AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i200_aful_mthe_300.orf -o200_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	RTH00601	195	M.thermo

Motif number 1

GTGGGATTATATTTCAGGGTCAACTTATAT	1	42	1	ATTTCAGGGT	    0.974498	-154
ATATATACCTTTGCCAGGATACATAAAGTT	1	68	1	TTGCCAGGAT	    0.981874	-128
AGTCTCATATCTGACAGGGTATCCCACGTG	1	106	1	CTGACAGGGT	    0.993574	-90
TGGGGGTATCATCACAGGATTATGGAACAC	1	133	0	ATCACAGGAT	    0.982468	-63
TTAAACATAAATCAGAGGATGGTAATGATA	1	174	1	ATCAGAGGAT	    0.972474	-22
          **********

Masking position 6
Map Score:   5.5611

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 92
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

CCACAATAGAATGAGGTTCTTATTTTAAGT	1	16	0	ATGAGGTTCT	    0.979294	-180
TCATTCTATTGTGGGATTATATTTCAGGGT	1	32	1	GTGGGATTAT	    0.989866	-164
CCTGTCAGATATGAGACTCCAGACTCAACT	1	94	0	ATGAGACTCC	    0.965175	-102
TATGGAACACGTGGGATACCCTGTCAGATA	1	113	0	GTGGGATACC	    0.986474	-83
AACAAGTTCAGTGGGGGTATCATCACAGGA	1	144	0	GTGGGGGTAT	    0.984247	-52
          **********

Masking position 2
Map Score:   2.70592

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 227
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

   AAATCACTTAAAATAAGAACCTCATTC	1	8	1	TTAAAATAAG	    0.842408	-188
AGTTGACCCTGAAATATAATCCCACAATAG	1	37	0	GAAATATAAT	    0.947294	-159
CTGGCAAAGGTATATATAAGTTGACCCTGA	1	55	0	TATATATAAG	    0.921341	-141
CCTTTGCCAGGATACATAAAGTTGAGTCTG	1	75	1	GATACATAAA	    0.974049	-121
TATCCCACGTGTTCCATAATCCTGTGATGA	1	125	1	GTTCCATAAT	     0.88828	-71
GAACTTGTTTTAAACATAAATCAGAGGATG	1	165	1	TAAACATAAA	    0.962048	-31
          **********

Masking position 6
Map Score:   1.9134

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 81
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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:   -3.30951e-14

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