AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i032_Pyruvate_Synthase_pyro_reg_100.orf -o032_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH01532	194	Pyrococcus_OT3

Motif number 1

AATTAACCTTTTTATCCAAATCATCTTCCAT	1	43	1	TTTTCCAAAT	    0.989438	-152
TATTTGAAAGTTTATCAAAATTTTCGAGCAT	1	76	0	TTTTCAAAAT	    0.969276	-119
CGTTGTTTCTTTTTTGAACATTAATGTCCAT	1	122	1	TTTTGAACAT	     0.92823	-73
GATGTTTACATTTGTCAACATTTAAAGCTTT	1	158	0	TTTTCAACAT	    0.994768	-37
          *** *******

Masking position 5
Map Score:   5.54451

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 25
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

 TTCTACCACCATCCTAAGATTCTGGGTTCGTTA	1	10	1	CTCCTAATCT	     0.99652	-185
TCCAAATCATCTTCCATAAATGCTCGAAAATTTT	1	57	1	CTCCAAATCT	     0.99862	-138
TTTTGATAAACTTTCAAATATCCTCCCATTTTGC	1	87	1	CTTCAAATCT	    0.994539	-108
CATTAATGTCCATCTACAAAAGCTTTAAATGTTG	1	140	1	CTCTAAAACT	    0.986316	-55
          * **** * ** **

Masking position 8
Map Score:   2.80603

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 38
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

    TTCTACCACCATCCTAAGATTCTGGG	1	7	1	CACCATCCTA	    0.977342	-188
TTTTTATCCAAATCATCTTCCATAAATGCT	1	51	1	AATCATCTTC	    0.951041	-144
AACTTTCAAATATCCTCCCATTTTGCTCGT	1	95	1	TATCCTCCCA	    0.987628	-100
         TTATCATCCCCACTCTGATGT	1	184	0	TATCATCCCC	    0.995264	-11
          **********

Masking position 6
Map Score:   0.997031

Number of sites scoring better than the average of aligned sites = 295
Number in coding regions = 277
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

AAGTTTATCAAAATTTTCGAGCATTTATGG	1	70	0	AAATTTTCGA	    0.967766	-125
AAATTTTGATAAACTTTCAAATATCCTCCC	1	84	1	AAACTTTCAA	    0.987198	-111
CCATCTACAAAAGCTTTAAATGTTGACAAA	1	149	1	AAGCTTTAAA	    0.966935	-46
TGACAAATGTAAACATCAGAGTGGGGATGA	1	172	1	AAACATCAGA	    0.947097	-23
          **********

Masking position 6
Map Score:   0.440867

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 201
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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