AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_SecDF_mthe_reg_100.orf -o118_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH01810	103	M.thermo

Motif number 1

          TCTATTTGACAGATGGGAGA	1	1	1	TCTATTTGAC	    0.927892	-103
AGGTGATCGTCTTGATTGACCGCATTTTAA	1	39	1	CTTGATTGAC	    0.981308	-65
CTATGAGTGGCCTGTATGACTTTAAAATGC	1	60	0	CCTGTATGAC	    0.997373	-44
GTTATGGCTGCTGGTATGGCTATGAGTGGC	1	79	0	CTGGTATGGC	    0.996514	-25
       TTACAGTTATGGCTGCTGGTATG	1	91	0	CAGTTATGGC	    0.976287	-13
          **********

Masking position 7
Map Score:   5.29615

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 345
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

       TCTATTTGACAGATGGGAGAAAC	1	4	1	ATTTGACAGA	     0.97247	-100
AAGACGATCACCTTTAAAGTTTCTCCCATC	1	22	0	CCTTTAAAGT	    0.514799	-82
GATTGACCGCATTTTAAAGTCATACAGGCC	1	52	1	ATTTTAAAGT	    0.536507	-52
          **********

Masking position 6
Map Score:   0.329093

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 31
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   -5.44113e-14

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 4

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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