AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_aquae_reg_300.orf -o194_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	RAA00545	31	Aquifex_aeolicus
#2	RAA00551	66	Aquifex_aeolicus
#3	RAA00585	38	Aquifex_aeolicus
#4	RAA00469	66	Aquifex_aeolicus
#5	RAA00774	178	Aquifex_aeolicus

Motif number 1

TTTCCCTTATAATACCTTCCT         	1	21	1	AATACCTTCC	    0.908184	-11
TTTTTATTGTAAAACATTCTCACTTCTTTT	2	27	0	AAAACATTCT	    0.941198	-40
GTTTTACAATAAAAAATTCTGTCTGGAGGA	2	42	1	AAAAAATTCT	    0.967744	-25
  TTAACTTTAATAAATTTTTAGAGTTAGG	3	9	1	AATAAATTTT	    0.926572	-30
TGTCAAGCTGAAGAAATACCTGTAAAATCA	4	15	0	AAGAAATACC	      0.9578	-52
TCAGAAATAAAATAAATTCTTTTGAGTG  	4	49	1	AATAAATTCT	    0.983657	-18
CCTCCTGGTTAGTAAATTCTAATCCACTTT	5	17	1	AGTAAATTCT	    0.962099	-162
TCCACTTTACAGGAAATTTCACGAGGTTTA	5	39	1	AGGAAATTTC	    0.873596	-140
AGGGTCCTAAAACAAATACCCTCCAGAGGT	5	154	1	AACAAATACC	    0.925008	-25
          **********

Masking position 4
Map Score:   10.3001

Number of sites scoring better than the average of aligned sites = 437
Number in coding regions = 395
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

AGGTATTATAAGGGAAAGGGAAGGGGA   	1	8	0	AGGGAAAGGG	     0.97958	-24
AGCCCTGCGGCGGGACAGGGTGAACTCCCC	5	81	1	CGGGACAGGG	     0.99823	-98
TGCTCCCTTTCGGGCCTGGGGGAGTTCACC	5	99	0	CGGGCCTGGG	    0.998387	-80
GGCCCGAAAGGGAGCAAGGGTAAGCCCGCC	5	113	1	GGAGCAAGGG	     0.98582	-66
ACCCTGCGCACGGGACGGCGGGCTTACCCT	5	129	0	CGGGACGGCG	    0.994214	-50
ATTTGTTTTAGGACCCTGCGCACGGGACGG	5	141	0	GGACCCTGCG	    0.945079	-38
          **********

Masking position 8
Map Score:   7.78207

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 153
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

AAAAATTCTGTCTGGAGGAAGTTA      	2	53	1	TCTGGAGGAA	    0.989558	-14
ATTTTTAGAGTTAGGAGGTAAGAGA     	3	24	1	TTAGGAGGTA	    0.954561	-15
AATTTACTAACCAGGAGGTGTAAA      	5	5	0	CCAGGAGGTG	     0.99429	-174
ACAGGAAATTTCACGAGGTTTATATTTATT	5	47	1	TCACGAGGTT	    0.968882	-132
CCCTTTCGGGCCTGGGGGAGTTCACCCTGT	5	95	0	CCTGGGGGAG	    0.977991	-84
  TTATTACCTCTGGAGGGTATTTGTTTTA	5	161	0	TCTGGAGGGT	    0.987601	-18
          **********

Masking position 5
Map Score:   5.83404

Number of sites scoring better than the average of aligned sites = 423
Number in coding regions = 373
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 4

TTACCTCCTAACTCTAAAAATTTATTAAAG	3	15	0	ACTCTAAAAA	    0.964946	-24
TGAAGAAATACCTGTAAAATCAAATT    	4	7	0	CCTGTAAAAT	    0.976482	-60
         CACTCAAAAGAATTTATTTTA	4	56	0	ACTCAAAAGA	    0.944008	-11
CGTGAAATTTCCTGTAAAGTGGATTAGAAT	5	32	0	CCTGTAAAGT	    0.951415	-147
          **********

Masking position 6
Map Score:   0.465958

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 76
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


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