AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_TRK_operon_aful_reg_100.orf -o107_aful_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	RAG02435	213	Archaeoglobus_fulgidus
#2	RAG46312	63	Archaeoglobus_fulgidus
#3	RAG46188	27	Archaeoglobus_fulgidus

Motif number 1

ATTCGAGGTAACTTAAACCTTACTCGGTTT	1	35	1	ACTTAAACCT	    0.952914	-179
TCCCTACAACGGAAAAACCGAGTAAGGTTT	1	49	0	GGAAAAACCG	    0.982093	-165
CTATTTTCGAACAAAAAACTTATATTTACG	1	90	0	ACAAAAAACT	    0.877627	-124
CGAAAATAGAACTAAAACCTCTCAAGTGAT	1	111	1	ACTAAAACCT	    0.982235	-103
TCAAAAGAATAGAAAAGCCGTGATGTGGGG	1	155	0	AGAAAAGCCG	    0.975514	-59
TCTATTCTTTTGATAAACCAGAATTGCCAA	1	172	1	TGATAAACCA	    0.820694	-42
TAGCGTCTCAAGTAAAAGCGGTCGTTGAAC	2	12	0	AGTAAAAGCG	    0.966482	-52
CTAACACTTTTATAAAACCGCAATCCAGAA	2	39	1	TATAAAACCG	    0.925946	-25
          **********

Masking position 5
Map Score:   6.08791

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 480
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

AATATGAATGAATGAGGTGGTGAG       	1	4	0	AATGAGGGGT	    0.917607	-210
TTTTCTATCACTTGAGAGGTTTTAGTTCTAT	1	116	0	CTTGAGAGTT	    0.971523	-98
CTCTCAAGTGATAGAAAAGGTCAGAGCCCCA	1	129	1	ATAGAAAGGT	    0.982255	-85
TATCAAAAGAATAGAAAAGCCGTGATGTGGG	1	156	0	ATAGAAAGCC	    0.909855	-58
ACCGCTTTTACTTGAGACGCTAACACTTTTA	2	20	1	CTTGAGAGCT	    0.973564	-44
TTGCGGTTTTATAAAAGTGTTAGCGTCTCAA	2	31	0	ATAAAAGGTT	    0.793946	-33
AAACCGCAATCCAGAAGTGGT          	2	53	1	CCAGAAGGGT	    0.942408	-11
          ATAGAGAAGTTTGGGGAGAAA	3	1	1	ATAGAGAGTT	    0.982406	-27
          ******* ***

Masking position 5
Map Score:   4.94279

Number of sites scoring better than the average of aligned sites = 1045
Number in coding regions = 971
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

TATTTACGAGAGCATTCTTTCCCTACAACG	1	68	0	AGCATTCTTT	    0.992337	-146
     GCTGAAGCATTCTTCGTATTGTTTG	1	199	0	AGCATTCTTC	    0.990921	-15
CTCAAGTAAAAGCGGTCGTTGAACA     	2	6	0	AGCGGTCGTT	     0.98093	-58
          **********

Masking position 1
Map Score:   0.577447

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 33
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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