Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019846.1 Corchorus olitorius cultivar O-4 contig19879, 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: 5952
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:58 original size:11 final size:11
Alignment explanation
Indices: 42--67 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32 CCTTTGCCTA
42 AAAACTAGAAG
1 AAAACTAGAAG
53 AAAACTAGAAG
1 AAAACTAGAAG
64 AAAA
1 AAAA
68 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:2167 original size:14 final size:15
Alignment explanation
Indices: 2148--2177 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2138 CAATCAAAGC
2148 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
2162 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
2177 A
1 A
2178 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:2563 original size:21 final size:21
Alignment explanation
Indices: 2537--2586 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2527 TGAATGGTGA
*
2537 TGGCACGGGCATAGCCGATGG
1 TGGCACGGGCATAACCGATGG
* *
2558 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGATGG
2579 TGGCACGG
1 TGGCACGG
2587 TGAATGGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGATGG
Found at i:4731 original size:33 final size:31
Alignment explanation
Indices: 4665--4766 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 31
4655 AACAATAAAG
* * *
4665 AAAATATTTTTTCTTTCTAAAAACGCAGGAACA
1 AAAAT-TTTTTTTTTTTTAAAAACGCA-AAACA
4698 AGAAATTTTTTTTTTTTTAGAAAACGCAAAAC-
1 A-AAATTTTTTTTTTTTTA-AAAACGCAAAACA
*
4730 --AATTTTTTTTTTTTCAAAAACGCAAAACTA
1 AAAATTTTTTTTTTTTTAAAAACGCAAAAC-A
4760 ATAAATT
1 A-AAATT
4767 AAAAACGCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
28 12 0.21
29 15 0.26
33 19 0.33
34 12 0.21
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
AAAATTTTTTTTTTTTTAAAAACGCAAAACA
Found at i:4749 original size:28 final size:29
Alignment explanation
Indices: 4701--4757 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
4691 AGGAACAAGA
*
4701 AATTTTTTTTTTTTTAGAAAACGCAAAAC
1 AATTTTTTTTTTTTCAGAAAACGCAAAAC
4730 AATTTTTTTTTTTTCA-AAAACGCAAAAC
1 AATTTTTTTTTTTTCAGAAAACGCAAAAC
4758 TAATAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (29 bp):
AATTTTTTTTTTTTCAGAAAACGCAAAAC
Found at i:4814 original size:26 final size:28
Alignment explanation
Indices: 4767--4821 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
4757 CTAATAAATT
4767 AAAAACGCAAGAAAACCCTTTTTTTATG
1 AAAAACGCAAGAAAACCCTTTTTTTATG
*
4795 AAAAACGC-A-AAAACCTTTTTTTTATG
1 AAAAACGCAAGAAAACCCTTTTTTTATG
4821 A
1 A
4822 TGCAGAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAAACGCAAGAAAACCCTTTTTTTATG
Found at i:4830 original size:22 final size:21
Alignment explanation
Indices: 4804--4875 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
4794 GAAAAACGCA
*
4804 AAAACCTTTTTTTTATGATGC
1 AAAACATTTTTTTTATGATGC
** *
4825 AGAAACAAATTTTTTATGACGC
1 A-AAACATTTTTTTTATGATGC
* *
4847 AAAAATATTTTTTTTTTCGATGC
1 -AAAACATTTTTTTTAT-GATGC
4870 AAAACA
1 AAAACA
4876 CAAAACAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.84
23 5 0.13
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAACATTTTTTTTATGATGC
Found at i:4856 original size:20 final size:22
Alignment explanation
Indices: 4812--4859 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4802 CAAAAACCTT
*
4812 TTTTTTATGATGCAGAAACAAA
1 TTTTTTATGACGCAGAAACAAA
*
4834 TTTTTTATGACGCA-AAA-ATA
1 TTTTTTATGACGCAGAAACAAA
4854 TTTTTT
1 TTTTTT
4860 TTTTCGATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 3 0.12
22 13 0.54
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTTTATGACGCAGAAACAAA
Found at i:5266 original size:16 final size:15
Alignment explanation
Indices: 5228--5269 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
5218 ACAGAGATTG
*
5228 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
5243 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
5258 ACTAGAAAACAA
1 AC-AGAAAACAA
5270 AGCAGAGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.