AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i032_mjan_pyro_300.orf -o032_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	RPH01532	194	Pyrococcus_OT3

Motif number 1

AATTAACCTTTTTATCCAAATCATCTTCCAT	1	43	1	TTTTCCAAAT	     0.98875	-152
TATTTGAAAGTTTATCAAAATTTTCGAGCAT	1	76	0	TTTTCAAAAT	    0.971024	-119
CGTTGTTTCTTTTTTGAACATTAATGTCCAT	1	122	1	TTTTGAACAT	    0.932519	-73
GATGTTTACATTTGTCAACATTTAAAGCTTT	1	158	0	TTTTCAACAT	    0.994615	-37
          *** *******

Masking position 5
Map Score:   5.54451

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 123
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

 TTCTACCACCATCCTAAGATTCTGGGTTCGTTA	1	10	1	CTCCTAATCT	    0.996848	-185
TCCAAATCATCTTCCATAAATGCTCGAAAATTTT	1	57	1	CTCCAAATCT	     0.99875	-138
TTTTGATAAACTTTCAAATATCCTCCCATTTTGC	1	87	1	CTTCAAATCT	    0.995052	-108
CATTAATGTCCATCTACAAAAGCTTTAAATGTTG	1	140	1	CTCTAAAACT	    0.987592	-55
          * **** * ** **

Masking position 8
Map Score:   2.80603

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 17
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 3

CCCAGAATCTTAGGATGGTGGTAGAA    	1	7	0	TAGGATGGTG	    0.979159	-188
AGCATTTATGGAAGATGATTTGGATAAAAA	1	51	0	GAAGATGATT	    0.954916	-144
ACGAGCAAAATGGGAGGATATTTGAAAGTT	1	95	0	TGGGAGGATA	    0.988641	-100
ACATCAGAGTGGGGATGATAA         	1	184	1	GGGGATGATA	    0.995654	-11
          **********

Masking position 5
Map Score:   0.997031

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 219
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

CCATAAATGCTCGAAAATTTTGATAAACTT	1	70	1	TCGAAAATTT	    0.969202	-125
GGGAGGATATTTGAAAGTTTATCAAAATTT	1	84	0	TTGAAAGTTT	     0.98778	-111
TTTGTCAACATTTAAAGCTTTTGTAGATGG	1	149	0	TTTAAAGCTT	    0.968407	-46
TCATCCCCACTCTGATGTTTACATTTGTCA	1	172	0	TCTGATGTTT	    0.949406	-23
          **********

Masking position 5
Map Score:   0.440867

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 293
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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 7

          **********

No masking
Map Score:   3.15071e-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