AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_aful_mthe_100.orf -o109_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	RTH00068	49	M.thermo
#2	RTH00701	136	M.thermo

Motif number 1

AAAAAGTCGGGGTCTTAAAAATAAAGTAGT	1	24	0	GGTCTTAAAA	    0.954308	-26
          CTTCAGAAAAAGTCGGGGTC	1	40	0	CTTCAGAAAA	    0.911176	-10
          GTTCTGGGAATAACTCCCTC	2	1	1	GTTCTGGGAA	    0.951784	-136
CAGAGTAGTCCTTCTTTATCTTTCAGGACG	2	30	1	CTTCTTTATC	    0.883889	-107
AACATGGGATCGTCCTGAAAGATAAAGAAG	2	40	0	CGTCCTGAAA	    0.953463	-97
ATACATATCGGTTCTGTGAAGGAATGAGAA	2	68	0	GTTCTGTGAA	    0.953537	-69
ACACCTATATCGACATGGACATATATACAT	2	92	0	CGACATGGAC	     0.87321	-45
GGTCTTTAACCTCCATTAACTCAGAACACC	2	117	0	CTCCATTAAC	    0.869639	-20
          GGTCTTTAACCTCCATTAAC	2	127	0	GGTCTTTAAC	     0.97939	-10
          **********

Masking position 4
Map Score:   5.09704

Number of sites scoring better than the average of aligned sites = 1240
Number in coding regions = 1164
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 2

AAGGACTACTCTGAGGGAGTTATTCCCAGA	2	13	0	CTGAGGGAGT	    0.996793	-124
TATCGGTTCTGTGAAGGAATGAGAACATGG	2	63	0	GTGAAGGAAT	    0.986593	-74
TATAGGTGTTCTGAGTTAATGGAGGTTAAA	2	113	1	CTGAGTTAAT	    0.980092	-24
          **********

Masking position 4
Map Score:   0.0528863

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 131
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   4.57179e-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 4

          **********

No masking
Map Score:   4.57179e-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 5

          **********

No masking
Map Score:   4.57179e-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