AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i177_aful_mthe_100.orf -o177_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	RAG26588	73	Archaeoglobus_fulgidus
#2	RTH01626	132	M.thermo

Motif number 1

GGCCGACAGAAGATGATGGAGTTTAGAGAC	2	15	0	AGATGATGGA	    0.997066	-118
TATCTTACGGGGCTGATGCATTCCATCAGC	2	51	1	GGCTGATGCA	    0.996673	-82
AAATGACCGGAGCTGATGGAATGCATCAGC	2	62	0	AGCTGATGGA	    0.998091	-71
          GTATGATGGTCAGCGCTCAA	2	123	0	GTATGATGGT	    0.981265	-10
          **********

Masking position 6
Map Score:   6.1582

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 149
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

AAAGCTAAATTACCGAAGTGAAACTTCTGC	1	52	1	TACCGAAGTG	    0.977395	-22
         TGGCAGAAGTTTCACTTCGGT	1	63	0	GGCAGAAGTT	    0.990087	-11
CCCTGCGGCCGACAGAAGATGATGGAGTTT	2	21	0	GACAGAAGAT	    0.981394	-112
ATCTTCTGTCGGCCGCAGGGTATCTTACGG	2	31	1	GGCCGCAGGG	    0.991624	-102
AGAGAAAAATGACCGGAGCTGATGGAATGC	2	68	0	GACCGGAGCT	    0.990346	-65
          **********

Masking position 7
Map Score:   4.15376

Number of sites scoring better than the average of aligned sites = 272
Number in coding regions = 263
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

         GCTAAGGTTTAACCTCAAAAC	1	2	1	CTAAGGTTTA	    0.964857	-72
AAACCTTAAATTAAGTTTTGAGGTTAAACC	1	16	0	TTAAGTTTTG	    0.971958	-58
AAAACTTAATTTAAGGTTTTCTGTAAAAGC	1	27	1	TTAAGGTTTT	    0.992098	-47
ACTTCGGTAATTTAGCTTTTACAGAAAACC	1	41	0	TTTAGCTTTT	    0.967033	-33
          **********

Masking position 4
Map Score:   2.30878

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 56
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

TGTAAAAGCTAAATTACCGAAGTGAAACTT	1	48	1	AAATTACCGA	    0.984896	-26
AAACAGAGAAAAATGACCGGAGCTGATGGA	2	72	0	AAATGACCGG	    0.996221	-61
AATTTAAATAAATTGAGCGCTGACCATCAT	2	111	1	AATTGAGCGC	     0.98784	-22
          **********

Masking position 6
Map Score:   0.306544

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 18
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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:   3.50598e-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