AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_protease_clp_mthe_reg_100.orf -o231_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	RTH00791	150	M.thermo

Motif number 1

ACAAATTTTTATTTTAATATATGGGGGTTC	1	45	0	ATTTTAATAT	    0.814514	-106
TACTTAAAATATTTTACTTACAAATTTTTA	1	64	0	ATTTTACTTA	    0.975954	-87
TAAGTAAAATATTTTAAGTAGGAGAAACAA	1	74	1	ATTTTAAGTA	    0.975127	-77
GATAACTGTGATTTTAATTTTAACCACTTC	1	106	1	ATTTTAATTT	    0.974228	-45
TAATGGAGGCATTTGAATAGAA        	1	139	1	ATTTGAATAG	    0.958911	-12
          **********

Masking position 6
Map Score:   5.81033

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 13
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

   ACCATGCAACATGGTGGAGATACCTTT	1	8	1	AACATGGTGG	     0.95262	-143
GAGATACCTTTATAAGGGGAACCCCCATAT	1	27	1	TATAAGGGGA	    0.976264	-124
TTTATTTTAATATATGGGGGTTCCCCTTAT	1	38	0	TATATGGGGG	    0.996759	-113
AGTAAAATATTTTAAGTAGGAGAAACAATT	1	76	1	TTTAAGTAGG	    0.948868	-75
ACCACTTCACTTAATGGAGGCATTTGAATA	1	128	1	TTAATGGAGG	    0.982119	-23
          **********

Masking position 4
Map Score:   3.69632

Number of sites scoring better than the average of aligned sites = 511
Number in coding regions = 430
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

CCCTTATAAAGGTATCTCCACCATGTTGCA	1	15	0	GGTATCTCCA	    0.989361	-136
TAATATATGGGGGTTCCCCTTATAAAGGTA	1	31	0	GGGTTCCCCT	    0.996185	-120
AGTTATCAATTGTTTCTCCTACTTAAAATA	1	83	0	TGTTTCTCCT	    0.993021	-68
          **********

Masking position 5
Map Score:   1.89864

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 108
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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