Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020053.1 Corchorus olitorius cultivar O-4 contig20086, 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: 21519
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3315 original size:5 final size:5
Alignment explanation
Indices: 3305--3329 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3295 AATTTTAAAT
3305 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
3330 CATATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:5507 original size:14 final size:14
Alignment explanation
Indices: 5488--5515 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5478 GCCACCCTGC
5488 CTAAAAAAATGTGT
1 CTAAAAAAATGTGT
5502 CTAAAAAAATGTGT
1 CTAAAAAAATGTGT
5516 ATATAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
CTAAAAAAATGTGT
Found at i:7086 original size:19 final size:19
Alignment explanation
Indices: 7062--7102 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
7052 TTACCAATGA
7062 CACCATGTATGGTTATTAC
1 CACCATGTATGGTTATTAC
7081 CACCATGTATGGTTATTAC
1 CACCATGTATGGTTATTAC
7100 CAC
1 CAC
7103 TAATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (19 bp):
CACCATGTATGGTTATTAC
Found at i:9038 original size:17 final size:17
Alignment explanation
Indices: 9016--9048 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9006 TTTTATGGAT
9016 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
9033 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
9049 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:10058 original size:22 final size:22
Alignment explanation
Indices: 10037--10079 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10027 TAGTTGAGTA
10037 AAAAT-ATAAAAGTAAAATAGT
1 AAAATGATAAAAGTAAAATAGT
*
10058 AAAATGATAAAATTAAAATAGT
1 AAAATGATAAAAGTAAAATAGT
10080 TATAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (22 bp):
AAAATGATAAAAGTAAAATAGT
Found at i:10059 original size:92 final size:93
Alignment explanation
Indices: 9973--10140 Score: 241
Period size: 92 Copynumber: 1.8 Consensus size: 93
9963 AGTAATATCG
**
9973 TAAAAATAAAATAGATATAAAAATATTATCTTTAATTAAAT-AAAATAGAGTTTCTAGTTGAG-T
1 TAAAAATAAAATAGATATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTG-GCT
10036 AAAAATATAAAAGTAAAATAGTAAAATGA
65 AAAAATATAAAAGTAAAATAGTAAAATGA
* * ** *
10065 TAAAATTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGGCTA
1 TAAAAATAAAATAGATATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGGCTA
*
10130 AAACTATAAAA
66 AAAATATAAAA
10141 ATTTAAACAA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
92 36 0.55
93 30 0.45
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (93 bp):
TAAAAATAAAATAGATATAAAAATATTAGATTTAATTAAATAAAAATAGAGTTTCTAGTTGGCTA
AAAATATAAAAGTAAAATAGTAAAATGA
Found at i:10223 original size:31 final size:31
Alignment explanation
Indices: 10176--10237 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
10166 ATATTCGACA
* * * *
10176 AATAAGGGTATGATAGGTGATTGAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
10207 AATAAGGATATAATAGGCGATTCAAAAGTTT
1 AATAAGGATATAATAGGCGATTCAAAAGTTT
10238 TACAAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (31 bp):
AATAAGGATATAATAGGCGATTCAAAAGTTT
Found at i:12632 original size:11 final size:11
Alignment explanation
Indices: 12616--12645 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12606 AAGGAAAATA
12616 TGAAGAACGAG
1 TGAAGAACGAG
12627 TGAAGAACGAG
1 TGAAGAACGAG
*
12638 TGATGAAC
1 TGAAGAAC
12646 AGGGTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.13
Consensus pattern (11 bp):
TGAAGAACGAG
Found at i:15845 original size:19 final size:18
Alignment explanation
Indices: 15821--15856 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15811 TGAAGATTTA
15821 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
15840 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
15857 ATGGAGCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:16711 original size:25 final size:25
Alignment explanation
Indices: 16665--16714 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16655 ATATATTAGG
**
16665 ATTTTTAAAAATATTCTCTTACAAT
1 ATTTTTAAAAATAAACTCTTACAAT
* *
16690 ATTTTTAGAAATAAACTTTTACAAT
1 ATTTTTAAAAATAAACTCTTACAAT
16715 TATTCTACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTTTAAAAATAAACTCTTACAAT
Found at i:19886 original size:14 final size:16
Alignment explanation
Indices: 19862--19899 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
19852 GAGGTTGACG
*
19862 GAAAGCAATTAAAC-A
1 GAAAACAATTAAACTA
19877 -AAAACAATTAAACTA
1 GAAAACAATTAAACTA
19892 GAAAACAA
1 GAAAACAA
19900 AGCAAAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.66, C:0.13, G:0.08, T:0.13
Consensus pattern (16 bp):
GAAAACAATTAAACTA
Done.