AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i101_aful_mthe_100.orf -o101_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	RAG50006	125	Archaeoglobus_fulgidus

Motif number 1

          TTTTCTTTCAATTTTTCTTCTCATAAA	1	1	1	TTCTTCATTC	    0.988543	-125
TCTCATAAATTTACTGTTCTTTGTAACCTTTGGTAAC	1	29	1	TTTTTCTTTC	    0.994806	-97
GATTAAAATTTTGGTTTTTGGTGTTACCAAAGGTTAC	1	51	0	TTTTTTGTTC	    0.997048	-75
AACCAAAATTTTAATCTTCAGTCTGCCATTAGCACAG	1	72	1	TTTTTCGTTC	    0.998687	-54
      CACCTTTTTGTGTGGTGTTACTAACAACTGT	1	105	0	TTTTGTGTTC	     0.99347	-21
          **  * *** ** *  *

Masking position 7
Map Score:   5.02646

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 21
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

GTGTTACCAAAGGTTACAAAGAACAGTAAA	1	38	0	AGGTTACAAA	    0.987764	-88
TTGGTTTTTGGTGTTACCAAAGGTTACAAA	1	48	0	GTGTTACCAA	    0.980363	-78
TTTTTGTGTGGTGTTACTAACAACTGTGCT	1	102	0	GTGTTACTAA	    0.995177	-24
          **********

Masking position 6
Map Score:   3.44169

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 6
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

   TTTTCTTTCAATTTTTCTTCTCATAAA	1	8	1	TCAATTTTTC	    0.977799	-118
CAAAGAACAGTAAATTTATGAGAAGAAAAA	1	22	0	TAAATTTATG	    0.981105	-104
GACTGAAGATTAAAATTTTGGTTTTTGGTG	1	65	0	TAAAATTTTG	    0.723818	-61
          **********

Masking position 4
Map Score:   1.21511

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 33
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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