AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_pyro_reg_300.orf -o316_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH01790	122	Pyrococcus_OT3

Motif number 1

  CTCCTTCACCTCCTCGCCAGGCCCGGTG	1	9	1	CCTCCTCGCC	    0.998846	-114
GAAAGGGAACCCACCGGGCCTGGCGAGGAG	1	20	0	CCACCGGGCC	     0.99695	-103
CTTTCGGACACCCCCGAGCCGTGCTAAGTG	1	45	1	CCCCCGAGCC	     0.99695	-78
          **********

Masking position 5
Map Score:   6.23369

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 12
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 2

         CTCCTTCACCTCCTCGCCAGGC	1	2	1	TCCTCACCTC	    0.985771	-121
CTTCACCTCCTCGCCAGGCCCGGTGGGTTCC	1	14	1	TCGCAGGCCC	    0.995524	-109
GGGTTCCCTTTCGGACACCCCCGAGCCGTGC	1	38	1	TCGGCACCCC	    0.997601	-85
CATGATCACTTAGCACGGCTCGGGGGTGTCC	1	50	0	TAGCCGGCTC	    0.991671	-73
          **** ******

Masking position 1
Map Score:   0.839235

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 86
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

TGGGTTATAAAGTACCTTTAAAAATCTTTA	1	87	1	AGTACCTTTA	    0.985177	-36
AGTACCTTTAAAAATCTTTACTTAAGATTC	1	97	1	AAAATCTTTA	    0.975889	-26
     CACTTGGAATCTTAAGTAAAGATTT	1	108	0	GGAATCTTAA	     0.98508	-15
          **********

Masking position 4
Map Score:   0.12119

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 97
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:   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