AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i077_aful_mthe_100.orf -o077_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	RTH00306	48	M.thermo
#2	RTH00146	60	M.thermo
#3	RTH01779	194	M.thermo

Motif number 1

     GTGGTCTGTCTTCACATGCAAGGGA	1	6	1	CTGTCTTCAC	    0.942958	-43
CAGTCCAGTCCAGTCCAGTCCATCCTATCC	3	103	0	CAGTCCAGTC	    0.998752	-92
CAGTCCAGTCCAGTCCAGTCCAGTCCAGTC	3	113	0	CAGTCCAGTC	    0.998752	-82
TTTATCAGTCCAGTCCAGTCCAGTCCAGTC	3	123	0	CAGTCCAGTC	    0.998752	-72
TCTGCATTCACTGTCTACTCCAGGATCTTT	3	151	0	CTGTCTACTC	    0.993935	-44
          **********

Masking position 4
Map Score:   12.4232

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 25
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

CTTCACATGCAAGGGAGTTAAGCGTGAGGA	1	20	1	AAGGGAGTTA	    0.899398	-29
GTTAAGCGTGAGGAGATGATGCC       	1	36	1	AGGAGATGAT	    0.970333	-13
GCATTCCTCATAGGGATTAACTCATCAGAG	2	28	1	TAGGGATTAA	    0.897933	-33
CTCATCAGAGAAAGGATGATTGA       	2	48	1	AAAGGATGAT	    0.928681	-13
CTGTAGGTTTAAGGGAGGAATAGGATAGGA	3	81	1	AAGGGAGGAA	    0.993705	-114
AGGGAGGAATAGGATAGGATGGACTGGACT	3	92	1	AGGATAGGAT	    0.836689	-103
CTCGAACATGGAGAGATGAAAA        	3	183	1	GAGAGATGAA	    0.958579	-12
          **********

Masking position 6
Map Score:   3.59339

Number of sites scoring better than the average of aligned sites = 1809
Number in coding regions = 1693
Number in noncoding regions = 116
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 3

  GGCATCATCTCCTCACGCTTAACTCCCTTG	1	29	0	CTCTCCGCTT	     0.98093	-20
        CACTTCTGGAGGTCCCGGCATTCC	2	3	1	CTCTGAGGTC	    0.989862	-58
CAGATTTTTACTGCTGTAGGTTTAAGGGAGGA	3	68	1	CTCTGAGGTT	    0.992599	-127
CATTCACTGTCTACTCCAGGATCTTTTATCAG	3	145	0	CTCTCAGGAT	    0.896473	-50
TCATCTCTCCATGTTCGAGGATCTGCATTCAC	3	170	0	ATTTCAGGAT	    0.674525	-25
          ** *** *****

Masking position 5
Map Score:   2.17954

Number of sites scoring better than the average of aligned sites = 341
Number in coding regions = 323
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

TGAGTTAATCCCTATGAGGAATGCCGGGAC	2	22	0	CCTATGAGGA	    0.991931	-39
AATCATCCTTTCTCTGATGAGTTAATCCCT	2	39	0	TCTCTGATGA	    0.976947	-22
TTAAACTTTTCGTATGATGATGTGGGGTGC	3	36	1	CGTATGATGA	    0.987632	-159
CATCTCTCCATGTTCGAGGATCTGCATTCA	3	171	0	TGTTCGAGGA	    0.956588	-24
          **********

Masking position 7
Map Score:   1.107

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 80
Number in noncoding regions = 3
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:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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