Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014861.1 Corchorus capsularis cultivar CVL-1 contig14882, 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: 6594
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1359 original size:3 final size:3
Alignment explanation
Indices: 1351--1380 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1341 ATTTCAACTG
1351 CTT CTT CTT CTT CTT CTT CTT CTTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT C-TT CTT CT
1381 CCCCATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:4734 original size:32 final size:32
Alignment explanation
Indices: 4693--4757 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
4683 TGCTTCTCCA
4693 GGGCCATGATGGATGTATATACGAAAAATATT
1 GGGCCATGATGGATGTATATACGAAAAATATT
*
4725 GGGCCATGATGGATGTGTATACGAAAAATATT
1 GGGCCATGATGGATGTATATACGAAAAATATT
4757 G
1 G
4758 TTGGTTTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (32 bp):
GGGCCATGATGGATGTATATACGAAAAATATT
Found at i:5392 original size:21 final size:21
Alignment explanation
Indices: 5367--5501 Score: 100
Period size: 21 Copynumber: 6.4 Consensus size: 21
5357 CGACGACGAT
5367 GAGGAGAAGAAGAGAAAGAAG
1 GAGGAGAAGAAGAGAAAGAAG
*
5388 GAGGAGGAGAAGGAGAAA-AAG
1 GAGGAGAAGAA-GAGAAAGAAG
* *
5409 GAGGAGGAGAAGAAAGAAAAGGAG
1 GAGGAGAAGAAG--AG-AAAGAAG
* * *
5433 GAGGAGAAGGAGAGGAAGAAA
1 GAGGAGAAGAAGAGAAAGAAG
*
5454 GAGGAGAA-AGAGAGGAAGAAG
1 GAGGAGAAGA-AGAGAAAGAAG
*
5475 GA-GA-AAGAGGA-AAAGAAG
1 GAGGAGAAGAAGAGAAAGAAG
* *
5493 AAGCAGAAG
1 GAGGAGAAG
5502 GAGAAGGAGG
Statistics
Matches: 92, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
18 7 0.08
19 5 0.05
20 7 0.08
21 48 0.52
22 10 0.11
23 3 0.03
24 12 0.13
ACGTcount: A:0.55, C:0.01, G:0.44, T:0.00
Consensus pattern (21 bp):
GAGGAGAAGAAGAGAAAGAAG
Found at i:5395 original size:6 final size:6
Alignment explanation
Indices: 5383--5510 Score: 68
Period size: 6 Copynumber: 23.3 Consensus size: 6
5373 AAGAAGAGAA
* *
5383 AGAAGG AGGAGG AGAAGG AGAA-- A-AAGG AGGAGG AGAA-G A-AA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
* * *
5425 AAAAGG AGGAGG AGAAGG AG-AGG AAGAA-- AG-AGG AGAAAG AG-AGG
1 AGAAGG AGAAGG AGAAGG AGAAGG -AGAAGG AGAAGG AGAAGG AGAAGG
* * *
5469 AAGAAGG AGAA-- AG-AGG AAAAGA AGAAGC AGAAGG AGAAGG AG
1 -AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AG
5511 GAAAAGAAGG
Statistics
Matches: 93, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
3 4 0.04
4 9 0.10
5 13 0.14
6 63 0.68
7 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.45, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:5396 original size:24 final size:23
Alignment explanation
Indices: 5367--5477 Score: 126
Period size: 21 Copynumber: 5.0 Consensus size: 23
5357 CGACGACGAT
5367 GAGGAGAAGAAGAGAAAGAAGGAG
1 GAGGAGAAG-AGAGAAAGAAGGAG
5391 GAGGAGAAG-GAGAAA-AAGGAG
1 GAGGAGAAGAGAGAAAGAAGGAG
*
5412 GAGGAGAAGAAAG-AA-AAGGAG
1 GAGGAGAAGAGAGAAAGAAGGAG
* *
5433 GAGGAGAAGGAGAGGAAGAAAGAG
1 GAGGAGAA-GAGAGAAAGAAGGAG
*
5457 GA-GA-AAGAGAGGAAGAAGGAG
1 GAGGAGAAGAGAGAAAGAAGGAG
5478 AAAGAGGAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
21 45 0.57
22 14 0.18
23 4 0.05
24 16 0.20
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (23 bp):
GAGGAGAAGAGAGAAAGAAGGAG
Found at i:5416 original size:15 final size:16
Alignment explanation
Indices: 5392--5510 Score: 58
Period size: 15 Copynumber: 7.7 Consensus size: 16
5382 AAGAAGGAGG
5392 AGGAGAAGGAGAA-AA
1 AGGAGAAGGAGAAGAA
*
5407 AGGAGGAGGAGAAGAA
1 AGGAGAAGGAGAAGAA
*
5423 A-GAAAAGGAG--G--
1 AGGAGAAGGAGAAGAA
*
5434 AGGAGAAGGAG-AGGA
1 AGGAGAAGGAGAAGAA
* *
5449 A-GAAAGAGGAGAAAGAG
1 AGGAGA-AGGAG-AAGAA
*
5466 AGGAAGAAGGAGAA-AG
1 AGG-AGAAGGAGAAGAA
* *
5482 AGGAAAAGAAGAAGCAGA
1 AGGAGAAGGAGAAG-A-A
5500 AGGAGAAGGAG
1 AGGAGAAGGAG
5511 GAAAAGAAGG
Statistics
Matches: 78, Mismatches: 13, Indels: 23
0.68 0.11 0.20
Matches are distributed among these distances:
11 1 0.01
12 8 0.10
13 2 0.03
14 3 0.04
15 33 0.42
16 8 0.10
17 6 0.08
18 15 0.19
19 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.45, T:0.00
Consensus pattern (16 bp):
AGGAGAAGGAGAAGAA
Found at i:5458 original size:42 final size:45
Alignment explanation
Indices: 5367--5477 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 45
5357 CGACGACGAT
* *
5367 GAGGAGAAGAAGAGAAAGAAGGAGGAGGAGAAGGAGAAAAAGGAG
1 GAGGAGAAGAAGAGAAAGAAGGAGGAGGAGAAGGAGAAAAAGAAA
**
5412 GAGGAGAAGAA-AG-AA-AAGGAGGAGGAGAAGGAGAGGAAGAAA
1 GAGGAGAAGAAGAGAAAGAAGGAGGAGGAGAAGGAGAAAAAGAAA
*
5454 GAGGAGAA-AGAGAGGAAGAAGGAG
1 GAGGAGAAGA-AGAGAAAGAAGGAG
5478 AAAGAGGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
41 1 0.02
42 32 0.55
43 4 0.07
44 4 0.07
45 17 0.29
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (45 bp):
GAGGAGAAGAAGAGAAAGAAGGAGGAGGAGAAGGAGAAAAAGAAA
Found at i:5500 original size:27 final size:27
Alignment explanation
Indices: 5449--5529 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
5439 AAGGAGAGGA
* *
5449 AGAAAGAGGAGAAAG-AGAGGAAGAAGG
1 AGAAAGAGGA-AAAGAAGAAGCAGAAGG
5476 AGAAAGAGGAAAAGAAGAAGCAGAAGG
1 AGAAAGAGGAAAAGAAGAAGCAGAAGG
* * *
5503 AGAAGGAGGAAAAGAAGGAGCACAAGG
1 AGAAAGAGGAAAAGAAGAAGCAGAAGG
5530 TCAAGGCAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.08
27 44 0.92
ACGTcount: A:0.56, C:0.04, G:0.41, T:0.00
Consensus pattern (27 bp):
AGAAAGAGGAAAAGAAGAAGCAGAAGG
Found at i:5897 original size:2 final size:2
Alignment explanation
Indices: 5890--5927 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5880 TAAATCTATT
5890 TA TA 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 TA TA
5928 CACTAGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6331 original size:36 final size:36
Alignment explanation
Indices: 6227--6331 Score: 87
Period size: 36 Copynumber: 3.1 Consensus size: 36
6217 TAGTGTGATT
*
6227 ATTCCTAAATCAAATGGACTATAATTTAAATCAACA
1 ATTCCTAAATCAAATAGACTATAATTTAAATCAACA
* * * * ** *
6263 A--CC-CAA--AAATAAAGT-TCAAATTAAGGCCACA
1 ATTCCTAAATCAAATAGACTAT-AATTTAAATCAACA
6294 ATTCCTAAATCAAATAGACTATAATTTAAATCAACA
1 ATTCCTAAATCAAATAGACTATAATTTAAATCAACA
6330 AT
1 AT
6332 AAGTAGAGAT
Statistics
Matches: 47, Mismatches: 15, Indels: 14
0.62 0.20 0.18
Matches are distributed among these distances:
30 1 0.02
31 17 0.36
33 4 0.09
34 4 0.09
36 20 0.43
37 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.27
Consensus pattern (36 bp):
ATTCCTAAATCAAATAGACTATAATTTAAATCAACA
Found at i:6536 original size:2 final size:2
Alignment explanation
Indices: 6529--6594 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
6519 GCTGAGCTTT
6529 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6571 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.