Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018905.1 Corchorus olitorius cultivar O-4 contig18938, 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: 10133
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Found at i:617 original size:17 final size:17
Alignment explanation
Indices: 595--636 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
585 AAGCCTTATA
595 CAAGGTATATATATAGT
1 CAAGGTATATATATAGT
612 CAAGGTATATATATAGT
1 CAAGGTATATATATAGT
629 CAAGGTAT
1 CAAGGTAT
637 GACTCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (17 bp):
CAAGGTATATATATAGT
Found at i:2232 original size:117 final size:116
Alignment explanation
Indices: 1996--2354 Score: 418
Period size: 117 Copynumber: 3.1 Consensus size: 116
1986 CTCTGTACTT
* ** * *
1996 GGTCGCACGACCTAGTGGGCATCCCCCCACTCGAACAATAAAAACGATCGAGCATCCCGCGGTCG
1 GGTCGCACGACCCAGTGGGCAT-CCCCCACTCGTGCAATAAGAACGATCGAGCATCCCTCGGTCG
* * *
2061 CACGACCTAGTGGGCATCCCCACTTGTTCCATAAGAACGATCGAGCATCCCTC
65 CACGACCTAGTGGGCATCCCCACTTGTGCAATAAGAA-AATCGAGCATCCCTC
* * * **
2114 GGTCGCACGGCCCAGTGGGCATCCCCCACTCGTGCAATGAGAACGATCGAACATCCCTTAGTCGC
1 GGTCGCACGACCCAGTGGGCATCCCCCACTCGTGCAATAAGAACGATCGAGCATCCCTCGGTCGC
** * * *
2179 ACGACCCGGTGGGCATCCACCACTTGTGCAATAAGAAAATCAAGTATCACTC
66 ACGACCTAGTGGGCATCC-CCACTTGTGCAATAAGAAAATCGAGCATCCCTC
* * *
2231 GGTCGTACGACCTC-GTGGGCATCCCCCACT-GATGCAAAAAGAA-AATCGAGCATCCCTCGGTC
1 GGTCGCACGACC-CAGTGGGCATCCCCCACTCG-TGCAATAAGAACGATCGAGCATCCCTCGGTC
* * * *
2293 ACACGACCTAATGGGCATCCCCCACTTGTGCAAAAAGAAAAACGAGCATCCCTC
64 GCACGACCTAGTGGGCAT-CCCCACTTGTGCAATAAGAAAATCGAGCATCCCTC
2347 GGTCGCAC
1 GGTCGCAC
2355 AACCTAAAAT
Statistics
Matches: 201, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
116 65 0.32
117 99 0.49
118 37 0.18
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (116 bp):
GGTCGCACGACCCAGTGGGCATCCCCCACTCGTGCAATAAGAACGATCGAGCATCCCTCGGTCGC
ACGACCTAGTGGGCATCCCCACTTGTGCAATAAGAAAATCGAGCATCCCTC
Found at i:2361 original size:58 final size:58
Alignment explanation
Indices: 1996--2360 Score: 394
Period size: 58 Copynumber: 6.2 Consensus size: 58
1986 CTCTGTACTT
* ** *
1996 GGTCGCACGACCTAGTGGGCATCCCCCCACTCGAACAATAA-AAACGATCGAGCATCCCGC
1 GGTCGCACGACCTAGTGGGCAT-CCCCCACTTGTGCAATAAGAAA--ATCGAGCATCCCTC
* * *
2056 GGTCGCACGACCTAGTGGGCAT-CCCCACTTGTTCCATAAGAACGATCGAGCATCCCTC
1 GGTCGCACGACCTAGTGGGCATCCCCCACTTGTGCAATAAGAA-AATCGAGCATCCCTC
* * * * * * *
2114 GGTCGCACGGCCCAGTGGGCATCCCCCACTCGTGCAATGAGAACGATCGAACATCCCTT
1 GGTCGCACGACCTAGTGGGCATCCCCCACTTGTGCAATAAGAA-AATCGAGCATCCCTC
* ** * * * *
2173 AGTCGCACGACCCGGTGGGCATCCACCACTTGTGCAATAAGAAAATCAAGTATCACTC
1 GGTCGCACGACCTAGTGGGCATCCCCCACTTGTGCAATAAGAAAATCGAGCATCCCTC
* * *
2231 GGTCGTACGACCTCGTGGGCATCCCCCAC-TGATGCAAAAAGAAAATCGAGCATCCCTC
1 GGTCGCACGACCTAGTGGGCATCCCCCACTTG-TGCAATAAGAAAATCGAGCATCCCTC
* * * *
2289 GGTCACACGACCTAATGGGCATCCCCCACTTGTGCAAAAAGAAAAACGAGCATCCCTC
1 GGTCGCACGACCTAGTGGGCATCCCCCACTTGTGCAATAAGAAAATCGAGCATCCCTC
*
2347 GGTCGCACAACCTA
1 GGTCGCACGACCTA
2361 AAATGGGTAC
Statistics
Matches: 258, Mismatches: 42, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
57 2 0.01
58 163 0.63
59 71 0.28
60 22 0.09
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (58 bp):
GGTCGCACGACCTAGTGGGCATCCCCCACTTGTGCAATAAGAAAATCGAGCATCCCTC
Found at i:3778 original size:15 final size:15
Alignment explanation
Indices: 3758--3790 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3748 CGCGAAACTA
3758 GGGTTTTTGATTTGG
1 GGGTTTTTGATTTGG
3773 GGG-TTTTGATTTGG
1 GGGTTTTTGATTTGG
3787 GGGT
1 GGGT
3791 ATAAAAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.06, C:0.00, G:0.45, T:0.48
Consensus pattern (15 bp):
GGGTTTTTGATTTGG
Found at i:5542 original size:98 final size:99
Alignment explanation
Indices: 5419--5665 Score: 343
Period size: 99 Copynumber: 2.5 Consensus size: 99
5409 AAGCGACCAT
* * * *
5419 GGGCATTTTTCACTTGCACTTGAGGATCATTCTCCATTTTGCGCTCGGCGAGAGTCCTACTCTTC
1 GGGCATTCTTCACTTGCACTCGAGGAGCATTCTCCATTTTGCGCTCGGCGAGAGTCCTACGCTTC
*
5484 GCG-TTCGGCGAGAGTTATCCGTTTCACCATTTC
66 GCGTTTCGGCGAGAGTTATCCGTTTCACCATCTC
* * * * *
5517 GGGCATTCTTCACTTGCTCTCGAGGAGCATTCTCCATTTCGCGCTCAGCGAGCGTCCTACGCTTT
1 GGGCATTCTTCACTTGCACTCGAGGAGCATTCTCCATTTTGCGCTCGGCGAGAGTCCTACGCTTC
* * *
5582 GCGTTTCGGCGAGCGTTATCTGTTTCGCCATCTC
66 GCGTTTCGGCGAGAGTTATCCGTTTCACCATCTC
* * *
5616 GGGCATTCTTTATTTGCACTCGAGGAGCATTCTCCATTTTCCGCTCGGCG
1 GGGCATTCTTCACTTGCACTCGAGGAGCATTCTCCATTTTGCGCTCGGCG
5666 GGCATTATCT
Statistics
Matches: 129, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
98 59 0.46
99 70 0.54
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.34
Consensus pattern (99 bp):
GGGCATTCTTCACTTGCACTCGAGGAGCATTCTCCATTTTGCGCTCGGCGAGAGTCCTACGCTTC
GCGTTTCGGCGAGAGTTATCCGTTTCACCATCTC
Found at i:5654 original size:24 final size:24
Alignment explanation
Indices: 5618--5800 Score: 72
Period size: 24 Copynumber: 7.5 Consensus size: 24
5608 GCCATCTCGG
**
5618 GCATTCTTTATTTGCACTCGAGGA
1 GCATTCTCCATTTGCACTCGAGGA
* * *
5642 GCATTCTCCATTTTCCGCTCG-GCGG
1 GCATTCTCCA-TTTGCACTCGAG-GA
* *
5667 GCATTATCTATTTCGTCATCTC-A-G-
1 GCATTCTCCATTT-G-CA-CTCGAGGA
* * *
5691 GCATTCTTCACTTGCTCTCGAGGA
1 GCATTCTCCATTTGCACTCGAGGA
* *
5715 GCATTCTCCATTTCGCGCTCGACGA
1 GCATTCTCCATTT-GCACTCGAGGA
* * * **
5740 GCGTTATCTATTTCGTCA-TCTTGG-
1 GCATTCTCCATTT-G-CACTCGAGGA
* **
5764 GCATTCTTCATTTGTGCTCGAGGA
1 GCATTCTCCATTTGCACTCGAGGA
5788 GCATTCTCCATTT
1 GCATTCTCCATTT
5801 CGCGTTCGAC
Statistics
Matches: 112, Mismatches: 34, Indels: 26
0.65 0.20 0.15
Matches are distributed among these distances:
21 3 0.03
22 2 0.02
23 7 0.06
24 53 0.47
25 42 0.38
26 2 0.02
27 3 0.03
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (24 bp):
GCATTCTCCATTTGCACTCGAGGA
Found at i:5681 original size:73 final size:74
Alignment explanation
Indices: 5587--5817 Score: 315
Period size: 73 Copynumber: 3.2 Consensus size: 74
5577 GCTTTGCGTT
* * *
5587 TCGGCGAGCGTTATCTGTTTCGCCATCTCGGGCATTCTTTATTTGCACTCGAGGAGCATTCTCCA
1 TCGGCGAGCGTTATCTATTTCGTCATCTCGGGCATTCTTCATTTGCACTCGAGGAGCATTCTCCA
5652 TTTTC-CGC
66 TTTTCGCGC
* * * * *
5660 TCGGCGGGCATTATCTATTTCGTCATCTCAGGCATTCTTCACTTGCTCTCGAGGAGCATTCTCCA
1 TCGGCGAGCGTTATCTATTTCGTCATCTCGGGCATTCTTCATTTGCACTCGAGGAGCATTCTCCA
5725 -TTTCGCGC
66 TTTTCGCGC
* * **
5733 TCGACGAGCGTTATCTATTTCGTCATCTTGGGCATTCTTCATTTGTGCTCGAGGAGCATTCTCCA
1 TCGGCGAGCGTTATCTATTTCGTCATCTCGGGCATTCTTCATTTGCACTCGAGGAGCATTCTCCA
*
5798 -TTTCGCGT
66 TTTTCGCGC
*
5806 TCGACGAGCGTT
1 TCGGCGAGCGTT
5818 CTACGCTTCG
Statistics
Matches: 140, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
72 4 0.03
73 136 0.97
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (74 bp):
TCGGCGAGCGTTATCTATTTCGTCATCTCGGGCATTCTTCATTTGCACTCGAGGAGCATTCTCCA
TTTTCGCGC
Found at i:5741 original size:25 final size:25
Alignment explanation
Indices: 5634--5819 Score: 84
Period size: 25 Copynumber: 7.6 Consensus size: 25
5624 TTTATTTGCA
*
5634 CTCGAGGAGCATTCTCCATTTTC-CG
1 CTCGACGAGCATTCTCCA-TTTCGCG
* * * * *
5659 CTCGGCGGGCATTATCTATTTCGTCAT
1 CTCGACGAGCATTCTCCATTTCG-C-G
* * *
5686 CTC-A-G-GCATTCTTCACTT-GCT
1 CTCGACGAGCATTCTCCATTTCGCG
*
5707 CTCGAGGAGCATTCTCCATTTCGCG
1 CTCGACGAGCATTCTCCATTTCGCG
* * * *
5732 CTCGACGAGCGTTATCTATTTCGTCAT
1 CTCGACGAGCATTCTCCATTTCG-C-G
* * *
5759 CTTG--G-GCATTCTTCATTT-GTG
1 CTCGACGAGCATTCTCCATTTCGCG
*
5780 CTCGAGGAGCATTCTCCATTTCGCG
1 CTCGACGAGCATTCTCCATTTCGCG
* *
5805 TTCGACGAGCGTTCT
1 CTCGACGAGCATTCT
5820 ACGCTTCGCA
Statistics
Matches: 116, Mismatches: 32, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
21 7 0.06
22 2 0.02
23 4 0.03
24 45 0.39
25 50 0.43
26 2 0.02
27 6 0.05
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (25 bp):
CTCGACGAGCATTCTCCATTTCGCG
Found at i:9291 original size:27 final size:28
Alignment explanation
Indices: 9253--9310 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
9243 AATTACTAAC
* *
9253 AAAACAAACCCAAAT-GTAAA-GAATTA
1 AAAAAAAACCCAAATAGCAAAGGAATTA
9279 AAAAAAAAGCCCAAATAGCAAAGGAATTA
1 AAAAAAAA-CCCAAATAGCAAAGGAATTA
9308 AAA
1 AAA
9311 GCCCAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
28 4 0.15
29 9 0.33
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (28 bp):
AAAAAAAACCCAAATAGCAAAGGAATTA
Found at i:9333 original size:24 final size:24
Alignment explanation
Indices: 9283--9334 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
9273 GAATTAAAAA
* *
9283 AAAAGCCCAAATAGCAAAGGAATT
1 AAAAGCCCAAATAACAAAGGAAAT
*
9307 AAAAGCCCAAAGTAACTAA-GAAAT
1 AAAAGCCCAAA-TAACAAAGGAAAT
9331 AAAA
1 AAAA
9335 AAGAACCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.12
Consensus pattern (24 bp):
AAAAGCCCAAATAACAAAGGAAAT
Done.