AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i123_aful_mthe_100.orf -o123_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	RAG50240	202	Archaeoglobus_fulgidus
#2	RTH00401	96	M.thermo

Motif number 1

TTAAATACGGGCTCGACGGGATTTGAACCC	1	27	1	GCTCGACGGG	    0.997634	-176
TTGAACCCGCGACCGACGGGTTAAAAGCCC	1	49	1	GACCGACGGG	     0.99873	-154
CAGCCAGGCAGAGCGACGGGCTTTTAACCC	1	66	0	GAGCGACGGG	     0.99931	-137
CTGCCTGGCTGAGCTACGAGCCCTCATCCA	1	85	1	GAGCTACGAG	    0.991946	-118
GTGCATTCGAGATTTGCGGGGAAAAGGC  	1	185	1	GATTTGCGGG	    0.972877	-18
          **********

Masking position 7
Map Score:   10.3515

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 44
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

CGTCGGTCGCGGGTTCAAATCCCGTCGAGCC	1	36	0	GGGTTAAATC	    0.992227	-167
CGCGACCGACGGGTTAAAAGCCCGTCGCTCT	1	56	1	GGGTTAAAGC	    0.992452	-147
GCGATGGTGAGGATTTAAATCTTTTTCGTGC	1	118	1	GGATTAAATC	    0.988408	-85
CGAGATTTGCGGGGAAAAGGC          	1	192	1	GGGGAAAGGC	    0.980157	-11
ATACTATCAGGGATAAAAATCTAACCATAAT	2	45	1	GGATAAAATC	     0.98984	-52
          ***** *****

Masking position 7
Map Score:   7.59673

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 38
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

CCTATTTTTAAATACGGGCTCGACGGGATTT	1	20	1	ATACGGGCTC	     0.92396	-183
TAACCCGTCGGTCGCGGGTTCAAATCCCGTC	1	41	0	GCGCGGGTTC	    0.994081	-162
GCCAGGCAGAGCGACGGGCTTTTAACCCGTC	1	63	0	GGACGGGCTT	    0.985515	-140
ATCGCTAATGGATGAGGGCTCGTAGCTCAGC	1	92	0	GTGAGGGCTC	    0.996491	-111
CATTAGCGATGGTGAGGATTTAAATCTTTTT	1	113	1	GTGAGGATTT	    0.969071	-90
TAGTGATGCTGTGGAGGGTGCATGA      	2	5	0	GGGAGGGTGC	    0.991361	-92
CTTCAGGGTCGCGGAGGATTTGG        	2	84	1	GGGAGGATTT	    0.980105	-13
          * *********

Masking position 6
Map Score:   8.9409

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 507
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

TTGATCCTCCTATTTTTAAATACGGGCTCGA	1	12	1	TATTTTAAAT	    0.871033	-191
TGAGGATTTAAATCTTTTTCGTGCTCTAAAG	1	125	1	AATTTTTTCG	    0.847005	-78
CCTTTGCTTGTATCTTTAGAGCACGAAAAAG	1	138	0	TATTTTAGAG	    0.981988	-65
AAAGGACAGATATATTTATCGGTGCATTCGA	1	164	1	TATTTTATCG	    0.976673	-39
TGATAGTATAAATTGTTATAGTGATGCTGTG	2	23	0	AATGTTATAG	    0.957339	-74
CATCGGGTATTATGGTTAGATTTTTATCCCT	2	53	0	TATGTTAGAT	    0.938547	-44
          *** *******

Masking position 6
Map Score:   1.27292

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 48
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

TGAACCCGCGACCGACGGGTTAAAAGCCCG	1	50	1	ACCGACGGGT	    0.945725	-153
GGGTTAAAAGCCCGTCGCTCTGCCTGGCTG	1	66	1	CCCGTCGCTC	    0.970342	-137
CTCATCCATTAGCGATGGTGAGGATTTAAA	1	107	1	AGCGATGGTG	    0.985605	-96
AAATTGTTATAGTGATGCTGTGGAGGGTGC	2	15	0	AGTGATGCTG	    0.956973	-82
AACCATAATACCCGATGCTTCAGGGTCGCG	2	67	1	CCCGATGCTT	    0.989715	-30
CCAAATCCTCCGCGACCCTGAAGCATCGGG	2	77	0	CGCGACCCTG	    0.987682	-20
          **********

Masking position 4
Map Score:   2.88327

Number of sites scoring better than the average of aligned sites = 546
Number in coding regions = 508
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 6

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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 8

          **********

No masking
Map Score:   1.16119e-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