AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i286_aful_mthe_300.orf -o286_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	RTH01355	147	M.thermo
#2	RTH00374	143	M.thermo
#3	RTH01852	135	M.thermo

Motif number 1

TCATGGGGTTATTACGGCAGCCTCTTCCCCT	1	16	1	ATACGGCAGC	    0.987834	-132
GGTGAGCAACATCGCTGCAGCGACTCAGAGA	2	20	0	ATGCTGCAGC	    0.990911	-124
CTCACCAGTAAGGCCGGCGCCAATGACTTTG	2	45	1	AGCCGGCGCC	    0.989347	-99
AGGTTAATTGATGCCTGCGGAGGTTTATAA 	2	124	1	ATCCTGCGGA	    0.992311	-20
AAAAATCCGTATACCTGCGGCAGGTGGGACA	3	92	0	ATCCTGCGGC	    0.998517	-44
          ** ********

Masking position 1
Map Score:   5.11429

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 94
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

 AGGACTCATGGGGTTATTACGGCAGCCTC	1	10	1	GGGGTTATTA	    0.847525	-138
TAGGGGATCCGATGATTAAACACTTGAAGG	1	44	0	GATGATTAAA	    0.753868	-104
CATGATTATTTATGATAATATAAAGTTTTC	1	93	0	TATGATAATA	    0.703696	-55
CATAAATAATCATGTTAATTATTGGTACTA	1	109	1	CATGTTAATT	    0.915628	-39
CAATGACTTTGAGGTTAAATTTCTGGGATT	2	65	1	GAGGTTAAAT	    0.925813	-79
ATTCTGACTTGAGGTTAATTGATGCCTGCG	2	113	1	GAGGTTAATT	    0.975303	-31
GATGCCTGCGGAGGTTTATAA         	2	133	1	GAGGTTTATA	    0.975303	-11
CTGATACGCTCATGTTTTTATTACAGCACT	3	29	1	CATGTTTTTA	    0.774237	-107
CAGCACTATAGATATTAATATGGGATAAGT	3	52	1	GATATTAATA	     0.85143	-84
          **********

Masking position 6
Map Score:   4.30408

Number of sites scoring better than the average of aligned sites = 625
Number in coding regions = 544
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 3

CATGGGGTTATTACGGCAGCCTCTTCCCCT	1	17	1	TTACGGCAGC	    0.960485	-131
TTTCTCTGAGTCGCTGCAGCGATGTTGCTC	2	18	1	TCGCTGCAGC	    0.989133	-126
TCAAAGTCATTGGCGCCGGCCTTACTGGTG	2	47	0	TGGCGCCGGC	     0.99143	-97
GGTTAATTGATGCCTGCGGAGGTTTATAA 	2	125	1	TGCCTGCGGA	    0.986354	-19
AAAATCCGTATACCTGCGGCAGGTGGGACA	3	92	0	TACCTGCGGC	    0.992825	-44
          **********

Masking position 1
Map Score:   2.67981

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 169
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

TTAAACACTTGAAGGGGAAGAGGCTGCCGTA	1	28	0	GAAGGGGAAA	    0.946934	-120
GTACTAAAGAGAAGGGAGCTATAAA      	1	133	1	GAAGGGAGCA	    0.989375	-15
GCCGGCCTTACTGGTGAGCAACATCGCTGCA	2	32	0	CTGGTGAGCA	     0.95105	-112
ATACCTGCGGCAGGTGGGACATACACTTATA	3	82	0	CAGGTGGGAA	    0.984599	-54
GATTTTTCCGGAAGTGGGCCAGCAATTCAG 	3	116	1	GAAGTGGGCA	    0.994881	-20
          ********* *

Masking position 11
Map Score:   0.660258

Number of sites scoring better than the average of aligned sites = 440
Number in coding regions = 412
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

TGATTAAACACTTGAAGGGGAAGAGGCTGC	1	32	0	CTTGAAGGGG	    0.871914	-116
TCTCTGAGTCGCTGCAGCGATGTTGCTCAC	2	20	1	GCTGCAGCGA	    0.964302	-124
ACCAGTAAGGCCGGCGCCAATGACTTTGAG	2	48	1	CCGGCGCCAA	     0.67822	-96
TTAATTGATGCCTGCGGAGGTTTATAA   	2	127	1	CCTGCGGAGG	    0.665714	-17
AATCCGTATACCTGCGGCAGGTGGGACATA	3	90	0	CCTGCGGCAG	    0.895377	-46
ACGGATTTTTCCGGAAGTGGGCCAGCAATT	3	113	1	CCGGAAGTGG	    0.960256	-23
          **********

Masking position 4
Map Score:   0.622975

Number of sites scoring better than the average of aligned sites = 1055
Number in coding regions = 992
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 6

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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 8

          **********

No masking
Map Score:   -2.03625e-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