AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i269_hypothetical14_mthe_reg_100.orf -o269_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	RTH00591	27	M.thermo
#2	RTH00127	109	M.thermo

Motif number 1

    GTTCTATTAATCAAGATGGTGTTTTAA 	1	7	1	TTATAAGATG	    0.996842	-21
GTGGGATGTGATGATGAAGCTGT         	2	2	0	ATATAAGCTG	     0.97739	-108
AATGGAAAGATTTATAAATATGAAAATTTGTG	2	31	0	TTATAATATG	    0.992486	-79
GGAATTATGATTAATATATATGTTATCCTTAC	2	68	0	TTATTATATG	    0.988595	-42
     TTAATTATTTTAATATGGTTGGAATTA	2	93	0	TATTAATATG	    0.944094	-17
          ** ** ******

Masking position 5
Map Score:   5.58431

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 41
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

 ACAGCTTCATCATCACATCCCACAAATTTT	2	10	1	TCTCACATCC	     0.99309	-100
TATTTATAAATCTTTCCATTCAATTGTAAGG	2	43	1	TCTTCCATTC	    0.995924	-67
ATATATGTTATCCTTACAATTGAATGGAAAG	2	54	0	TCTTACAATT	    0.975538	-56
ATATTAATCATAATTCCAACCATATTAAAAT	2	83	1	TATTCCAACC	    0.989607	-27
          ** ********

Masking position 4
Map Score:   1.77172

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 235
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

          **********

No masking
Map Score:   1.87173e-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 4

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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