Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017281.1 Corchorus olitorius cultivar O-4 contig17314, 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: 17886
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Found at i:2507 original size:43 final size:42
Alignment explanation
Indices: 2460--2742 Score: 367
Period size: 43 Copynumber: 6.6 Consensus size: 42
2450 AAAATGCCTT
*
2460 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAA-TGCCCC
*
2503 TGTGTTATATATGTGTTTGGGGACTTTG-ATATAG-ATGCCTC
1 TGTGTTATATATGTGTTTGGGGACTTTGTA-ATAGAATGCCCC
* * *
2544 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCA
1 TGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG-AATGCCCC
2588 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAACTGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAA-TGCCCC
* * *
2631 TGTGTTATATATGTGTTTGGGGACTTGGGT-ATA-TATGCCTC
1 TGTGTTATATATGTGTTTGGGGACTT-TGTAATAGAATGCCCC
* *
2672 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCC
1 TGTGTTATATATGTGTTTGGGGAC-TTTGTAATAG-AATGCCCC
*
2716 TGTGTTATATATTTGTTTGGGGACTTT
1 TGTGTTATATATGTGTTTGGGGACTTT
2743 TTTGTTATTG
Statistics
Matches: 211, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
41 57 0.27
42 18 0.09
43 78 0.37
44 58 0.27
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (42 bp):
TGTGTTATATATGTGTTTGGGGACTTTGTAATAGAATGCCCC
Found at i:2600 original size:128 final size:128
Alignment explanation
Indices: 2451--2742 Score: 503
Period size: 128 Copynumber: 2.3 Consensus size: 128
2441 CCATAAGGAA
** * *
2451 AAATGCCTTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATG
1 AAATGCCCATGTGTTATATATGTGTTTGGGGACTTTGTAATAGAACTGCCCCTGTGTTATATATG
*
2516 TGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
2579 AAATGCCCATGTGTTATATATGTGTTTGGGGACTTTGTAATAGAACTGCCCCTGTGTTATATATG
1 AAATGCCCATGTGTTATATATGTGTTTGGGGACTTTGTAATAGAACTGCCCCTGTGTTATATATG
* *
2644 TGTTTGGGGACTTGGGTATATATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
66 TGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
* *
2707 AAATGCCCCTGTGTTATATATTTGTTTGGGGACTTT
1 AAATGCCCATGTGTTATATATGTGTTTGGGGACTTT
2743 TTTGTTATTG
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 155 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (128 bp):
AAATGCCCATGTGTTATATATGTGTTTGGGGACTTTGTAATAGAACTGCCCCTGTGTTATATATG
TGTTTGGGGACTTGGATATAGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAG
Found at i:2608 original size:85 final size:84
Alignment explanation
Indices: 2460--2742 Score: 360
Period size: 85 Copynumber: 3.3 Consensus size: 84
2450 AAAATGCCTT
* *
2460 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGTGTTTGGGG
1 TGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATG-CCCTGTGTTATATATGTGTTTGGGG
*
2525 ACTTTGATATAG-ATGCCTC
65 ACTTTGATATAGAATGCCCC
2544 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCATGTGTTATATATGTGTTTGGG
1 TGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAAATGCCC-TGTGTTATATATGTGTTTGGG
2609 GACTTTG-TAATAGAACTGCCCC
64 GACTTTGAT-ATAGAA-TGCCCC
* * * * *
2631 TGTGTTATATATGTGTTTGGGGAC-TTGG-GTATATATGCCTCTGTGTTATATATGTGTTTGAGG
1 TGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCC-CTGTGTTATATATGTGTTTGGGG
2694 ACTTTTGGA-ATAGAAATGCCCC
65 AC-TTT-GATATAG-AATGCCCC
* *
2716 TGTGTTATATATTTGTTTGGGGACTTT
1 TGTGTTATATATGTGTTTGAGGACTTT
2743 TTTGTTATTG
Statistics
Matches: 179, Mismatches: 9, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
84 59 0.33
85 86 0.48
86 6 0.03
87 28 0.16
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42
Consensus pattern (84 bp):
TGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCTGTGTTATATATGTGTTTGGGGA
CTTTGATATAGAATGCCCC
Found at i:4568 original size:21 final size:21
Alignment explanation
Indices: 4544--4614 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
4534 CTTAGACAAT
*
4544 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4565 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
4586 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
4607 TCCAATGA
1 TCCAATGA
4615 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:7875 original size:25 final size:24
Alignment explanation
Indices: 7838--7884 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
7828 CTAGAAAATT
7838 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
7864 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
7885 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 (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:8776 original size:21 final size:21
Alignment explanation
Indices: 8752--8822 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
8742 CTTAGACAAT
*
8752 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8773 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
8794 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
8815 TCCAATGA
1 TCCAATGA
8823 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:17015 original size:74 final size:75
Alignment explanation
Indices: 16905--17051 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 75
16895 AATGCCAAAG
16905 GTGCCCATGCCAAGATTTTTTTGGTATTTTCAAAATGCAATTTAGATGACTGAAAATGGATTAGT
1 GTGCCCATGCCAAGATTTTTTTGGTATTTTCAAAATGCAATTTAGATGACTGAAAATGGATTAGT
16970 TAATCTAATT
66 TAATCTAATT
16980 GTGCCCATGCCAAGA-TTTTTTGGTATTTTCAAAATGCAATTTAGATGACTGAAAATGGATTAGT
1 GTGCCCATGCCAAGATTTTTTTGGTATTTTCAAAATGCAATTTAGATGACTGAAAATGGATTAGT
17044 TAATCTAA
66 TAATCTAA
17052 ATTAAATGTG
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 57 0.79
75 15 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (75 bp):
GTGCCCATGCCAAGATTTTTTTGGTATTTTCAAAATGCAATTTAGATGACTGAAAATGGATTAGT
TAATCTAATT
Found at i:17140 original size:28 final size:28
Alignment explanation
Indices: 17103--17166 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
17093 GCCAATGACA
17103 AAAATGCCCCTAAATATAAAAATGACCC
1 AAAATGCCCCTAAATATAAAAATGACCC
*
17131 AAAATGCCCCTGAATATAAAAATGACCC
1 AAAATGCCCCTAAATATAAAAATGACCC
17159 AAAATGCC
1 AAAATGCC
17167 TCCAGATGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.17
Consensus pattern (28 bp):
AAAATGCCCCTAAATATAAAAATGACCC
Done.