AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i168_aful_mthe_300.orf -o168_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	RTH01904	139	M.thermo
#2	RTH01526	71	M.thermo
#3	RTH00989	16	M.thermo
#4	RTH00935	20	M.thermo
#5	RTH00563	107	M.thermo
#6	RTH02097	37	M.thermo

Motif number 1

         CCTCTTCACCTCACTCTCTACTCA	1	2	1	CTTTCATCAC	    0.967661	-138
TCACCTCACTCTCTACTCATAACCTTTATCTGT	1	16	1	CTTACTTAAC	    0.676248	-124
TTTAACAGTCCCCTTCATGTTATCTTCAGTGTC	1	78	0	CCTTCATTAT	    0.963721	-62
CCTCAAGTTCCCTTCCATCTATTCTAAATTTAA	1	106	0	CCTCCATATT	    0.940206	-34
  CCACACACCTATATATATATTTTTCTATTTG	2	9	1	CTTATATATT	     0.79888	-63
ATATATTTTTCTATTTGATTTTTGTAGAAAATT	2	25	1	CTTTTGTTTT	    0.769513	-47
CATTTAGCCGCCGTCCATATAATAATTTTCTAC	2	48	0	CCTCCATAAT	    0.919498	-24
TCTATTTTTCCCATTTTCTTCTCATGAAAACTG	5	29	1	CCTTTTTCTC	    0.895869	-79
CTCATGAAAACTGTTCAGTTTTTGCTTTTTTGT	5	49	1	CTTTCATTTT	    0.969296	-59
TCAGTTTTTGCTTTTTTGTTCTTTATTTTAACC	5	63	1	CTTTTTTCTT	    0.900278	-45
          CTATTTAAATTTTTTGGTAAATG	5	95	0	CTTTTATTTT	    0.934595	-13
TCAAGTAAGTCCATTCAATTCACT         	6	2	0	CCTTCATCAC	    0.971959	-36
          ** ****  ****

Masking position 4
Map Score:   9.16985

Number of sites scoring better than the average of aligned sites = 1057
Number in coding regions = 955
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

CTTCCATCTATTCTAAATTTAACAGTCCCC	1	98	0	TTCTAAATTT	     0.92222	-42
ACACCTATATATATATTTTTCTATTTGATT	2	15	1	ATATATTTTT	     0.85413	-57
GCCGTCCATATAATAATTTTCTACAAAAAT	2	42	0	TAATAATTTT	    0.730738	-30
CCTAAATAAATTCTATTTTTCCCATTTTCT	5	18	1	TTCTATTTTT	    0.984273	-90
ATGAAAACTGTTCAGTTTTTGCTTTTTTGT	5	52	1	TTCAGTTTTT	    0.908816	-56
TGCTTTTTTGTTCTTTATTTTAACCATTTA	5	71	1	TTCTTTATTT	    0.870532	-37
      CTATTTAAATTTTTTGGTAAATGG	5	94	0	TTAAATTTTT	     0.92862	-14
          **********

Masking position 8
Map Score:   3.43534

Number of sites scoring better than the average of aligned sites = 401
Number in coding regions = 231
Number in noncoding regions = 170
Number of orfs with sites within 600 bp upstream = 179
Fraction of orfs with sites within 600 bp upstream = 0.0287504


Motif number 3

          **********

No masking
Map Score:   -7.57276e-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 4

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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