AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i329_mjan_pyro_100.orf -o329_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	RPH00798	50	Pyrococcus_OT3
#2	RPH00797	116	Pyrococcus_OT3

Motif number 1

TTAACTTCCTTCATTGGATAATTTCTCCAG	1	22	1	TCATTGGATA	    0.996924	-29
    TTTTCATCACTGGAGAAATTATCCAA	1	35	0	TCACTGGAGA	    0.992793	-16
CTTAACAAATTCATTGGAACTGGGAGTGGG	2	20	0	TCATTGGAAC	    0.983098	-97
GTTAAGTTCCTTACGGGATAAAATATCCAT	2	44	1	TTACGGGATA	    0.975296	-73
AAATATTGTTTCATAGAATAGAATCCCAGG	2	87	1	TCATAGAATA	    0.961146	-30
          **********

Masking position 3
Map Score:   5.82137

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 85
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

  CCCTTATCTTTTTAACTTCCTTCATTGGATA	1	9	1	TTTTTATTCT	    0.979024	-42
ACTTCCTTCATTGGATAATTTCTCCAGTGATGA	1	25	1	TTGGAATTCT	    0.995725	-26
TCCAATGAATTTGTTAAGTTCCTTACGGGATAA	2	32	1	TTGTTATTCT	    0.990579	-85
AGTTGCTAGTATGGATATTTTATCCCGTAAGGA	2	51	0	ATGGAATTAT	    0.930463	-66
TGAAACAATATTTAAGAGTTGCTAGTATGGATA	2	67	0	TTTAAATTCT	    0.974257	-50
          ***** * ** **

Masking position 7
Map Score:   2.24529

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 209
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

TCATTGGATAATTTCTCCAGTGATGAAAA 	1	32	1	ATTTCTCCAG	    0.988478	-19
AGTATGGATATTTTATCCCGTAAGGAACTT	2	47	0	TTTTATCCCG	    0.993428	-70
          TTTTCTCACCCCTGGGATTC	2	107	0	TTTTCTCACC	    0.987981	-10
          **********

Masking position 6
Map Score:   0.435699

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 35
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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