AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_pyro_reg_100.orf -o039_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	RPH00208	300	Pyrococcus_OT3

Motif number 1

ACTATGAATATTTTCTTCTCCTGGGTTTCC	1	39	1	TTTTCTTCTC	    0.971791	-262
TAAATGATGATTTTATTCTCGTGGAAACCC	1	61	0	TTTTATTCTC	    0.993263	-240
TAAAATCATCATTTATGCTCTTTATTCTTC	1	76	1	ATTTATGCTC	    0.947564	-225
CAGACAAGAGTTTTATTATGCCAACTACAT	1	121	1	TTTTATTATG	    0.946933	-180
CCCCATTGCCATTAATTCTCACCAGAGGGT	1	175	1	ATTAATTCTC	    0.960693	-126
ATATAAAAATTTAAATTCTCGTATGAAAAA	1	208	0	TTAAATTCTC	    0.960693	-93
ATTTAAATTTTTATATTATAGGAGGCTAGT	1	222	1	TTATATTATA	     0.70203	-79
AGGGACCTTTATATATTCTGACTAACAGAA	1	261	1	ATATATTCTG	    0.961445	-40
TCACCTGATCTGTTATTCTGTTAGTCAGAA	1	276	0	TGTTATTCTG	    0.954902	-25
          **********

Masking position 6
Map Score:   12.7856

Number of sites scoring better than the average of aligned sites = 405
Number in coding regions = 350
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 2

TCGTGGAAACCCAGGAGAAGAAAATATTCA	1	43	0	CCAGGAGAAG	    0.970618	-258
ATGATTTTATTCTCGTGGAAACCCAGGAGA	1	55	0	TCTCGTGGAA	     0.93764	-246
AAAACTCTTGTCTGGGGAAGTCTTGATAGG	1	105	0	TCTGGGGAAG	     0.99359	-196
AAAATTACCCTCTGGTGAGAATTAATGGCA	1	181	0	TCTGGTGAGA	    0.979663	-120
GAATAACAGATCAGGTGAAGTGA       	1	288	1	TCAGGTGAAG	    0.994631	-13
          **********

Masking position 5
Map Score:   3.74169

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 166
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

          **********

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 4

          **********

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 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