Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024537.1 Corchorus olitorius cultivar O-4 contig24570, 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: 9490
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:2475 original size:24 final size:24
Alignment explanation
Indices: 2448--2504 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2438 AAAAATAAAA
*
2448 AAATAGGTATAGAG-ATAAATAGAT
1 AAATAGGTACAGAGAAT-AATAGAT
*
2472 AAATAGATACAGAGAATAATAGAT
1 AAATAGGTACAGAGAATAATAGAT
2496 AAATAGGTA
1 AAATAGGTA
2505 GCTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (24 bp):
AAATAGGTACAGAGAATAATAGAT
Found at i:2522 original size:30 final size:31
Alignment explanation
Indices: 2486--2567 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 31
2476 AGATACAGAG
2486 AATAATAGATAAATAGGTAGCTAAAAAAAT-
1 AATAATAGATAAATAGGTAGCTAAAAAAATA
* **
2516 AATAATAAATAAATAGATAGTAGCTAAATTAATA
1 AATAATAGATAAATAG---GTAGCTAAAAAAATA
*
2550 AATAAAAAGATAAATAGG
1 AAT-AATAGATAAATAGG
2568 AAGTAAATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
30 15 0.36
32 1 0.02
33 12 0.29
34 3 0.07
35 11 0.26
ACGTcount: A:0.61, C:0.02, G:0.12, T:0.24
Consensus pattern (31 bp):
AATAATAGATAAATAGGTAGCTAAAAAAATA
Found at i:2606 original size:27 final size:27
Alignment explanation
Indices: 2576--2627 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2566 GGAAGTAAAT
*
2576 AGAT-AATAGCTAAATTAATAAATAAGA
1 AGATAAATAG-TAAATAAATAAATAAGA
*
2603 AGATAAATAGTAAATAAATAGATAA
1 AGATAAATAGTAAATAAATAAATAA
2628 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.25
Consensus pattern (27 bp):
AGATAAATAGTAAATAAATAAATAAGA
Found at i:2616 original size:19 final size:18
Alignment explanation
Indices: 2594--2708 Score: 66
Period size: 19 Copynumber: 6.4 Consensus size: 18
2584 GCTAAATTAA
2594 TAAATAAGAAGATAAATAG
1 TAAATAA-AAGATAAATAG
2613 TAAATAAATAGAT-AATAG
1 TAAATAAA-AGATAAATAG
*
2631 TTAAA-AATAA-ATAAAAAG
1 -TAAATAA-AAGATAAATAG
*
2649 ATAAATAGTAA-ATAAATAG
1 -TAAATA-AAAGATAAATAG
* *
2668 ---ATAATAGTTAAA-AG
1 TAAATAAAAGATAAATAG
*
2682 TTAATAAAAAGATAAATAG
1 TAAAT-AAAAGATAAATAG
2701 TAAATAAA
1 TAAATAAA
2709 TAGACAATAG
Statistics
Matches: 74, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
14 3 0.04
15 7 0.09
17 4 0.05
18 28 0.38
19 32 0.43
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (18 bp):
TAAATAAAAGATAAATAG
Found at i:2645 original size:25 final size:25
Alignment explanation
Indices: 2613--2710 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 25
2603 AGATAAATAG
*
2613 TAAATAAATAGATAATAGTTAAAAA
1 TAAATAAAAAGATAATAGTTAAAAA
2638 TAAATAAAAAGATAAATAG-T--AAA
1 TAAATAAAAAGAT-AATAGTTAAAAA
*
2661 TAAAT----AGATAATAGTTAAAAG
1 TAAATAAAAAGATAATAGTTAAAAA
* *
2682 TTAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAAAAGAT-AATAGTTAA-AAA
2709 TA
1 TA
2711 GACAATAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
18 5 0.09
19 5 0.09
21 6 0.11
23 8 0.14
25 17 0.30
26 13 0.23
27 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (25 bp):
TAAATAAAAAGATAATAGTTAAAAA
Found at i:2684 original size:51 final size:44
Alignment explanation
Indices: 2550--2724 Score: 233
Period size: 44 Copynumber: 3.9 Consensus size: 44
2540 TAAATTAATA
* * * * * *
2550 AATAAAAAGATAAATAGGAAGTAAATAGATAATAGCTAAATTAATA
1 AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAA--AGTT
* * * *
2596 AATAAGAAGATAAATAGTAAATAAATAGATAATAGTTAAAAATA
1 AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAAAGTT
*
2640 AATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAAAGTT
1 AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAAAGTT
2684 AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAAA
1 AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAAA
2725 AAAATCTTTT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 85 0.70
46 36 0.30
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.25
Consensus pattern (44 bp):
AATAAAAAGATAAATAGTAAATAAATAGACAATAGTTAAAAGTT
Found at i:2717 original size:11 final size:11
Alignment explanation
Indices: 2592--2711 Score: 56
Period size: 11 Copynumber: 10.8 Consensus size: 11
2582 TAGCTAAATT
2592 AATAAATAAG-A
1 AATAAAT-AGTA
2603 AGATAAATAGTA
1 A-ATAAATAGTA
2615 AATAAATAG-A
1 AATAAATAGTA
** *
2625 TAATAGTTA-AA
1 -AATAAATAGTA
**
2636 AATAAATAAAA
1 AATAAATAGTA
2647 AGATAAATAGTA
1 A-ATAAATAGTA
2659 AATAAATAGATA
1 AATAAATAG-TA
*
2671 ATAGTTAAA-AGTT
1 A-A--TAAATAGTA
2684 AATAAA-A--A
1 AATAAATAGTA
*
2692 GATAAATAGTA
1 AATAAATAGTA
2703 AATAAATAG
1 AATAAATAG
2712 ACAATAGTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
8 5 0.06
9 1 0.01
10 12 0.14
11 38 0.44
12 21 0.24
13 3 0.03
14 2 0.02
15 4 0.05
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (11 bp):
AATAAATAGTA
Found at i:4376 original size:53 final size:54
Alignment explanation
Indices: 4294--4484 Score: 253
Period size: 54 Copynumber: 3.5 Consensus size: 54
4284 TTCTTGGAGT
* * *
4294 GACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCGAAAACTTTTTG-AAC
1 GACCACACTGGATC--ATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
* *
4348 GAGCATACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
* * * *
4402 GACCACACCGGATCATTTGAAGATCAACTCTGATCTTCAAAAACTTCTTGAAAC
1 GACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
4456 GACCACA-TCGGATCATCTGGAGATCAACT
1 GACCACACT-GGATCATCTGGAGATCAACT
4485 TTGAAAACTT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
52 2 0.02
53 31 0.25
54 89 0.73
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (54 bp):
GACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAAC
Found at i:4594 original size:53 final size:54
Alignment explanation
Indices: 4515--4651 Score: 188
Period size: 53 Copynumber: 2.6 Consensus size: 54
4505 CCGCACTCGA
* * *
4515 AAACATCTTGTAAGGACCGCACTGGATCATCTG-GAGATCAACTCTGATCATCA-
1 AAACTTCTTGGAATGACCGCACTGGATCATCTGAG-GATCAACTCTGATCATCAT
* * *
4568 AAACTTCTTTGAATGACCGCACTGGATCATCTGAGGATCAAGTCTGATCATTAT
1 AAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATCAT
*
4622 AAACTTCTTGGAATGACCACACTGGATCAT
1 AAACTTCTTGGAATGACCGCACTGGATCAT
4652 TTGAACACCT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
53 45 0.61
54 29 0.39
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (54 bp):
AAACTTCTTGGAATGACCGCACTGGATCATCTGAGGATCAACTCTGATCATCAT
Found at i:9047 original size:4 final size:4
Alignment explanation
Indices: 9040--9065 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9030 TACCAAAGGA
9040 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
9066 GTGAATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.