AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mjan_pyro_300.orf -o316_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	RPH01790	122	Pyrococcus_OT3

Motif number 1

  CTCCTTCACCTCCTCGCCAGGCCCGGTG	1	9	1	CCTCCTCGCC	    0.998825	-114
GAAAGGGAACCCACCGGGCCTGGCGAGGAG	1	20	0	CCACCGGGCC	    0.996991	-103
CTTTCGGACACCCCCGAGCCGTGCTAAGTG	1	45	1	CCCCCGAGCC	    0.996991	-78
          **********

Masking position 5
Map Score:   6.23369

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

         CTCCTTCACCTCCTCGCCAGGC	1	2	1	TCCTCACCTC	    0.985522	-121
CTTCACCTCCTCGCCAGGCCCGGTGGGTTCC	1	14	1	TCGCAGGCCC	    0.995487	-109
GGGTTCCCTTTCGGACACCCCCGAGCCGTGC	1	38	1	TCGGCACCCC	     0.99756	-85
CATGATCACTTAGCACGGCTCGGGGGTGTCC	1	50	0	TAGCCGGCTC	    0.991639	-73
          **** ******

Masking position 1
Map Score:   0.839235

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 5
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

TAAAGATTTTTAAAGGTACTTTATAACCCA	1	87	0	TAAAGGTACT	     0.98583	-36
GAATCTTAAGTAAAGATTTTTAAAGGTACT	1	97	0	TAAAGATTTT	    0.976496	-26
AAATCTTTACTTAAGATTCCAAGTG     	1	108	1	TTAAGATTCC	    0.985728	-15
          **********

Masking position 4
Map Score:   0.12119

Number of sites scoring better than the average of aligned sites = 88
Number in coding regions = 88
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:   1.23224e-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:   1.23224e-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:   1.23224e-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