AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i269_aful_mthe_100.orf -o269_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 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	    0.996309	-21
GTGGGATGTGATGATGAAGCTGT         	2	2	0	ATATAAGCTG	     0.97366	-108
AATGGAAAGATTTATAAATATGAAAATTTGTG	2	31	0	TTATAATATG	    0.992505	-79
GGAATTATGATTAATATATATGTTATCCTTAC	2	68	0	TTATTATATG	    0.986776	-42
     TTAATTATTTTAATATGGTTGGAATTA	2	93	0	TATTAATATG	    0.941231	-17
          ** ** ******

Masking position 5
Map Score:   5.58431

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 49
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

 ACAGCTTCATCATCACATCCCACAAATTTT	2	10	1	TCTCACATCC	     0.99284	-100
TATTTATAAATCTTTCCATTCAATTGTAAGG	2	43	1	TCTTCCATTC	    0.995777	-67
ATATATGTTATCCTTACAATTGAATGGAAAG	2	54	0	TCTTACAATT	    0.974669	-56
ATATTAATCATAATTCCAACCATATTAAAAT	2	83	1	TATTCCAACC	    0.989233	-27
          ** ********

Masking position 4
Map Score:   1.77172

Number of sites scoring better than the average of aligned sites = 320
Number in coding regions = 303
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


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