AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i117_aful_mthe_300.orf -o117_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	RAG45695	300	Archaeoglobus_fulgidus

Motif number 1

ACAAGAAAAAGGAAGAGAGGCTTTAGCATCA	1	39	1	GGAAGAGGGC	    0.999582	-262
AATAATTAACGGAAGAGTGGCACTACACGTT	1	69	0	GGAAGAGGGC	    0.999561	-232
TTATCTGAGGGAAAGAGGGGCACATTGTTGT	1	210	0	GAAAGAGGGC	    0.998865	-91
          ******* ***

Masking position 6
Map Score:   7.13504

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 16
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 2

AAGCCTCTCTTCCTTTTTCTTGTTTCATGA	1	32	0	TCCTTTTTCT	    0.950961	-269
AAAGAACCATGTCGATTTCGGGAGAAATAA	1	95	0	GTCGATTTCG	    0.969526	-206
ATCGACATGGTTCTTTTTCACTATCGTTTT	1	109	1	TTCTTTTTCA	    0.924995	-192
CTTTTTCACTATCGTTTTCGAGCCTTCTCA	1	121	1	ATCGTTTTCG	    0.986038	-180
ACATTGTTGTACCTTTATCGCCTGAAGATT	1	190	0	ACCTTTATCG	    0.955488	-111
CTCAAACGTATCCGATGTCGTCACTGCCGG	1	258	1	TCCGATGTCG	    0.974632	-43
          **********

Masking position 6
Map Score:   3.29407

Number of sites scoring better than the average of aligned sites = 492
Number in coding regions = 457
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

TTTCGAGCCTTCTCAGAAGTGCCATGAGCT	1	136	1	TCTCAGAAGT	    0.920296	-165
GTGCCATGAGCTTCAAACGTGCATCTGATG	1	154	1	CTTCAAACGT	    0.978021	-147
GATTGTATTTCATCAGATGCACGTTTGAAG	1	164	0	CATCAGATGC	    0.951083	-137
GAAATACAATCTTCAGGCGATAAAGGTACA	1	183	1	CTTCAGGCGA	    0.971096	-118
CCCCTCTTTCCCTCAGATAAATTTTTAAGC	1	221	1	CCTCAGATAA	    0.934287	-80
AAGCCAAACACCTCAAACGTATCCGATGTC	1	247	1	CCTCAAACGT	    0.990124	-54
          **********

Masking position 5
Map Score:   2.9776

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 404
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

CCGAAATCGACATGGTTCTTTTTCACTATC	1	104	1	CATGGTTCTT	    0.994772	-197
GTTTGAAGCTCATGGCACTTCTGAGAAGGC	1	142	0	CATGGCACTT	    0.989023	-159
TACATAATAACAAGGTTTTTA         	1	290	1	CAAGGTTTTT	    0.975284	-11
          **********

Masking position 2
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 48
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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