Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020231.1 Corchorus olitorius cultivar O-4 contig20264, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34031
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:4240 original size:24 final size:24
Alignment explanation
Indices: 4208--4266 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
4198 GCTTCCTTCC
4208 GTTCCTCCTCCCCCTCCCCCAACT
1 GTTCCTCCTCCCCCTCCCCCAACT
*
4232 GTTCCTCCTCCTCCTCCCCCAACT
1 GTTCCTCCTCCCCCTCCCCCAACT
*
4256 GTTCCGCCTCC
1 GTTCCTCCTCC
4267 AGCTCTTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.07, C:0.59, G:0.07, T:0.27
Consensus pattern (24 bp):
GTTCCTCCTCCCCCTCCCCCAACT
Found at i:17223 original size:24 final size:24
Alignment explanation
Indices: 17191--17239 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17181 CTGTAGTGCC
17191 AGAGTCCAAATTAAGATGATTTGA
1 AGAGTCCAAATTAAGATGATTTGA
*
17215 AGAGTCCAAATTAAGATTATTTGA
1 AGAGTCCAAATTAAGATGATTTGA
17239 A
1 A
17240 ACCAAACTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (24 bp):
AGAGTCCAAATTAAGATGATTTGA
Found at i:27740 original size:1 final size:1
Alignment explanation
Indices: 27729--27768 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
27719 TTTTCGCAGC
* *
27729 AAAACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27769 CTCTTATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27746 original size:12 final size:12
Alignment explanation
Indices: 27729--27769 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
27719 TTTTCGCAGC
27729 AAAACAAAAAAA
1 AAAACAAAAAAA
27741 AAAACAAAAAAA
1 AAAACAAAAAAA
*
27753 AAAAAAAAAAAA
1 AAAACAAAAAAA
27765 AAAAC
1 AAAAC
27770 TCTTATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAA
Found at i:33233 original size:14 final size:14
Alignment explanation
Indices: 33216--33259 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
33206 TGAACAATGT
*
33216 AAAGTGAAAAAAAG
1 AAAGAGAAAAAAAG
33230 AAAGAGAAAAAAAG
1 AAAGAGAAAAAAAG
*
33244 -AAGAAGAAAAAGAG
1 AAAG-AGAAAAAAAG
33258 AA
1 AA
33260 CTATTTGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 3 0.12
14 22 0.85
15 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAAAAAG
Found at i:33647 original size:37 final size:37
Alignment explanation
Indices: 33597--33670 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
33587 CATCTAACCT
*
33597 TGTTCCAAGCACGAAATTGAGGTGAAGATCGAAATCG
1 TGTTCCAAGCACGAAATTGAGATGAAGATCGAAATCG
*
33634 TGTTCCAAGCACGAAATTGAGATGAAGATTGAAATCG
1 TGTTCCAAGCACGAAATTGAGATGAAGATCGAAATCG
33671 AGTTGACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (37 bp):
TGTTCCAAGCACGAAATTGAGATGAAGATCGAAATCG
Done.