Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019314.1 Corchorus olitorius cultivar O-4 contig19347, 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: 8979
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:578 original size:22 final size:22
Alignment explanation
Indices: 536--578 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
526 TTTCTGATTA
**
536 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
558 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
579 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Found at i:3028 original size:27 final size:27
Alignment explanation
Indices: 2975--3030 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2965 AGATTTTAAT
***
2975 AAAACTTTGATTCTCTTTGTGTCAAAA
1 AAAACTTTGATTCTCTACATGTCAAAA
3002 AAAACTTTGATTCTCTACATAGT-AAAA
1 AAAACTTTGATTCTCTACAT-GTCAAAA
3029 AA
1 AA
3031 GAAAAGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (27 bp):
AAAACTTTGATTCTCTACATGTCAAAA
Found at i:4630 original size:11 final size:11
Alignment explanation
Indices: 4613--4644 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4603 ACAGCGCAAG
4613 AAAAACAAAAC
1 AAAAACAAAAC
*
4624 GAAAACAAAAC
1 AAAAACAAAAC
4635 AAAAACAAAA
1 AAAAACAAAA
4645 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:5081 original size:390 final size:379
Alignment explanation
Indices: 4296--5036 Score: 1074
Period size: 390 Copynumber: 1.9 Consensus size: 379
4286 TTGTTTGAGC
* * *
4296 TTGTTTGACATCGTTTTTGTTTCCTGTTTTCTGTTACCAATTTCCTGTTTTTGGAAACAAAACAG
1 TTGTTTGACATCGTTTCTGTTTCCTGTTTTATGTTACCAATTTCCTGTTTTTCGAAACAAAACAG
* *
4361 TGAAAACATGTTTGGCAGGCTGTTTCTGTTTTCAAAAATTTTGGAAACAGAAGCAGTGTTTTGGA
66 TGAAAACATGTTTGGCAGGCTGTTTCCGTTTTCAAAAATTATGGAAACAGAAGCAGTGTTTTGGA
* *
4426 AAAAAGTGGAAGCAAGAAATTTTGTGTTTTCATGTTTTTCCAAAACACTTCCAAAACATATAAGC
131 AAAAAGTGGAAGCAAGAAATTTTGTGCTTTCATGTTTTTCCAAAACA---CC--AACA-AGAAGC
* * * ** *
4491 ACAATGATGAACAGTAACTCACATGCTTTTTAACCATTTTTTCTTTTACTTTTTTATTTAAAAAC
190 ACAATCATAAACAGTAACTCACATACTTTTTAACCATTTTTTCTTAAACTTATTTATTTAAAAAC
* * * *
4556 ATACAACTGAATTGTATATCCAAACATTTTTTTGTTTTCAAAAATTGACAGCGCAAGAAAAACAA
255 ATACAACTAAATTGTATATCCAAACATGTTTTTGTTTTCAAAAATTGACAGCACAACAAAAACAA
4621 AACGAAAACAAAACAAAAACAAAAAACAGAAAAACGAAAACGATGCCAAACGACCCCTTAAGGGG
320 AACG-----AAAACAAAAACAAAAAACAGAAAAACGAAAACGATGCCAAACGACCCCTTAAGGGG
* * *
4686 TTGTTTGACATTGTTTCTGTTTCCTGTTTTATGTTGCCAATTTTCTGTTTTTCGAAACAAAACAG
1 TTGTTTGACATCGTTTCTGTTTCCTGTTTTATGTTACCAATTTCCTGTTTTTCGAAACAAAACAG
* *
4751 TGAAAACATGTTTGGCAGGCTGTTTCCGTTTTCAAAAATTATGGAAACAGAATCATTGTTTTGGA
66 TGAAAACATGTTTGGCAGGCTGTTTCCGTTTTCAAAAATTATGGAAACAGAAGCAGTGTTTTGGA
4816 AAAAAGTGGAAGCAA-AAATTTTGTGCTTTCATGTTTTTCC-AAA-A-C-AC-AGAAGCACAATC
131 AAAAAGTGGAAGCAAGAAATTTTGTGCTTTCATGTTTTTCCAAAACACCAACAAGAAGCACAATC
4875 ATAAACAGTAACTCACATACATTTTT-A-CA-TTTTT-TTAAACTTATTTATTTAAAAACATACA
196 ATAAACAGTAACTCACATAC-TTTTTAACCATTTTTTCTTAAACTTATTTATTTAAAAACATACA
4936 A-TAAAATTGTATATCCAAACATGTTTTTGTTTTCAAAAAATTGACAGCACAACAAAAACAAAAC
260 ACT-AAATTGTATATCCAAACATGTTTTTGTTTTC-AAAAATTGACAGCACAACAAAAACAAAAC
5000 G-AAACAAAAACAAAAAACAGAAAAACGAAAACGATGC
323 GAAAACAAAAACAAAAAACAGAAAAACGAAAACGATGC
5037 TAAATGGCCC
Statistics
Matches: 326, Mismatches: 22, Indels: 26
0.87 0.06 0.07
Matches are distributed among these distances:
370 36 0.11
374 1 0.00
375 54 0.17
376 33 0.10
377 2 0.01
378 29 0.09
379 5 0.02
380 2 0.01
383 1 0.00
387 1 0.00
388 3 0.01
389 24 0.07
390 135 0.41
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (379 bp):
TTGTTTGACATCGTTTCTGTTTCCTGTTTTATGTTACCAATTTCCTGTTTTTCGAAACAAAACAG
TGAAAACATGTTTGGCAGGCTGTTTCCGTTTTCAAAAATTATGGAAACAGAAGCAGTGTTTTGGA
AAAAAGTGGAAGCAAGAAATTTTGTGCTTTCATGTTTTTCCAAAACACCAACAAGAAGCACAATC
ATAAACAGTAACTCACATACTTTTTAACCATTTTTTCTTAAACTTATTTATTTAAAAACATACAA
CTAAATTGTATATCCAAACATGTTTTTGTTTTCAAAAATTGACAGCACAACAAAAACAAAACGAA
AACAAAAACAAAAAACAGAAAAACGAAAACGATGCCAAACGACCCCTTAAGGGG
Found at i:8324 original size:30 final size:31
Alignment explanation
Indices: 8263--8339 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
8253 AAAAAAAAAG
*
8263 TCAGGGACCCAATTGCTCAATTAAATTCACT
1 TCAGGGACCCAATTGCTCAACTAAATTCACT
* **
8294 TCAGGGACTCAATTGCTC-ACTACGTTCACT
1 TCAGGGACCCAATTGCTCAACTAAATTCACT
*
8324 TCAGGGACCCATTTGC
1 TCAGGGACCCAATTGC
8340 ACATTTTCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (31 bp):
TCAGGGACCCAATTGCTCAACTAAATTCACT
Done.