AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i014_aful_mthe_100.orf -o014_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	RAG25887	68	Archaeoglobus_fulgidus
#2	RTH01963	195	M.thermo

Motif number 1

AAAACTTTCTGAAAATTTTAATTTACCTGCT	1	23	0	GAAAATTTTA	    0.971481	-46
AAAATTTTCAGAAAGTTTTTAATTTCACCTT	1	35	1	GAAAGTTTTA	    0.980115	-34
          TATAATGTTTACAATTTAATT	2	1	1	TATAATGTTA	    0.894406	-195
AAAGCTGTTGGATGATGTTAAACCAGTGAAA	2	32	0	GATGATGTTA	    0.988674	-164
CCCACATAGTGAAGGTGTTAAATGCAGAAAG	2	59	0	GAAGGTGTTA	     0.99611	-137
GGGAGTTGTTGAAGGGGTTCATGAATGAATT	2	112	0	GAAGGGGTTA	    0.989433	-84
          ********* *

Masking position 8
Map Score:   7.17044

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 327
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

AGAAAGTTTTTAATTTCACCTTCCGAATTG	1	44	1	TAATTTCACC	    0.782737	-25
          CACTTCAATTCGGAAGGTGA	1	59	0	CACTTCAATT	    0.938963	-10
ATAATGTTTACAATTTAATTTTTCACTGGT	2	12	1	CAATTTAATT	    0.913934	-184
CTGCATTTAACACCTTCACTATGTGGGGAT	2	63	1	CACCTTCACT	    0.987926	-133
ATATTACAGGCAAATTCATTCATGAACCCC	2	100	1	CAAATTCATT	    0.921598	-96
CATTCATGAACCCCTTCAACAACTCCCGCA	2	116	1	CCCCTTCAAC	    0.948711	-80
TTTTATAATACACCTCAACCATACTATGAG	2	162	1	CACCTCAACC	    0.978873	-34
TATGAGATATCCCATTAATC          	2	186	1	CCCATTAATC	    0.944533	-10
          **********

Masking position 8
Map Score:   4.44564

Number of sites scoring better than the average of aligned sites = 1952
Number in coding regions = 1818
Number in noncoding regions = 134
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

ATAGTGAAGGTGTTAAATGCAGAAAGCTGT	2	55	0	TGTTAAATGC	    0.945533	-141
TGAATTTGCCTGTAATATCCAGCGCATCCC	2	88	0	TGTAATATCC	    0.990883	-108
TAAAATATGCTGTGACATCCGTGCGGGAGT	2	137	0	TGTGACATCC	    0.990296	-59
AGGTGTATTATAAAATATGCTGTGACATCC	2	147	0	TAAAATATGC	    0.911852	-49
AACCATACTATGAGATATCCCATTAATC  	2	178	1	TGAGATATCC	    0.986388	-18
          **********

Masking position 5
Map Score:   4.25931

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 87
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

TGAAAATTTTAATTTACCTGCTCAGAATTG	1	15	0	AATTTACCTG	    0.991758	-54
AAAGTTTTTAATTTCACCTTCCGAATTGAA	1	46	1	ATTTCACCTT	    0.964454	-23
TTCATGAATGAATTTGCCTGTAATATCCAG	2	96	0	AATTTGCCTG	    0.986036	-100
CATATTTTATAATACACCTCAACCATACTA	2	158	1	AATACACCTC	    0.975728	-38
          **********

Masking position 3
Map Score:   1.9322

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 30
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

          **********

No masking
Map Score:   -4.30999e-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:   -4.30999e-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:   -4.30999e-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