Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012348.1 Corchorus capsularis cultivar CVL-1 contig12369, 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: 17632
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:5312 original size:21 final size:21
Alignment explanation
Indices: 5288--5355 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5278 ATGATTTTAC
5288 CATATCCATAATAATTTGTTG
1 CATATCCATAATAATTTGTTG
** * **
5309 CATATGTATATATGATTT-TAC
1 CATATCCATA-ATAATTTGTTG
5330 CATATCCATAATAATTTGTCTG
1 CATATCCATAATAATTTGT-TG
5352 CATA
1 CATA
5356 CGTATATGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
20 6 0.18
21 18 0.53
22 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
CATATCCATAATAATTTGTTG
Found at i:5320 original size:42 final size:42
Alignment explanation
Indices: 5261--5362 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
5251 TTAGAACGTC
5261 TTGTTGCATATGTATATATGATTTTACCATATCCATAATAAT
1 TTGTTGCATATGTATATATGATTTTACCATATCCATAATAAT
5303 TTGTTGCATATGTATATATGATTTTACCATATCCATAATAAT
1 TTGTTGCATATGTATATATGATTTTACCATATCCATAATAAT
*
5345 TTGTCTGCATACGTATAT
1 TTGT-TGCATATGTATAT
5363 GTGTCTCTGC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 46 0.79
43 12 0.21
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (42 bp):
TTGTTGCATATGTATATATGATTTTACCATATCCATAATAAT
Found at i:5753 original size:26 final size:26
Alignment explanation
Indices: 5724--5778 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
5714 TAGACTTGAT
5724 AAGTTTGGCCCAATTCTAACATATAA
1 AAGTTTGGCCCAATTCTAACATATAA
*
5750 AAGTTTGGCCCAATTCTAGCATATAA
1 AAGTTTGGCCCAATTCTAACATATAA
5776 AAG
1 AAG
5779 CAGACTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (26 bp):
AAGTTTGGCCCAATTCTAACATATAA
Found at i:6652 original size:21 final size:20
Alignment explanation
Indices: 6624--6662 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
6614 TCTCTCTCTC
6624 TCAAAAGCCAGTACTTCATT
1 TCAAAAGCCAGTACTTCATT
6644 TCAAGAAGCCAGTACTTCA
1 TCAA-AAGCCAGTACTTCA
6663 CTCAGTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TCAAAAGCCAGTACTTCATT
Found at i:11555 original size:12 final size:12
Alignment explanation
Indices: 11548--11605 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
11538 CACTTTTCTT
11548 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
11560 TTATCTTCTTTTC
1 TTTTCTT-TTTTC
11573 TTTCTCATTTTCTTC
1 TTT-TC-TTTT-TTC
*
11588 TTTTC-TTTCTC
1 TTTTCTTTTTTC
11599 TTTTCTT
1 TTTTCTT
11606 CAACCCTCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 7 0.18
12 10 0.26
13 7 0.18
14 6 0.16
15 8 0.21
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:11596 original size:20 final size:19
Alignment explanation
Indices: 11540--11606 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
11530 AAAAAAATCA
*
11540 CTTTTCTT-TTTTCTTTTTT
1 CTTTTCTTCTTTTC-TTTCT
*
11559 CTTATCTTCTTTTCTTTCT
1 CTTTTCTTCTTTTCTTTCT
11578 CATTTTCTTCTTTTCTTTCT
1 C-TTTTCTTCTTTTCTTTCT
11598 CTTTTCTTC
1 CTTTTCTTC
11607 AACCCTCGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 20 0.47
20 23 0.53
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (19 bp):
CTTTTCTTCTTTTCTTTCT
Found at i:17528 original size:30 final size:29
Alignment explanation
Indices: 17461--17528 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
17451 ACACCGAACC
****
17461 GTCAAATAAGCCCCTGAACTATTATTTCG
1 GTCAAATAAGCCCCTGAACTATTAAAAAG
* *
17490 GCCAAATAAGCCCCTGAACTCTTAAAAAAG
1 GTCAAATAAGCCCCTGAACTATT-AAAAAG
17520 GTCAAATAA
1 GTCAAATAA
17529 ACCCTGTTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAG
Done.