Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020974.1 Corchorus olitorius cultivar O-4 contig21007, 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: 53284
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:4797 original size:15 final size:15
Alignment explanation
Indices: 4777--4807 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4767 GTGAAGATTG
4777 TTGAAAATTTGGCCT
1 TTGAAAATTTGGCCT
4792 TTGAAAATTTGGCCT
1 TTGAAAATTTGGCCT
4807 T
1 T
4808 CCTTGATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TTGAAAATTTGGCCT
Found at i:9579 original size:101 final size:100
Alignment explanation
Indices: 9469--9717 Score: 277
Period size: 101 Copynumber: 2.5 Consensus size: 100
9459 GGAACTTTCC
* * * * *
9469 CTAAATTGAAAAC-TGAAACCTGATGGGAACCTTCCCAATTTAAAAACCAGCTAAATTGAATGCT
1 CTAAATTGAAAACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAA-CAGCTAAATTGAATACT
9533 TTGAAAACTGATGGGAACTTTCCCAATTTAAAAAGAG
65 TTGAAAACTGATGGGAACTTTCCCAATTTAAAAA-AG
* * * ** **
9570 CTAAATTGAATACTTTAAAAACTGGTGGGAACTTTCCCGACCTGAAAA-ATTTAAATTGAATACT
1 CTAAATTGAAAAC-TTAAAAACTGATGGGAACTTTCCCAATTTGAAAACAGCTAAATTGAATACT
* ** * *
9634 TTGAAGACTGATGGGAACTTTCCTGATTTGAAAAAT
65 TTGAAAACTGATGGGAACTTTCCCAATTTAAAAAAG
* * *
9670 TTAAATTGAACACTTAAAAACTGATGGGAACTTTCTCAATTTGAAAAC
1 CTAAATTGAAAACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAAC
9718 TTAAACCTGA
Statistics
Matches: 121, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
99 29 0.24
100 12 0.10
101 55 0.45
103 25 0.21
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (100 bp):
CTAAATTGAAAACTTAAAAACTGATGGGAACTTTCCCAATTTGAAAACAGCTAAATTGAATACTT
TGAAAACTGATGGGAACTTTCCCAATTTAAAAAAG
Found at i:9712 original size:49 final size:50
Alignment explanation
Indices: 9488--9716 Score: 253
Period size: 50 Copynumber: 4.5 Consensus size: 50
9478 AAACTGAAAC
* * ** * *
9488 CTGATGGGAACCTTCCCAATTTAAAAACCAGCTAAATTGAATGCTTTGAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAA--ATTTAAATTGAATACTTTAAAAA
* **
9540 CTGATGGGAACTTTCCCAATTTAAAAAGAGCTAAATTGAATACTTTAAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAA-ATTTAAATTGAATACTTTAAAAA
* * ** * *
9591 CTGGTGGGAACTTTCCCGACCTGAAAAATTTAAATTGAATACTTTGAAGA
1 CTGATGGGAACTTTCCCAATTTGAAAAATTTAAATTGAATACTTTAAAAA
** *
9641 CTGATGGGAACTTTCCTGATTTGAAAAATTTAAATTGAACAC-TTAAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAAATTTAAATTGAATACTTTAAAAA
*
9690 CTGATGGGAACTTTCTCAATTTGAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAA
9717 CTTAAACCTG
Statistics
Matches: 154, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
49 29 0.19
50 56 0.36
51 43 0.28
52 26 0.17
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (50 bp):
CTGATGGGAACTTTCCCAATTTGAAAAATTTAAATTGAATACTTTAAAAA
Found at i:10394 original size:22 final size:21
Alignment explanation
Indices: 10314--10394 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 21
10304 AACTCTCAAC
10314 AAAGCCCAAATTAAATAAA-A
1 AAAGCCCAAATTAAATAAAGA
*
10334 AGGAAGCCCAACTGTAAAGAATAAAGAA
1 A--AAGCCCAAAT-T--A-AATAAAG-A
10362 AAAGGCCCAAATTAAATAAAGGA
1 AAA-GCCCAAATTAAATAAA-GA
10385 AAAGCCCAAA
1 AAAGCCCAAA
10395 GTTAGAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
20 1 0.02
22 16 0.33
23 11 0.22
24 2 0.04
25 1 0.02
26 9 0.18
27 7 0.14
28 2 0.04
ACGTcount: A:0.58, C:0.16, G:0.15, T:0.11
Consensus pattern (21 bp):
AAAGCCCAAATTAAATAAAGA
Found at i:13337 original size:22 final size:22
Alignment explanation
Indices: 13309--13350 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
13299 ATGAGCTATG
*
13309 CTAAATGCCAAAATTGAATTTA
1 CTAAATGCCAAAAGTGAATTTA
13331 CTAAATGCCAAAAGTGAATT
1 CTAAATGCCAAAAGTGAATT
13351 AGAAAATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (22 bp):
CTAAATGCCAAAAGTGAATTTA
Found at i:13485 original size:21 final size:22
Alignment explanation
Indices: 13461--13506 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
13451 GGCTTGGAAT
13461 GGTGATGGCACGG-GCATGGCC
1 GGTGATGGCACGGTGCATGGCC
* *
13482 GGTGGTGGCACGGTGGATGGCC
1 GGTGATGGCACGGTGCATGGCC
13504 GGT
1 GGT
13507 TGAGGCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (22 bp):
GGTGATGGCACGGTGCATGGCC
Found at i:18766 original size:31 final size:31
Alignment explanation
Indices: 18703--18789 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
18693 GAAAATATTC
* *
18703 AATTAGCGGCGTTTTACACCT-TAAGCGCCACT
1 AATTAGCGGCG-TTT-CAGCTGTAAACGCCACT
18735 AATTAGCGGCGTTTCAGCTGTAAACGCCACT
1 AATTAGCGGCGTTTCAGCTGTAAACGCCACT
* * * *
18766 AATTGGTGGCGTTTCTGGTGTAAA
1 AATTAGCGGCGTTTCAGCTGTAAA
18790 ATGCCGCTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.08
31 33 0.69
32 11 0.23
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (31 bp):
AATTAGCGGCGTTTCAGCTGTAAACGCCACT
Found at i:19520 original size:32 final size:32
Alignment explanation
Indices: 19478--19545 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
19468 CATTTTTGCA
*
19478 AATTAGTGGCG-TTTATTG-AGTAAAACGCCACT
1 AATTACTGGCGTTTTA-TGAAG-AAAACGCCACT
*
19510 AATTACTGGCGTTTTATGAAGAAAACGCCCCT
1 AATTACTGGCGTTTTATGAAGAAAACGCCACT
19542 AATT
1 AATT
19546 TGCAATCCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (32 bp):
AATTACTGGCGTTTTATGAAGAAAACGCCACT
Found at i:24262 original size:2 final size:2
Alignment explanation
Indices: 24255--24280 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24245 GATATAATTC
24255 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
24281 GTCTCCAAGT
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:24444 original size:2 final size:2
Alignment explanation
Indices: 24437--24481 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
24427 CAGATGCTTG
*
24437 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24478 TA TA
1 TA TA
24482 ATTCTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28769 original size:12 final size:12
Alignment explanation
Indices: 28752--28779 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28742 AATCATCCAA
28752 TGAGGGGTTTTG
1 TGAGGGGTTTTG
28764 TGAGGGGTTTTG
1 TGAGGGGTTTTG
28776 TGAG
1 TGAG
28780 AACATCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (12 bp):
TGAGGGGTTTTG
Found at i:35725 original size:15 final size:15
Alignment explanation
Indices: 35694--35735 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
35684 TCACTTTGCT
*
35694 TTGTTTTCTAATTTAA
1 TTGTTTTCT-GTTTAA
35710 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
35725 TTGCTTTCTGT
1 TTGTTTTCTGT
35736 CAACATCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:36112 original size:24 final size:22
Alignment explanation
Indices: 36083--36145 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
36073 TTGTTTTGTG
36083 TTTTGCGTCAAGAAAAAAAAATAT
1 TTTTGCGTCAA-AAAAAAAAA-AT
* *
36107 TTTTGCGT-AAAAAAAAAGAGT
1 TTTTGCGTCAAAAAAAAAAAAT
*
36128 TTTTGCGTCATAAAAAAA
1 TTTTGCGTCAAAAAAAAA
36146 TTTTGTGTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.26
22 16 0.46
23 2 0.06
24 8 0.23
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (22 bp):
TTTTGCGTCAAAAAAAAAAAAT
Found at i:36121 original size:21 final size:21
Alignment explanation
Indices: 36095--36146 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36085 TTGCGTCAAG
36095 AAAAAAAAATATTTTTGCGTA
1 AAAAAAAAATATTTTTGCGTA
* *
36116 AAAAAAAAGA-GTTTTTGCGTC
1 AAAAAAAA-ATATTTTTGCGTA
*
36137 ATAAAAAAAT
1 AAAAAAAAAT
36147 TTTGTGTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAAAAATATTTTTGCGTA
Found at i:41145 original size:29 final size:31
Alignment explanation
Indices: 41093--41152 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
41083 GAAGTTCGTG
*
41093 TTTGAAGACCATTTGAAGACTTATTTGAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
*
41124 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
41153 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTGAAGACCATTTGAAGACTTATTTCAAGA
Found at i:42536 original size:15 final size:16
Alignment explanation
Indices: 42508--42548 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
42498 TCACTTTGCT
*
42508 TTGTTTTTTAGTTTAA
1 TTGTTTTCTAGTTTAA
42524 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
*
42539 TTGCTTTCTA
1 TTGTTTTCTA
42549 TCAACCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.66
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:48889 original size:21 final size:21
Alignment explanation
Indices: 48865--48935 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
48855 CTTAAGCAAT
48865 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
48886 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
48907 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
48928 TCCAATGA
1 TCCAATGA
48936 TCTCCTAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:52255 original size:26 final size:23
Alignment explanation
Indices: 52225--52271 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
52215 CTTGAAAATT
52225 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
52251 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
52272 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Done.