AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i297_mixed12_aquae_reg_300.orf -o297_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	RAA00952	300	Aquifex_aeolicus

Motif number 1

GCCGAAGGAGGCAAAGTTATGCGACATGTA	1	12	0	GCAAAGTTAT	    0.911001	-289
GCCTCCTTCGGCAAAATAAAAGTATAATAC	1	30	1	GCAAAATAAA	     0.92348	-271
CAACAATTGTGAAAAAAAAAGTTTAAATTA	1	59	1	GAAAAAAAAA	    0.798197	-242
AAAGAGATCAACAAAAGTAAGACCGCTTAT	1	144	0	ACAAAAGTAA	    0.884364	-157
TCCCGTTCCCGCAAAGAGATCAACAAAAGT	1	156	0	GCAAAGAGAT	    0.924011	-145
AAAGGAGGGTGCAAAGGTCATTTTCGTAGA	1	205	1	GCAAAGGTCA	    0.989702	-96
CATTTTCGTAGAAAAGAACAGGAAACTTGC	1	223	1	GAAAAGAACA	    0.895755	-78
CAGGAAACTTGCAAACGAAATAAAGAAGAA	1	241	1	GCAAACGAAA	    0.962895	-60
GAAAACTAAGGGAAAGGTAATTGTCGGGGA	1	268	1	GGAAAGGTAA	     0.97949	-33
       AAAAGAAAGGGCATCCCCGACAA	1	288	0	AGAAAGGGCA	    0.829736	-13
          **********

Masking position 5
Map Score:   8.6762

Number of sites scoring better than the average of aligned sites = 2229
Number in coding regions = 2118
Number in noncoding regions = 111
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 2

TCGCATAACTTTGCCTCCTTCGGCAAAATAA	1	18	1	TTGCCCCTTC	     0.99563	-283
CAGTCCAATCTGTCCCGTTCCCGCAAAGAGA	1	167	0	TGTCCGTTCC	    0.969012	-134
TGCACCCTCCTTTCCGCCTCCAGTCCAATCT	1	187	0	TTTCCCCTCC	     0.99563	-114
AAAATGACCTTTGCACCCTCCTTTCCGCCTC	1	198	0	TTGCACCTCC	     0.99563	-103
TTTATTTCGTTTGCAAGTTTCCTGTTCTTTT	1	234	0	TTGCAGTTTC	    0.968564	-67
          ***** *****

Masking position 9
Map Score:   4.46797

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 180
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

CATCTTTAACATACTCGGAGACATAAGCGGT	1	122	1	ATATCGGAGA	    0.994139	-179
TGCAAAGGTCATTTTCGTAGAAAAGAACAGG	1	214	1	ATTTCGTAGA	    0.990963	-87
GGGAAAGGTAATTGTCGGGGATGCCCTTTCT	1	277	1	ATTTCGGGGA	    0.996038	-24
          *** *******

Masking position 1
Map Score:   0.629145

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 25
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

AACTTTGCCTCCTTCGGCAAAATAAAAGTA	1	24	1	CCTTCGGCAA	     0.98656	-277
CCGACGAAATCCATCGTTAAAAACGCCATC	1	96	1	CCATCGTTAA	    0.994501	-205
GTTAAAAACGCCATCTTTAACATACTCGGA	1	111	1	CCATCTTTAA	    0.985329	-190
          **********

Masking position 9
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 10
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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