AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i173_1_17_4_2_pyro_reg_100.orf -o173_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	RPH01018	214	Pyrococcus_OT3

Motif number 1

       TTGATATTTTGTTCAACTTTTCGCT	1	4	1	ATATTTGTCA	    0.998683	-211
AATTGCAGTTATATTTTGTACATAAGACGGAT	1	71	0	ATATTTGTCA	    0.998683	-144
ATATCCAATAATATTTAGTCAAAATTCTAAAA	1	102	0	ATATTTGTAA	    0.993164	-113
ATATTATTGGATATTTTATCCAATTCTCAAGC	1	120	1	ATATTTATCA	    0.993165	-95
CACCTCTTGGATATTTTGTCCAACTTGGAGAT	1	188	0	ATATTTGTCA	    0.998683	-27
          ****** ** **

Masking position 6
Map Score:   14.4064

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 5
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

TGATATTTTGTTCAACTTTTCGCTTTATTGATTT	1	12	1	TCACTTTGCT	    0.995474	-203
TTGATTTACTTTCATCTATTTGATAATAATGTAT	1	39	1	TCACTTTGAT	     0.98363	-176
AAAATATAACTGCAATTTTTAGAATTTTGACTAA	1	86	1	TCATTTTGAA	    0.970385	-129
GGATATTTTGTCCAACTTGGAGATAGCAGATTCA	1	178	0	TCACTGGGAT	    0.990449	-37
       ACTTTCACCTCTTGGATATTTTGTCCA	1	198	0	TCACTTTGAT	    0.997956	-17
          * ** ** ** ***

Masking position 7
Map Score:   6.36881

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 40
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

AATTCTAAAAATTGCAGTTATATTTTGTAC	1	82	0	ATTGCAGTTA	    0.927091	-133
ACTGCAATTTTTAGAATTTTGACTAAATAT	1	94	1	TTAGAATTTT	    0.879838	-121
ACTAAATATTATTGGATATTTTATCCAATT	1	115	1	ATTGGATATT	    0.976572	-100
TTCAAGGCTTTTAGGATTTATGGCATGAGG	1	152	0	TTAGGATTTA	     0.93973	-63
CAACTTGGAGATAGCAGATTCAAGGCTTTT	1	170	0	ATAGCAGATT	    0.959555	-45
ACTTTCACCTCTTGGATATTTTGTCCAACT	1	195	0	CTTGGATATT	     0.96071	-20
          **********

Masking position 6
Map Score:   2.453

Number of sites scoring better than the average of aligned sites = 385
Number in coding regions = 353
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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