AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i123_Daunorubicin_Resistance_Pump_aful_reg_100.orf -o123_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	RAG50240	202	Archaeoglobus_fulgidus

Motif number 1

GGGTTCAAATCCCGTCGAGCCCGTATTTAA	1	27	0	CCCGTCGAGC	    0.998373	-176
GGGCTTTTAACCCGTCGGTCGCGGGTTCAA	1	49	0	CCCGTCGGTC	    0.999127	-154
GGGTTAAAAGCCCGTCGCTCTGCCTGGCTG	1	66	1	CCCGTCGCTC	    0.999526	-137
TGGATGAGGGCTCGTAGCTCAGCCAGGCAG	1	85	0	CTCGTAGCTC	    0.994456	-118
  GCCTTTTCCCCGCAAATCTCGAATGCAC	1	185	0	CCCGCAAATC	    0.981217	-18
          **********

Masking position 4
Map Score:   12.284

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	    0.992054	-167
CGCGACCGACGGGTTAAAAGCCCGTCGCTCT	1	56	1	GGGTTAAAGC	    0.994319	-147
TAATGGATGAGGGCTCGTAGCTCAGCCAGGC	1	87	0	GGGCTGTAGC	    0.977772	-116
GCGATGGTGAGGATTTAAATCTTTTTCGTGC	1	118	1	GGATTAAATC	    0.975201	-85
CGAGATTTGCGGGGAAAAGGC          	1	192	1	GGGGAAAGGC	    0.977754	-11
          ***** *****

Masking position 2
Map Score:   4.62967

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 194
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

GGCTTTTAACCCGTCGGTCGCGGGTTCAAATC	1	46	0	CCGTCGTGCG	    0.988961	-157
AAGCCCGTCGCTCTGCCTGGCTGAGCTACGAG	1	73	1	CTCTGCTGCT	    0.996173	-130
GATTTAAATCCTCACCATCGCTAATGGATGAG	1	107	0	CTCACCTGCT	    0.996401	-96
ATAAATATATCTGTCCTTTGCTTGTATCTTTA	1	151	0	CTGTCCTGCT	    0.998573	-52
          ****** * ***

Masking position 8
Map Score:   1.74428

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 62
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

TCGGTCGCGGGTTCAAATCCCGTCGAGCCCG	1	34	0	GTTAAATCCC	    0.984914	-169
CGACCGACGGGTTAAAAGCCCGTCGCTCTGC	1	58	1	GTTAAAGCCC	    0.997074	-145
GCCTGGCTGAGCTACGAGCCCTCATCCATTA	1	87	1	GCTCGAGCCC	    0.986829	-116
TTGCTTGTATCTTTAGAGCACGAAAAAGATT	1	135	0	CTTAGAGCAC	    0.991188	-68
CCCCGCAAATCTCGAATGCACCGATAAATAT	1	175	0	CTCAATGCAC	    0.934492	-28
          *** *******

Masking position 9
Map Score:   2.38485

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 315
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

AGCTCAGCCAGGCAGAGCGACGGGCTTTTA	1	70	0	GGCAGAGCGA	     0.99775	-133
CGCTCTGCCTGGCTGAGCTACGAGCCCTCA	1	81	1	GGCTGAGCTA	     0.99667	-122
ACAAGCAAAGGACAGATATATTTATCGGTG	1	158	1	GACAGATATA	    0.962958	-45
          **********

Masking position 6
Map Score:   0.863347

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 107
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 6

GAGGATTTAAATCTTTTTCGTGCTCTAAAG	1	126	1	ATCTTTTTCG	    0.989823	-77
CTTTGCTTGTATCTTTAGAGCACGAAAAAG	1	138	0	ATCTTTAGAG	    0.978918	-65
AAGGACAGATATATTTATCGGTGCATTCGA	1	165	1	ATATTTATCG	    0.984254	-38
          **********

Masking position 1
Map Score:   0.81895

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 20
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 7

          **********

No masking
Map Score:   3.22176e-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:   3.22176e-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 9

          **********

No masking
Map Score:   3.22176e-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