Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015598.1 Corchorus olitorius cultivar O-4 contig15631, 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: 11083
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1598 original size:19 final size:19
Alignment explanation
Indices: 1571--1627 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1561 CTTGAGCCAG
*
1571 CCGGCTTGGCCGATCCGAA
1 CCGGTTTGGCCGATCCGAA
*
1590 CCGGTTTGGTCGGAT-CGAA
1 CCGGTTTGG-CCGATCCGAA
*
1609 CCGGTTTGACCCGATCCGA
1 CCGGTTTG-GCCGATCCGA
1628 CCCAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (19 bp):
CCGGTTTGGCCGATCCGAA
Found at i:5328 original size:20 final size:20
Alignment explanation
Indices: 5303--5343 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5293 TTGGGCTCGA
*
5303 ACCCATGGATGTATCTACTT
1 ACCCATGGATGGATCTACTT
5323 ACCCATGGATGGATCTACTT
1 ACCCATGGATGGATCTACTT
5343 A
1 A
5344 GAGCTAGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (20 bp):
ACCCATGGATGGATCTACTT
Found at i:5708 original size:27 final size:27
Alignment explanation
Indices: 5668--5746 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 27
5658 AATGGACTAT
* *
5668 AAATGACCAGAATGCCCCTAGGTGCAA
1 AAATGACCAAAATGCCCCTAGATGCAA
**
5695 AAATGACCAAAATGCCCCCTAGATTTAA
1 AAATGACCAAAATG-CCCCTAGATGCAA
*
5723 AAATGACCAAAATCCCCCTAGATG
1 AAATGACCAAAATGCCCCTAGATG
5747 ATTCTAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 22 0.49
28 23 0.51
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTAGATGCAA
Found at i:5724 original size:28 final size:28
Alignment explanation
Indices: 5668--5746 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
5658 AATGGACTAT
* *
5668 AAATGACCAGAATG-CCCCTAGGTGCAA
1 AAATGACCAAAATGCCCCCTAGATGCAA
**
5695 AAATGACCAAAATGCCCCCTAGATTTAA
1 AAATGACCAAAATGCCCCCTAGATGCAA
5723 AAATGACCAAAAT-CCCCCTAGATG
1 AAATGACCAAAATGCCCCCTAGATG
5747 ATTCTAATGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 23 0.50
28 23 0.50
ACGTcount: A:0.41, C:0.27, G:0.15, T:0.18
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCTAGATGCAA
Found at i:6296 original size:30 final size:30
Alignment explanation
Indices: 6260--6747 Score: 632
Period size: 30 Copynumber: 16.1 Consensus size: 30
6250 ACTGATGAAA
6260 CAATGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
6290 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
6320 CAATGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
6350 CAATGATCCTCAAA-CAGGATTAAAAATAAAG
1 CAATGATCCT-AAACCAGGATT-AAAATAAAG
*
6381 CAATGATCCTTAAA-CAGGATTAAAAATGAAG
1 CAATGATCC-TAAACCAGGATT-AAAATAAAG
* *
6412 CAATGATCCTCAAA-CAGTATTAAAATGAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
*
6442 CAATGATCCTCAAA-CAAGATTAAAAATAAAG
1 CAATGATCCT-AAACCAGGATT-AAAATAAAG
6473 CAATGATCCTCAAA-CAGGATTAAAATAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
* *
6503 CAACGATCCTCAAA-CAGGATTAAAGTAAAG
1 CAATGATCCT-AAACCAGGATTAAAATAAAG
*
6533 CAATGATCCTCAAA-CAAGATTAAAAATAAAG
1 CAATGATCCT-AAACCAGGATT-AAAATAAAG
* *
6564 CAATGATCCTCAACCAGGATTAAAAAAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
*
6594 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* *
6624 CAACGATCCTCAACCAGGATTAAAA-AAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* *
6653 AAATGATCCTCAACCAGGATTACAAATAAAG
1 CAATGATCCTAAACCAGGATTA-AAATAAAG
* *
6684 CAATGATCGTCAACCAGGATTAAAATAAAG
1 CAATGATCCTAAACCAGGATTAAAATAAAG
* * *
6714 CAATGATCCTCAACCAGGATTAGAATAAAA
1 CAATGATCCTAAACCAGGATTAAAATAAAG
6744 CAAT
1 CAAT
6748 CACGCAATGA
Statistics
Matches: 424, Mismatches: 25, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
29 24 0.06
30 265 0.62
31 134 0.32
32 1 0.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (30 bp):
CAATGATCCTAAACCAGGATTAAAATAAAG
Found at i:6399 original size:91 final size:91
Alignment explanation
Indices: 6260--6735 Score: 703
Period size: 91 Copynumber: 5.2 Consensus size: 91
6250 ACTGATGAAA
6260 CAATGATCCT-AAACCAGGATT-AAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAA
1 CAATGATCCTCAAA-CAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAA
6323 TGATCCTAAACCAGGATTAAAATAAAG
65 TGATCCTAAACCAGGATTAAAATAAAG
* * *
6350 CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTTAAACAGGATTAAAAATGAAGCAA
1 CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATT-AAAATAAAGCAA
* *
6415 TGATCCTCAAA-CAGTATTAAAATGAAG
65 TGATCCT-AAACCAGGATTAAAATAAAG
* * *
6442 CAATGATCCTCAAACAAGATTAAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAC
1 CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAAT
*
6507 GATCCTCAAA-CAGGATTAAAGTAAAG
66 GATCCT-AAACCAGGATTAAAATAAAG
* *
6533 CAATGATCCTCAAACAAGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAAAAAAGCAAT
1 CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAAT
*
6598 GATCCTCAACCAGGATTAAAATAAAG
66 GATCCTAAACCAGGATTAAAATAAAG
* * *
6624 CAACGATCCTCAACCAGGATT-AAAA-AAAGAAATGATCCTCAACCAGGATTACAAATAAAGCAA
1 CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTA-AAATAAAGCAA
* *
6687 TGATCGTCAACCAGGATTAAAATAAAG
65 TGATCCTAAACCAGGATTAAAATAAAG
*
6714 CAATGATCCTCAACCAGGATTA
1 CAATGATCCTCAAACAGGATTA
6736 GAATAAAACA
Statistics
Matches: 355, Mismatches: 24, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
89 25 0.07
90 79 0.22
91 166 0.47
92 82 0.23
93 3 0.01
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (91 bp):
CAATGATCCTCAAACAGGATTAAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAAT
GATCCTAAACCAGGATTAAAATAAAG
Found at i:6437 original size:61 final size:60
Alignment explanation
Indices: 6260--6747 Score: 703
Period size: 61 Copynumber: 8.1 Consensus size: 60
6250 ACTGATGAAA
*
6260 CAATGATCCT-AAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
6320 CAATGATCCT-AAACCAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAAATAAAG
1 CAATGATCCTCAAA-CAGGATTAAAATAAAGCAATGATCCTCAAACAGGATT-AAAATAAAG
* * * *
6381 CAATGATCCTTAAACAGGATTAAAAATGAAGCAATGATCCTCAAACAGTATTAAAATGAAG
1 CAATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
*
6442 CAATGATCCTCAAACAAGATTAAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
* * *
6503 CAACGATCCTCAAACAGGATTAAAGTAAAGCAATGATCCTCAAACAAGATTAAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATT-AAAATAAAG
* * *
6564 CAATGATCCTCAACCAGGATTAAAAAAAAGCAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
* * * *
6624 CAACGATCCTCAACCAGGATTAAAA-AAAGAAATGATCCTCAACCAGGATTACAAATAAAG
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTA-AAATAAAG
* * * * *
6684 CAATGATCGTCAACCAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAGAATAAAA
1 CAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
6744 CAAT
1 CAAT
6748 CACGCAATGA
Statistics
Matches: 396, Mismatches: 26, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
59 25 0.06
60 152 0.38
61 188 0.47
62 31 0.08
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.19
Consensus pattern (60 bp):
CAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAG
Found at i:7426 original size:26 final size:26
Alignment explanation
Indices: 7397--7455 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
7387 AACTGAAATG
7397 AACTGAAGAAAAGATCGCCCTGGATA
1 AACTGAAGAAAAGATCGCCCTGGATA
* *
7423 AACTGAAGAAAAGATTGCCCTGGATC
1 AACTGAAGAAAAGATCGCCCTGGATA
7449 AACTGAA
1 AACTGAA
7456 ATAAATGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (26 bp):
AACTGAAGAAAAGATCGCCCTGGATA
Found at i:7605 original size:177 final size:177
Alignment explanation
Indices: 7309--7629 Score: 579
Period size: 177 Copynumber: 1.8 Consensus size: 177
7299 AAGAAAATAC
* *
7309 CTTTGGAAAATAACTCTGAATCTGATGTTGAAATTGAAAACTTCTTGGTTGATGATGAAAGAGGA
1 CTTTGGAAAATAACTCTAAATCTGATGTTGAAATTGAAAACTTCATGGTTGATGATGAAAGAGGA
*
7374 CCAATTTGCGATCAACTGAAATGAACTGAAGAAAAGATCGCCCTGGATAAACTGAAGAAAAGATT
66 CCAATTTGCGATCAACTGAAATGAACTGAAGAAAAGATCGCCCTGGATAAACTGAAGAAAAGATC
* *
7439 GCCCTGGATCAACTGAAATAAATGGAAGAAAGACCGCCCTGGATCAA
131 CCCCTAGATCAACTGAAATAAATGGAAGAAAGACCGCCCTGGATCAA
7486 CTTTGGAAAATAACTCTAAATCTGATGTTGAAATTGAAAACTTCATGGTTGATGATGAAAGAGGA
1 CTTTGGAAAATAACTCTAAATCTGATGTTGAAATTGAAAACTTCATGGTTGATGATGAAAGAGGA
* *
7551 CCAATTTGCGGTCAACTGAAATGAACTGCAGAAAAGATCGCCCTGGATAAACTGAAGAAAAGATC
66 CCAATTTGCGATCAACTGAAATGAACTGAAGAAAAGATCGCCCTGGATAAACTGAAGAAAAGATC
7616 CCCCTAGATCAACT
131 CCCCTAGATCAACT
7630 CCCTTGGTCA
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 137 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (177 bp):
CTTTGGAAAATAACTCTAAATCTGATGTTGAAATTGAAAACTTCATGGTTGATGATGAAAGAGGA
CCAATTTGCGATCAACTGAAATGAACTGAAGAAAAGATCGCCCTGGATAAACTGAAGAAAAGATC
CCCCTAGATCAACTGAAATAAATGGAAGAAAGACCGCCCTGGATCAA
Found at i:7610 original size:26 final size:26
Alignment explanation
Indices: 7574--7629 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
7564 AACTGAAATG
* * *
7574 AACTGCAGAAAAGATCGCCCTGGATA
1 AACTGAAGAAAAGATCCCCCTAGATA
*
7600 AACTGAAGAAAAGATCCCCCTAGATC
1 AACTGAAGAAAAGATCCCCCTAGATA
7626 AACT
1 AACT
7630 CCCTTGGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (26 bp):
AACTGAAGAAAAGATCCCCCTAGATA
Found at i:9175 original size:14 final size:13
Alignment explanation
Indices: 9141--9181 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
9131 AGCATCCTCG
* *
9141 TGAAAACAAATTT
1 TGAAAACCATTTT
9154 TGAAAACCATTTT
1 TGAAAACCATTTT
9167 TGAAAAACCATTTT
1 TG-AAAACCATTTT
9181 T
1 T
9182 TTGAAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (13 bp):
TGAAAACCATTTT
Found at i:9195 original size:15 final size:16
Alignment explanation
Indices: 9151--9189 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9141 TGAAAACAAA
9151 TTTTG-AAAACCA--T
1 TTTTGAAAAACCATTT
9164 TTTTGAAAAACCATTT
1 TTTTGAAAAACCATTT
9180 TTTTGAAAAA
1 TTTTGAAAAA
9190 TCTTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
16 11 0.48
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (16 bp):
TTTTGAAAAACCATTT
Found at i:9596 original size:2 final size:2
Alignment explanation
Indices: 9589--9621 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9579 AACAGTAAAG
9589 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9622 GGAAAGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.