AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i255_heat_shock_tpal_reg_100.orf -o255_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00279	205	AE000520
#2	RTP00278	115	AE000520

Motif number 1

GGGCGTATTCCGCGCATGGATTCTGTAGAG	1	26	0	CGCGCATGGA	    0.996854	-180
TAGACGTTACCGCTTTTGGTTACCAGAAAG	1	55	0	CGCTTTTGGT	    0.980236	-151
AACACACAAGCGCTCATCGAGAGCACCTGC	1	125	1	CGCTCATCGA	    0.950098	-81
GAGTTTGGTGCGCGTGTGCTTATCAATACA	1	161	0	CGCGTGTGCT	    0.993101	-45
TACTCATTTCGGAGTTTGGTGCGCGTGTGC	1	172	0	GGAGTTTGGT	    0.897308	-34
      AGTGCGCGCAACGAGTTACCATGC	2	5	1	CGCGCAACGA	    0.938432	-111
TGCTTATTGTGGCGCATGGTAACTCGTTGC	2	18	0	GGCGCATGGT	    0.995329	-98
ATTTCCGGACAGCGTGTGCTTATTGTGGCG	2	34	0	AGCGTGTGCT	    0.935787	-82
GATACCGTTGCGCGTGTGGTGCCGTATTTT	2	88	0	CGCGTGTGGT	    0.998217	-28
          **********

Masking position 2
Map Score:   16.1103

Number of sites scoring better than the average of aligned sites = 1134
Number in coding regions = 1056
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 2

   CGTGTTCGCAGTCCACTCTACAGAATC	1	8	1	GCAGTCCACT	    0.960307	-198
CCCTTTCTGGTAACCAAAAGCGGTAACGTC	1	53	1	TAACCAAAAG	    0.840355	-153
CCTGTATTGATAAGCACACGCGCACCAAAC	1	159	1	TAAGCACACG	    0.984571	-47
AAGCACACGCGCACCAAACTCCGAAATGAG	1	170	1	GCACCAAACT	     0.98821	-36
     GCTTTGCACTCAACTACTCATTTCG	1	191	0	GCACTCAACT	    0.938972	-15
TGCGCCACAATAAGCACACGCTGTCCGGAA	2	32	1	TAAGCACACG	    0.984571	-84
TCAAAATACGGCACCACACGCGCAACGGTA	2	86	1	GCACCACACG	    0.997211	-30
          **********

Masking position 3
Map Score:   7.64361

Number of sites scoring better than the average of aligned sites = 837
Number in coding regions = 769
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 3

CGCGCATGGATTCTGTAGAGTGGACTGCGAA	1	15	0	TTCTGTGAGT	    0.955617	-191
CAGTGCAGCATGATGTAGACGTTACCGCTTT	1	69	0	TGATGTGACG	     0.96767	-137
ATGTGCTAGTTTCTGTCGATGCAGTGCAGCA	1	90	0	TTCTGTGATG	    0.992303	-116
AGCGCTTGTGTGTTTTTGATGTGCTAGTTTC	1	108	0	TGTTTTGATG	    0.945181	-98
GAATTGCAGGTGCTCTCGATGAGCGCTTGTG	1	129	0	TGCTCTGATG	    0.982929	-77
TGGTGCCGTATTTTGAAGAGGAAATCAAACC	2	71	0	TTTTGAGAGG	    0.938421	-45
          ****** ****

Masking position 4
Map Score:   2.64993

Number of sites scoring better than the average of aligned sites = 170
Number in coding regions = 160
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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