Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015956.1 Corchorus olitorius cultivar O-4 contig15989, 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: 10441
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:2014 original size:42 final size:42
Alignment explanation
Indices: 1957--2051 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
1947 ATAGCCATTG
*
1957 ATATATG-TCATACATCC-TCCATGCATCGTCCATGT-CTTTGT
1 ATATATGTTCATACATCCAT-CATGCATCATCCAT-TCCTTTGT
*
1998 ATATATGTTCATACATCCATCGTGCATCATCCATTCCTTTGT
1 ATATATGTTCATACATCCATCATGCATCATCCATTCCTTTGT
2040 ATATATGTTCAT
1 ATATATGTTCAT
2052 GCATAGGTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
41 8 0.16
42 40 0.82
43 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (42 bp):
ATATATGTTCATACATCCATCATGCATCATCCATTCCTTTGT
Found at i:3739 original size:22 final size:19
Alignment explanation
Indices: 3696--3733 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3686 CAAGAAATTC
*
3696 AAAAATCATCAAAAATAAA
1 AAAAATCATCAAAAAAAAA
3715 AAAAATCATCATAAAAAAA
1 AAAAATCATCA-AAAAAAA
3734 TCAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAATCATCAAAAAAAAA
Found at i:4408 original size:50 final size:50
Alignment explanation
Indices: 4323--4470 Score: 208
Period size: 50 Copynumber: 3.0 Consensus size: 50
4313 GTTTTATAAC
* *
4323 AAGATTTCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
1 AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
* *
4373 -AGAATTGCTTTCCATTTGTGAGTTCAAGATTAAAATTCGCTTTTCAAAGT
1 AAG-ATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
* * * *
4423 AAGATTGCATTCCAGTTGTGGGTCCAAGATCAAAATTCGCTTTTCAAA
1 AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAA
4471 GGGCATTTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 2 0.02
50 83 0.95
51 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (50 bp):
AAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAT
Found at i:4994 original size:35 final size:35
Alignment explanation
Indices: 4954--5166 Score: 315
Period size: 35 Copynumber: 6.1 Consensus size: 35
4944 AGTTATTTTC
4954 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
1 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
4989 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
1 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
* *
5024 CAAAGCTGA-ATCCAGATGACTCGGTGTAGCATCTT
1 CAAAG-TTATATTCAGATGACTCGGTGTAGCATCTT
*
5059 CGAAA-TTGA-ATCCAGATGACTCGGTGTAGCATCTT
1 C-AAAGTT-ATATTCAGATGACTCGGTGTAGCATCTT
5094 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
1 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
* * * *
5129 CAAAGATAAACTCAGATGACTCGATGTAGCATCTT
1 CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
5164 CAA
1 CAA
5167 TATGGACTCA
Statistics
Matches: 165, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
34 5 0.03
35 155 0.94
36 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (35 bp):
CAAAGTTATATTCAGATGACTCGGTGTAGCATCTT
Found at i:5148 original size:105 final size:105
Alignment explanation
Indices: 4966--5164 Score: 355
Period size: 105 Copynumber: 1.9 Consensus size: 105
4956 AAGTTATATT
*
4966 CAGATGACTCGGTGTAGCATCTTCAAAGTTATATTCAGATGACTCGGTGTAGCATCTTCAAAGCT
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTATATTCAGATGACTCGGTGTAGCATCTTCAAAGAT
* *
5031 GAATCCAGATGACTCGGTGTAGCATCTTCGAAATTGAATC
66 AAATCCAGATGACTCGATGTAGCATCTTCGAAATTGAATC
5071 CAGATGACTCGGTGTAGCATCTTCAAAGTTATATTCAGATGACTCGGTGTAGCATCTTCAAAGAT
1 CAGATGACTCGGTGTAGCATCTTCAAAGTTATATTCAGATGACTCGGTGTAGCATCTTCAAAGAT
5136 AAA-CTCAGATGACTCGATGTAGCATCTTC
66 AAATC-CAGATGACTCGATGTAGCATCTTC
5165 AATATGGACT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 1 0.01
105 89 0.99
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (105 bp):
CAGATGACTCGGTGTAGCATCTTCAAAGTTATATTCAGATGACTCGGTGTAGCATCTTCAAAGAT
AAATCCAGATGACTCGATGTAGCATCTTCGAAATTGAATC
Found at i:5520 original size:29 final size:28
Alignment explanation
Indices: 5458--5532 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 28
5448 AAAAACCCAT
*
5458 GGGCATTTTGGTCATTTTTCACATTCAG
1 GGGCATTTTGGTCATTTTGCACATTCAG
* *
5486 GGGCATTATGGTCATTTCTGCATATTCAG
1 GGGCATTTTGGTCATTT-TGCACATTCAG
5515 GGGCATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
5533 AAGTTCATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.40
29 25 0.60
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATTCAG
Found at i:8078 original size:41 final size:41
Alignment explanation
Indices: 7951--8079 Score: 204
Period size: 41 Copynumber: 3.1 Consensus size: 41
7941 TTTCCGTGTT
*
7951 CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGACA
1 CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGATA
7992 CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGATA
1 CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGATA
* * * * *
8033 CAATTTAGTCCCTAATTTAGGTTTCTAGTTACTATTTGTTT
1 CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGATA
8074 CAATTT
1 CAATTT
8080 GATCCTTATT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (41 bp):
CAATTTAGTCCCTGATTTAGGATTCTATTTACTATTTGATA
Done.