Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012766.1 Corchorus olitorius cultivar O-4 contig12799, 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: 25163
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:374 original size:29 final size:29
Alignment explanation
Indices: 341--396 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
331 ATACGGACTG
* *
341 TCACTTTGCATCC-AACTTTTTTATTTTGA
1 TCACTTTGCACCCTAA-TGTTTTATTTTGA
370 TCACTTTGCACCCTAATGTTTTATTTT
1 TCACTTTGCACCCTAATGTTTTATTTT
397 TGTTCTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (29 bp):
TCACTTTGCACCCTAATGTTTTATTTTGA
Found at i:2800 original size:2 final size:2
Alignment explanation
Indices: 2793--2820 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2783 TACTTACTAG
2793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2821 GTTAATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3810 original size:21 final size:21
Alignment explanation
Indices: 3786--3852 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3776 AATTCTCTGT
3786 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
3807 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
3828 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
3849 AAAT
1 AAAT
3853 CCTAATCCTT
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:3832 original size:42 final size:42
Alignment explanation
Indices: 3773--3853 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
3763 GCTAAGTCTT
3773 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
3815 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
3854 CTAATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:3991 original size:56 final size:56
Alignment explanation
Indices: 3919--4028 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
3909 TTTATTTTGT
* *
3919 AGAATAATTAAGTAGAGATAAAGGAATATGATTTATTATAGCATTTATTGTGTGGA
1 AGAATAATTAAGTAGAGATAAAGGAATAGGATTTATTATAACATTTATTGTGTGGA
** *
3975 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTG
1 AGAATAATTAAGTAGAGATAAAGGAATAGGATTTATTATAACATTTATTGTGTG
4029 AAAGGAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAAAGGAATAGGATTTATTATAACATTTATTGTGTGGA
Found at i:5592 original size:1 final size:1
Alignment explanation
Indices: 5586--5620 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
5576 CTTGGTTTTG
5586 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5621 GAGAGAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13690 original size:2 final size:2
Alignment explanation
Indices: 13638--13671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13628 ACCATATCCA
13638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13672 TAATTAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15180 original size:2 final size:2
Alignment explanation
Indices: 15173--15206 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15163 TTGCTTATTT
15173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15207 GGACTCCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17567 original size:123 final size:127
Alignment explanation
Indices: 17335--17586 Score: 395
Period size: 131 Copynumber: 2.0 Consensus size: 127
17325 TAAGAAATAA
* *
17335 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAAT---ATA-
* *
17400 GTATAAGGATATTGGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTA
62 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTA
17465 T
127 T
17466 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAAT-TA-TA-
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAATATAGTAT
*
17528 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
17587 TTAAACAATG
Statistics
Matches: 116, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
123 54 0.47
124 2 0.02
125 2 0.02
127 2 0.02
131 56 0.48
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAT
Found at i:18114 original size:21 final size:24
Alignment explanation
Indices: 18085--18135 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
18075 TTTTGAACTC
18085 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
18108 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
18131 ATTAT
1 ATTAT
18136 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:18130 original size:25 final size:25
Alignment explanation
Indices: 18085--18133 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18075 TTTTGAACTC
*
18085 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
18110 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
18134 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:19657 original size:9 final size:9
Alignment explanation
Indices: 19639--19669 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
19629 TGTTCGATTC
19639 ATAT-TAGT
1 ATATATAGT
19647 ATATATAGT
1 ATATATAGT
19656 ATATATAGT
1 ATATATAGT
19665 ATATA
1 ATATA
19670 CTCTCTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (9 bp):
ATATATAGT
Found at i:20865 original size:24 final size:24
Alignment explanation
Indices: 20838--20886 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20828 ATCCAGTCAA
20838 ACAAAGTTAACTTGTAGAAAGTAT
1 ACAAAGTTAACTTGTAGAAAGTAT
20862 ACAAAGTTAACTTGTAGAAAGTAT
1 ACAAAGTTAACTTGTAGAAAGTAT
20886 A
1 A
20887 TGAAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (24 bp):
ACAAAGTTAACTTGTAGAAAGTAT
Found at i:24570 original size:27 final size:27
Alignment explanation
Indices: 24512--24564 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
24502 CTTATGTTTT
24512 GTTTTTGAGACAAAATAATCCCTTATA
1 GTTTTTGAGACAAAATAATCCCTTATA
* * *
24539 TTTTTTGGGGACAAATTAATCCCTTA
1 GTTTTT-GAGACAAAATAATCCCTTA
24565 CGTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (27 bp):
GTTTTTGAGACAAAATAATCCCTTATA
Found at i:24706 original size:30 final size:31
Alignment explanation
Indices: 24672--24735 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
24662 AAGGGACTAA
*
24672 TTTGTCCCATAA-AAAAACATAAGAGATTAT
1 TTTGTCCCAAAAGAAAAACATAAGAGATTAT
* *
24702 TTTGTTCCAAAAGAAAAACATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAGATTAT
24733 TTT
1 TTT
24736 TATATTTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGAGATTAT
Done.