AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_TRK_operon_aful_reg_300.orf -o107_aful_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	RAG02435	213	Archaeoglobus_fulgidus
#2	RAG46312	63	Archaeoglobus_fulgidus
#3	RAG46188	27	Archaeoglobus_fulgidus

Motif number 1

AAACCGAGTAAGGTTTAAGTTACCTCGAAT	1	35	0	AGGTTTAAGT	    0.952369	-179
AAACCTTACTCGGTTTTTCCGTTGTAGGGA	1	49	1	CGGTTTTTCC	    0.981879	-165
CGTAAATATAAGTTTTTTGTTCGAAAATAG	1	90	1	AGTTTTTTGT	    0.876323	-124
ATCACTTGAGAGGTTTTAGTTCTATTTTCG	1	111	0	AGGTTTTAGT	    0.982023	-103
CCCCACATCACGGCTTTTCTATTCTTTTGA	1	155	1	CGGCTTTTCT	    0.975223	-59
TTGGCAATTCTGGTTTATCAAAAGAATAGA	1	172	0	TGGTTTATCA	    0.818909	-42
GTTCAACGACCGCTTTTACTTGAGACGCTA	2	12	1	CGCTTTTACT	    0.966088	-52
TTCTGGATTGCGGTTTTATAAAAGTGTTAG	2	39	0	CGGTTTTATA	    0.925113	-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

TACGAGAGCATTCTTTCCCTACAACGGAAA	1	64	0	TTCTTTCCCT	    0.988302	-150
GAGGTTTTAGTTCTATTTTCGAACAAAAAA	1	102	0	TTCTATTTTC	    0.943316	-112
CTCTGACCTTTTCTATCACTTGAGAGGTTT	1	125	0	TTCTATCACT	    0.977965	-89
ATCACGGCTTTTCTATTCTTTTGATAAACC	1	161	1	TTCTATTCTT	    0.959751	-53
       ATCTTCTTTCTCCCCAAACTTCT	3	15	0	TTCTTTCTCC	    0.983322	-13
          **********

Masking position 6
Map Score:   3.70488

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 253
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

AGAACTAAAACCTCTCAAGTGATAGAAAAG	1	118	1	CCTCTCAAGT	    0.996567	-96
AAAGTGTTAGCGTCTCAAGTAAAAGCGGTC	2	19	0	CGTCTCAAGT	    0.997062	-45
          **********

Masking position 5
Map Score:   0.617159

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 4

GTTGTAGGGAAAGAATGCTCTCGTAAATAT	1	69	1	AAGAATGCTC	    0.930773	-145
AAACAATACGAAGAATGCTTCAGC      	1	200	1	AAGAATGCTT	    0.696917	-14
    TGTTCAACGACCGCTTTTACTTGAGA	2	7	1	ACGACCGCTT	    0.986245	-57
          **********

Masking position 4
Map Score:   0.577447

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 33
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

TATGAATGAATGAGGTGGTGAG        	1	3	0	TGAGGTGGTG	    0.990573	-211
TCGGTTTTTCCGTTGTAGGGAAAGAATGCT	1	58	1	CGTTGTAGGG	    0.983473	-156
AGAAAAGCCGTGATGTGGGGCTCTGACCTT	1	145	0	TGATGTGGGG	    0.997076	-69
          **********

Masking position 6
Map Score:   0.185642

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 92
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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


Motif number 7

          **********

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 8

          **********

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