AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i173_aful_mthe_100.orf -o173_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	RTH01486	123	M.thermo
#2	RTH00930	246	M.thermo

Motif number 1

TATTATTCATTTAATAAGGCATTCATATCG	2	102	0	TTAATAAGGC	    0.983144	-145
TAATAACACCTTTATAAGGGTTTAAATAAT	2	140	0	TTTATAAGGG	    0.995544	-107
CAGCCGATGATTTTTAAGGGGGGCGCGGCA	2	172	1	TTTTTAAGGG	    0.985486	-75
CGCGGCACCTTTAATATGGGTGGTGAACAT	2	195	1	TTAATATGGG	    0.979356	-52
GACATTAGATTCTATAAGGAG         	2	236	1	TCTATAAGGA	    0.954537	-11
          **********

Masking position 5
Map Score:   5.94367

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 29
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ACAGGGAACAGGCCGATGGAATGATCCCAG	1	44	0	GGCCGATGGA	     0.98529	-80
GTTTCCTTGTGGATGATGAGGGCTCTGACT	1	94	1	GGATGATGAG	    0.986635	-30
AAAACAGAGAGGATGATGCAGAGCCCCTTA	2	47	1	GGATGATGCA	    0.989703	-200
AAAAATCATCGGCTGATTAATAACACCTTT	2	157	0	GGCTGATTAA	    0.979828	-90
CCTTTAATATGGGTGGTGAACATAAAATTA	2	202	1	GGGTGGTGAA	    0.984139	-45
          **********

Masking position 7
Map Score:   3.89282

Number of sites scoring better than the average of aligned sites = 223
Number in coding regions = 206
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

TGTGGATGATGAGGGCTCTGACTACACCGA	1	101	1	GAGGGCTCTG	     0.98195	-23
AGGGAAATTAAGGGGCTCTGCATCATCCTC	2	55	0	AGGGGCTCTG	    0.995293	-192
GATTTTTAAGGGGGGCGCGGCACCTTTAAT	2	180	1	GGGGGCGCGG	    0.998156	-67
          **********

Masking position 5
Map Score:   3.11222

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 13
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

ACAGGCCGATGGAATGATCCCAGCTGTCCAGCT	1	34	0	GGAAGATCCG	     0.98576	-90
TCATTCCATCGGCCTGTTCCCTGTCAGCAAGTA	1	50	1	GGCCGTTCCG	    0.995693	-74
GTACCAGTTTGAACGTTTCCTTGTGGATGATGA	1	80	1	GAACTTTCCG	    0.989139	-44
CCCTCTATACGAACAGTTCCACGATATGAATGC	2	81	1	GAACGTTCCG	    0.997901	-166
CCACCCATATTAAAGGTGCCGCGCCCCCCTTAA	2	185	0	TAAAGTGCCG	    0.947948	-62
          **** *****  *

Masking position 9
Map Score:   1.80477

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 43
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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