Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012469.1 Corchorus olitorius cultivar O-4 contig12502, 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: 7004
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Found at i:4581 original size:21 final size:21
Alignment explanation
Indices: 4552--4601 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
4542 ATGTAGGTTT
* *
4552 TGAAATTTGATTTTTAAGTCA
1 TGAATTTTGAGTTTTAAGTCA
* **
4573 TGAATTTTGAGTTTTGAGTTT
1 TGAATTTTGAGTTTTAAGTCA
4594 TGAATTTT
1 TGAATTTT
4602 AAATTTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (21 bp):
TGAATTTTGAGTTTTAAGTCA
Found at i:4589 original size:7 final size:7
Alignment explanation
Indices: 4573--4624 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
4563 TTTTAAGTCA
4573 TGAATTT
1 TGAATTT
*
4580 TGAGTTT
1 TGAATTT
*
4587 TGAGTTT
1 TGAATTT
4594 TGAATTT
1 TGAATTT
*
4601 TAAATTT
1 TGAATTT
4608 TGAATTT
1 TGAATTT
4615 TGAATTT
1 TGAATTT
4622 TGA
1 TGA
4625 GTAATGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (7 bp):
TGAATTT
Found at i:4802 original size:33 final size:33
Alignment explanation
Indices: 4760--4837 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
4750 AGAAACTGTG
* * * *
4760 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATAAAATGCA
4793 GATTTTGAACTTTGAATTTTGAAATAAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATAAAATGCA
*
4826 AATTTTGAACTT
1 GATTTTGAACTT
4838 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATAAAATGCA
Found at i:5013 original size:54 final size:54
Alignment explanation
Indices: 4900--5445 Score: 683
Period size: 54 Copynumber: 10.3 Consensus size: 54
4890 TTCTTGGAAT
* ** * *
4900 GACCGCACTGGGTCAGTTTAGAGATCAACTCT-GATCATC-GTAAACTTCT-TGGAAT
1 GACCACACTGGGTCAACTTA-AGATCAACT-TAGATC-TCTGAAAACTTCTAT-GAAA
* * * *
4955 GACCACACTGGATCAACTTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * * *
5009 GACCACACAGGGTCATCTGAAGATCAACTTAGACCTCT-AAAAGCTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAA-CTTCTATGAAA
5063 GACCACACTGGGTCATA-TTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGGTCA-ACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * *
5117 GACCACACTGGGTCACCTTAAAATCAACTTAGATCTCTGAAAACTTCTATTAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * *
5171 GATCACACTGAGTCACCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* * **
5225 GATCAAACTGGGTCATTTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
*
5279 GACCACATTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
* *
5333 GACCACATTGGGTCATCTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
*
5387 GACCACACT--G--------A-ATCAACTTAGATCTCTGAAAAGTTCTATGAAA
1 GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
5430 GACCACACTGGGTCAA
1 GACCACACTGGGTCAA
5446 AGACCACACT
Statistics
Matches: 438, Mismatches: 40, Indels: 32
0.86 0.08 0.06
Matches are distributed among these distances:
43 40 0.09
44 1 0.00
45 1 0.00
52 1 0.00
53 6 0.01
54 368 0.84
55 21 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (54 bp):
GACCACACTGGGTCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATGAAA
Found at i:5449 original size:17 final size:17
Alignment explanation
Indices: 5427--5461 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5417 AAGTTCTATG
5427 AAAGACCACACTGGGTC
1 AAAGACCACACTGGGTC
5444 AAAGACCACACTGGGTC
1 AAAGACCACACTGGGTC
5461 A
1 A
5462 TCTTAAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (17 bp):
AAAGACCACACTGGGTC
Found at i:5716 original size:111 final size:111
Alignment explanation
Indices: 5587--6265 Score: 597
Period size: 111 Copynumber: 6.1 Consensus size: 111
5577 TTGAAGAGAC
* * ** *
5587 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATTTTGAACAAGATTT
1 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAACCTTAAACAAGATTT
* * * *
5652 TGATGAGACATCTAAATAGGGACCTTAAATAAGGATTTGATAAGAA
66 TGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * * * ** * * *
5698 AGCTAAACCGAGATCTTAAACAAAAATTTTGACAA-AAATCCTAAACAGGCACCTTAAACAAAAA
1 ACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAA-CCTAAACAGGAACCTTAAAC-AAGA
* * * *
5762 TTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAA
63 TTTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * * * * *
5811 ACCTAAACAGGGATCTTAAACAA-GATTTTGATGAGACACCTAAATAGGGACCTTAAATAAAGA-
1 ACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAACCTAAACAGGAACCTTAAA-CAAGAT
* * * * * * *
5874 TTTAATAAGAAACCTAAACAGGAATCTTGAACAA-GATGTTGATGAGAC
64 TTTGATAAGACACCTAAACAGGGACCTTAAACAAGGAT-TTGATAAGAA
* *
5922 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACATGG-ACCTTAAATAAGGA-
1 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACA-GGAACCTTAAACAA-GAT
* * * *
5985 TTTAATAAGACACCTAAACAAGGATCTTAAACAAGGATTTGATAAGAC
64 TTTGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
* * * *
6033 ACCTAAACAGGGGCCTTAAATAAGGATTTGATAAGAAACCTAAATAGGGATCTTAAACAAGATTT
1 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAACCTTAAACAAGATTT
* *** ** *
6098 TGATGAGACACCTAAACATAAATATTGAACAA-GATTTTGAT--GAA
66 TGATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTGATAAGAA
* * * * *
6142 ACAACTAAATATGGACATTAAATAAGGATTTGATAA-AACACCTAAACAGGAATCTTGAACAAGA
1 AC--CTAAACAGGGACCTTAAATAAGGATTTGATAAGAA-ACCTAAACAGGAACCTTAAACAAGA
* * * *
6206 TTTTGATGAA-ACACCTAAATATGGACCTTAAATAAGGATTTGATAAGAC
63 TTTTGAT-AAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
6255 ACCTAAACAGG
1 ACCTAAACAGG
6266 AATCTTGAAC
Statistics
Matches: 467, Mismatches: 81, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
109 4 0.01
110 13 0.03
111 318 0.68
112 60 0.13
113 72 0.15
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.24
Consensus pattern (111 bp):
ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAACCTTAAACAAGATTT
TGATAAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA
Found at i:6266 original size:74 final size:74
Alignment explanation
Indices: 5774--6288 Score: 592
Period size: 74 Copynumber: 7.0 Consensus size: 74
5764 TTGACAAGAA
* * * * *
5774 ACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTT
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTT
*
5839 TGATGAGAC
66 TGATGAAAC
* * * *
5848 ACCTAAATAGGGACCTTAAATAAAGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAGATGT
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTT
*
5913 TGATGAGAC
66 TGATGAAAC
* * * *
5922 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACATGG-ACCTTAAATAAGGA-
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACA-GGAATCTTGAACAA-GAT
*
5985 TTTAAT-AAGAC
64 TTTGATGAA-AC
* * * * *** * *
5996 ACCTAAACAAGGATCTTAAACAAGGATTTGATAAGACACCTAAACAGGGGCCTTAAATAAGGA-T
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAA-GATT
*
6060 TTGAT-AAGAA
65 TTGATGAA-AC
* * * ** *
6070 ACCTAAATAGGGATCTTAAACAA-GATTTTGATGAGACACCTAAACATAAATATTGAACAAGATT
1 ACCTAAATAGGGACCTTAAATAAGGA-TTTGATAAGACACCTAAACAGGAATCTTGAACAAGATT
6134 TTGATGAAAC
65 TTGATGAAAC
* * * *
6144 AACTAAATATGGACATTAAATAAGGATTTGATAAAACACCTAAACAGGAATCTTGAACAAGATTT
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTT
6209 TGATGAAAC
66 TGATGAAAC
* *
6218 ACCTAAATATGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGGTTT
1 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTT
6283 TGATGA
66 TGATGA
6289 GACTGAATTT
Statistics
Matches: 384, Mismatches: 49, Indels: 16
0.86 0.11 0.04
Matches are distributed among these distances:
73 7 0.02
74 369 0.96
75 8 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.24
Consensus pattern (74 bp):
ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTT
TGATGAAAC
Found at i:6285 original size:37 final size:37
Alignment explanation
Indices: 5583--6291 Score: 537
Period size: 37 Copynumber: 19.1 Consensus size: 37
5573 GATTTTGAAG
* * *
5583 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* ** * *
5620 AGAAACCTAAACAGGAATTTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGAACCTTAAACAAGGA-TTTGATA
* * * *
5657 AGACATCTAAATAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* * * * ** *
5694 AGAAAGCTAAAC-CGAGATCTTAAACAAAAATTTTGACA
1 AGACACCTAAACAGGA-ACCTTAAACAAGGA-TTTGATA
* * ** *
5732 A-AAATCCTAAACAGGCACCTTAAACAAAAATTTTGACA
1 AGACA-CCTAAACAGGAACCTTAAACAAGGA-TTTGATA
* * *
5770 AGAAACCTAAACAGGCACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* * * *
5807 AGAAACCTAAACAGGGATCTTAAACAA-GATTTTGATG
1 AGACACCTAAACAGGAACCTTAAACAAGGA-TTTGATA
* * * * *
5844 AGACACCTAAATAGGGACCTTAAATAAAGATTTAATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* * * *
5881 AGAAACCTAAACAGGAATCTTGAACAA-GATGTTGATG
1 AGACACCTAAACAGGAACCTTAAACAAGGAT-TTGATA
* *
5918 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* *
5955 AGACACCTAAACATGG-ACCTTAAATAAGGATTTAATA
1 AGACACCTAAACA-GGAACCTTAAACAAGGATTTGATA
*
5992 AGACACCTAAACAAGG-ATCTTAAACAAGGATTTGATA
1 AGACACCTAAAC-AGGAACCTTAAACAAGGATTTGATA
** *
6029 AGACACCTAAACAGGGGCCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
* * * * *
6066 AGAAACCTAAATAGGGATCTTAAACAA-GATTTTGATG
1 AGACACCTAAACAGGAACCTTAAACAAGGA-TTTGATA
** ** *
6103 AGACACCTAAACATAAATATTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGAACCTTAAACAAGGA-TTTGAT-A
* * * *
6141 A-ACAACTAAATATGG-ACATTAAATAAGGATTTGATA
1 AGACACCTAAACA-GGAACCTTAAACAAGGATTTGATA
* * *
6177 AAACACCTAAACAGGAATCTTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGAACCTTAAACAAGGA-TTTGAT-A
* *
6215 A-ACACCTAAATATGG-ACCTTAAATAAGGATTTGATA
1 AGACACCTAAACA-GGAACCTTAAACAAGGATTTGATA
* * * *
6251 AGACACCTAAACAGGAATCTTGAACAAGGTTTTGATG
1 AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
6288 AGAC
1 AGAC
6292 TGAATTTTTC
Statistics
Matches: 543, Mismatches: 103, Indels: 52
0.78 0.15 0.07
Matches are distributed among these distances:
36 23 0.04
37 440 0.81
38 76 0.14
39 4 0.01
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (37 bp):
AGACACCTAAACAGGAACCTTAAACAAGGATTTGATA
Found at i:6916 original size:2 final size:2
Alignment explanation
Indices: 6911--6939 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6901 ATATTCAGGA
6911 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6940 AAATAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.