Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013919.1 Corchorus olitorius cultivar O-4 contig13952, 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: 32632
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:8945 original size:20 final size:21
Alignment explanation
Indices: 8904--8945 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
8894 AATGGTTATG
*
8904 AGGAATAAAAAATGAAAGAAA
1 AGGAATAAAAAATGAAACAAA
*
8925 AGGAAT-AAAAATGGAACAAA
1 AGGAATAAAAAATGAAACAAA
8945 A
1 A
8946 CACTTTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (21 bp):
AGGAATAAAAAATGAAACAAA
Found at i:15310 original size:3 final size:3
Alignment explanation
Indices: 15298--15330 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
15288 AAAACGTCAA
15298 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
15331 CTCGTTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:17874 original size:27 final size:27
Alignment explanation
Indices: 17844--17914 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
17834 AGTGGACTTA
* *
17844 AAATTACCAAAATGCCC-CTGAATGTAC
1 AAATGACCAAAATGCCCTCTG-ATGCAC
* *
17871 AAATGACCAAAATGCCCTTTGGTGCAC
1 AAATGACCAAAATGCCCTCTGATGCAC
17898 AAATGACCAAAATGCCC
1 AAATGACCAAAATGCCC
17915 AAGGGTGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 37 0.95
28 2 0.05
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCTCTGATGCAC
Found at i:17921 original size:27 final size:27
Alignment explanation
Indices: 17869--17921 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
17859 CCCTGAATGT
***
17869 ACAAATGACCAAAATGCCCTTTGGTGC
1 ACAAATGACCAAAATGCCCAAGGGTGC
17896 ACAAATGACCAAAATGCCCAAGGGTG
1 ACAAATGACCAAAATGCCCAAGGGTG
17922 ATCCTAATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (27 bp):
ACAAATGACCAAAATGCCCAAGGGTGC
Found at i:19041 original size:17 final size:17
Alignment explanation
Indices: 19021--19054 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19011 GCTAATAATA
19021 ATTATGAAATAATTATT
1 ATTATGAAATAATTATT
**
19038 ATTATTCAATAATTATT
1 ATTATGAAATAATTATT
19055 CCTTAATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATGAAATAATTATT
Found at i:19550 original size:36 final size:36
Alignment explanation
Indices: 19396--19591 Score: 173
Period size: 36 Copynumber: 5.4 Consensus size: 36
19386 AAAAATGCTT
* * * *
19396 TTGATGGGAACTTTCCCACTTTGAAAACTAAAACTGAAA
1 TTGATGGGAACTTTCCCAATTTGAAAATTTAAA---AAC
* * * * *
19435 ATGACGAGAACTTTCCCTAAATTGAAAA-CT-AAAAC
1 TTGATGGGAACTTTCCC-AATTTGAAAATTTAAAAAC
* * *
19470 CTGATGGGAACTTTCCCAATTTAAAAACTTTGAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAA-TTTAAAAAC
*
19507 -TGAATGGGAACTTTCCCAATTTGAAAAGTTAAAAAC
1 TTG-ATGGGAACTTTCCCAATTTGAAAATTTAAAAAC
* *
19543 TTGATGGGAATTTTCTCAATTTGAAAATTTAAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAATTTAAAAAC
*
19579 TTGTTGGGAACTT
1 TTGATGGGAACTT
19592 AACTAAAACC
Statistics
Matches: 129, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
34 8 0.06
35 16 0.12
36 51 0.40
37 30 0.23
38 2 0.02
39 14 0.11
40 8 0.06
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (36 bp):
TTGATGGGAACTTTCCCAATTTGAAAATTTAAAAAC
Found at i:19591 original size:72 final size:72
Alignment explanation
Indices: 19397--19579 Score: 187
Period size: 73 Copynumber: 2.5 Consensus size: 72
19387 AAAATGCTTT
* *
19397 TGATGGGAACTTTCCCACTTTGAAAAC--T-AAAACTGAAAATGACGAGAACTTTCCCTAAATTG
1 TGATGGGAACTTTCCCAATTTAAAAACTTTAAAAACTG--AATG--G-GAACTTTCCCTAAATTG
19459 AAAACTAAAACC
61 AAAACTAAAACC
* *
19471 TGATGGGAACTTTCCCAATTTAAAAACTTTGAAAACTGAATGGGAACTTTCCC-AATTTGAAAAG
1 TGATGGGAACTTTCCCAATTTAAAAACTTTAAAAACTGAATGGGAACTTTCCCTAAATTGAAAA-
* *
19535 TTAAAAACT
65 CT-AAAACC
* * *
19544 TGATGGGAATTTTCTCAATTTGAAAA-TTTAAAAACT
1 TGATGGGAACTTTCCCAATTTAAAAACTTTAAAAACT
19580 TGTTGGGAAC
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
71 9 0.09
72 20 0.21
73 29 0.31
74 25 0.26
75 4 0.04
76 1 0.01
77 7 0.07
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (72 bp):
TGATGGGAACTTTCCCAATTTAAAAACTTTAAAAACTGAATGGGAACTTTCCCTAAATTGAAAAC
TAAAACC
Found at i:19708 original size:39 final size:39
Alignment explanation
Indices: 19637--19740 Score: 93
Period size: 39 Copynumber: 2.7 Consensus size: 39
19627 ACTAAAACCT
* * * * **
19637 GAAC-TTTCCCAATTTGAAAACTTCTAAAAAACTTGATGG
1 GAACTTTTCCAAAATTGAAAACTT-TGAAAAACTGGACAG
* *
19676 GAACTTTTCCAAAATTGAAAACTTTGATAAACTGGACAT
1 GAACTTTTCCAAAATTGAAAACTTTGAAAAACTGGACAG
* * *
19715 GATCTTTCCCTAAATTGAAAACTTTG
1 GAACTTTTCCAAAATTGAAAACTTTG
19741 GAAATTTCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 36 0.68
40 17 0.32
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (39 bp):
GAACTTTTCCAAAATTGAAAACTTTGAAAAACTGGACAG
Found at i:24713 original size:3 final size:3
Alignment explanation
Indices: 24705--24738 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
24695 GATTAGTTCC
24705 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
24739 TTTTTTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:25434 original size:33 final size:33
Alignment explanation
Indices: 25392--25473 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
25382 TCTTTCAGCC
25392 TTGAGGATGGTTTCCTGGAAGACAATACCATGA
1 TTGAGGATGGTTTCCTGGAAGACAATACCATGA
25425 TTGAGGATGGTTTCCTGGAAGACAATACCATGA
1 TTGAGGATGGTTTCCTGGAAGACAATACCATGA
25458 TTGAGGATGGTTTCCT
1 TTGAGGATGGTTTCCT
25474 TGCAGTTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (33 bp):
TTGAGGATGGTTTCCTGGAAGACAATACCATGA
Found at i:32510 original size:28 final size:28
Alignment explanation
Indices: 32470--32525 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
32460 TGTTGTGGTA
32470 TAATTGGTATGGAATTGATTATCATTTG
1 TAATTGGTATGGAATTGATTATCATTTG
* *
32498 TAATTGGTTTGGACTTGATTATCATTTG
1 TAATTGGTATGGAATTGATTATCATTTG
32526 GTGTAGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.21, T:0.48
Consensus pattern (28 bp):
TAATTGGTATGGAATTGATTATCATTTG
Done.