Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024050.1 Corchorus olitorius cultivar O-4 contig24083, 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: 15287
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Found at i:1523 original size:5 final size:6
Alignment explanation
Indices: 1501--1549 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
1491 GAAAAACACA
*
1501 AAAACAC AAAAAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
1550 CTAAAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 27 0.71
7 7 0.18
8 4 0.11
ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:1523 original size:20 final size:20
Alignment explanation
Indices: 1493--1549 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1483 AAAATTAAGA
1493 AAAACACAAAAACACAAAAAC-
1 AAAA-ACAAAAACA-AAAAACG
*
1514 AAAAACAAAAACAAAATACG
1 AAAAACAAAAACAAAAAACG
*
1534 AAAAATAAAAACAAAA
1 AAAAACAAAAACAAAA
1550 CTAAAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.73
21 4 0.12
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.04
Consensus pattern (20 bp):
AAAAACAAAAACAAAAAACG
Found at i:1527 original size:26 final size:27
Alignment explanation
Indices: 1493--1550 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1483 AAAATTAAGA
1493 AAAACACAAAA-ACACAAAAACAAAAAC
1 AAAACACAAAATAC-CAAAAACAAAAAC
* *
1520 AAAA-ACAAAATACGAAAAATAAAAAC
1 AAAACACAAAATACCAAAAACAAAAAC
1546 AAAAC
1 AAAAC
1551 TAAAGGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.78, C:0.17, G:0.02, T:0.03
Consensus pattern (27 bp):
AAAACACAAAATACCAAAAACAAAAAC
Found at i:2957 original size:14 final size:14
Alignment explanation
Indices: 2938--2966 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2928 AAATCTACTT
2938 TTATTCACAATATA
1 TTATTCACAATATA
2952 TTATTCACAATATA
1 TTATTCACAATATA
2966 T
1 T
2967 AAAGTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATTCACAATATA
Found at i:5755 original size:23 final size:23
Alignment explanation
Indices: 5724--5774 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5714 ATTTAATTTT
5724 TTTAATAAA-AGAAATAATTAAAA
1 TTTAATAAATAGAAA-AATTAAAA
* *
5747 TTTATTAAATATAAAAATTAAAA
1 TTTAATAAATAGAAAAATTAAAA
*
5770 ATTAA
1 TTTAA
5775 AACACACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TTTAATAAATAGAAAAATTAAAA
Found at i:8922 original size:12 final size:12
Alignment explanation
Indices: 8905--8930 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8895 CTGATGCCTG
8905 ATGGATACATAT
1 ATGGATACATAT
8917 ATGGATACATAT
1 ATGGATACATAT
8929 AT
1 AT
8931 CTAATACTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGGATACATAT
Found at i:12760 original size:76 final size:77
Alignment explanation
Indices: 12597--12921 Score: 386
Period size: 76 Copynumber: 4.2 Consensus size: 77
12587 AAAAAGACAA
* *
12597 GATGGGATCTTTCCCTAAAT-TAAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
1 GATGGGATCTTTCCCTAAATCGAAAACTTCTAAAAAACTTGATGGGATCTTTCCC-AAATTAAAA
12661 ACTTTGAAGACTG
65 ACTTTGAAGACTG
*
12674 GATGGGATCTTTCCCTAAATCGAAAGAC-T-TAAACAAACTTGATGGGATCTTTCCC-AATTAGA
1 GATGGGATCTTTCCCTAAATCGAAA-ACTTCTAAA-AAACTTGATGGGATCTTTCCCAAATTAAA
*
12736 AA-TCTTGAA-AGCTT
64 AACT-TTGAAGA-CTG
* * *
12750 GATGGGATCTTTCCCTAATTTTG-AAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAA
1 GATGGGATCTTTCCCTAA-ATCGAAAACTTCTAAAAAACTTGATGGGATCTTTCCC-AAATTAAA
12814 AACTTTGAAGACTG
64 AACTTTGAAGACTG
*
12828 GATGGGATCTTTCCCTAAATCGAAAGAC-TC-AAACAAACTTGATGGGATCTTTCCC-AATTAGA
1 GATGGGATCTTTCCCTAAATCGAAA-ACTTCTAAA-AAACTTGATGGGATCTTTCCCAAATTAAA
*
12890 AA-TCTTGAA-AGCTT
64 AACT-TTGAAGA-CTG
12904 GATGGGATCTTTCCCTAA
1 GATGGGATCTTTCCCTAA
12922 TTTTGAAATC
Statistics
Matches: 217, Mismatches: 14, Indels: 35
0.82 0.05 0.13
Matches are distributed among these distances:
75 6 0.03
76 90 0.41
77 32 0.15
78 83 0.38
79 6 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (77 bp):
GATGGGATCTTTCCCTAAATCGAAAACTTCTAAAAAACTTGATGGGATCTTTCCCAAATTAAAAA
CTTTGAAGACTG
Found at i:12843 original size:78 final size:76
Alignment explanation
Indices: 12597--12964 Score: 380
Period size: 76 Copynumber: 4.8 Consensus size: 76
12587 AAAAAGACAA
*
12597 GATGGGATCTTTCCCTAAATTAAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAAA
1 GATGGGATCTTTCCCTAAATTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAAA
12662 CTTTGAAGACTG
66 CTTTGAA-ACTG
* * *
12674 GATGGGATCTTTCCCTAAATCGAAAGAC-T-TAAACAAACTTGATGGGATCTTTCCC--AATTAG
1 GATGGGATCTTTCCCTAAATTG-AA-ACTTCTGAA-AAACTTGATGGGATCTTTCCCTAAATTAA
*
12735 AAA-TCTTGAAAGCTT
63 AAACT-TTGAAA-CTG
*
12750 GATGGGATCTTTCCCTAATTTTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
1 GATGGGATCTTTCCCTAA-ATTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
12815 ACTTTGAAGACTG
65 ACTTTGAA-ACTG
* * *
12828 GATGGGATCTTTCCCTAAATCGAAAGAC-TC-AAACAAACTTGATGGGATCTTTCCC--AATTAG
1 GATGGGATCTTTCCCTAAATTG-AA-ACTTCTGAA-AAACTTGATGGGATCTTTCCCTAAATTAA
*
12889 AAA-TCTTGAAAGCTT
63 AAACT-TTGAAA-CTG
* * *
12904 GATGGGATCTTTCCCTAATTTTGAAA-TCCTTGAAAAATACTTTGGTGGGATCTTTCCCTAA
1 GATGGGATCTTTCCCTAA-ATTGAAACTTC-TG-AAAA-AC-TTGATGGGATCTTTCCCTAA
12965 TTTTGAAATC
Statistics
Matches: 245, Mismatches: 20, Indels: 48
0.78 0.06 0.15
Matches are distributed among these distances:
75 8 0.03
76 92 0.38
77 36 0.15
78 86 0.35
79 22 0.09
81 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (76 bp):
GATGGGATCTTTCCCTAAATTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAAA
CTTTGAAACTG
Found at i:12899 original size:154 final size:154
Alignment explanation
Indices: 12597--12964 Score: 641
Period size: 154 Copynumber: 2.4 Consensus size: 154
12587 AAAAAGACAA
* *
12597 GATGGGATCTTTCCCTAA-ATTAAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
1 GATGGGATCTTTCCCTAATTTTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
*
12661 ACTTTGAAGACTGGATGGGATCTTTCCCTAAATCGAAAGACTTAAACAAACTTGATGGGATCTTT
66 ACTTTGAAGACTGGATGGGATCTTTCCCTAAATCGAAAGACTCAAACAAACTTGATGGGATCTTT
12726 CCCAATTAGAAATCTTGAAAGCTT
131 CCCAATTAGAAATCTTGAAAGCTT
12750 GATGGGATCTTTCCCTAATTTTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
1 GATGGGATCTTTCCCTAATTTTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
12815 ACTTTGAAGACTGGATGGGATCTTTCCCTAAATCGAAAGACTCAAACAAACTTGATGGGATCTTT
66 ACTTTGAAGACTGGATGGGATCTTTCCCTAAATCGAAAGACTCAAACAAACTTGATGGGATCTTT
12880 CCCAATTAGAAATCTTGAAAGCTT
131 CCCAATTAGAAATCTTGAAAGCTT
* *
12904 GATGGGATCTTTCCCTAATTTTGAAA-TCCTTGAAAAATACTTTGGTGGGATCTTTCCCTAA
1 GATGGGATCTTTCCCTAATTTTGAAACTTC-TG-AAAA-AC-TTGATGGGATCTTTCCCTAA
12965 TTTTGAAATC
Statistics
Matches: 205, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
153 20 0.10
154 160 0.78
155 4 0.02
156 2 0.01
157 19 0.09
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (154 bp):
GATGGGATCTTTCCCTAATTTTGAAACTTCTGAAAAACTTGATGGGATCTTTCCCTAAATTAAAA
ACTTTGAAGACTGGATGGGATCTTTCCCTAAATCGAAAGACTCAAACAAACTTGATGGGATCTTT
CCCAATTAGAAATCTTGAAAGCTT
Found at i:12967 original size:43 final size:43
Alignment explanation
Indices: 12752--13026 Score: 225
Period size: 43 Copynumber: 6.8 Consensus size: 43
12742 GAAAGCTTGA
*
12752 TGGGATCTTTCCCTAATTTTGAAA-CTTCTG-AAAA-AC-TTGA
1 TGGGATCTTTCCCTAATTTTGAAATCTT-TGAAAAATACTTTGG
* * * *
12792 TGGGATCTTTCCCTAA-ATTAAAAACTTTG---AAGAC--TGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
* * * * *
12829 ATGGGATCTTTCCCTAA-ATCGAAAGAC--TCAAACAA-AC-TTGA
1 -TGGGATCTTTCCCTAATTTTGAAA-TCTTTGAAA-AATACTTTGG
* * *
12870 TGGGATCTTTCCC-AA-TTAGAAATC-TTG--AAA-GC-TTGA
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
*
12906 TGGGATCTTTCCCTAATTTTGAAATCCTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
12949 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
*
12992 TGGAATCTTTCCCTAATTTTGAAATCTTTGAAAAA
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAA
13027 CTTGATTTTT
Statistics
Matches: 201, Mismatches: 17, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
36 20 0.10
37 8 0.04
38 32 0.16
39 20 0.10
40 34 0.17
41 7 0.03
42 1 0.00
43 79 0.39
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (43 bp):
TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
Found at i:13070 original size:29 final size:31
Alignment explanation
Indices: 13005--13076 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
12995 AATCTTTCCC
*
13005 TAATTTTGAAATCTTTGAAAAACTTGATTTT
1 TAATTTTGAAATCTTTGAAAAACTTGATTAT
* * * *
13036 TGATTTTG-AATTTTTGAAAACCTT-CTTAT
1 TAATTTTGAAATCTTTGAAAAACTTGATTAT
*
13065 TAATTTGGAAAT
1 TAATTTTGAAAT
13077 ATTCAATTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 9 0.27
30 17 0.52
31 7 0.21
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (31 bp):
TAATTTTGAAATCTTTGAAAAACTTGATTAT
Found at i:14689 original size:21 final size:22
Alignment explanation
Indices: 14651--14691 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14641 TCACCGAATC
*
14651 GAAATTTCGAACCCTCCGATCT
1 GAAAATTCGAACCCTCCGATCT
*
14673 GAAAATTC-AACCGTCCGAT
1 GAAAATTCGAACCCTCCGAT
14692 GTTTCTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (22 bp):
GAAAATTCGAACCCTCCGATCT
Done.