Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019198.1 Corchorus olitorius cultivar O-4 contig19231, 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: 69139
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:688 original size:28 final size:27
Alignment explanation
Indices: 646--700 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
636 TTTTTATTTG
*
646 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
672 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
701 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:15298 original size:4 final size:4
Alignment explanation
Indices: 15273--15312 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
15263 TCTCATGATA
*
15273 AAAG AAA- AAA- AAA- AAAG TAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
15313 CACAACCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 9 0.27
4 24 0.73
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:17700 original size:3 final size:3
Alignment explanation
Indices: 17692--17746 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
17682 TCAGTGATCC
17692 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
17740 AAG AAG A
1 AAG AAG A
17747 GGAGGATGCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41866 original size:13 final size:13
Alignment explanation
Indices: 41850--41881 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41840 AACGCAGAAA
41850 AAGAAAGCAGGAG
1 AAGAAAGCAGGAG
41863 AAGAAAGCAGGAG
1 AAGAAAGCAGGAG
41876 AAGAAA
1 AAGAAA
41882 CGAAACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.34, T:0.00
Consensus pattern (13 bp):
AAGAAAGCAGGAG
Found at i:41906 original size:15 final size:17
Alignment explanation
Indices: 41874--41910 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
41864 AGAAAGCAGG
41874 AGAAGAAACGAAACCAAA
1 AGAAGAAAC-AAACCAAA
41892 AGAAGAAA-AAA-CAAA
1 AGAAGAAACAAACCAAA
41907 AGAA
1 AGAA
41911 AACGATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
18 8 0.42
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAGAAACAAACCAAA
Found at i:41922 original size:21 final size:21
Alignment explanation
Indices: 41898--41943 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41888 CAAAAGAAGA
*
41898 AAAAACAAA-AGAAAACGATAG
1 AAAAACAAAGA-AAAACGAAAG
41919 AAAAACAAAGAAAAACGAAAG
1 AAAAACAAAGAAAAACGAAAG
41940 AAAA
1 AAAA
41944 TAGCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (21 bp):
AAAAACAAAGAAAAACGAAAG
Found at i:41923 original size:11 final size:11
Alignment explanation
Indices: 41898--41943 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 11
41888 CAAAAGAAGA
*
41898 AAAAACAAAAG
1 AAAAACGAAAG
*
41909 -AAAACGATAG
1 AAAAACGAAAG
41919 AAAAAC-AAAG
1 AAAAACGAAAG
41929 AAAAACGAAAG
1 AAAAACGAAAG
41940 AAAA
1 AAAA
41944 TAGCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 17 0.57
11 13 0.43
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAACGAAAG
Found at i:42981 original size:30 final size:30
Alignment explanation
Indices: 42947--43007 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
42937 ATTTTTATAT
42947 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
* *
42977 TGACTTTTCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
43007 T
1 T
43008 ATCTTATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:48940 original size:83 final size:83
Alignment explanation
Indices: 48801--49003 Score: 406
Period size: 83 Copynumber: 2.4 Consensus size: 83
48791 ATCACAAGCA
48801 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAATTAGTAGTAAGCCTATCATGAGCAGCCAG
1 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAATTAGTAGTAAGCCTATCATGAGCAGCCAG
48866 CCAAAGAAACTACCAAGG
66 CCAAAGAAACTACCAAGG
48884 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAATTAGTAGTAAGCCTATCATGAGCAGCCAG
1 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAATTAGTAGTAAGCCTATCATGAGCAGCCAG
48949 CCAAAGAAACTACCAAGG
66 CCAAAGAAACTACCAAGG
48967 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAAT
1 ATATTATCAGAGATTTGTCTATTATAAAGCATGAAAT
49004 GTGCAATCTC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 120 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (83 bp):
ATATTATCAGAGATTTGTCTATTATAAAGCATGAAATTAGTAGTAAGCCTATCATGAGCAGCCAG
CCAAAGAAACTACCAAGG
Found at i:49399 original size:2 final size:2
Alignment explanation
Indices: 49387--49440 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
49377 TCAATATGAA
* *
49387 AT AT AT GT AT AT AT AT AT AT AT AT AT -T AT AT A- AA AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49426 AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT A
49441 AAATAATTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:49424 original size:22 final size:22
Alignment explanation
Indices: 49397--49445 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
49387 ATATATGTAT
*
49397 ATATATATATATATATTATATAAA
1 ATATA-ATATA-ATATAATATAAA
49421 ATATAATATAATATAATATAAA
1 ATATAATATAATATAATATAAA
49443 ATA
1 ATA
49446 ATTGAGTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.58
23 5 0.21
24 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAATATAATATAATATAAA
Found at i:49428 original size:5 final size:5
Alignment explanation
Indices: 49395--49447 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
49385 AAATATATGT
* * *
49395 ATATA TATATA TATATA TTAT- ATAAA ATATA ATATA ATATA ATATA AAATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
49446 AT
1 AT
49448 TGAGTGGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.05
5 27 0.68
6 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:49676 original size:23 final size:22
Alignment explanation
Indices: 49620--49686 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
49610 TAAATTTTTT
*
49620 TATAAACAAATATTAAT-ATATA
1 TATAAA-ACATATTAATAATATA
*
49642 TATATAAC-TATTAATAATATA
1 TATAAAACATATTAATAATATA
*
49663 TTTCAAAACATATT-A-AATATA
1 TAT-AAAACATATTAATAATATA
49684 TAT
1 TAT
49687 CTTATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 7 0.19
21 16 0.43
22 10 0.27
23 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
TATAAAACATATTAATAATATA
Found at i:53061 original size:18 final size:20
Alignment explanation
Indices: 53019--53063 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
53009 CACGACATGA
*
53019 ATATTATTACATTACATTAT
1 ATATAATTACATTACATTAT
53039 A-ATAATTA-ATTA-ATTAT
1 ATATAATTACATTACATTAT
53056 ATATAATT
1 ATATAATT
53064 CCTATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 6 0.26
20 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATAATTACATTACATTAT
Found at i:64414 original size:23 final size:23
Alignment explanation
Indices: 64384--64431 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
64374 CCAACCTAAA
64384 ACCAATTGACTATAGTTGGAGAG
1 ACCAATTGACTATAGTTGGAGAG
64407 ACCAATTGACTATAGTTGGAGAG
1 ACCAATTGACTATAGTTGGAGAG
64430 AC
1 AC
64432 TCTTCATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (23 bp):
ACCAATTGACTATAGTTGGAGAG
Found at i:68508 original size:101 final size:101
Alignment explanation
Indices: 68397--68584 Score: 322
Period size: 101 Copynumber: 1.9 Consensus size: 101
68387 GAGGGAGTAG
* *
68397 TTAATTAAAAAAATGGACATGTGTCAATTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGT
1 TTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGC
68462 CAGTGTATCAAATAATTACCCATATTTAAAACTTAA
66 CAGTGTATCAAATAATTACCCATATTTAAAACTTAA
* * *
68498 TTAATTAAAAAGATGGACATGTGTCAACTCCATAACCCGCTTGTGGAGTCCAAATTTTACACCGC
1 TTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGC
*
68563 CGGTGTATCAAATAATTACCCA
66 CAGTGTATCAAATAATTACCCA
68585 AAATAAAAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (101 bp):
TTAATTAAAAAAATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGC
CAGTGTATCAAATAATTACCCATATTTAAAACTTAA
Done.