AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i329_mjan_pyro_300.orf -o329_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	RPH00798	50	Pyrococcus_OT3
#2	RPH00797	116	Pyrococcus_OT3

Motif number 1

CTGGAGAAATTATCCAATGAAGGAAGTTAA	1	22	0	TATCCAATGA	    0.996876	-29
TTGGATAATTTCTCCAGTGATGAAAA    	1	35	1	TCTCCAGTGA	    0.992754	-16
CCCACTCCCAGTTCCAATGAATTTGTTAAG	2	20	1	GTTCCAATGA	    0.982836	-97
ATGGATATTTTATCCCGTAAGGAACTTAAC	2	44	0	TATCCCGTAA	    0.974918	-73
CCTGGGATTCTATTCTATGAAACAATATTT	2	87	0	TATTCTATGA	    0.960556	-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

CTTTTTAACTTCCTTCATTGGATAATTTCT	1	18	1	TCCTTCATTG	    0.943306	-33
       TTTTCATCACTGGAGAAATTATC	1	38	0	TCATCACTGG	    0.993015	-13
TTTGTTAAGTTCCTTACGGGATAAAATATC	2	41	1	TCCTTACGGG	     0.98768	-76
GGATAAAATATCCATACTAGCAACTCTTAA	2	59	1	TCCATACTAG	     0.96957	-58
     TTTTCTCACCCCTGGGATTCTATTC	2	102	0	TCACCCCTGG	    0.989796	-15
          **********

Masking position 1
Map Score:   3.84955

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 98
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

TTTTTAACTTCCTTCATTGGATAATTTCTC	1	19	1	CCTTCATTGG	    0.995681	-32
       TTTTCATCACTGGAGAAATTATC	1	38	0	TCATCACTGG	    0.989544	-13
GAACTTAACAAATTCATTGGAACTGGGAGT	2	23	0	AATTCATTGG	    0.987404	-94
          **********

Masking position 6
Map Score:   1.48185

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 30
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


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