AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i335_mjan_pyro_100.orf -o335_mjan_pyro_100.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

GAAATATCTCATTACTTTGCAAAAGTTTTTT	1	14	1	ATTACTTGCA	    0.927173	-287
TGACCTAATGAATATTTTAAAAAAACTTTTG	1	33	0	AATATTTAAA	    0.908952	-268
CTAATGAAGTCATATTATAGATTGCTTGGAC	1	77	1	CATATTTAGA	    0.864961	-224
AGTAACAAATAATAATGTCCAAGCAATCTAT	1	93	0	AATAATTCCA	    0.963964	-208
TTACACCTAAAATATTCTCGAGCTCTAATAA	1	161	0	AATATTTCGA	    0.939521	-140
AAAAGGTACCAATATATTACACCTAAAATAT	1	177	0	AATATATACA	    0.924868	-124
TTCAAACAAAAGTATTCTACACGTTGCAGAT	1	206	1	AGTATTTACA	    0.969485	-95
TATTCGTCTGATTAATATACAACTCACTACA	1	239	0	ATTAATTACA	    0.972207	-62
ATAAACCCCTATTATTTTGCATCCGCATGTA	1	269	1	ATTATTTGCA	    0.976376	-32
      TTTCTTTAATTTACATGCGGATGCA	1	286	0	TTTAATTACA	    0.824458	-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

TTAGAAATATCTCATTACTTTGCAAAAGTT	1	11	1	CTCATTACTT	    0.949029	-290
TTTTAAAATATTCATTAGGTCATTAACTGG	1	42	1	TTCATTAGGT	    0.987967	-259
ATAATATGACTTCATTAGGATCACCAGTTA	1	65	0	TTCATTAGGA	    0.982831	-236
ATCTAGGTGTTTCATTATTAGAGCTCGAGA	1	147	1	TTCATTATTA	    0.951128	-154
         TTTCTTTAATTTACATGCGGA	1	290	0	TTCTTTAATT	     0.89447	-11
          **********

Masking position 5
Map Score:   1.97719

Number of sites scoring better than the average of aligned sites = 185
Number in coding regions = 166
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

TCTCATTACTTTGCAAAAGTTTTTTTAAAA	1	20	1	TTGCAAAAGT	    0.990004	-281
ATACTTTTGTTTGAAAAGGTACCAATATAT	1	191	0	TTGAAAAGGT	    0.981757	-110
ATTCTACACGTTGCAGATGTTGTAGTGAGT	1	219	1	TTGCAGATGT	    0.988129	-82
          **********

Masking position 5
Map Score:   0.42009

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 37
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


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


Motif number 6

          **********

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