AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_aful_mthe_300.orf -o061_aful_mthe_300.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	RTH00475	137	M.thermo

Motif number 1

   TTACAATTCTCATTTAATGATAAAATATT	1	8	1	TTATTTAATG	    0.995401	-130
TAGATAATTATATATTTTAAGGAGAATATTTT	1	32	0	TTTTTTAAGG	    0.997292	-106
TTTTCCATGCTGTAATTTAAGGTTTCCCATTT	1	78	0	TTATTTAAGG	    0.997274	-60
TGTTTTAACATGTTTTTTAATGAACAATTTTC	1	105	0	TTTTTTAATG	    0.995811	-33
          * * ********

Masking position 6
Map Score:   7.79341

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 4
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

         TTACAATTCTCATTTAATGAT	1	2	1	TACAATTCTC	    0.984248	-136
CATTTAATGATAAAATATTCTCCTTAAAAT	1	21	1	TAAAATATTC	    0.946501	-117
CCTTAAAATATATAATTATCTACCTGGTCT	1	42	1	TATAATTATC	    0.845714	-96
TTTTTTAATGAACAATTTTCCATGCTGTAA	1	95	0	AACAATTTTC	    0.948248	-43
          **********

Masking position 5
Map Score:   3.91388

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 62
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

ATTTCTGGAAAGACCAGGTAGATAATTATA	1	52	0	AGACCAGGTA	    0.984559	-86
TGGTCTTTCCAGAAATGGGAAACCTTAAAT	1	66	1	AGAAATGGGA	    0.986873	-72
GTTCATTAAAAAACATGTTAAAACAGGGGA	1	112	1	AAACATGTTA	    0.850688	-26
AAACATGTTAAAACAGGGGATGTTAG    	1	122	1	AAACAGGGGA	    0.992967	-16
          **********

Masking position 3
Map Score:   2.10443

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 96
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

GGAGAATATTTTATCATTAAATGAGAATTG	1	14	0	TTATCATTAA	    0.982799	-124
TGATAAAATATTCTCCTTAAAATATATAAT	1	28	1	TTCTCCTTAA	     0.99049	-110
CATGGAAAATTGTTCATTAAAAAACATGTT	1	101	1	TGTTCATTAA	    0.986766	-37
          **********

Masking position 9
Map Score:   1.90134

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 40
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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 7

          **********

No masking
Map Score:   2.15595e-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