AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i187_aful_mthe_300.orf -o187_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	RAG31052	182	Archaeoglobus_fulgidus

Motif number 1

TTAGGAAAATCATGAAAAGTTGTAAAGCTA	1	34	0	CATGAAAAGT	    0.890262	-149
TCATGATTTTCCTAAAAATCGGATTTGATA	1	49	1	CCTAAAAATC	    0.991672	-134
CAAGCTGATTCAGAAAACTTTATCAAATCC	1	69	0	CAGAAAACTT	    0.955187	-114
TAACTTTAAACCTAAAACTTAACCAAAAAC	1	99	1	CCTAAAACTT	    0.994268	-84
TAAAACTTAACCAAAAACGAAGTCAGGCAG	1	111	1	CCAAAAACGA	    0.950033	-72
GGCAGAACTCCCAAAAAATTTAAATCACGA	1	136	1	CCAAAAAATT	    0.987176	-47
TGGGACACTTCCTACAAATCACCGAATCGT	1	162	0	CCTACAAATC	    0.973432	-21
          **********

Masking position 6
Map Score:   9.19732

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 275
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

GCTTCAATTTTCGTAGCTTTACAACTTTTC	1	21	1	TCGTAGCTTT	    0.987623	-162
TTACAACTTTTCATGATTTTCCTAAAAATC	1	39	1	TCATGATTTT	    0.971622	-144
CTGAATCAGCTTGTAACTTTAAACCTAAAA	1	86	1	TTGTAACTTT	    0.971622	-97
AATCACCGAATCGTGATTTAAATTTTTTGG	1	146	0	TCGTGATTTA	    0.981764	-37
          **********

Masking position 4
Map Score:   1.55218

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 103
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

AAGCTACGAAAATTGAAGCCGTGCTCACA 	1	10	0	AATTGAAGCC	    0.992822	-173
TCAGCTTGTAACTTTAAACCTAAAACTTAA	1	91	1	ACTTTAAACC	    0.970156	-92
ACTTAACCAAAAACGAAGTCAGGCAGAACT	1	115	1	AAACGAAGTC	    0.954509	-68
ACTCCCAAAAAATTTAAATCACGATTCGGT	1	142	1	AATTTAAATC	    0.878153	-41
          **********

Masking position 6
Map Score:   1.00138

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 100
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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