Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018691.1 Corchorus olitorius cultivar O-4 contig18724, 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: 27860
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3035 original size:21 final size:21
Alignment explanation
Indices: 3011--3063 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
3001 AAAGCTTCCT
3011 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
3032 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
3053 AATGGCATCTT
1 AATGGCATCTT
3064 AAGCAACTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGGCATCTTCAATGGATCA
Found at i:8588 original size:26 final size:23
Alignment explanation
Indices: 8558--8604 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
8548 CTTGAAAATT
8558 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
8584 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
8605 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 (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:14065 original size:2 final size:2
Alignment explanation
Indices: 14058--14085 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14048 TGGTTTCGAG
14058 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14086 GTTGATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18352 original size:16 final size:17
Alignment explanation
Indices: 18329--18367 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
18319 ATTTAGAGAT
**
18329 AGAAAAAGATCAAAATC
1 AGAAAAAGAGAAAAATC
18346 A-AAAAAGAGAAAAATC
1 AGAAAAAGAGAAAAATC
18362 AGAAAA
1 AGAAAA
18368 TAAAAAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.72, C:0.08, G:0.13, T:0.08
Consensus pattern (17 bp):
AGAAAAAGAGAAAAATC
Found at i:21346 original size:82 final size:82
Alignment explanation
Indices: 21255--21478 Score: 430
Period size: 82 Copynumber: 2.7 Consensus size: 82
21245 TATATATAAT
21255 AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTATCTAT
1 AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTATCTAT
21320 ACAATATTAAAAAGTAC
66 ACAATATTAAAAAGTAC
21337 AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTATCTAT
1 AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTATCTAT
21402 ACAATATTAAAAAGTAC
66 ACAATATTAAAAAGTAC
* *
21419 AACCTCTTGTAAAACTTTTGAATTGCACATTATACCCTTATTTTTCGAATATATTTCTTA
1 AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTA
21479 AATGCCATTG
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 140 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.42
Consensus pattern (82 bp):
AAACTCTTGTAAAACTTTTGAATTGCCCATTATACCCTTATTTTTCGAATATATTTCTTATCTAT
ACAATATTAAAAAGTAC
Found at i:21644 original size:131 final size:129
Alignment explanation
Indices: 21493--21751 Score: 375
Period size: 131 Copynumber: 2.0 Consensus size: 129
21483 CCATTGTTTC
*
21493 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTT-ATTTAATTAAATCTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTAT-TTTCATTTAATTAAATATAATATCCTTATAACT
* *
21557 ATTTTATTTTTACC-TTTTAC-CATTTCAATT-AAAAACTTAAGTATATATTAGAATTTTTTAAA
65 ATTTTA---TTACCATTTTACTAATTT-AATTAAAAAACTT-AG-ATATATTAGAATTTTTAAAA
21619 TATACA
124 TATACA
*
21625 TTTT-TAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATATAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATATAATATCCTTATAACTA
21689 TTTTATTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAAATATA
66 TTTTATTACCATTTTACTAATTTAATT-AAAAAACTTAGATATATTAGAATTTTTAAAATATA
21752 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
128 5 0.04
129 33 0.28
130 9 0.08
131 67 0.57
132 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (129 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATATAATATCCTTATAACTA
TTTTATTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATACA
Found at i:22331 original size:15 final size:15
Alignment explanation
Indices: 22289--22331 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
22279 AATTTTCTCG
*
22289 GGTCATTCGGGTTTC
1 GGTCATTCGGGTTTA
22304 GGCTCA-TCTGGGTTTA
1 GG-TCATTC-GGGTTTA
22320 GGTCATTCGGGT
1 GGTCATTCGGGT
22332 CTGGGTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.09, C:0.19, G:0.35, T:0.37
Consensus pattern (15 bp):
GGTCATTCGGGTTTA
Found at i:22338 original size:15 final size:15
Alignment explanation
Indices: 22288--22338 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
22278 TAATTTTCTC
22288 GGGTCATTCGGGTTT
1 GGGTCATTCGGGTTT
*
22303 CGGCTCA-TCTGGGTTT
1 -GGGTCATTC-GGGTTT
* *
22319 AGGTCATTCGGGTCT
1 GGGTCATTCGGGTTT
22334 GGGTC
1 GGGTC
22339 TGCTGATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.08, C:0.20, G:0.37, T:0.35
Consensus pattern (15 bp):
GGGTCATTCGGGTTT
Found at i:22403 original size:16 final size:16
Alignment explanation
Indices: 22379--22412 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22369 TTTGGCCTCA
22379 GTCACTCGAGTTCTGG
1 GTCACTCGAGTTCTGG
* *
22395 GTCATTCGAGTTTTGG
1 GTCACTCGAGTTCTGG
22411 GT
1 GT
22413 TTTTCAGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.18, G:0.32, T:0.38
Consensus pattern (16 bp):
GTCACTCGAGTTCTGG
Found at i:23474 original size:19 final size:20
Alignment explanation
Indices: 23452--23495 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
23442 AGGCTGAAAT
23452 TAATTAATTA-TTAATTAAA
1 TAATTAATTATTTAATTAAA
* *
23471 TAA-TAATTATTTTATTGAA
1 TAATTAATTATTTAATTAAA
23490 TAATTA
1 TAATTA
23496 TCATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 13 0.62
20 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATTAATTATTTAATTAAA
Done.