Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015509.1 Corchorus olitorius cultivar O-4 contig15542, 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: 7233
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1477 original size:23 final size:24
Alignment explanation
Indices: 1431--1478 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1421 ACTTGGTGTC
1431 AACTGTCATGAAACCAAAAAAAAA
1 AACTGTCATGAAACCAAAAAAAAA
1455 AACTGTCATGAAACCAAAAAAAAA
1 AACTGTCATGAAACCAAAAAAAAA
1479 GTGGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.12
Consensus pattern (24 bp):
AACTGTCATGAAACCAAAAAAAAA
Found at i:5214 original size:22 final size:21
Alignment explanation
Indices: 5154--5650 Score: 387
Period size: 22 Copynumber: 22.9 Consensus size: 21
5144 CCGTGTTAGA
* **
5154 TAACTACCCTATTAAATTTTAC
1 TAACT-CCCTATGAAATTTTGG
* *
5176 TAACCTCCATACGAAATTTTGG
1 TAA-CTCCCTATGAAATTTTGG
* * *
5198 TAATCTCACTATCAAATTTCGG
1 TAA-CTCCCTATGAAATTTTGG
*
5220 TAACTTCCCTATGAAATTTTTG
1 TAAC-TCCCTATGAAATTTTGG
*
5242 TAACACCCTATG-AATTTTGG
1 TAACTCCCTATGAAATTTTGG
*
5262 TAA-TCCCCTTATGAAAATTTGG
1 TAACT-CCC-TATGAAATTTTGG
* *
5284 TAATCTCTCTATGAAATTTCGG
1 TAA-CTCCCTATGAAATTTTGG
*
5306 TAACCTTCCTATGAAATTTTGG
1 TAA-CTCCCTATGAAATTTTGG
**
5328 TAAGCT-TTTATGAAATTTTGG
1 TAA-CTCCCTATGAAATTTTGG
* * *
5349 TAACCTTCATATGAAAATTTGG
1 TAA-CTCCCTATGAAATTTTGG
*
5371 TAACATCACTATGAAATTTTGG
1 TAAC-TCCCTATGAAATTTTGG
* *
5393 TAAC-CCCTACGAAATTTTTG
1 TAACTCCCTATGAAATTTTGG
* *
5413 TAAACTCCGTATGAAATTTTGA
1 T-AACTCCCTATGAAATTTTGG
* * *
5435 TAACACCATATGAAATTTTTG
1 TAACTCCCTATGAAATTTTGG
5456 TAAACTCCCTATGAAATTTTGG
1 T-AACTCCCTATGAAATTTTGG
5478 TAAC-CCCTATGAAATTTTGG
1 TAACTCCCTATGAAATTTTGG
5498 TGAAACTCCCTATGAAATTTTGG
1 T--AACTCCCTATGAAATTTTGG
* *
5521 TAACCTCTCTATGAAATTTTGA
1 TAA-CTCCCTATGAAATTTTGG
* * *
5543 AAACAGATCCATTTGAAATTTTGG
1 TAAC---TCCCTATGAAATTTTGG
*
5567 TAA-TCCCCTATGAAATTTTTG
1 TAACT-CCCTATGAAATTTTGG
* * *
5588 TAAATTCTCTATGAAATTTTGT
1 T-AACTCCCTATGAAATTTTGG
* *
5610 TAACCCCCTATGAACTGTTT-G
1 TAACTCCCTATGAAAT-TTTGG
*
5631 TAACCTCCCTATTAAATTTT
1 TAA-CTCCCTATGAAATTTT
5651 TTTAACCTCT
Statistics
Matches: 378, Mismatches: 73, Indels: 49
0.76 0.15 0.10
Matches are distributed among these distances:
20 45 0.12
21 88 0.23
22 207 0.55
23 22 0.06
24 16 0.04
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (21 bp):
TAACTCCCTATGAAATTTTGG
Found at i:5296 original size:43 final size:42
Alignment explanation
Indices: 5155--5650 Score: 428
Period size: 43 Copynumber: 11.4 Consensus size: 42
5145 CGTGTTAGAT
* ** *
5155 AACTACCCTATTAAATTTTACTAACCTCCATACGAAATTTTGGTA
1 AACT-CCCTATGAAATTTTGGTAACC-CC-TATGAAATTTTGGTA
* * * * *
5200 ATCTCACTATCAAATTTCGGTAACTTCCCTATGAAATTTTTGT-
1 AACTCCCTATGAAATTTTGGTAAC--CCCTATGAAATTTTGGTA
* *
5243 AACACCCTATG-AATTTTGGTAATCCCCTTATGAAAATTTGGTA
1 AACTCCCTATGAAATTTTGGTAA-CCCC-TATGAAATTTTGGTA
* * *
5286 ATCTCTCTATGAAATTTCGGTAACCTTCCTATGAAATTTTGGTA
1 AACTCCCTATGAAATTTTGGTAACC--CCTATGAAATTTTGGTA
* ** * *
5330 AGCT-TTTATGAAATTTTGGTAACCTTCATATGAAAATTTGGT-
1 AACTCCCTATGAAATTTTGGTAACC--CCTATGAAATTTTGGTA
* * *
5372 AACATCACTATGAAATTTTGGTAACCCCTACGAAATTTTTGTA
1 AAC-TCCCTATGAAATTTTGGTAACCCCTATGAAATTTTGGTA
* * * *
5415 AACTCCGTATGAAATTTTGATAACACCATATGAAATTTTTGTA
1 AACTCCCTATGAAATTTTGGTAAC-CCCTATGAAATTTTGGTA
5458 AACTCCCTATGAAATTTTGGTAACCCCTATGAAATTTTGGTGA
1 AACTCCCTATGAAATTTTGGTAACCCCTATGAAATTTTGGT-A
*
5501 AACTCCCTATGAAATTTTGGTAACCTCTCTATGAAATTTT-GAA
1 AACTCCCTATGAAATTTTGGTAACC-C-CTATGAAATTTTGGTA
* * *
5544 AACAGATCCATTTGAAATTTTGGTAATCCCCTATGAAATTTTTGTA
1 AAC---TCCCTATGAAATTTTGGTAA-CCCCTATGAAATTTTGGTA
* * * *
5590 AATTCTCTATGAAATTTTGTTAACCCCCTATGAACTGTTT-GTA
1 AACTCCCTATGAAATTTTGGTAA-CCCCTATGAAAT-TTTGGTA
* *
5633 ACCTCCCTATTAAATTTT
1 AACTCCCTATGAAATTTT
5651 TTTAACCTCT
Statistics
Matches: 374, Mismatches: 56, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.01
42 69 0.18
43 168 0.45
44 77 0.21
45 31 0.08
46 24 0.06
47 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (42 bp):
AACTCCCTATGAAATTTTGGTAACCCCTATGAAATTTTGGTA
Found at i:5341 original size:65 final size:65
Alignment explanation
Indices: 5188--5659 Score: 316
Period size: 65 Copynumber: 7.3 Consensus size: 65
5178 ACCTCCATAC
* * * * *
5188 GAAATTTTGGTAATCTCACTATCAAATTTCGGTAACT-TCCCTATGAAATTTTTGTAACAC--CC
1 GAAATTTTGGTAACCTC-CTATGAAATTTTGGTAACTCT-CATATGAAATTTTGGTAAC-CTTCC
5250 TAT
63 TAT
* *
5253 G-AATTTTGGTAATCC-CCTTATGAAAATTTGGTAATCTCTC-TATGAAATTTCGGTAACCTTCC
1 GAAATTTTGGTAA-CCTCC-TATGAAATTTTGGTAA-CTCTCATATGAAATTTTGGTAACCTTCC
5315 TAT
63 TAT
* ** * *
5318 GAAATTTTGGTAAGCTTTTATGAAATTTTGGTAAC-CTTCATATGAAAATTTGGTAA-CATCACT
1 GAAATTTTGGTAACCTCCTATGAAATTTTGGTAACTC-TCATATGAAATTTTGGTAACCTTC-CT
5381 AT
64 AT
* * * * *
5383 GAAATTTTGGTAACC-CCTACGAAATTTTTGTAAACTC-CGTATGAAATTTTGATAACAC--CAT
1 GAAATTTTGGTAACCTCCTATGAAATTTTGGT-AACTCTCATATGAAATTTTGGTAAC-CTTCCT
5444 AT
64 AT
* * * * *
5446 GAAATTTTTGTAAACTCCCTATGAAATTTTGGTAAC-C-CCTATGAAATTTTGGTGAAACTCCCT
1 GAAATTTTGGTAACCT-CCTATGAAATTTTGGTAACTCTCATATGAAATTTTGGT-AACCTTCCT
5509 AT
64 AT
** *
5511 GAAATTTTGGTAACCTCTCTATGAAATTTTGAAAACAGATC-CATTTGAAATTTTGGTAATCC--
1 GAAATTTTGGTAACCTC-CTATGAAATTTTGGTAAC---TCTCATATGAAATTTTGGTAA-CCTT
5573 CCTAT
61 CCTAT
* ** * * * * *
5578 GAAATTTTTGTAAATTCTCTATGAAATTTTGTTAAC-CCCCTATGAACTGTTT-GTAACCTCCCT
1 GAAATTTTGGTAACCTC-CTATGAAATTTTGGTAACTCTCATATGAAAT-TTTGGTAACCTTCCT
5641 AT
64 AT
* **
5643 TAAATTTTTTTAACCTC
1 GAAATTTTGGTAACCTC
5660 TTTTTTTATT
Statistics
Matches: 328, Mismatches: 49, Indels: 60
0.75 0.11 0.14
Matches are distributed among these distances:
63 38 0.12
64 91 0.28
65 131 0.40
66 14 0.04
67 36 0.11
68 2 0.01
69 16 0.05
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (65 bp):
GAAATTTTGGTAACCTCCTATGAAATTTTGGTAACTCTCATATGAAATTTTGGTAACCTTCCTAT
Found at i:6087 original size:241 final size:240
Alignment explanation
Indices: 5664--6149 Score: 927
Period size: 241 Copynumber: 2.0 Consensus size: 240
5654 AACCTCTTTT
5664 TTTATTAAAGGCAAATTAGATGAATTTTATTGAAAATAAAAGTCCAAACAATTACAACAACAACA
1 TTTATTAAAGGCAAATTAGATGAATTTTATTGAAAATAAAAGTCCAAACAATTACAACAACAACA
5729 CAGTCTAAGAACCAACAGCTTTGGATATTTTAAAATGCCAAAGTCTAGTTGACAACAAGGAGGCT
66 CAGTCTAAGAACCAACAGCTTTGGATATTTTAAAATGCCAAAGTCTAGTTGACAACAAGGAGGCT
5794 ATGGATATTGTATTGCAAGCTGGAGGTTCAAATGCTTCCTCAGTTCCCATAACCAAATCCTTAGC
131 ATGGATATTGTATTGCAAGCTGGAGGTTCAAATGCTTCCTCAGTTCCCATAACCAAATCCTTAGC
*
5859 TGAGCTCTTAAGGTTTAAAGTTGGAATTTCTGAAAGATTAATGATA
196 TGAGCT-TTAAAGTTTAAAGTTGGAATTTCTGAAAGATTAATGATA
* *
5905 TTTATTAAAGGCAAATTAGATGAATTTTATTGAAAATAAAAGTCCAAACAATTACAGCAGCAACA
1 TTTATTAAAGGCAAATTAGATGAATTTTATTGAAAATAAAAGTCCAAACAATTACAACAACAACA
5970 CAGTCTAAGAACCAACAGCTTTGGATATTTTAAAATGCCAAAGTCTAGTTGACAACAAGGAGGCT
66 CAGTCTAAGAACCAACAGCTTTGGATATTTTAAAATGCCAAAGTCTAGTTGACAACAAGGAGGCT
*
6035 GTGGATATTGTATTGCAAGCTGGAGGTTCAAATGCTTCCTCAGTTCCCATAACCAAATCCTTAGC
131 ATGGATATTGTATTGCAAGCTGGAGGTTCAAATGCTTCCTCAGTTCCCATAACCAAATCCTTAGC
6100 TGAGCTTTAAAGTTTAAAGTTGGAATTTCTGAAAGATTAATGATA
196 TGAGCTTTAAAGTTTAAAGTTGGAATTTCTGAAAGATTAATGATA
6145 TTTAT
1 TTTAT
6150 AACTCGAGCC
Statistics
Matches: 241, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
240 43 0.18
241 198 0.82
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (240 bp):
TTTATTAAAGGCAAATTAGATGAATTTTATTGAAAATAAAAGTCCAAACAATTACAACAACAACA
CAGTCTAAGAACCAACAGCTTTGGATATTTTAAAATGCCAAAGTCTAGTTGACAACAAGGAGGCT
ATGGATATTGTATTGCAAGCTGGAGGTTCAAATGCTTCCTCAGTTCCCATAACCAAATCCTTAGC
TGAGCTTTAAAGTTTAAAGTTGGAATTTCTGAAAGATTAATGATA
Done.