Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011231.1 Corchorus olitorius cultivar O-4 contig11264, 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: 13089
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2013 original size:15 final size:15
Alignment explanation
Indices: 1993--2024 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1983 AAGAAGAAGG
1993 AAAGAAGAAGAAAAA
1 AAAGAAGAAGAAAAA
2008 AAAGAAGAAGAAAAA
1 AAAGAAGAAGAAAAA
2023 AA
1 AA
2025 TCTGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAAAA
Found at i:2021 original size:14 final size:14
Alignment explanation
Indices: 1982--2024 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1972 AAATAGAGAG
**
1982 GAAGAAGAAGGAAA
1 GAAGAAGAAAAAAA
1996 GAAGAAGAAAAAAAA
1 GAAGAAG-AAAAAAA
2011 GAAGAAGAAAAAAA
1 GAAGAAGAAAAAAA
2025 TCTGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAAAAA
Found at i:4627 original size:42 final size:42
Alignment explanation
Indices: 4571--4665 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
4561 ATATCCGTTG
*
4571 ATATATG-TCATACATCC-TCCATGCATCGTCCATGT-CTTTGT
1 ATATATGTTCATACATCCAT-CATGCATCATCCAT-TCCTTTGT
4612 ATATATGTTCATACATCCATCATGCATCATCCATTCCTTTGT
1 ATATATGTTCATACATCCATCATGCATCATCCATTCCTTTGT
4654 ATATATGTTCAT
1 ATATATGTTCAT
4666 GCATAGGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
41 8 0.16
42 41 0.82
43 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.41
Consensus pattern (42 bp):
ATATATGTTCATACATCCATCATGCATCATCCATTCCTTTGT
Found at i:6334 original size:17 final size:15
Alignment explanation
Indices: 6309--6353 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
6299 ATTCAAAAAA
6309 AAATC-AAATCAATC
1 AAATCAAAATCAATC
6323 AAAATCAAAAATCAAATC
1 -AAATC-AAAATC-AATC
6341 AAATCAAAATCAA
1 AAATCAAAATCAA
6354 GAGAGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 10 0.37
18 4 0.15
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATCAAAATCAATC
Found at i:6335 original size:22 final size:23
Alignment explanation
Indices: 6307--6353 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
6297 AAATTCAAAA
6307 AAAAATCAAATC-AATCAAAATC
1 AAAAATCAAATCAAATCAAAATC
6329 AAAAATCAAATCAAATCAAAATC
1 AAAAATCAAATCAAATCAAAATC
6352 AA
1 AA
6354 GAGAGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAAATCAAATCAAATCAAAATC
Found at i:6660 original size:8 final size:8
Alignment explanation
Indices: 6647--6675 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
6637 TCGAGGTGCA
6647 AAAAAAAT
1 AAAAAAAT
6655 AAAAAAAT
1 AAAAAAAT
6663 AAAAAAAT
1 AAAAAAAT
6671 AAAAA
1 AAAAA
6676 GGAGAGCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:7402 original size:50 final size:50
Alignment explanation
Indices: 6961--7401 Score: 720
Period size: 50 Copynumber: 8.8 Consensus size: 50
6951 AACAAGATTT
*
6961 CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
*
7011 CTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* *
7061 CTTTCCATTTGAGAGTTCAAGATCAAAATTCCCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
*
7111 CTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * *
7161 CTTTCCATTTGAGAGTTCAAGATTAAAATTCGCTTTTCGAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* *
7211 CTTTCCATTTATGGGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
*
7261 CTTTCCATTTGTGGGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * *
7311 CTTTCCATTTGTGAGTTCAAGATTAAAATTCGCTTTTCAAAGTAAGATTG
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
* * * *
7361 CATTCCAGTTGTGAGTCCAAGATCAAAATTCACTTTTCAAA
1 CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAA
7402 GGGCATTTAA
Statistics
Matches: 370, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 370 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (50 bp):
CTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAATAAAATTG
Found at i:8065 original size:50 final size:50
Alignment explanation
Indices: 8006--8140 Score: 180
Period size: 50 Copynumber: 2.7 Consensus size: 50
7996 TGAATGTTTC
8006 GGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAATTATCAACATA
* * * * *
8056 GGCTTTTCCACAGGGCAAACTCGTTTTCATACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAATTATCAACATA
* ** *
8106 GGCTTTTCCATAAGCCACAGTTTGTTTCCATACGA
1 GGCTTTTCCACAAGCCA-AACTAGTTTCCATACGA
8141 TACATTACCA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 59 0.82
51 13 0.18
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTAGTTTCCATACGAGTCAATTATCAACATA
Found at i:8204 original size:35 final size:34
Alignment explanation
Indices: 8158--8427 Score: 364
Period size: 35 Copynumber: 7.7 Consensus size: 34
8148 CCATCTTCTT
*
8158 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTA-ATCC
* *
8193 AGATGACTCGGTGTAGCATCTTCAAAATTATATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTA-ATCC
*
8228 AGATGACTCGGTGTAGCATCTTCAAAGATGAATCC
1 AGATGACTCGGTGTAGCATCTTCAAAG-TTAATCC
*
8263 AGATGACTCGGTGTAGCATCTTCAAAATTGAATCC
1 AGATGACTCGGTGTAGCATCTTCAAAGTT-AATCC
* *
8298 AGATGACTCAGTGTAGCATCTTC-GAGATTGAATCC
1 AGATGACTCGGTGTAGCATCTTCAAAG-TT-AATCC
*
8333 AGATGACTCGGTGTAGCATCTTCGAAA-TCGAATCC
1 AGATGACTCGGTGTAGCATCTTC-AAAGT-TAATCC
8368 AGATGACTCGGTGTAGCATCTTCAAAGTTGAATCC
1 AGATGACTCGGTGTAGCATCTTCAAAGTT-AATCC
*
8403 AGATGACTCGGTGTAACATCTTCAA
1 AGATGACTCGGTGTAGCATCTTCAA
8428 TATGGACTCA
Statistics
Matches: 213, Mismatches: 14, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
34 5 0.02
35 205 0.96
36 2 0.01
37 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (34 bp):
AGATGACTCGGTGTAGCATCTTCAAAGTTAATCC
Found at i:8340 original size:105 final size:105
Alignment explanation
Indices: 8158--8427 Score: 420
Period size: 105 Copynumber: 2.6 Consensus size: 105
8148 CCATCTTCTT
*
8158 AGATGACTCGGTGTAGCATCTTCAAAGTT-ATATTCAGATGACTCGGTGTAGCATCTTCAAAATT
1 AGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATCCAGATGACTCGGTGTAGCATCTTCAAAATT
*
8222 ATATTCAGATGACTCGGTGTAGCATCTTCAAAGAT-GAATCC
65 ATATCCAGATGACTCGGTGTAGCATCTTCAAA-ATCGAATCC
* * * *
8263 AGATGACTCGGTGTAGCATCTTCAAAATTGAATCCAGATGACTCAGTGTAGCATCTTCGAGATTG
1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAAAATT-
*
8328 A-ATCCAGATGACTCGGTGTAGCATCTTCGAAATCGAATCC
65 ATATCCAGATGACTCGGTGTAGCATCTTCAAAATCGAATCC
*
8368 AGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAACATCTTCAA
1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAA
8428 TATGGACTCA
Statistics
Matches: 151, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
104 2 0.01
105 147 0.97
106 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (105 bp):
AGATGACTCGGTGTAGCATCTTCAAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAAAATTA
TATCCAGATGACTCGGTGTAGCATCTTCAAAATCGAATCC
Found at i:8917 original size:26 final size:26
Alignment explanation
Indices: 8876--8928 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
8866 CATTTGCACA
**
8876 TTCAGGGGCATTTTGGTCATTTTAAG
1 TTCAGGGGCACATTGGTCATTTTAAG
8902 TTCAGGGGCACATTGGTCATTTTAAG
1 TTCAGGGGCACATTGGTCATTTTAAG
8928 T
1 T
8929 ACACTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCACATTGGTCATTTTAAG
Found at i:11469 original size:14 final size:14
Alignment explanation
Indices: 11450--11490 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
11440 AAATAGAGAG
**
11450 GAAGAAGAAGGAAA
1 GAAGAAGAAAAAAA
11464 GAAGAAGAAAAAAA
1 GAAGAAGAAAAAAA
11478 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
11491 TCTGAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAAAAA
Done.