Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010145.1 Corchorus capsularis cultivar CVL-1 contig10166, 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: 29814
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:284 original size:33 final size:33
Alignment explanation
Indices: 221--328 Score: 168
Period size: 33 Copynumber: 3.3 Consensus size: 33
211 AAATTAGCCG
221 GTGGGGCGGCCTGCCC-TGGCT-AAGCCGCCCCA
1 GTGGGGCGGCCTGCCCATGG-TGAAGCCGCCCCA
253 GTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCA
1 GTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCA
*
286 GTGGGGCGGCCTGTCCATGGTGAAGCCGCCCCA
1 GTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCA
319 -TGAGGGCGGC
1 GTG-GGGCGGC
329 TTCGCCACGG
Statistics
Matches: 72, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
32 19 0.26
33 53 0.74
ACGTcount: A:0.11, C:0.35, G:0.41, T:0.13
Consensus pattern (33 bp):
GTGGGGCGGCCTGCCCATGGTGAAGCCGCCCCA
Found at i:5387 original size:2 final size:2
Alignment explanation
Indices: 5380--5413 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5370 CTCATTATCT
5380 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
5414 GATCAGTATT
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:5824 original size:23 final size:23
Alignment explanation
Indices: 5793--5838 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5783 CAAACAATCT
*
5793 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGATCTCTA
*
5816 TGAGTACTCTCGCTCGATCTCTA
1 TGAGCACTCTCGCTCGATCTCTA
5839 ACAAACTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.20, T:0.33
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGATCTCTA
Found at i:5864 original size:21 final size:22
Alignment explanation
Indices: 5835--5877 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5825 TCGCTCGATC
*
5835 TCTAACAAA-CTAACAATCACA
1 TCTAACAAACCAAACAATCACA
*
5856 TCTACCAAACCAAACAATCACA
1 TCTAACAAACCAAACAATCACA
5878 CAAACACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (22 bp):
TCTAACAAACCAAACAATCACA
Found at i:6851 original size:46 final size:46
Alignment explanation
Indices: 6760--6851 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
6750 TTCAAGCCAA
**
6760 CAGGGTAAGAAGTTAAAATCCTTCTAACAAATCTGTTTTTGAGGAT
1 CAGGGTAAGAAGTTAAAATCCTTCTAACAAATCCATTTTTGAGGAT
* *
6806 CAGGGTGAA-AAGTTAAAGTTCTTCTAACAAATCCATTTATT-AGGAT
1 CAGGGT-AAGAAGTTAAAATCCTTCTAACAAATCCATTT-TTGAGGAT
6852 GCAACTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
46 36 0.90
47 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (46 bp):
CAGGGTAAGAAGTTAAAATCCTTCTAACAAATCCATTTTTGAGGAT
Found at i:8792 original size:20 final size:20
Alignment explanation
Indices: 8751--8793 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8741 CTCTTATACG
* *
8751 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
8771 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
8791 TTT
1 TTT
8794 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:9805 original size:25 final size:25
Alignment explanation
Indices: 9769--9819 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
9759 ATTGTTGGTT
9769 AATAGAGACCGAGCGAGAGTGCTCA
1 AATAGAGACCGAGCGAGAGTGCTCA
* *
9794 AATAGAGGCCGAGCGAGAGTGTTCA
1 AATAGAGACCGAGCGAGAGTGCTCA
9819 A
1 A
9820 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
AATAGAGACCGAGCGAGAGTGCTCA
Found at i:15108 original size:13 final size:13
Alignment explanation
Indices: 15090--15117 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15080 TGTTGACTAA
15090 GTCAACCTGCCAC
1 GTCAACCTGCCAC
15103 GTCAACCTGCCAC
1 GTCAACCTGCCAC
15116 GT
1 GT
15118 TATCAGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.43, G:0.18, T:0.18
Consensus pattern (13 bp):
GTCAACCTGCCAC
Found at i:23300 original size:41 final size:41
Alignment explanation
Indices: 23243--23330 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
23233 CCCTTTAGCA
23243 GCACCATTGACATAGAATTTAAGGAACCCAGCTTGTGGCTT
1 GCACCATTGACATAGAATTTAAGGAACCCAGCTTGTGGCTT
23284 GCACCATTGACATAGAATTTAAGGAACCCAGCTTGTGGCTT
1 GCACCATTGACATAGAATTTAAGGAACCCAGCTTGTGGCTT
23325 GCACCA
1 GCACCA
23331 ATGAACTGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (41 bp):
GCACCATTGACATAGAATTTAAGGAACCCAGCTTGTGGCTT
Found at i:23380 original size:39 final size:39
Alignment explanation
Indices: 23321--23397 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
23311 CCAGCTTGTG
*
23321 GCTTGCACCAATGAACTGACCTCCAACTTACATTTAGGA
1 GCTTACACCAATGAACTGACCTCCAACTTACATTTAGGA
23360 GCTTACACCAATGAACTGACCTCCAACTTACATTTAGG
1 GCTTACACCAATGAACTGACCTCCAACTTACATTTAGG
23398 CCTCAGCATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (39 bp):
GCTTACACCAATGAACTGACCTCCAACTTACATTTAGGA
Done.