AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_tpal_reg_100.orf -o043_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	RTP00711	151	AE000520

Motif number 1

        CACGCAGCCGCTCCACCACCCG	1	3	1	CGCAGCCGCT	    0.906616	-149
CAGCCGCTCCACCACCCGCTTGTCAGAAAT	1	15	1	ACCACCCGCT	    0.911726	-137
GCAGTGGACACCGGCGCCATTTCTGACAAG	1	33	0	CCGGCGCCAT	    0.944793	-119
TCCGGGCACTCTGACGCACTCAGCGCAGTG	1	57	0	CTGACGCACT	    0.988005	-95
CATTCCCCTTTCCGGGCACTCTGACGCACT	1	67	0	TCCGGGCACT	    0.962359	-85
GGAAAGGGGAATGACGAGCTGCGTTTTTCC	1	84	1	ATGACGAGCT	    0.896786	-68
CTGCGTTTTTCCCGGCCACTGATCGAAACG	1	102	1	CCCGGCCACT	    0.989537	-50
ACTGATCGAAACGGCGCGCAATACCGACGT	1	119	1	ACGGCGCGCA	    0.869954	-33
GCGCGCAATACCGACGTGCTCGGGGGAGAG	1	132	1	CCGACGTGCT	    0.989366	-20
          **********

Masking position 10
Map Score:   13.2255

Number of sites scoring better than the average of aligned sites = 2871
Number in coding regions = 2668
Number in noncoding regions = 203
Number of orfs with sites within 600 bp upstream = 137
Fraction of orfs with sites within 600 bp upstream = 0.0220045


Motif number 2

         CACGCAGCCGCTCCACCACCC	1	2	1	ACGCAGCCGC	    0.977083	-150
GCAGCCGCTCCACCACCCGCTTGTCAGAAA	1	14	1	CACCACCCGC	     0.97985	-138
AGCGCAGTGGACACCGGCGCCATTTCTGAC	1	36	0	ACACCGGCGC	    0.905803	-116
TTCCGGGCACTCTGACGCACTCAGCGCAGT	1	58	0	TCTGACGCAC	    0.900157	-94
TCATTCCCCTTTCCGGGCACTCTGACGCAC	1	68	0	TTCCGGGCAC	    0.941529	-84
AAAGGGGAATGACGAGCTGCGTTTTTCCCG	1	86	1	GACGAGCTGC	    0.905359	-66
GCTGCGTTTTTCCCGGCCACTGATCGAAAC	1	101	1	TCCCGGCCAC	    0.987569	-51
CACTGATCGAAACGGCGCGCAATACCGACG	1	118	1	AACGGCGCGC	    0.990256	-34
GGCGCGCAATACCGACGTGCTCGGGGGAGA	1	131	1	ACCGACGTGC	    0.981573	-21
          **********

Masking position 10
Map Score:   8.30547

Number of sites scoring better than the average of aligned sites = 4184
Number in coding regions = 3871
Number in noncoding regions = 313
Number of orfs with sites within 600 bp upstream = 186
Fraction of orfs with sites within 600 bp upstream = 0.0298747


Motif number 3

GGTGGTGGAGCGGCTGCGTG          	1	1	0	CGGCTGCGTG	    0.982821	-151
CCATTTCTGACAAGCGGGTGGTGGAGCGGC	1	17	0	CAAGCGGGTG	    0.768133	-135
CAGTGGACACCGGCGCCATTTCTGACAAGC	1	32	0	CGGCGCCATT	    0.860845	-120
CTGACGCACTCAGCGCAGTGGACACCGGCG	1	47	0	CAGCGCAGTG	    0.992557	-105
GCGCTGAGTGCGTCAGAGTGCCCGGAAAGG	1	61	1	CGTCAGAGTG	    0.924371	-91
AGTGCCCGGAAAGGGGAATGACGAGCTGCG	1	77	1	AAGGGGAATG	    0.925195	-75
TGGCCGGGAAAAACGCAGCTCGTCATTCCC	1	90	0	AAACGCAGCT	    0.735511	-62
CGTTTCGATCAGTGGCCGGGAAAAACGCAG	1	102	0	AGTGGCCGGG	    0.889807	-50
CCACTGATCGAAACGGCGCGCAATACCGAC	1	117	1	AAACGGCGCG	    0.966795	-35
CCGACGTGCTCGGGGGAGAG          	1	142	1	CGGGGGAGAG	    0.982554	-10
          **********

Masking position 8
Map Score:   5.92663

Number of sites scoring better than the average of aligned sites = 5865
Number in coding regions = 5286
Number in noncoding regions = 579
Number of orfs with sites within 600 bp upstream = 295
Fraction of orfs with sites within 600 bp upstream = 0.0473819


Motif number 4

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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