Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023422.1 Corchorus olitorius cultivar O-4 contig23455, 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: 19143
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:205 original size:28 final size:28
Alignment explanation
Indices: 158--234 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
148 TCTGTTTTAC
* *
158 TTGTTGAATTGGGATGATTTTGTGTG-TT
1 TTGTTGAATTGGAATAATTTTGTG-GATT
186 TTGTTGAATTGGAATAATTTTGTGGATT
1 TTGTTGAATTGGAATAATTTTGTGGATT
214 TTGTTGAATTGGAATAATTTT
1 TTGTTGAATTGGAATAATTTT
235 TTGGGTGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (28 bp):
TTGTTGAATTGGAATAATTTTGTGGATT
Found at i:794 original size:28 final size:28
Alignment explanation
Indices: 747--823 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
737 TCTGTTTTAC
* *
747 TTGTTGAATTGGGATGATTTTGTGTG-TT
1 TTGTTGAATTGGAATAATTTTGTG-GATT
775 TTGTTGAATTGGAATAATTTTGTGGATT
1 TTGTTGAATTGGAATAATTTTGTGGATT
803 TTGTTGAATTGGAATAATTTT
1 TTGTTGAATTGGAATAATTTT
824 TTGGGTGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (28 bp):
TTGTTGAATTGGAATAATTTTGTGGATT
Found at i:3386 original size:34 final size:34
Alignment explanation
Indices: 3343--3413 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
3333 GGAGGAGGAG
3343 GAGCAAACAAACAACTAAGCGAGAAAACTAAAGA
1 GAGCAAACAAACAACTAAGCGAGAAAACTAAAGA
*
3377 GAGCAAACAAATAACTAAGCGAGAAAACTAAAGA
1 GAGCAAACAAACAACTAAGCGAGAAAACTAAAGA
3411 GAG
1 GAG
3414 AATAGAGGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.58, C:0.15, G:0.20, T:0.07
Consensus pattern (34 bp):
GAGCAAACAAACAACTAAGCGAGAAAACTAAAGA
Found at i:4522 original size:34 final size:34
Alignment explanation
Indices: 4484--4553 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
4474 AAATATTTTA
*
4484 TTTTTACCATTTTACTATTTTAATTAAAAAAAAC
1 TTTTTACCATTTCACTATTTTAATTAAAAAAAAC
4518 TTTTTACCATTTCACTATTTTAATTAAAAAAAAC
1 TTTTTACCATTTCACTATTTTAATTAAAAAAAAC
4552 TT
1 TT
4554 AGATATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (34 bp):
TTTTTACCATTTCACTATTTTAATTAAAAAAAAC
Found at i:5339 original size:29 final size:28
Alignment explanation
Indices: 5296--5352 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
5286 CTATCTAATG
*
5296 AAGTACTAGAATTTATTTTAACAAAAAAA
1 AAGTACTAGAATTTATTCTAA-AAAAAAA
* *
5325 AAGTACTATACTTTATTCTAAAAAAAAA
1 AAGTACTAGAATTTATTCTAAAAAAAAA
5353 TTTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (28 bp):
AAGTACTAGAATTTATTCTAAAAAAAAA
Found at i:5470 original size:47 final size:47
Alignment explanation
Indices: 5417--5509 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
5407 TATTTAGTGT
5417 ATTGCTAGTTTAATTTATTTGAGTGTGTAACAAGAATTTAAAGTTTA
1 ATTGCTAGTTTAATTTATTTGAGTGTGTAACAAGAATTTAAAGTTTA
5464 ATTGCTAGTTTAATTTATTTGAGTGTGTAACAAGAATTTAAAGTTT
1 ATTGCTAGTTTAATTTATTTGAGTGTGTAACAAGAATTTAAAGTTT
5510 TTTAAAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.45
Consensus pattern (47 bp):
ATTGCTAGTTTAATTTATTTGAGTGTGTAACAAGAATTTAAAGTTTA
Found at i:9619 original size:5 final size:5
Alignment explanation
Indices: 9609--9644 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
9599 CAGGAAAGAA
9609 AAAAG AAAAG AAAAG AAAAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG AAAA
9645 AAGATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 24 0.83
7 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:9620 original size:12 final size:12
Alignment explanation
Indices: 9603--9648 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
9593 CTCTTACAGG
9603 AAAGAAAAAAGA
1 AAAGAAAAAAGA
9615 AAAG--AAAAGA
1 AAAGAAAAAAGA
9625 AAA-AAGAAAAGA
1 AAAGAA-AAAAGA
9637 AAAGAAAAAAGA
1 AAAGAAAAAAGA
9649 TCTTTAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.30
12 19 0.63
13 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:9625 original size:17 final size:17
Alignment explanation
Indices: 9603--9648 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
9593 CTCTTACAGG
9603 AAAGAAAAAAGAAAAGA
1 AAAGAAAAAAGAAAAGA
9620 AAAGAAAAAAGAAAAGA
1 AAAGAAAAAAGAAAAGA
9637 AAAGAAAAAAGA
1 AAAGAAAAAAGA
9649 TCTTTAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAGA
Found at i:11001 original size:20 final size:20
Alignment explanation
Indices: 10978--11048 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
10968 CCGACCAATT
10978 TTGCAACGACCCGAGAGATG
1 TTGCAACGACCCGAGAGATG
* *
10998 TTGCAACAACCCGAGGGATG
1 TTGCAACGACCCGAGAGATG
* *
11018 TTGTAACGACCCGAGAGATA
1 TTGCAACGACCCGAGAGATG
11038 TTGCAACGACC
1 TTGCAACGACC
11049 AATGGGAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (20 bp):
TTGCAACGACCCGAGAGATG
Found at i:19053 original size:16 final size:15
Alignment explanation
Indices: 19015--19056 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
19005 ACAGAGGTTG
19015 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
19030 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
19045 ACTAGAAAACAA
1 AC-AGAAAACAA
19057 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.