT	1	9	1	TTTTCTCCTC	    0.948278	-81
GCTAACTAGATCTTCCTTTACCTCTATAAG	1	47	1	TCTTCCTTTA	    0.968498	-43
        GATTTTCTATTGTATACTCAAT	1	78	0	TTTTCTATTG	    0.900426	-12
AAGCTATAATTTTTCAATTATGGGCAAGCT	2	25	1	TTTTCAATTA	    0.893604	-239
CAGCAAATAAAATTCCCTTATTAAGGGATA	2	111	1	AATTCCCTTA	    0.813778	-153
TTCTTTTAATTTATCCCTTAATAAGGGAAT	2	122	0	TTATCCCTTA	    0.942086	-142
TATAAACACGTATTCTTTTAATTTATCCCT	2	134	0	TATTCTTTTA	    0.946971	-130
AGCTTTTTTCTTTTCCTTTCCAAGTTTTTA	2	171	0	TTTTCCTTTC	    0.974784	-93
AGAAAAAAGCTTTTCCATTAAGAATCTTGA	2	190	1	TTTTCCATTA	     0.98191	-74
GTAGATTATTTCTTCTTCTAAATCAAGATT	2	224	0	TCTTCTTCTA	    0.923518	-40
GAAGAAGAAATAATCTACTCAAAGCTTAAG	2	236	1	TAATCTACTC	    0.663975	-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

CATCGGATATAATTAAGCTAACTAGATCTT	1	31	1	AATTAAGCTA	    0.981111	-59
AATTAGGTTATTTTAAGCTATAATTTTTCA	2	11	1	TTTTAAGCTA	    0.907767	-253
CTTTTTGGTTTATAATGCTAAATTTTCAAG	2	58	1	TATAATGCTA	     0.88282	-206
TAATTACCCTAAATATGCTTGAAAATTTAG	2	75	0	AAATATGCTT	    0.930154	-189
AAAGGAAAAGAAAAAAGCTTTTCCATTAAG	2	182	1	AAAAAAGCTT	    0.930199	-82
TTAGAAGAAGAAATAATCTACTCAAAGCTT	2	233	1	AAATAATCTA	    0.838036	-31
   TTTATGTTCTTAAGCTTTGAGTAGATT	2	247	0	TCTTAAGCTT	    0.918051	-17
          **********

Masking position 5
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

TAGTTAGCTTAATTATATCCGATGAAGAGG	1	25	0	AATTATATCC	    0.968941	-65
ATAATTGAAAAATTATAGCTTAAAATAACC	2	16	0	AATTATAGCT	    0.943441	-248
ATATGCTTGAAAATTTAGCATTATAAACCA	2	63	0	AAATTTAGCA	    0.937004	-201
TATTTAGGGTAATTATAACAACAGCAAATA	2	90	1	AATTATAACA	    0.894725	-174
TTAATAAGGGAATTTTATTTGCTGTTGTTA	2	105	0	AATTTTATTT	    0.694739	-159
CGTATTCTTTTAATTTATCCCTTAATAAGG	2	126	0	TAATTTATCC	      0.8008	-138
AGTTTTTACTAAATATATAAACACGTATTC	2	149	0	AAATATATAA	    0.766928	-115
          **********

Masking position 7
Map Score:   0.924988

Number of sites scoring better than the average of aligned sites = 188
Number in coding regions = 138
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 4

GTATACTCAATTCTTATAGAGGTAAAGGAA	1	59	0	TTCTTATAGA	    0.854344	-31
   AATTAGGTTATTTTAAGCTATAATTTT	2	8	1	TTATTTTAAG	    0.788818	-256
GGGCAAGCTGTTCTTTTTGGTTTATAATGC	2	46	1	TTCTTTTTGG	    0.974332	-218
ATTTTCAAGCATATTTAGGGTAATTATAAC	2	79	1	ATATTTAGGG	     0.90207	-185
TAAAATTCCCTTATTAAGGGATAAATTAAA	2	118	1	TTATTAAGGG	    0.971399	-146
ACCTTCAAGATTCTTAATGGAAAAGCTTTT	2	194	0	TTCTTAATGG	    0.971853	-70
          **********

Masking position 5
Map Score:   1.28807

Number of sites scoring better than the average of aligned sites = 572
Number in coding regions = 533
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


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


Motif number 7

          **********

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