Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021986.1 Corchorus olitorius cultivar O-4 contig22019, 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: 35720
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3863 original size:2 final size:2
Alignment explanation
Indices: 3856--3881 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3846 CATATAATCA
3856 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3882 CTCACTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11622 original size:42 final size:42
Alignment explanation
Indices: 11563--11647 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
11553 AGGTGTTTGA
11563 AGTCTTCCACCAGCTCCTATGGACCTTGCAATCTCTTCATGT
1 AGTCTTCCACCAGCTCCTATGGACCTTGCAATCTCTTCATGT
11605 AGTCTTCCACCAGCTCCTATGGACCTTGCAATCTCTTCATGT
1 AGTCTTCCACCAGCTCCTATGGACCTTGCAATCTCTTCATGT
11647 A
1 A
11648 TTAAAAGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.33
Consensus pattern (42 bp):
AGTCTTCCACCAGCTCCTATGGACCTTGCAATCTCTTCATGT
Found at i:12278 original size:27 final size:27
Alignment explanation
Indices: 12236--12309 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
12226 TAGTGGACTT
* *
12236 AAAATGACCAACATGCCCCTGAATATG
1 AAAATGACCAAAATGCCCCTGAATATA
* * *
12263 CAAATGACCAAAATG-CCCTTAGTATA
1 AAAATGACCAAAATGCCCCTGAATATA
12289 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
12310 GATAACCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 22 0.56
27 17 0.44
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATATA
Found at i:15449 original size:21 final size:21
Alignment explanation
Indices: 15422--15629 Score: 256
Period size: 21 Copynumber: 9.9 Consensus size: 21
15412 TATATGAAAC
15422 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * * *
15443 TTCGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
15464 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
15485 TTTGGGGGTTGACCATCAAAT
1 TTTGGGGTTTGACTATCAAAA
15506 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* **
15527 TTTGGGGTTTGACAATCAATC
1 TTTGGGGTTTGACTATCAAAA
15548 TTT-GGGTGTTGACTATCAAAA
1 TTTGGGGT-TTGACTATCAAAA
* * * *
15569 TTTGGGGGTTGACCATTAAAC
1 TTTGGGGTTTGACTATCAAAA
15590 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* *
15611 TTTGGGGATTGACCATCAA
1 TTTGGGGTTTGACTATCAA
15630 TGGGATTTGA
Statistics
Matches: 155, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
20 4 0.03
21 148 0.95
22 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAAAA
Found at i:15477 original size:42 final size:42
Alignment explanation
Indices: 15418--15629 Score: 345
Period size: 42 Copynumber: 5.0 Consensus size: 42
15408 GAAATATATG
*
15418 AAACTTTGGGGTTTGACTATCAAAATTCGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
15460 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* * *
15502 AAATTTTGGGGTTTGACTATCAAAATTTGGGGTTTGACAATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* *
15544 AATCTTT-GGGTGTTGACTATCAAAATTTGGGGGTTGACCATT
1 AAACTTTGGGGT-TTGACTATCAAAATTTGGGGGTTGACCATC
*
15586 AAACTTTGGGGTTTGACTATCAAAATTTGGGGATTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
15628 AA
1 AA
15630 TGGGATTTGA
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 4 0.03
42 148 0.95
43 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.34
Consensus pattern (42 bp):
AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
Found at i:15753 original size:17 final size:17
Alignment explanation
Indices: 15727--15760 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15717 TAATTAAATT
15727 TTGATAGTCAAACCCCA
1 TTGATAGTCAAACCCCA
*
15744 TTGATGGTCAAACCCCA
1 TTGATAGTCAAACCCCA
15761 CATTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (17 bp):
TTGATAGTCAAACCCCA
Found at i:16606 original size:26 final size:26
Alignment explanation
Indices: 16577--16642 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
16567 GGTTATTTAT
* **
16577 TATTATATTATTATCAAATTTGTATA
1 TATTTTATTATTAAAAAATTTGTATA
* * *
16603 TATTTTTTTGTGAAAAAATTTGTATA
1 TATTTTATTATTAAAAAATTTGTATA
16629 TATTTTATTATTAA
1 TATTTTATTATTAA
16643 TAATACTCAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
TATTTTATTATTAAAAAATTTGTATA
Found at i:28817 original size:41 final size:40
Alignment explanation
Indices: 28729--28822 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
28719 GTTTAGTCTA
* * ** *
28729 GCCCCTGATTTAGTGTAATGTTGTTAATTGCTTCAATTTT
1 GCCCCTGATTTAGAGTAATGTTATTAATTAATTCAATTTC
* * *
28769 GTCCCTGATTTAGAGTAATATTTATTTATTAATTCAATTTC
1 GCCCCTGATTTAGAGTAAT-GTTATTAATTAATTCAATTTC
28810 GCCCCTGATTTAG
1 GCCCCTGATTTAG
28823 GATTTTATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 17 0.39
41 27 0.61
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (40 bp):
GCCCCTGATTTAGAGTAATGTTATTAATTAATTCAATTTC
Found at i:31654 original size:41 final size:41
Alignment explanation
Indices: 31597--31699 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
31587 TTTTTCCGTT
* * * *
31597 TTCAATATAGTCCCTGATTTAG-GTTTATGTTTGTTAATTGA
1 TTCAATTTAGTCCCTGATTTAGAG-TAATATTTATTAATTGA
* *
31638 TTCAATTTTGTCCCTGATTTAGAGTAATATTTATTTATTGA
1 TTCAATTTAGTCCCTGATTTAGAGTAATATTTATTAATTGA
* *
31679 TTCAATTTCGCCCCTGATTTA
1 TTCAATTTAGTCCCTGATTTA
31700 AGATTTTACT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (41 bp):
TTCAATTTAGTCCCTGATTTAGAGTAATATTTATTAATTGA
Found at i:32700 original size:16 final size:15
Alignment explanation
Indices: 32662--32703 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
32652 ACAGAGGTTG
*
32662 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
32677 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
32692 ACTAGAAAACAA
1 AC-AGAAAACAA
32704 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.