Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020757.1 Corchorus olitorius cultivar O-4 contig20790, 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: 72956
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:99 original size:39 final size:42
Alignment explanation
Indices: 18--132 Score: 164
Period size: 39 Copynumber: 2.7 Consensus size: 42
8 GTTTAGAGAA
18 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTTAGATGAGGATTTGG
1 TTGCGAAGGCAAGAGAGAAGGGGAGGC-TTT--ATGAGGATTTGG
*
63 TTGCGAAGGCAAGAGAGAGGGGGAGGCTTT-T-A-GATTTGG
1 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTATGAGGATTTGG
*
102 TTGCGAAGGCAAGAGGGAAGGGGAGGCTTTA
1 TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTA
133 AAAGGATGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
39 35 0.53
40 1 0.02
41 1 0.02
44 3 0.05
45 26 0.39
ACGTcount: A:0.28, C:0.08, G:0.43, T:0.21
Consensus pattern (42 bp):
TTGCGAAGGCAAGAGAGAAGGGGAGGCTTTATGAGGATTTGG
Found at i:353 original size:30 final size:29
Alignment explanation
Indices: 319--386 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
309 ACCGTACAGG
319 TCCCTCTACTTACTAAAA-GGATCAATTTGA
1 TCCCTCTACTTA-TAAAACGG-TCAATTTGA
* *
349 TCCCTATAC-TATAAAACTGTCAATTTGA
1 TCCCTCTACTTATAAAACGGTCAATTTGA
*
377 TCCATCTACT
1 TCCCTCTACT
387 AACAATTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 21 0.66
29 3 0.09
30 8 0.25
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.35
Consensus pattern (29 bp):
TCCCTCTACTTATAAAACGGTCAATTTGA
Found at i:861 original size:42 final size:42
Alignment explanation
Indices: 814--901 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
804 TGTGTGTGAT
814 AGAAGTTAGGTTGGATGGGGTTTTAGTGGATTGATGATTATG
1 AGAAGTTAGGTTGGATGGGGTTTTAGTGGATTGATGATTATG
856 AGAAGTTAGGTTGGATGGGGTTTTAGTGGATTGATGATTATG
1 AGAAGTTAGGTTGGATGGGGTTTTAGTGGATTGATGATTATG
898 AGAA
1 AGAA
902 TGCTGAATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (42 bp):
AGAAGTTAGGTTGGATGGGGTTTTAGTGGATTGATGATTATG
Found at i:7795 original size:35 final size:35
Alignment explanation
Indices: 7754--7857 Score: 144
Period size: 35 Copynumber: 3.0 Consensus size: 35
7744 TCTTTCCATA
7754 ATCAAACTTTTAAATCTTTAAAATCC-CGGAATAAT
1 ATCAAACTTTTAAATCTTTAAAATCCTC-GAATAAT
* *
7789 ATCAAACTTTTAAATCTCTAAATTCCTCG---AAT
1 ATCAAACTTTTAAATCTTTAAAATCCTCGAATAAT
7821 ATCAAACTTTTAAATCTTTAAAAATCCTCGAATAAT
1 ATCAAACTTTTAAATCTTT-AAAATCCTCGAATAAT
7857 A
1 A
7858 GTTACTCGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
32 21 0.35
33 9 0.15
35 25 0.42
36 5 0.08
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (35 bp):
ATCAAACTTTTAAATCTTTAAAATCCTCGAATAAT
Found at i:7914 original size:68 final size:69
Alignment explanation
Indices: 7822--7957 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 69
7812 TCCTCGAATA
* * *
7822 TCAAACTTTTAAATCTTTAAAAATCCTCGAATAATAGTTACTCGAACTTTAAAGTGAAGAGATGC
1 TCAAACATTTAAATCTTTAAAAATCCTCAAATAATAGTTACTCAAACTTTAAAGTGAAGAGATGC
7887 ATAC
66 ATAC
7891 TCAAACATTTAAATCTTT-AAAATCCTCAAATAATAGTTACTCAAACTTTAAAGTGAAGAGATGC
1 TCAAACATTTAAATCTTTAAAAATCCTCAAATAATAGTTACTCAAACTTTAAAGTGAAGAGATGC
7955 ATA
66 ATA
7958 ATAGGTACTC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 47 0.73
69 17 0.27
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (69 bp):
TCAAACATTTAAATCTTTAAAAATCCTCAAATAATAGTTACTCAAACTTTAAAGTGAAGAGATGC
ATAC
Found at i:8134 original size:90 final size:86
Alignment explanation
Indices: 8039--8203 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 86
8029 GGATTTAAGC
*
8039 CCTACATAAGTTTAGAGACTCTATCCTAATAGAAAAC-AAAAGAGCATTTACAGGATTAAAGTAG
1 CCTACATAAGTTCAGAGA--CTATCCTAATAGAAAACAAAAAGAGCATTTACAGGATT-AA--AG
8103 TTCACATATCCTGCTAAATTAGAAGG
61 TTCACATATCCTGCTAAATTAGAAGG
*
8129 CCTACATAAGTTCAGAGACTATCCTAATAGGAAACAAAAAGAGCATTTACAGGATTAAAGTTCAC
1 CCTACATAAGTTCAGAGACTATCCTAATAGAAAACAAAAAGAGCATTTACAGGATTAAAGTTCAC
8194 ATATCCTGCT
66 ATATCCTGCT
8204 GTTACATGCC
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
86 17 0.24
88 18 0.25
89 20 0.28
90 17 0.24
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (86 bp):
CCTACATAAGTTCAGAGACTATCCTAATAGAAAACAAAAAGAGCATTTACAGGATTAAAGTTCAC
ATATCCTGCTAAATTAGAAGG
Found at i:9476 original size:29 final size:29
Alignment explanation
Indices: 9439--9495 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9429 GAGTAATAAG
*
9439 TTTAGCATTACTAAAAAAGCATCTGAAAA
1 TTTAACATTACTAAAAAAGCATCTGAAAA
**
9468 TTTAACATTACTTGAAAAGCATCTGAAA
1 TTTAACATTACTAAAAAAGCATCTGAAA
9496 TTGAGAGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (29 bp):
TTTAACATTACTAAAAAAGCATCTGAAAA
Found at i:9791 original size:15 final size:15
Alignment explanation
Indices: 9771--9803 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9761 TTTTTTCCCT
9771 AAATCTCAGAAATTC
1 AAATCTCAGAAATTC
9786 AAATCTCAGAAATTC
1 AAATCTCAGAAATTC
9801 AAA
1 AAA
9804 ACCCTAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (15 bp):
AAATCTCAGAAATTC
Found at i:10005 original size:19 final size:19
Alignment explanation
Indices: 9978--10017 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9968 ATGGAATAAA
*
9978 AGTAAAAAAACAGAAAAAG
1 AGTAAAAAAAAAGAAAAAG
* *
9997 AGTAGAAAAAAAGAGAAAG
1 AGTAAAAAAAAAGAAAAAG
10016 AG
1 AG
10018 AATGAAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (19 bp):
AGTAAAAAAAAAGAAAAAG
Found at i:28688 original size:30 final size:30
Alignment explanation
Indices: 28654--28739 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
28644 GCAAGTCTTT
*
28654 CTCAATGTCAATAGCATCTGATCCATGACC
1 CTCAATGTCAATAGCATCAGATCCATGACC
* * *
28684 CTCAATATCAACAGCATCAGATCCATTACC
1 CTCAATGTCAATAGCATCAGATCCATGACC
*
28714 TTCAATGTCAACT-GCATCAGATCCAT
1 CTCAATGTCAA-TAGCATCAGATCCAT
28740 CACCATCTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (30 bp):
CTCAATGTCAATAGCATCAGATCCATGACC
Found at i:29016 original size:21 final size:21
Alignment explanation
Indices: 28990--29056 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
28980 TGTGGCTTCC
28990 ACTGTCACT-TCCACTATCACT
1 ACTGTCACTGT-CACTATCACT
*
29011 ACTGTCACTGTCACTGTCACTAT
1 ACTGTCACTGTCACTATCAC--T
* *
29034 CACTGCCACTGTCACTAGCACT
1 -ACTGTCACTGTCACTATCACT
29056 A
1 A
29057 TGCGCCTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 18 0.47
22 2 0.05
23 1 0.03
24 17 0.45
ACGTcount: A:0.24, C:0.36, G:0.10, T:0.30
Consensus pattern (21 bp):
ACTGTCACTGTCACTATCACT
Found at i:29038 original size:18 final size:18
Alignment explanation
Indices: 29015--29055 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
29005 ATCACTACTG
*
29015 TCACTGTCACTGTCACTA
1 TCACTGCCACTGTCACTA
29033 TCACTGCCACTGTCACTA
1 TCACTGCCACTGTCACTA
*
29051 GCACT
1 TCACT
29056 ATGCGCCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.12, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTGTCACTA
Found at i:29055 original size:12 final size:12
Alignment explanation
Indices: 28988--29049 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
28978 GCTGTGGCTT
*
28988 CCACTGTCACTT
1 CCACTGTCACTG
*
29000 CCACTATCACTACTG
1 CCACTGT--C-ACTG
*
29015 TCACTGTCACTG
1 CCACTGTCACTG
* *
29027 TCACTATCACTG
1 CCACTGTCACTG
29039 CCACTGTCACT
1 CCACTGTCACT
29050 AGCACTATGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
12 30 0.75
13 1 0.03
14 1 0.03
15 8 0.20
ACGTcount: A:0.21, C:0.39, G:0.10, T:0.31
Consensus pattern (12 bp):
CCACTGTCACTG
Found at i:29336 original size:22 final size:22
Alignment explanation
Indices: 29308--29349 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29298 AAAAATAAAA
29308 ACAACAATATGATCAGATGCAG
1 ACAACAATATGATCAGATGCAG
* *
29330 ACAACAATATTATCCGATGC
1 ACAACAATATGATCAGATGC
29350 TGCAACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (22 bp):
ACAACAATATGATCAGATGCAG
Found at i:33432 original size:20 final size:22
Alignment explanation
Indices: 33407--33447 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
33397 TTTTTTTAAA
33407 TATATA-C-ATACAATTTGAAG
1 TATATAGCAATACAATTTGAAG
33427 TATATAGCAATACAATTTGAA
1 TATATAGCAATACAATTTGAA
33448 TAAGATAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (22 bp):
TATATAGCAATACAATTTGAAG
Found at i:42618 original size:43 final size:43
Alignment explanation
Indices: 42557--42642 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
42547 ATTAGTCTCG
42557 GTTTAATAAGGTCTAAGGATACTTACTCTTGGTTATATACCAT
1 GTTTAATAAGGTCTAAGGATACTTACTCTTGGTTATATACCAT
42600 GTTTAATAAGGTCTAAGGATACTTACTCTTGGTTATATACCAT
1 GTTTAATAAGGTCTAAGGATACTTACTCTTGGTTATATACCAT
42643 TTCTTGGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (43 bp):
GTTTAATAAGGTCTAAGGATACTTACTCTTGGTTATATACCAT
Found at i:47595 original size:2 final size:2
Alignment explanation
Indices: 47583--47612 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
47573 CCAGACACTG
*
47583 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47613 ATGTGGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:70728 original size:32 final size:32
Alignment explanation
Indices: 70652--70742 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
70642 CTTCTCCTTC
*
70652 AGGAGATAAAATGTCTTGAATTTAGGAAG-TTT
1 AGGAGACAAAATGTCTTGAATTTA-GAAGTTTT
*
70684 AGGAGACCAAATGTCTTGAATTTAGAAGTTTT
1 AGGAGACAAAATGTCTTGAATTTAGAAGTTTT
* *
70716 GAGGTGA-AAAATGTCCTG-ATTT-GAAGT
1 -AGGAGACAAAATGTCTTGAATTTAGAAGT
70743 CCAAGGGGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
30 5 0.10
31 8 0.15
32 34 0.65
33 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (32 bp):
AGGAGACAAAATGTCTTGAATTTAGAAGTTTT
Done.