Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013048.1 Corchorus olitorius cultivar O-4 contig13081, 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: 6861
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:884 original size:15 final size:15
Alignment explanation
Indices: 854--895 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
844 TTACTCTGCT
854 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
870 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
885 TTGCTTTCTGT
1 TTGTTTTCTGT
896 CAATCTCTGT
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:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4790 original size:27 final size:27
Alignment explanation
Indices: 4729--4958 Score: 85
Period size: 27 Copynumber: 8.0 Consensus size: 27
4719 GTAGCTAAAA
* *
4729 AAATAATAATAATAAATAAATAAATAAT
1 AAATAA-ATTAATAAATAAAAAAATAAT
** *
4757 AGCTAAATTAATAAATAAAAAAATAGT
1 AAATAAATTAATAAATAAAAAAATAAT
* *
4784 AAATAAA-TAGAT-AATAATTAAATTAAT
1 AAATAAATTA-ATAAATAA-AAAAATAAT
*
4811 AAATAAA-AAGATAAATAGTAAATAAATAGAT
1 AAATAAATTA-ATAAATA--AAA-AAATA-AT
* * **
4842 AGTAGTTAAATTAATAAATAAAAGAATCGT
1 A--A-ATAAATTAATAAATAAAAAAATAAT
* *
4872 AAATAAA-TAGAT-AATAATTAAATTAAT
1 AAATAAATTA-ATAAATAA-AAAAATAAT
*
4899 AAATAAA-AAGATAAATAGTAAATAAATAGAT
1 AAATAAATTA-ATAAATA--AAA-AAATA-AT
*
4930 AATAGTTAAATTAATAAATAAAAGAATAA
1 AA-A--TAAATTAATAAATAAAAAAATAA
4959 GTAGTAAATA
Statistics
Matches: 151, Mismatches: 29, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
26 14 0.09
27 63 0.42
28 13 0.09
29 2 0.01
30 13 0.09
31 14 0.09
32 7 0.05
33 1 0.01
34 22 0.15
35 2 0.01
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (27 bp):
AAATAAATTAATAAATAAAAAAATAAT
Found at i:4816 original size:46 final size:45
Alignment explanation
Indices: 4726--5021 Score: 365
Period size: 46 Copynumber: 6.6 Consensus size: 45
4716 TAGGTAGCTA
* * *
4726 AAAAAATAATAATAATAAATAAATAAATAATAGCTAAATTAATAAAT
1 AAAAAAT-A-AATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
*
4773 --AAAA-AAATAGTAAATAAATAGATAATAATTAAATTAATAAAT
1 AAAAAATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
*
4815 AAAAAGATAAATAGTAAATAAATAGATAGTAGTTAAATTAATAAAT
1 AAAAA-ATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
* * *
4861 --AAAA-GAATCGTAAATAAATAGATAATAATTAAATTAATAAAT
1 AAAAAATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
4903 AAAAAGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
1 AAAAA-ATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
* *
4949 AAAAGAATAAGTAGTAAATAAATAGATGATAGTTAAA--AATAAAT
1 AAAA-AATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
* * *
4993 AAATAGATAAATAGTGAATAAATAAATAA
1 AAA-AAATAAATAGTAAATAAATAGATAA
5022 AAAAATTTTT
Statistics
Matches: 219, Mismatches: 20, Indels: 23
0.84 0.08 0.09
Matches are distributed among these distances:
42 67 0.31
43 2 0.01
44 38 0.17
45 7 0.03
46 104 0.47
47 1 0.00
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (45 bp):
AAAAAATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAAT
Found at i:4833 original size:88 final size:88
Alignment explanation
Indices: 4736--5021 Score: 423
Period size: 88 Copynumber: 3.2 Consensus size: 88
4726 AAAAAATAAT
* *
4736 AATAATAAATAAATAAATAATAGCTAAATTAATAAATAAAAAAATAGTAAATAAATAGATAATAA
1 AATAGTAAATAAATAAATAATAGTTAAATTAATAAATAAAAAAATAGTAAATAAATAGATAATAA
4801 TTAAATTAATAAATAAAAAGATA
66 TTAAATTAATAAATAAAAAGATA
* * * *
4824 AATAGTAAATAAATAGATAGTAGTTAAATTAATAAATAAAAGAATCGTAAATAAATAGATAATAA
1 AATAGTAAATAAATAAATAATAGTTAAATTAATAAATAAAAAAATAGTAAATAAATAGATAATAA
4889 TTAAATTAATAAATAAAAAGATA
66 TTAAATTAATAAATAAAAAGATA
* *
4912 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAGAATAAGTAGTAAATAAATAGATG
1 AATAGTAAATAAATAAATAATAGTTAAATTAATAAAT-AAA-AA-AA-TAGTAAATAAATAGATA
* *
4977 ATAGTTAAA--AATAAATAAATAGATA
62 ATAATTAAATTAATAAATAAAAAGATA
*
5002 AATAGTGAATAAATAAATAA
1 AATAGTAAATAAATAAATAA
5022 AAAAATTTTT
Statistics
Matches: 180, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
88 118 0.66
89 3 0.02
90 34 0.19
91 2 0.01
92 23 0.13
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (88 bp):
AATAGTAAATAAATAAATAATAGTTAAATTAATAAATAAAAAAATAGTAAATAAATAGATAATAA
TTAAATTAATAAATAAAAAGATA
Found at i:4931 original size:8 final size:8
Alignment explanation
Indices: 4677--4834 Score: 51
Period size: 8 Copynumber: 20.1 Consensus size: 8
4667 ATAGGTATAG
4677 AGATAAAT
1 AGATAAAT
*
4685 AGATAAGT
1 AGATAAAT
* *
4693 AGATACAG
1 AGATAAAT
4701 AGA-ATAAT
1 AGATA-AAT
4709 AGATAAAT
1 AGATAAAT
* **
4717 AGGTAGCT
1 AGATAAAT
* *
4725 AAAAAAAT
1 AGATAAAT
4733 A-ATAATAAT
1 AGAT-A-AAT
*
4742 AAATAAAT
1 AGATAAAT
*
4750 AAAT-AAT
1 AGATAAAT
*
4757 AGCTAAATT
1 AGATAAA-T
4766 A-ATAAAT
1 AGATAAAT
* *
4773 AAAAAAAT
1 AGATAAAT
4781 AG-TAAAT
1 AGATAAAT
* *
4788 AAATAGAT
1 AGATAAAT
*
4796 A-ATAATT
1 AGATAAAT
* *
4803 AAATTAAT
1 AGATAAAT
* *
4811 AAATAAAA
1 AGATAAAT
4819 AGATAAAT
1 AGATAAAT
4827 AG-TAAAT
1 AGATAAAT
4834 A
1 A
4835 AATAGATAGT
Statistics
Matches: 109, Mismatches: 31, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
7 25 0.23
8 74 0.68
9 8 0.07
10 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:4945 original size:19 final size:18
Alignment explanation
Indices: 4810--5021 Score: 70
Period size: 19 Copynumber: 11.8 Consensus size: 18
4800 ATTAAATTAA
*
4810 TAAATAAAAAGATAAATAG
1 TAAATAAATAGAT-AATAG
*
4829 TAAATAAATAGATAGTAG
1 TAAATAAATAGATAATAG
* * *
4847 TTAAATTAATAAATAAAAG
1 -TAAATAAATAGATAATAG
*
4866 -AATCGTAAAT--A-AATAG
1 TAA--ATAAATAGATAATAG
* * *
4882 -ATAATAATTA-A-ATTAA
1 TA-AATAAATAGATAATAG
*
4898 TAAATAAAAAGATAAATAG
1 TAAATAAATAGAT-AATAG
4917 TAAATAAATAGATAATAG
1 TAAATAAATAGATAATAG
* * *
4935 TTAAATTAATAAATAAAAG
1 -TAAATAAATAGATAATAG
*
4954 --AATAAGTAG-TAA-A-
1 TAAATAAATAGATAATAG
* * *
4967 TAAATAGATGATAGTTAAAAA
1 TAAATA-A--ATAGATAATAG
4988 TAAATAAATAGATAAATAG
1 TAAATAAATAGAT-AATAG
* *
5007 TGAATAAATAAATAA
1 TAAATAAATAGATAA
5022 AAAAATTTTT
Statistics
Matches: 144, Mismatches: 30, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.01
15 11 0.08
16 22 0.15
17 6 0.04
18 19 0.13
19 77 0.53
20 2 0.01
21 6 0.04
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (18 bp):
TAAATAAATAGATAATAG
Found at i:4966 original size:27 final size:27
Alignment explanation
Indices: 4871--5006 Score: 80
Period size: 27 Copynumber: 5.4 Consensus size: 27
4861 AAAAGAATCG
*
4871 TAAATAAATAGATAATAATTAAAT---
1 TAAATAAATAGATAATAGTTAAATAAA
* *
4895 T-AATAAATA-A-AA-AGATAAAT-AG
1 TAAATAAATAGATAATAGTTAAATAAA
*
4917 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAATAGTTAAATAAA
4944 TAAATAAA-AGAATAAGTAG-TAAATAAA
1 TAAATAAATAG-ATAA-TAGTTAAATAAA
* * * **
4971 TAGAT-GATAGTTAA-AAATAAATAAA
1 TAAATAAATAGATAATAGTTAAATAAA
*
4996 TAGATAAATAG
1 TAAATAAATAG
5007 TGAATAAATA
Statistics
Matches: 90, Mismatches: 10, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.07
21 2 0.02
22 2 0.02
23 16 0.18
24 3 0.03
25 15 0.17
26 17 0.19
27 26 0.29
28 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (27 bp):
TAAATAAATAGATAATAGTTAAATAAA
Found at i:6371 original size:35 final size:35
Alignment explanation
Indices: 6326--6687 Score: 404
Period size: 35 Copynumber: 10.0 Consensus size: 35
6316 ATCAATGTGA
*
6326 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
** *
6361 AGATCAACTCTGATCATAAAAAAAAAAAAAAGCTTCTTGAAAGG
1 AGATCAACTCTGATCAT--------CGAAAA-CTTCTTGAAATG
* **
6405 AGATCAACTCTGACCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCGAAAACTTCTTGAAATG
* * *
6442 AGATCAACTCTCATCAACGAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTC-TTGAAATG
6477 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* * *
6512 AGATCAACTCTGACCAT-AAAAACATCTTGAATATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAA-ATG
** * *
6547 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
6582 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
6617 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
6652 AGATCAACTCTGATCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
6687 A
1 A
6688 CCGCACTGGA
Statistics
Matches: 282, Mismatches: 30, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
34 14 0.05
35 194 0.69
36 14 0.05
37 24 0.09
38 6 0.02
43 4 0.01
44 24 0.09
46 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:6398 original size:44 final size:43
Alignment explanation
Indices: 6345--6429 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 43
6335 CTGATCATCG
* *
6345 AAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAAAA
1 AAAACTTCTTGAAAGAAGATCAACTCTGACCATAAAAAAAAAA
* *
6388 AAAAGCTTCTTGAAAGGAGATCAACTCTGACCATATAAAAAA
1 AAAA-CTTCTTGAAAGAAGATCAACTCTGACCATAAAAAAAA
6430 CTTCTTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAACTTCTTGAAAGAAGATCAACTCTGACCATAAAAAAAAAA
Found at i:6734 original size:54 final size:54
Alignment explanation
Indices: 6652--6811 Score: 266
Period size: 54 Copynumber: 3.0 Consensus size: 54
6642 TCTTGAAACG
* * *
6652 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTCA
* *
6706 AGATCAACTCTGACCATTGAAAACTTCTTGGAACGACCGCAATGGATCATCTCA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTCA
*
6760 GGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCT
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCT
6812 TAACACCTGT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTCA
Done.