Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021754.1 Corchorus olitorius cultivar O-4 contig21787, 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: 29898
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:612 original size:6 final size:6
Alignment explanation
Indices: 598--691 Score: 125
Period size: 6 Copynumber: 15.7 Consensus size: 6
588 TAAAATTTTT
* * * * *
598 CTCGGA CTTGGA CTTGGA CTTGGA CTCGGA TTCGGA CTCGGA CACGGA
1 CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA
* *
646 CTTGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGAA CTCG
1 CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCGGA CTCG
692 CGGGTACCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.18, C:0.29, G:0.32, T:0.21
Consensus pattern (6 bp):
CTCGGA
Found at i:4433 original size:44 final size:45
Alignment explanation
Indices: 4319--4447 Score: 206
Period size: 45 Copynumber: 2.9 Consensus size: 45
4309 TTCTGATCTC
4319 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
4364 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
** * * *
4409 TTTG-TTGTGAAGGAGAGGATTCTGAGTTTGTTATTGATG
1 TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATG
4448 GAAAAAGATT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 30 0.38
45 49 0.62
ACGTcount: A:0.25, C:0.05, G:0.29, T:0.41
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAACAATCTGATTTTGTTCTTGATGAAGGA
Found at i:5444 original size:45 final size:45
Alignment explanation
Indices: 5387--5516 Score: 199
Period size: 45 Copynumber: 2.9 Consensus size: 45
5377 AATCTTTTTC
* * * **
5387 CATCAATAACAAACTCAGAATCCTCTCCTTCACAAACAAAT-CTAT
1 CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAATCCT-T
5432 CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAATCCTT
1 CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAATCCTT
5477 CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAA
1 CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAA
5517 GAGATCAGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 77 0.97
46 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (45 bp):
CATCAAGAACAAAATCAGATTGTTCTCCTTCACAAACAAATCCTT
Found at i:5537 original size:21 final size:22
Alignment explanation
Indices: 5513--5557 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
5503 CCTTCACAAA
5513 CAAAGAGATCAGAATCTT-CTC
1 CAAAGAGATCAGAATCTTCCTC
5534 CAAAGAGATCAGAATCTTCCTC
1 CAAAGAGATCAGAATCTTCCTC
5556 CA
1 CA
5558 CATCATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (22 bp):
CAAAGAGATCAGAATCTTCCTC
Found at i:8499 original size:33 final size:33
Alignment explanation
Indices: 8462--8802 Score: 187
Period size: 33 Copynumber: 10.6 Consensus size: 33
8452 GGTAATAATA
8462 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * * **
8495 ATTTGGTAATCAAAGTAAAAAGA-AAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
*
8527 ATTTGGTAACTAAAGT--------TAAA-TGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* *
8551 ATCTGGTAATTAAAGTCAAAAGAGTAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
* * * * **
8584 ATTTGGCAATCAAAGTAAAAAGAGAAAAAATGAA
1 ATTTGGTAATTAAAGTAAAAAGAG-TAAATTGGT
* **
8618 ATTTGGCAATTAAAACAAAAAGAGT-AATATGGT
1 ATTTGGTAATTAAAGTAAAAAGAGTAAAT-TGGT
****
8651 AAAAAG-AGATTAAAGTAAAAAGAGTAGAA-TGGT
1 ATTTGGTA-ATTAAAGTAAAAAGAGTA-AATTGGT
** * ** *
8684 AAAAT-GAAATT-TGGTAACTAAAG-TTAAA-TGGT
1 -ATTTGGTAATTAAAGTAA--AAAGAGTAAATTGGT
* *
8716 ATTCGGTAATTAGAA-TAAAAAGAGTAAATTAGT
1 ATTTGGTAATTA-AAGTAAAAAGAGTAAATTGGT
* *
8749 ATTTGGTAAATATAGTAAAAAGAGTAAAATTGGT
1 ATTTGGTAATTAAAGTAAAAAGAGT-AAATTGGT
*
8783 ATTTGATAATTAAAGTAAAA
1 ATTTGGTAATTAAAGTAAAA
8803 TTGGTAAAAA
Statistics
Matches: 231, Mismatches: 52, Indels: 49
0.70 0.16 0.15
Matches are distributed among these distances:
24 16 0.07
25 3 0.01
31 5 0.02
32 46 0.20
33 101 0.44
34 58 0.25
35 2 0.01
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28
Consensus pattern (33 bp):
ATTTGGTAATTAAAGTAAAAAGAGTAAATTGGT
Found at i:8547 original size:24 final size:24
Alignment explanation
Indices: 8520--8566 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
8510 TAAAAAGAAA
*
8520 AAATGAAATTTGGTAACTAAAGTT
1 AAATGAAATCTGGTAACTAAAGTT
** *
8544 AAATGGTATCTGGTAATTAAAGT
1 AAATGAAATCTGGTAACTAAAGT
8567 CAAAAGAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (24 bp):
AAATGAAATCTGGTAACTAAAGTT
Found at i:8656 original size:17 final size:17
Alignment explanation
Indices: 8634--8687 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
8624 CAATTAAAAC
8634 AAAAAGAGTAATATGGT
1 AAAAAGAGTAATATGGT
* **
8651 AAAAAGAG-ATTAAAGT
1 AAAAAGAGTAATATGGT
8667 AAAAAGAGTAGA-ATGGT
1 AAAAAGAGTA-ATATGGT
8684 AAAA
1 AAAA
8688 TGAAATTTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (17 bp):
AAAAAGAGTAATATGGT
Found at i:8810 original size:34 final size:33
Alignment explanation
Indices: 8712--8856 Score: 100
Period size: 33 Copynumber: 4.2 Consensus size: 33
8702 TAAAGTTAAA
* *
8712 TGGTATTCGGTAATTAGAA-TAAAAAGAGT-AAAT
1 TGGTATTTGATAATTA-AAGTAAAAAG-GTAAAAT
* * * *
8745 TAGTATTTGGTAAATATAGTAAAAAGAGTAAAAT
1 TGGTATTTGATAATTAAAGTAAAAAG-GTAAAAT
*
8779 TGGTATTTGATAATTAAAGTAAAATTGGTAAAAAGAT
1 TGGTATTTGATAATTAAAGTAAAA-AGGT--AAA-AT
8816 ATGGTATTT-AGTAATTAAAG-AAAAAGGGTAAAAT
1 -TGGTATTTGA-TAATTAAAGTAAAAA-GGTAAAAT
*
8850 TGATATT
1 TGGTATT
8857 CAGTAATCAG
Statistics
Matches: 92, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
32 1 0.01
33 29 0.32
34 28 0.30
35 4 0.04
36 3 0.03
37 10 0.11
38 17 0.18
ACGTcount: A:0.47, C:0.01, G:0.19, T:0.33
Consensus pattern (33 bp):
TGGTATTTGATAATTAAAGTAAAAAGGTAAAAT
Found at i:8855 original size:38 final size:38
Alignment explanation
Indices: 8747--8848 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 38
8737 GAGTAAATTA
* * * *
8747 GTATTTGGTAAATATAGTAAAAAGAGT--AAA-AT-TG
1 GTATTTGATAATTAAAGTAAAAAGGGTAAAAAGATATG
**
8781 GTATTTGATAATTAAAGTAAAATTGGTAAAAAGATATG
1 GTATTTGATAATTAAAGTAAAAAGGGTAAAAAGATATG
8819 GTATTT-AGTAATTAAAG-AAAAAGGGTAAAA
1 GTATTTGA-TAATTAAAGTAAAAAGGGTAAAA
8849 TTGATATTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
34 21 0.38
36 3 0.05
37 14 0.25
38 17 0.31
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (38 bp):
GTATTTGATAATTAAAGTAAAAAGGGTAAAAAGATATG
Found at i:17416 original size:21 final size:23
Alignment explanation
Indices: 17387--17430 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
17377 CTTCAGTCCT
17387 GTTTCGACCCAGA-GAAGGTCGA
1 GTTTCGACCCAGATGAAGGTCGA
*
17409 GTTT-GACCCTGATGAAGGTCGA
1 GTTTCGACCCAGATGAAGGTCGA
17431 AACAGGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (23 bp):
GTTTCGACCCAGATGAAGGTCGA
Found at i:18166 original size:31 final size:31
Alignment explanation
Indices: 18119--18179 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
18109 AGTTTTGTAA
*
18119 AACTTTTAAAATGCCTATTATA-CTCTTATTT
1 AACTTTTAAAACGCCTATTATATC-CTTATTT
*
18150 AACTTTTGAAACGCCTATTATATCCTTATT
1 AACTTTTAAAACGCCTATTATATCCTTATT
18180 GTCTAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAACGCCTATTATATCCTTATTT
Found at i:22251 original size:21 final size:21
Alignment explanation
Indices: 22225--22268 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
22215 ACCCTCCAAA
22225 CAACCATGGTAATAGCTTTGT
1 CAACCATGGTAATAGCTTTGT
22246 CAACCATGGTAATAGCTTTGT
1 CAACCATGGTAATAGCTTTGT
22267 CA
1 CA
22269 TTTTGGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (21 bp):
CAACCATGGTAATAGCTTTGT
Done.