AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_aquae_reg_100.orf -o320_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	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

TATTCGTCCGAAAATTTACGGAGGTACGGG	1	14	0	AAAATTTACG	    0.883141	-68
TTATTGTGTTAAAATTATTCGTCCGAAAAT	1	29	0	AAAATTATTC	    0.962213	-53
TTTTTGTGGTAAACTTATTGTGTTAAAATT	1	43	0	AAACTTATTG	    0.891644	-39
   AAAGATAAATATTAAAGGTTTTTTGTG	1	65	0	AATATTAAAG	    0.966048	-17
 CGGATAAGGAAAATTTAAGGAAAAGAGAG	2	14	0	AAAATTTAAG	    0.966047	-19
    AGGTGGTAAATTAATCCTTG      	3	7	1	TAAATTAATC	    0.882463	-14
CCTCCGCTAAACAATTATAGCAATACC   	4	8	0	ACAATTATAG	     0.97924	-26
TTATTAAAGGAAAATTAAACGGGAGGTAAA	5	14	0	AAAATTAAAC	    0.985257	-91
CTCAAGAAATATTATTAAAGGAAAATTAAA	5	25	0	ATTATTAAAG	    0.899913	-80
AAAGGTTGACACAATTATACTCAAGAAATA	5	44	0	ACAATTATAC	    0.964898	-61
     AGAAATTAATTATAGTGGAGGGAGT	5	90	0	TTAATTATAG	    0.883264	-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

GGTAAACTTATTGTGTTAAAATTATTCGTC	1	36	0	TTGTGTTAAA	    0.932574	-46
TAAAGGTTTTTTGTGGTAAACTTATTGTGT	1	50	0	TTGTGGTAAA	      0.9859	-32
TAAGGAAAATTTAAGGAAAAGAGAGGGA  	2	9	0	TTAAGGAAAA	    0.982047	-24
       CGGATAAGGAAAATTTAAGGAAA	2	20	0	ATAAGGAAAA	    0.960143	-13
          AGGTGGTAAATTAATCCTTG	3	1	1	AGGTGGTAAA	    0.953675	-20
AAAATTAAACGGGAGGTAAAAGT       	5	4	0	GGGAGGTAAA	    0.983794	-101
GAAATATTATTAAAGGAAAATTAAACGGGA	5	20	0	TAAAGGAAAA	    0.960116	-85
ATAATATTTCTTGAGTATAATTGTGTCAAC	5	40	1	TTGAGTATAA	    0.771014	-65
GAGTGTGCACGAAAGGTATAAAAGGTTGAC	5	64	0	GAAAGGTATA	     0.75897	-41
          **********

Masking position 10
Map Score:   10.1217

Number of sites scoring better than the average of aligned sites = 2115
Number in coding regions = 1965
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 3

GTCCGAAAATTTACGGAGGTACGGGAAA   	1	8	0	TTCGGAGGTA	    0.992578	-74
CTCCGTAAATTTTCGGACGAATAATTTTAAC	1	21	1	TTCGGACGAA	    0.970114	-61
AATTTAAGGAAAAGAGAGGGA          	2	1	0	AAGAGAGGGA	    0.958994	-32
TATAATTGTTTAGCGGAGGAGAAGA      	4	19	1	TACGGAGGAG	    0.989791	-15
AGGAAAATTAAACGGGAGGTAAAAGT     	5	6	0	AAGGGAGGTA	    0.989677	-99
AAATTAATTATAGTGGAGGGAGTGTGCACGA	5	82	0	TATGGAGGGA	    0.990421	-23
          ** ********

Masking position 7
Map Score:   5.20471

Number of sites scoring better than the average of aligned sites = 474
Number in coding regions = 428
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

          **********

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 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