Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012798.1 Corchorus olitorius cultivar O-4 contig12831, 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: 17314
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:174 original size:100 final size:100
Alignment explanation
Indices: 1--188 Score: 349
Period size: 100 Copynumber: 1.9 Consensus size: 100
*
1 TTAGATTCATTTTCAGCTGTTAAACAATCTCATGATTGTAACATTGATTTTTCTAGCAATGGGGT
1 TTAGATTCATTTTCAGCTGTTAAACAATCTCACGATTGTAACATTGATTTTTCTAGCAATGGGGT
*
66 GTTTTAGAAATAGTGAATTATGGTATATATAATAA
66 GTTTTAGAAATAGTGAACTATGGTATATATAATAA
*
101 TTAGATTCATTTTCAGCTGTTAAACAATCTCACGATTGTCACATTGATTTTTCTAGCAATGGGGT
1 TTAGATTCATTTTCAGCTGTTAAACAATCTCACGATTGTAACATTGATTTTTCTAGCAATGGGGT
166 GTTTTAGAAATAGTGAACTATGG
66 GTTTTAGAAATAGTGAACTATGG
189 AGTAATCAAC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (100 bp):
TTAGATTCATTTTCAGCTGTTAAACAATCTCACGATTGTAACATTGATTTTTCTAGCAATGGGGT
GTTTTAGAAATAGTGAACTATGGTATATATAATAA
Found at i:1846 original size:25 final size:25
Alignment explanation
Indices: 1812--1885 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 25
1802 TCAAACAATC
*
1812 TTGAGCACTCTCGTTCAGTCTCTAT
1 TTGAGTACTCTCGTTCAGTCTCTAT
1837 TTGAGTACTCTCGTTCAGTCTCTAT
1 TTGAGTACTCTCGTTCAGTCTCTAT
* *
1862 TTGAGTACTCTCGCTCGGTCTCTA
1 TTGAGTACTCTCGTTCAGTCTCTA
1886 CAAACCAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.41
Consensus pattern (25 bp):
TTGAGTACTCTCGTTCAGTCTCTAT
Found at i:2399 original size:21 final size:21
Alignment explanation
Indices: 2370--2411 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2360 TCGCTCGGTC
*
2370 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
2390 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
2412 CACACCCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:2409 original size:25 final size:25
Alignment explanation
Indices: 2374--2465 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 25
2364 TCGGTCTCTA
2374 CAAACCAATCATCACATCTACCAAAC
1 CAAA-CAATCATCACATCTACCAAAC
*
2400 CAAACAATCACACACACCCTCCTAAACCAAACC
1 CAAACAATCA-TCACA---T-CT--ACCAAA-C
* *
2433 CAAACAATCTTGA-ATCTACCAAAC
1 CAAACAATCATCACATCTACCAAAC
2457 CAAACAATC
1 CAAACAATC
2466 TCGCTCGGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
24 10 0.19
25 12 0.22
26 8 0.15
27 2 0.04
28 1 0.02
29 1 0.02
30 2 0.04
31 1 0.02
32 7 0.13
33 10 0.19
ACGTcount: A:0.47, C:0.38, G:0.01, T:0.14
Consensus pattern (25 bp):
CAAACAATCATCACATCTACCAAAC
Found at i:2548 original size:80 final size:80
Alignment explanation
Indices: 2464--2912 Score: 263
Period size: 80 Copynumber: 5.5 Consensus size: 80
2454 AACCAAACAA
2464 TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCCA
1 TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCCA
2529 AACAATCTTGAGCAC
66 AACAATCTTGAGCAC
* * ** * *
2544 TCTCGCTCGGTCTCTACAAGCCAATCATCACATCTACCAAACCAAACAAT-C-ACA-CACACCCT
1 TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCC-
* * *
2606 TAACCAATCATCA-CA-
65 -AAACAATCTTGAGCAC
* *** * * * * * *
2621 TC-CTAC-CAAAC-CAACACACACC-CTCCT-AAACCAAACCAAACACACACCCTCCTAAACCAA
1 TCTC-GCTCGGTCTCTACA-A-ACCAATCATCACATC-TACCAAAC-CACACCCTCCTAAACCAA
2681 A-CCAAACAATC---A-CAC
61 ACCCAAACAATCTTGAGCAC
* * ** *
2696 ACAC-CTC---CTAAACCAAACCCAAACAATCTTGA-ATCTACCAAACCAAACAATCTCACACAC
1 TCTCGCTCGGTCTCTA-CAAA-CCAATC-ATC---ACATCT-----ACC--A-AA-C-CACA--C
*
2756 CCTCCTAAACCAAACCCAAACAATGTTGAGCAC
48 CCTCCTAAACCAAACCCAAACAATCTTGAGCAC
*
2789 TCTCGCTCGGTCTCTACAAATCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCCA
1 TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCCA
2854 AACAATCTTGAGCAC
66 AACAATCTTGAGCAC
* ** *
2869 TCTCACTCGGTCTCTACAAGTCAATCATCACATCTAGCAAACCA
1 TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCA
2913 AATAATCACA
Statistics
Matches: 281, Mismatches: 45, Indels: 86
0.68 0.11 0.21
Matches are distributed among these distances:
72 2 0.01
73 5 0.02
74 7 0.02
75 10 0.04
76 15 0.05
77 23 0.08
78 7 0.02
79 15 0.05
80 123 0.44
82 7 0.02
83 1 0.00
84 3 0.01
85 3 0.01
86 5 0.02
87 3 0.01
88 15 0.05
89 9 0.03
91 1 0.00
92 5 0.02
93 5 0.02
94 6 0.02
95 4 0.01
96 4 0.01
97 3 0.01
ACGTcount: A:0.38, C:0.39, G:0.05, T:0.17
Consensus pattern (80 bp):
TCTCGCTCGGTCTCTACAAACCAATCATCACATCTACCAAACCACACCCTCCTAAACCAAACCCA
AACAATCTTGAGCAC
Found at i:2651 original size:20 final size:20
Alignment explanation
Indices: 2595--2654 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2585 CCAAACAATC
2595 ACACACACCCT--T-AACCA
1 ACACACACCCTCCTAAACCA
*
2612 ATCATCACATCCTACC-AAACCA
1 A-CA-CACACCCT-CCTAAACCA
2634 ACACACACCCTCCTAAACCA
1 ACACACACCCTCCTAAACCA
2654 A
1 A
2655 ACCAAACACA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
17 1 0.03
18 2 0.06
19 9 0.26
20 14 0.41
21 2 0.06
22 6 0.18
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.13
Consensus pattern (20 bp):
ACACACACCCTCCTAAACCA
Found at i:2661 original size:30 final size:29
Alignment explanation
Indices: 2625--2721 Score: 137
Period size: 26 Copynumber: 3.3 Consensus size: 29
2615 ATCACATCCT
2625 ACCAAACCAACACACACCCTCCTAAACCAA
1 ACCAAA-CAACACACACCCTCCTAAACCAA
2655 ACC--A-AACACACACCCTCCTAAACCAA
1 ACCAAACAACACACACCCTCCTAAACCAA
2681 ACCAAACAATCACACACACCTCCTAAACCAA
1 ACCAAACAA-CACACAC-CCTCCTAAACCAA
2712 ACCCAAACAA
1 A-CCAAACAA
2722 TCTTGAATCT
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
26 25 0.41
28 2 0.03
29 2 0.03
30 10 0.16
31 14 0.23
32 8 0.13
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.07
Consensus pattern (29 bp):
ACCAAACAACACACACCCTCCTAAACCAA
Found at i:2685 original size:31 final size:31
Alignment explanation
Indices: 2625--2719 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
2615 ATCACATCCT
2625 ACCAAACC-AACACACACCCTCCT-----AA
1 ACCAAACCAAACACACACCCTCCTAAACCAA
2650 ACCAAACCAAACACACACCCTCCTAAACCAA
1 ACCAAACCAAACACACACCCTCCTAAACCAA
*
2681 ACCAAA-CAATCACACACACCTCCTAAACCAA
1 ACCAAACCAAACACACAC-CCTCCTAAACCAA
2712 ACCCAAAC
1 A-CCAAAC
2720 AATCTTGAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
25 8 0.13
26 15 0.25
30 10 0.17
31 22 0.37
32 5 0.08
ACGTcount: A:0.47, C:0.45, G:0.00, T:0.07
Consensus pattern (31 bp):
ACCAAACCAAACACACACCCTCCTAAACCAA
Found at i:2712 original size:57 final size:57
Alignment explanation
Indices: 2625--2777 Score: 170
Period size: 56 Copynumber: 2.7 Consensus size: 57
2615 ATCACATCCT
**
2625 ACCAAACCAA-CACACAC-CCTCCTAAACCAAACCAAACACACACCCT-CCTAAACCAA
1 ACCAAA-CAATCACACACACCTCCTAAACCAAACCAAACACA-ACCCTGAATAAACCAA
* * * **
2681 ACCAAACAATCACACACACCTCCTAAACCAAACCCAA-ACAATCTTGAATCTACCAA
1 ACCAAACAATCACACACACCTCCTAAACCAAACCAAACACAACCCTGAATAAACCAA
*
2737 ACCAAACAATCTCACACACCCTCCTAAACCAAACCCAAACA
1 ACCAAACAATCACACACA-CCTCCTAAACCAAA-CCAAACA
2778 ATGTTGAGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
55 6 0.07
56 39 0.48
57 32 0.39
58 4 0.05
59 1 0.01
ACGTcount: A:0.46, C:0.42, G:0.01, T:0.10
Consensus pattern (57 bp):
ACCAAACAATCACACACACCTCCTAAACCAAACCAAACACAACCCTGAATAAACCAA
Found at i:2736 original size:56 final size:57
Alignment explanation
Indices: 2676--2784 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 57
2666 ACCCTCCTAA
2676 ACCAAACCAAACAATCACACACA-CCTCCTAAACCAAACCCAAACAATCTTGAATCT
1 ACCAAACCAAACAATCACACACACCCTCCTAAACCAAACCCAAACAATCTTGAATCT
* *
2732 ACCAAACCAAACAATCTCACACACCCTCCTAAACCAAACCCAAACAATGTTGA
1 ACCAAACCAAACAATCACACACACCCTCCTAAACCAAACCCAAACAATCTTGA
2785 GCACTCTCGC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 22 0.44
57 28 0.56
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.14
Consensus pattern (57 bp):
ACCAAACCAAACAATCACACACACCCTCCTAAACCAAACCCAAACAATCTTGAATCT
Found at i:4335 original size:32 final size:32
Alignment explanation
Indices: 4294--4359 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
4284 GCTACCCAAC
4294 CATGGAGGATGGGGGTGCCCTGCCATAGTCTA
1 CATGGAGGATGGGGGTGCCCTGCCATAGTCTA
4326 CATGGAGGATGGGGGTGCCCTGCCATAGTCTA
1 CATGGAGGATGGGGGTGCCCTGCCATAGTCTA
4358 CA
1 CA
4360 GCCGGGCGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (32 bp):
CATGGAGGATGGGGGTGCCCTGCCATAGTCTA
Found at i:7191 original size:45 final size:45
Alignment explanation
Indices: 7140--7231 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 45
7130 CTTGATACTT
7140 ACAATTTGTAGTAAATGAAACAGTACTCTGAAGAAGATA-AAGAAA
1 ACAATTTGTAGTAAATGAAACAGTACTCTGAAGAAGA-AGAAGAAA
7185 ACAATTTGTAGTAAATGAAACAGTACTCTGAAGAAGAAGAAGAAA
1 ACAATTTGTAGTAAATGAAACAGTACTCTGAAGAAGAAGAAGAAA
7230 AC
1 AC
7232 GGCAGACCGC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (45 bp):
ACAATTTGTAGTAAATGAAACAGTACTCTGAAGAAGAAGAAGAAA
Found at i:8055 original size:29 final size:29
Alignment explanation
Indices: 8023--8080 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
8013 ATGAAGAACA
8023 ACAAATGAAGAAGAAGAAGGAGAGCAGCG
1 ACAAATGAAGAAGAAGAAGGAGAGCAGCG
8052 ACAAATGAAGAAGAAGAAGGAGAGCAGCG
1 ACAAATGAAGAAGAAGAAGGAGAGCAGCG
8081 GTGATTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.34, T:0.03
Consensus pattern (29 bp):
ACAAATGAAGAAGAAGAAGGAGAGCAGCG
Found at i:9628 original size:20 final size:20
Alignment explanation
Indices: 9599--9636 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9589 ATCTCTAACA
*
9599 GAATACACTTGATTTTTCCG
1 GAATAAACTTGATTTTTCCG
9619 GAATAAACTTGATTTTTC
1 GAATAAACTTGATTTTTC
9637 ACCCATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
GAATAAACTTGATTTTTCCG
Found at i:15076 original size:37 final size:37
Alignment explanation
Indices: 15030--15100 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
15020 AGTTATCGGG
*
15030 AAAAAAGGACATGACTATGGAGAAGGCAGAATAGGGA
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
15067 AAAAAAGGACATGAATATGGAGAAGGCAGAATAG
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAG
15101 TACATATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.31, T:0.11
Consensus pattern (37 bp):
AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
Done.