AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_pyro_reg_300.orf -o039_pyro_300.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	     0.97079	-262
TAAATGATGATTTTATTCTCGTGGAAACCC	1	61	0	TTTTATTCTC	    0.993019	-240
TAAAATCATCATTTATGCTCTTTATTCTTC	1	76	1	ATTTATGCTC	    0.945752	-225
CAGACAAGAGTTTTATTATGCCAACTACAT	1	121	1	TTTTATTATG	    0.945101	-180
CCCCATTGCCATTAATTCTCACCAGAGGGT	1	175	1	ATTAATTCTC	    0.959315	-126
ATATAAAAATTTAAATTCTCGTATGAAAAA	1	208	0	TTAAATTCTC	    0.959315	-93
ATTTAAATTTTTATATTATAGGAGGCTAGT	1	222	1	TTATATTATA	     0.69447	-79
AGGGACCTTTATATATTCTGACTAACAGAA	1	261	1	ATATATTCTG	    0.960093	-40
TCACCTGATCTGTTATTCTGTTAGTCAGAA	1	276	0	TGTTATTCTG	    0.953331	-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

TGAATATTTTCTTCTCCTGGGTTTCCACGA	1	43	1	CTTCTCCTGG	    0.973416	-258
TCTCCTGGGTTTCCACGAGAATAAAATCAT	1	55	1	TTCCACGAGA	    0.943363	-246
CCTATCAAGACTTCCCCAGACAAGAGTTTT	1	105	1	CTTCCCCAGA	    0.994207	-196
TGCCATTAATTCTCACCAGAGGGTAATTTT	1	181	1	TCTCACCAGA	    0.981238	-120
       TCACTTCACCTGATCTGTTATTC	1	288	0	CTTCACCTGA	    0.995153	-13
          **********

Masking position 6
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