AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i297_mixed12_tpal_reg_100.orf -o297_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	RTP00388	141	AE000520
#2	RTP00389	73	AE000520
#3	RTP00834	177	AE000520

Motif number 1

GCTCGATTTTTCTGTGGAAGAGAATA     	1	6	0	TCGTGGAAGA	    0.967638	-136
ACAGAAAAATCGAGCACAAGGCCGTGCTTCC	1	22	1	CGGCACAAGG	    0.881171	-120
TTCCTGAGGATCGGCGGAAGCACGGCCTTGT	1	37	0	TCGCGGAAGC	    0.982948	-105
AACGCACTTCCGTGCGCGAGCGTGTTCTGCG	1	82	0	CGGCGCGAGC	    0.993922	-60
TTCTGCTTGACGGGTGCGAGATACAACGCAC	1	106	0	CGGTGCGAGA	    0.988287	-36
CAGTGGGAGAGCTGTGCGAGCGCTACGGACT	2	19	0	GCGTGCGAGC	    0.995931	-55
TGCGCATCGCGCAGTGGGAGAGCTGTGCGAG	2	30	0	GCGTGGGAGA	    0.987889	-44
TGCGCGATGCGCAGCACGAACATCCGTGCGA	2	48	1	GCGCACGAAC	    0.910567	-26
AGCACGAACATCCGTGCGAGCAAA       	2	60	1	TCGTGCGAGC	    0.995595	-14
      TACCGCTGTGGAAAATTTTCTCCAG	3	5	1	GCGTGGAAAA	    0.803977	-173
GCCTGGGTAATGAGCTGGAGAAAATTTTCCA	3	19	0	TGGCTGGAGA	     0.86623	-159
CGAAAGTAGATGGGTACGCGCCTGGGTAATG	3	38	0	TGGTACGCGC	    0.908237	-140
GGAAAAATCTTGCGTACAAGGTACGCAAATT	3	70	1	TGGTACAAGG	    0.898193	-108
          ** ********

Masking position 4
Map Score:   21.2097

Number of sites scoring better than the average of aligned sites = 2355
Number in coding regions = 2183
Number in noncoding regions = 172
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


Motif number 2

GCTCGCGCACGGAAGTGCGTTGTATCTCGC	1	92	1	GGAAGTGCGT	    0.978237	-50
     CCACCGCAAGTCCGTAGCGCTCGCA	2	6	1	GCAAGTCCGT	    0.986508	-68
TTGCTCGCACGGATGTTCGTGCTGCGCATC	2	53	0	GGATGTTCGT	    0.978262	-21
 TACCGCTGTGGAAAATTTTCTCCAGCTCA	3	10	1	GGAAAATTTT	    0.812004	-168
TACCTTGTACGCAAGATTTTTCCCCGAAAG	3	63	0	GCAAGATTTT	    0.968472	-115
TACAAGGTACGCAAATTTGTTGAAGACATT	3	84	1	GCAAATTTGT	    0.943532	-94
AAAACGTGCGGCATGTTCGTTTTTTTGGAA	3	141	0	GCATGTTCGT	    0.986513	-37
   TCGATTTGCAAGAATTTAAAACGTGCG	3	161	0	GCAAGAATTT	    0.883446	-17
          **********

Masking position 3
Map Score:   8.8744

Number of sites scoring better than the average of aligned sites = 331
Number in coding regions = 321
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

GATTTTTCTGTGGAAGAGAATA        	1	3	0	TGGAAGAGAA	    0.840617	-139
TGAGGATCGGCGGAAGCACGGCCTTGTGCT	1	34	0	CGGAAGCACG	    0.978753	-108
CACTTCCGTGCGCGAGCGTGTTCTGCGTGG	1	79	0	CGCGAGCGTG	    0.982412	-63
CGCTCGCGCACGGAAGTGCGTTGTATCTCG	1	91	1	CGGAAGTGCG	    0.954692	-51
TTCTGCTTGACGGGTGCGAGATACAACGCA	1	107	0	CGGGTGCGAG	    0.976136	-35
GGGAGAGCTGTGCGAGCGCTACGGACTTGC	2	16	0	TGCGAGCGCT	     0.98699	-58
CATCGCGCAGTGGGAGAGCTGTGCGAGCGC	2	27	0	TGGGAGAGCT	    0.978402	-47
CGAACATCCGTGCGAGCAAA          	2	64	1	TGCGAGCAAA	    0.878044	-10
CGAAAGTAGATGGGTACGCGCCTGGGTAAT	3	39	0	TGGGTACGCG	    0.858605	-139
    TCGATTTGCAAGAATTTAAAACGTGC	3	162	0	TGCAAGAATT	    0.501825	-16
          **********

Masking position 2
Map Score:   9.4891

Number of sites scoring better than the average of aligned sites = 2782
Number in coding regions = 2578
Number in noncoding regions = 204
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 4

CTTCCGTGCGCGAGCGTGTTCTGCGTGGTG	1	77	0	CGAGCGTGTT	    0.922548	-65
CGCGCACGGAAGTGCGTTGTATCTCGCACC	1	95	1	AGTGCGTTGT	     0.95845	-47
GCGCTACGGACTTGCGGTGG          	2	1	0	CTTGCGGTGG	    0.916828	-73
TGCTGCGCATCGCGCAGTGGGAGAGCTGTG	2	34	0	CGCGCAGTGG	    0.948565	-40
TAGATGGGTACGCGCCTGGGTAATGAGCTG	3	33	0	CGCGCCTGGG	    0.980473	-145
AACAAATTTGCGTACCTTGTACGCAAGATT	3	75	0	CGTACCTTGT	    0.953428	-103
ACGTGCGGCATGTTCGTTTTTTTGGAATTC	3	138	0	TGTTCGTTTT	    0.582475	-40
ACGAACATGCCGCACGTTTTAAATTCTTGC	3	151	1	CGCACGTTTT	    0.957181	-27
          **********

Masking position 5
Map Score:   1.75694

Number of sites scoring better than the average of aligned sites = 2557
Number in coding regions = 2387
Number in noncoding regions = 170
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 5

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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