AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i335_mjan_pyro_300.orf -o335_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00685	300	Pyrococcus_OT3
#2	RPH00684	21	Pyrococcus_OT3

Motif number 1

AAAAAACTTTTGCAAAGTAATGAGATATTTC	1	14	0	TGCAAGTAAT	    0.914962	-287
CAAAAGTTTTTTTAAAATATTCATTAGGTCA	1	33	1	TTTAAATATT	    0.894214	-268
GTCCAAGCAATCTATAATATGACTTCATTAG	1	77	0	TCTAAATATG	    0.844079	-224
ATAGATTGCTTGGACATTATTATTTGTTACT	1	93	1	TGGAATTATT	    0.957636	-208
TTATTAGAGCTCGAGAATATTTTAGGTGTAA	1	161	1	TCGAAATATT	    0.929213	-140
ATATTTTAGGTGTAATATATTGGTACCTTTT	1	177	1	TGTATATATT	     0.91293	-124
ATCTGCAACGTGTAGAATACTTTTGTTTGAA	1	206	0	TGTAAATACT	    0.964433	-95
TGTAGTGAGTTGTATATTAATCAGACGAATA	1	239	1	TGTAATTAAT	    0.968062	-62
TACATGCGGATGCAAAATAATAGGGGTTTAT	1	269	0	TGCAAATAAT	    0.972176	-32
TGCATCCGCATGTAAATTAAAGAAA      	1	286	1	TGTAATTAAA	    0.808274	-15
          **** ******

Masking position 4
Map Score:   9.46026

Number of sites scoring better than the average of aligned sites = 366
Number in coding regions = 290
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

CTAATGAATATTTTAAAAAAACTTTTGCAA	1	30	0	TTTTAAAAAA	    0.698566	-271
CCAGTTAATGACCTAATGAATATTTTAAAA	1	42	0	ACCTAATGAA	    0.975761	-259
TAACTGGTGATCCTAATGAAGTCATATTAT	1	65	1	TCCTAATGAA	    0.975618	-236
TCCCTCAAATTCTTAAAAAATCGAAGTAAC	1	118	0	TCTTAAAAAA	    0.924238	-183
TCTCGAGCTCTAATAATGAAACACCTAGAT	1	147	0	TAATAATGAA	    0.788809	-154
AATATATTACACCTAAAATATTCTCGAGCT	1	168	0	ACCTAAAATA	     0.90234	-133
TACCTTTTCAAACAAAAGTATTCTACACGT	1	200	1	AACAAAAGTA	    0.672075	-101
TCCGCATGTAAATTAAAGAAA         	1	290	1	AATTAAAGAA	    0.937966	-11
          **********

Masking position 5
Map Score:   3.48482

Number of sites scoring better than the average of aligned sites = 1072
Number in coding regions = 976
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 3

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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:   -5.09159e-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