AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i014_aful_mthe_300.orf -o014_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	RAG25887	68	Archaeoglobus_fulgidus
#2	RTH01930	300	M.thermo
#3	RTH01963	195	M.thermo

Motif number 1

AAAAACTTTCTGAAAATTTTAATTTACCTG	1	25	0	TGAAAATTTT	    0.742857	-44
AAGGTGAAATTAAAAACTTTCTGAAAATTT	1	36	0	TAAAAACTTT	    0.948923	-33
TAAAAAAATCTGAAAGCCTTTTAAATTAAA	2	17	0	TGAAAGCCTT	    0.980668	-284
TTGGAAAAAATAAAACCTTTTAACAGAGTA	2	65	1	TAAAACCTTT	    0.925934	-236
AAAAGCATTATATAAGCCTTTTTGTCTTAT	2	142	1	TATAAGCCTT	    0.943747	-159
CACCACTATATATAAACCTTTGTTTCCGGA	2	172	0	TATAAACCTT	    0.961437	-129
AAAATTAAATTGTAAACATTATA       	3	4	0	TGTAAACATT	    0.859507	-192
CTTTCTGCATTTAACACCTTCACTATGTGG	3	59	1	TTAACACCTT	     0.87595	-137
AATTCATTCATGAACCCCTTCAACAACTCC	3	112	1	TGAACCCCTT	    0.961235	-84
          **********

Masking position 4
Map Score:   8.32365

Number of sites scoring better than the average of aligned sites = 484
Number in coding regions = 408
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 2

 CACTTCAATTCGGAAGGTGAAATTAAAAA	1	50	0	TCGGAAGGTG	     0.97091	-19
TTATATATAGTGGTGATGTGATTAAGGTTC	2	187	1	TGGTGATGTG	    0.961631	-114
TTAAGGTTCATGGTAAGGTCGGCGGGTAGA	2	208	1	TGGTAAGGTC	    0.890154	-93
TCCTGCCATCAGTGGAGGCGGTAAGATTAA	2	238	1	AGTGGAGGCG	    0.978116	-63
AAGTAGAGCGAGGTAACGCGAGTGTCTCTT	2	266	0	AGGTAACGCG	    0.871663	-35
ATCCCCACATAGTGAAGGTGTTAAATGCAG	3	63	0	AGTGAAGGTG	    0.965011	-133
CTTCACTATGTGGGGATGCGCTGGATATTA	3	76	1	TGGGGATGCG	    0.975971	-120
TGACATCCGTGCGGGAGTTGTTGAAGGGGT	3	125	0	GCGGGAGTTG	    0.842009	-71
CTCATAGTATGGTTGAGGTGTATTATAAAA	3	162	0	GGTTGAGGTG	    0.967504	-34
          **********

Masking position 6
Map Score:   6.53004

Number of sites scoring better than the average of aligned sites = 2027
Number in coding regions = 1920
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

TCTGAAAATTTTAATTTACCTGCTCAGAAT	1	17	0	TTAATTTACC	    0.959055	-52
CAGAAAGTTTTTAATTTCACCTTCCGAATT	1	43	1	TTAATTTCAC	     0.97101	-26
   TGCTGATTTAATTTAAAAGGCTTTCAG	2	8	1	TTAATTTAAA	    0.859613	-293
TTAAAAGGTTTTATTTTTTCCAAAGAATGA	2	58	0	TTATTTTTTC	    0.907848	-243
CGAGTGTCTCTTAATCTTACCGCCTCCACT	2	248	0	TTAATCTTAC	    0.953198	-53
TGTTTACAATTTAATTTTTCACTGGTTTAA	3	16	1	TTAATTTTTC	    0.975511	-180
          **********

Masking position 5
Map Score:   2.76474

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 49
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 4

GGGATGCGCTGGATATTACAGGCAAATTCA	3	88	1	GGATATTACA	    0.983877	-108
ACTCCCGCACGGATGTCACAGCATATTTTA	3	137	1	GGATGTCACA	    0.993044	-59
  GATTAATGGGATATCTCATAGTATGGTT	3	178	0	GGATATCTCA	    0.985474	-18
          **********

Masking position 3
Map Score:   0.942817

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 11
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

TCCAAAGAATGAATATGGGGCCCTAAAAAA	2	40	0	GAATATGGGG	    0.982555	-261
CCTTTTAACAGAGTATTGGGGCGCCATTAT	2	80	1	GAGTATTGGG	    0.973718	-221
ATCATGAATTGATAATGGCGCCCCAATACT	2	91	0	GATAATGGCG	    0.941162	-210
TGCGGGAGTTGTTGAAGGGGTTCATGAATG	3	116	0	GTTGAAGGGG	    0.946543	-80
          GATTAATGGGATATCTCATA	3	186	0	GATTAATGGG	    0.977817	-10
          **********

Masking position 5
Map Score:   0.882505

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 342
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   1.48036e-12

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:   1.48036e-12

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 8

          **********

No masking
Map Score:   1.48036e-12

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