AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_aquae_reg_300.orf -o320_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	RAA01072	81	Aquifex_aeolicus
#2	RAA00533	32	Aquifex_aeolicus
#3	RAA00534	20	Aquifex_aeolicus
#4	RAA00541	33	Aquifex_aeolicus
#5	RAA00627	104	Aquifex_aeolicus

Motif number 1

CCCGTACCTCCGTAAATTTTCGGACGAATA	1	14	1	CGTAAATTTT	    0.862699	-68
ATTTTCGGACGAATAATTTTAACACAATAA	1	29	1	GAATAATTTT	    0.954896	-53
AATTTTAACACAATAAGTTTACCACAAAAA	1	43	1	CAATAAGTTT	    0.872475	-39
CACAAAAAACCTTTAATATTTATCTTT   	1	65	1	CTTTAATATT	    0.959442	-17
CTCTCTTTTCCTTAAATTTTCCTTATCCG 	2	14	1	CTTAAATTTT	    0.959442	-19
      CAAGGATTAATTTACCACCT    	3	7	0	GATTAATTTA	    0.861922	-14
   GGTATTGCTATAATTGTTTAGCGGAGG	4	8	1	CTATAATTGT	    0.975136	-26
TTTACCTCCCGTTTAATTTTCCTTTAATAA	5	14	1	GTTTAATTTT	     0.98232	-91
TTTAATTTTCCTTTAATAATATTTCTTGAG	5	25	1	CTTTAATAAT	    0.882013	-80
TATTTCTTGAGTATAATTGTGTCAACCTTT	5	44	1	GTATAATTGT	    0.958079	-61
ACTCCCTCCACTATAATTAATTTCT     	5	90	1	CTATAATTAA	    0.862841	-15
          **********

Masking position 5
Map Score:   15.2174

Number of sites scoring better than the average of aligned sites = 376
Number in coding regions = 313
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 2

GTAAACTTATTGTGTTAAAATTATTCGTCC	1	35	0	TGTGTTAAAA	    0.721871	-47
AAAGGTTTTTTGTGGTAAACTTATTGTGTT	1	49	0	TGTGGTAAAC	    0.939503	-33
          AAAGATAAATATTAAAGGTT	1	72	0	AAAGATAAAT	    0.782343	-10
AAGGAAAATTTAAGGAAAAGAGAGGGA   	2	8	0	TAAGGAAAAG	     0.96433	-25
      CGGATAAGGAAAATTTAAGGAAAA	2	19	0	TAAGGAAAAT	    0.970246	-14
         AGGTGGTAAATTAATCCTTG 	3	2	1	GGTGGTAAAT	    0.976542	-19
ATTGTTTAGCGGAGGAGAAGA         	4	23	1	GGAGGAGAAG	    0.915664	-11
AAATTAAACGGGAGGTAAAAGT        	5	3	0	GGAGGTAAAA	    0.986035	-102
AAATATTATTAAAGGAAAATTAAACGGGAG	5	19	0	AAAGGAAAAT	    0.961603	-86
AGTGTGCACGAAAGGTATAAAAGGTTGACA	5	63	0	AAAGGTATAA	    0.798469	-42
          **********

Masking position 9
Map Score:   9.74169

Number of sites scoring better than the average of aligned sites = 2725
Number in coding regions = 2515
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 3

TCCGAAAATTTACGGAGGTACGGGAAA   	1	8	0	TACGGAGGTA	    0.978882	-74
TCCGTAAATTTTCGGACGAATAATTTTAAC	1	22	1	TTCGGACGAA	    0.923525	-60
ATTTAAGGAAAAGAGAGGGA          	2	1	0	AAGAGAGGGA	     0.89633	-32
ATAATTGTTTAGCGGAGGAGAAGA      	4	20	1	AGCGGAGGAG	    0.984216	-14
GGAAAATTAAACGGGAGGTAAAAGT     	5	6	0	ACGGGAGGTA	    0.973131	-99
GTGGAGGGAGTGTGCACGAAAGGTATAAAA	5	71	0	TGTGCACGAA	    0.848516	-34
AATTAATTATAGTGGAGGGAGTGTGCACGA	5	82	0	AGTGGAGGGA	    0.989805	-23
          **********

Masking position 6
Map Score:   3.04781

Number of sites scoring better than the average of aligned sites = 1392
Number in coding regions = 1286
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 4

TGGTAAACTTATTGTGTTAAAATTATTCGT	1	37	0	ATTGTGTTAA	      0.9876	-45
TTAAAGGTTTTTTGTGGTAAACTTATTGTG	1	51	0	TTTGTGGTAA	    0.979881	-31
CCGCTAAACAATTATAGCAATACC      	4	5	0	ATTATAGCAA	    0.923277	-29
CTTGAGTATAATTGTGTCAACCTTTTATAC	5	49	1	ATTGTGTCAA	    0.991944	-56
          **********

Masking position 5
Map Score:   2.82159

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 28
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 5

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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 7

          **********

No masking
Map Score:   -2.46258e-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