AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i103_mjan_pyro_100.orf -o103_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	RMJ04246	104	M_jannaschii_chromosome
#2	RPH01106	123	Pyrococcus_OT3

Motif number 1

TAGTTAAAATTTTTAACCGTAGTTAAATAA	1	46	0	TTTTAACCGT	    0.988659	-59
CGGTTAAAAATTTTAACTATAATTAAATCA	1	57	1	TTTTAACTAT	      0.9861	-48
TAATTAAATCATTTAACCATATATAAATGT	1	76	1	ATTTAACCAT	    0.983263	-29
AGGTTCCTACTTTGAACGATTTCAGATAAA	2	30	1	TTTGAACGAT	    0.988633	-94
CAACCTAATTTTTTAATGATGCCTTTAAAT	2	76	0	TTTTAATGAT	    0.973742	-48
          **********

Masking position 5
Map Score:   6.73405

Number of sites scoring better than the average of aligned sites = 132
Number in coding regions = 112
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

AAAATTTTTAACCGTAGTTAAATAATAACATGC	1	38	0	ACCTATAAAT	    0.995308	-67
AAAAATTTTAACTATAATTAAATCATTTAACCA	1	62	1	ACTTATAAAT	    0.986719	-43
AAATCATTTAACCATATATAAATGTTGTGGTAT	1	81	1	ACCTATAAAT	    0.995439	-24
ACTTTGAACGATTTCAGATAAATTCTCGAACAA	2	38	1	ATTCATAAAT	    0.894369	-86
ATTTAAAGGCATCATTAAAAAATTAGGTTGCCC	2	76	1	ATCTTAAAAT	    0.888623	-48
          *** **  *****

Masking position 10
Map Score:   2.45171

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 78
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

AATAACATGCAGGGTATAAAAACCTTTCGG	1	18	0	AGGGTATAAA	    0.933827	-87
AAGAGATTTAAAGGCATCATTAAAAAATTA	2	71	1	AAGGCATCAT	    0.982325	-53
CATTATTATTAGGGCAACCTAATTTTTTAA	2	90	0	AGGGCAACCT	    0.879899	-34
TAATAATGGGAGGTCATCCAAT        	2	112	1	AGGTCATCCA	    0.978365	-12
          **********

Masking position 6
Map Score:   0.940614

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 106
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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:   1.87173e-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