Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022358.1 Corchorus olitorius cultivar O-4 contig22391, 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: 15186
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2095 original size:21 final size:21
Alignment explanation
Indices: 2048--2102 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2038 GGCTTGGAAT
* **
2048 GGTGATGGCACGGGCATGGCC
1 GGTGGTGGCACGGGCATAACC
* *
2069 GATGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
*
2090 GGTGGTGTCACGG
1 GGTGGTGGCACGG
2103 TGAACGGCCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:5587 original size:16 final size:15
Alignment explanation
Indices: 5549--5590 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5539 ACAGAGATTG
*
5549 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
5564 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
5579 ACTAGAAAACAA
1 AC-AGAAAACAA
5591 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:6366 original size:11 final size:11
Alignment explanation
Indices: 6350--6375 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6340 CCTTTGCCTA
6350 AAAACTAGAAG
1 AAAACTAGAAG
6361 AAAACTAGAAG
1 AAAACTAGAAG
6372 AAAA
1 AAAA
6376 TAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:13115 original size:33 final size:33
Alignment explanation
Indices: 13078--13357 Score: 427
Period size: 33 Copynumber: 8.4 Consensus size: 33
13068 GTAATCAGTG
13078 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
*
13111 AAAATGGAATTTGGTAATTAAAGTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
* *
13144 AAAATGATATCTGGTAATTAAAGTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
* *
13177 AAAATGGAATGTGGTAATTAAAGTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
*
13210 AAAATGGTATTTGGTAATCAAAGTTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAG-TAAAAAGAGT
*
13244 AAAATGGTACTTGGTAATTAAAGTAAAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
13277 AAGAATGGTATTTGGTAATTAAAGAGTAAAAAGAGT
1 AA-AATGGTATTTGGTAATT-AA-AGTAAAAAGAGT
*
13313 AAAATGGCATTTGGTAATTAAAGT-AAAAGAGT
1 AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
*
13345 AAAAATAGTATTT
1 -AAAATGGTATTT
13358 AAAAAGTAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
32 8 0.04
33 137 0.61
34 49 0.22
35 18 0.08
36 14 0.06
ACGTcount: A:0.49, C:0.01, G:0.21, T:0.28
Consensus pattern (33 bp):
AAAATGGTATTTGGTAATTAAAGTAAAAAGAGT
Found at i:13367 original size:20 final size:21
Alignment explanation
Indices: 13336--13378 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
13326 GTAATTAAAG
13336 TAAAAGAGTAAAAATAGTATT
1 TAAAAGAGTAAAAATAGTATT
* *
13357 TAAAA-AGTAAAATTGGTATT
1 TAAAAGAGTAAAAATAGTATT
13377 TA
1 TA
13379 GTAATTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (21 bp):
TAAAAGAGTAAAAATAGTATT
Found at i:14645 original size:37 final size:35
Alignment explanation
Indices: 14530--14665 Score: 134
Period size: 37 Copynumber: 3.7 Consensus size: 35
14520 AAATGCTTTG
*
14530 GATGGGAACTTTCCCATTTTGAAAACTAAAACTGAAAA-T
1 GATGGGAACTTTCCCAATTTGAAAACT-----TGAAAACT
* *
14569 GACGGGAACTTTCCCTAAATTGAAAA--TGAAAACCT
1 GATGGGAACTTTCCC-AATTTGAAAACTTGAAAA-CT
14604 GATGGGAACTTTCCCAATTTGAAAACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAAC-TTGAAAACT
*
14640 GGATGGGAACTTTCGCAATTTGAAAA
1 -GATGGGAACTTTCCCAATTTGAAAA
14666 AAGAGAGATA
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
33 6 0.07
34 9 0.11
35 15 0.18
36 2 0.02
37 30 0.36
39 14 0.17
40 8 0.10
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (35 bp):
GATGGGAACTTTCCCAATTTGAAAACTTGAAAACT
Found at i:14746 original size:36 final size:37
Alignment explanation
Indices: 14690--14763 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
14680 GAATGCTTTG
*
14690 AAAACTGAATGGGAACTTTCCCAATTTGAAAACTTAA
1 AAAACTGAATGGGAACTTTCCCAATTTAAAAACTTAA
* *
14727 AAAACTG-GTGGGAACTTTCCTAATTTAAAAACTTAA
1 AAAACTGAATGGGAACTTTCCCAATTTAAAAACTTAA
14763 A
1 A
14764 CCTGATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 27 0.79
37 7 0.21
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (37 bp):
AAAACTGAATGGGAACTTTCCCAATTTAAAAACTTAA
Done.