Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012179.1 Corchorus olitorius cultivar O-4 contig12212, 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: 11770
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1805 original size:21 final size:21
Alignment explanation
Indices: 1766--1805 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1756 AATTAAAGAA
* *
1766 TATTATATTATCTTATATTAT
1 TATTATACTATATTATATTAT
*
1787 TATTATACTATATTTTATT
1 TATTATACTATATTATATT
1806 TGTAACTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATACTATATTATATTAT
Found at i:5722 original size:11 final size:10
Alignment explanation
Indices: 5706--5758 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
5696 TGCCTCTTGA
5706 AATAATTCTTC
1 AATAA-TCTTC
5717 AATAATCTTC
1 AATAATCTTC
5727 -A-AATCTTC
1 AATAATCTTC
*
5735 AAATTATCTTC
1 -AATAATCTTC
5746 AATAAATCTTC
1 AAT-AATCTTC
5757 AA
1 AA
5759 ACACGAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 9 0.25
11 19 0.53
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (10 bp):
AATAATCTTC
Found at i:5745 original size:19 final size:18
Alignment explanation
Indices: 5712--5747 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5702 TTGAAATAAT
5712 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
5730 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
5748 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:7675 original size:21 final size:21
Alignment explanation
Indices: 7641--7695 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
7631 GGCTTGGAAT
* * *
7641 GGTGATGGCACGGGCATGACC
1 GGTGGTGGCTCGGGCATAACC
* * *
7662 GGTGGTTGCTCGGGCTTAACT
1 GGTGGTGGCTCGGGCATAACC
7683 GGTGGTGGCTCGG
1 GGTGGTGGCTCGG
7696 TGATGGCATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.45, T:0.24
Consensus pattern (21 bp):
GGTGGTGGCTCGGGCATAACC
Found at i:10733 original size:32 final size:32
Alignment explanation
Indices: 10652--10734 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
10642 AAAAATTTTT
** *
10652 AAACGCAAAACACAAAACAATTTTTTTAAAAAA
1 AAACGCAAAA-ACAAAATTATTTTTTAAAAAAA
** *
10685 AAA-TTAAAAACGAAAATTCTTTTTTAAAAAAA
1 AAACGCAAAAAC-AAAATTATTTTTTAAAAAAA
10717 AAACGCAAAAACAAAATT
1 AAACGCAAAAACAAAATT
10735 TTCAGAGAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
31 2 0.05
32 29 0.73
33 9 0.22
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.23
Consensus pattern (32 bp):
AAACGCAAAAACAAAATTATTTTTTAAAAAAA
Found at i:11507 original size:10 final size:10
Alignment explanation
Indices: 11475--11524 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
11465 TTGGTTCAAT
11475 TGGGGAGGGG
1 TGGGGAGGGG
* **
11485 TGGGGTGAAG
1 TGGGGAGGGG
*
11495 TGGGAAGGGG
1 TGGGGAGGGG
*
11505 TGGGGTGGGG
1 TGGGGAGGGG
11515 TGGGGAGGGG
1 TGGGGAGGGG
11525 GAGGGTTTGG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.12, C:0.00, G:0.74, T:0.14
Consensus pattern (10 bp):
TGGGGAGGGG
Found at i:11530 original size:20 final size:20
Alignment explanation
Indices: 11475--11524 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
11465 TTGGTTCAAT
11475 TGGGGAGGGGTGGGGTGAAG
1 TGGGGAGGGGTGGGGTGAAG
* **
11495 TGGGAAGGGGTGGGGTGGGG
1 TGGGGAGGGGTGGGGTGAAG
11515 TGGGGAGGGG
1 TGGGGAGGGG
11525 GAGGGTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.74, T:0.14
Consensus pattern (20 bp):
TGGGGAGGGGTGGGGTGAAG
Done.