Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022016.1 Corchorus olitorius cultivar O-4 contig22049, 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: 20087
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3751 original size:21 final size:21
Alignment explanation
Indices: 3727--3793 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3717 AATTCTCTGT
3727 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
3748 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
3769 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
3790 AAAT
1 AAAT
3794 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:3774 original size:42 final size:42
Alignment explanation
Indices: 3715--3794 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
3705 CTAAGTCTTT
3715 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
*
3757 AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
3795 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
AAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAG
Found at i:3949 original size:56 final size:56
Alignment explanation
Indices: 3860--3973 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
3850 TTAATTTTGT
*
3860 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
3916 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
3972 AG
1 AG
3974 GAAACAAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:4464 original size:3 final size:3
Alignment explanation
Indices: 4458--4488 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4448 TCCAAACGAT
4458 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
4489 CACGTTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6289 original size:7 final size:7
Alignment explanation
Indices: 6277--6301 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6267 ATCAAACCAC
6277 CTCAAGG
1 CTCAAGG
6284 CTCAAGG
1 CTCAAGG
6291 CTCAAGG
1 CTCAAGG
6298 CTCA
1 CTCA
6302 GCGTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (7 bp):
CTCAAGG
Found at i:7406 original size:62 final size:62
Alignment explanation
Indices: 7333--7456 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
7323 TTTCCCTTGT
7333 GAGTGTTTCCTCTTGTCCTCGTATAAGCTCTCTTGGCGGCTGAATTTCTACTATTTTTTTTG
1 GAGTGTTTCCTCTTGTCCTCGTATAAGCTCTCTTGGCGGCTGAATTTCTACTATTTTTTTTG
*
7395 GAGTGTTTCCTCTTGTCCTCGTATAAGCTCTCTTGGCGGCTGAATTTCTACTTTTTTTTTTG
1 GAGTGTTTCCTCTTGTCCTCGTATAAGCTCTCTTGGCGGCTGAATTTCTACTATTTTTTTTG
7457 ATTACACTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.48
Consensus pattern (62 bp):
GAGTGTTTCCTCTTGTCCTCGTATAAGCTCTCTTGGCGGCTGAATTTCTACTATTTTTTTTG
Found at i:9050 original size:26 final size:27
Alignment explanation
Indices: 9021--9071 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9011 GTTGGTCTTT
9021 TTAAGTTCA-CTT-GTAATTTAGATTAG
1 TTAA-TTCATCTTGGTAATTTAGATTAG
*
9047 TTAATTCATCTTGGTCATTTAGATT
1 TTAATTCATCTTGGTAATTTAGATT
9072 GCATTTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 7 0.32
27 11 0.50
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (27 bp):
TTAATTCATCTTGGTAATTTAGATTAG
Found at i:15812 original size:38 final size:38
Alignment explanation
Indices: 15769--16002 Score: 161
Period size: 40 Copynumber: 5.8 Consensus size: 38
15759 AAAAACTTTG
15769 ATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAACTGA
1 ATGGGATCTTT-CCCTAAATTGAAAACTTTGAAAACTGA
* * *
15807 ATGGGATCTTTCCCTAAATCGCAAATTTTGAAAAAACTTG-
1 ATGGGATCTTTCCCTAAATTGAAAACTTTG--AAAAC-TGA
* *
15847 ATGGGATCTTTCCCTAAATTAAAAACTTTGAAGACT-A
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAACTGA
* * * *
15884 GATAGGATCTTTCCCTAAATAAATAAAAAACTTTAAAAAGAAACTGG
1 -ATGGGATCTTTCCCTAAAT---T-GAAAACTTT---GA-AAACTGA
* * * **
15931 ATAGGATCTTTCCCTAAATCGCAAGACTTAAACAAACCTG-
1 ATGGGATCTTTCCCTAAATTG-AAAACTTTGA-AAA-CTGA
*
15971 ATGGGATCTTTCCCTAAATTAAAAACTTTGAA
1 ATGGGATCTTTCCCTAAATTGAAAACTTTGAA
16003 TTGAAAACTT
Statistics
Matches: 156, Mismatches: 23, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
37 5 0.03
38 45 0.29
39 7 0.04
40 54 0.35
41 6 0.04
42 9 0.06
43 6 0.04
45 1 0.01
46 23 0.15
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (38 bp):
ATGGGATCTTTCCCTAAATTGAAAACTTTGAAAACTGA
Found at i:15848 original size:78 final size:79
Alignment explanation
Indices: 15753--15903 Score: 227
Period size: 78 Copynumber: 1.9 Consensus size: 79
15743 GACTCAATTT
* *
15753 TTTTAAAAAAACTTTGATGGGATCTTTCCCCT-AATTGAAAACTTTGAAAACT-GAATGGGATCT
1 TTTTAAAAAAACTTTGATGGGATCTTT-CCCTAAATTAAAAACTTTGAAAACTAG-ATAGGATCT
15816 TTCCCTAAATCGCAAA
64 TTCCCTAAATCGCAAA
* *
15832 TTTTGAAAAAAC-TTGATGGGATCTTTCCCTAAATTAAAAACTTTGAAGACTAGATAGGATCTTT
1 TTTTAAAAAAACTTTGATGGGATCTTTCCCTAAATTAAAAACTTTGAAAACTAGATAGGATCTTT
15896 CCCTAAAT
66 CCCTAAAT
15904 AAATAAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
77 4 0.06
78 50 0.76
79 12 0.18
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (79 bp):
TTTTAAAAAAACTTTGATGGGATCTTTCCCTAAATTAAAAACTTTGAAAACTAGATAGGATCTTT
CCCTAAATCGCAAA
Found at i:15854 original size:40 final size:40
Alignment explanation
Indices: 15753--15903 Score: 143
Period size: 38 Copynumber: 3.9 Consensus size: 40
15743 GACTCAATTT
* *
15753 TTTTAAAAAAACTTTGATGGGATCTTTCCCCT-AATTGAAAA
1 TTTTGAAAAAAC-TTGATGGGATCTTT-CCCTAAATCGAAAA
* *
15794 CTTTG--AAAAC-TGAATGGGATCTTTCCCTAAATCGCAAA
1 TTTTGAAAAAACTTG-ATGGGATCTTTCCCTAAATCGAAAA
**
15832 TTTTGAAAAAACTTGATGGGATCTTTCCCTAAATTAAAAA
1 TTTTGAAAAAACTTGATGGGATCTTTCCCTAAATCGAAAA
* * * *
15872 CTTTG--AAGACTAGATAGGATCTTTCCCTAAAT
1 TTTTGAAAAAACTTGATGGGATCTTTCCCTAAAT
15904 AAATAAAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
37 6 0.06
38 46 0.49
39 5 0.05
40 31 0.33
41 5 0.05
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (40 bp):
TTTTGAAAAAACTTGATGGGATCTTTCCCTAAATCGAAAA
Found at i:19949 original size:62 final size:63
Alignment explanation
Indices: 19868--20016 Score: 212
Period size: 63 Copynumber: 2.4 Consensus size: 63
19858 TCTTAAAAAT
* *
19868 TTTTAGGAACTGTCTTCAGAACCCATCTTTGTGAACT-ATCTTCAGATTCTCTCTTA-ATTACC
1 TTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAACTGATCTTCAGATTCACTCTTATA-TACC
* * *
19930 TTTTAGGAACTGTCCTCAGAACCCATCTTCGTGAACTGTTCTTCAGATTCACTCTTATATATC
1 TTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAACTGATCTTCAGATTCACTCTTATATACC
* *
19993 ATTCAGGAACTGTCTTCAGAACCC
1 TTTTAGGAACTGTCTTCAGAACCC
20017 GTCTATGAGC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
62 35 0.45
63 41 0.53
64 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (63 bp):
TTTTAGGAACTGTCTTCAGAACCCATCTTCGTGAACTGATCTTCAGATTCACTCTTATATACC
Done.