Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021286.1 Corchorus olitorius cultivar O-4 contig21319, 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: 15358
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:252 original size:31 final size:31
Alignment explanation
Indices: 180--252 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
170 GTCTATCAGC
*
180 TTTTTAATTTGTTTAATTTAAGACTTTCATT
1 TTTTTAATTTGTTTAATTTAAGACTTTAATT
*
211 TTAATT-ATTTGTTTAATTTAATG-C-TTAATT
1 TT-TTTAATTTGTTTAATTTAA-GACTTTAATT
241 TGTTTTAATTTG
1 T-TTTTAATTTG
253 CAATAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
30 8 0.23
31 24 0.69
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.62
Consensus pattern (31 bp):
TTTTTAATTTGTTTAATTTAAGACTTTAATT
Found at i:542 original size:13 final size:12
Alignment explanation
Indices: 506--552 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
496 TCAATCTTTA
*
506 TATATATTGATAA
1 TATATATT-ATAT
*
519 TA-ATGTTATAT
1 TATATATTATAT
530 TATATTATTATAT
1 TATA-TATTATAT
543 TATATATTAT
1 TATATATTAT
553 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:688 original size:6 final size:6
Alignment explanation
Indices: 677--730 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
667 ATCAAAATCA
* * * *
677 AACCCG AGCCCG AACCCG -ACCCG AGCCCG AACCC- TACCCG AGCCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
723 AACCCG AA
1 AACCCG AA
731 AATACCCAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.28, C:0.50, G:0.20, T:0.02
Consensus pattern (6 bp):
AACCCG
Found at i:700 original size:17 final size:17
Alignment explanation
Indices: 678--729 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
668 TCAAAATCAA
678 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
*
695 ACCCGAGCCCGAACCCT
1 ACCCGAGCCCGAACCCG
712 ACCCGAGCCCGAACCCG
1 ACCCGAGCCCGAACCCG
729 A
1 A
730 AAATACCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.25, C:0.52, G:0.21, T:0.02
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:761 original size:32 final size:32
Alignment explanation
Indices: 719--839 Score: 156
Period size: 32 Copynumber: 3.8 Consensus size: 32
709 CCTACCCGAG
* *
719 CCCGAACCCGAAAATACCCAAACCCGACATAA
1 CCCGAGCCCGAAAATACCCGAACCCGACATAA
*
751 CCCGAGCCCGAAAATACCCGAACCCGACTTAA
1 CCCGAGCCCGAAAATACCCGAACCCGACATAA
*
783 CCCGAGCCCGAAAATACCCGAACCCGA-AAATA
1 CCCGAGCCCGAAAATACCCGAACCCGACATA-A
* * *
815 CCCGAACTCG-AAGTACCCGAACCCG
1 CCCGAGCCCGAAAATACCCGAACCCG
840 CCCGAGCCCG
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.19
32 65 0.81
ACGTcount: A:0.37, C:0.40, G:0.15, T:0.07
Consensus pattern (32 bp):
CCCGAGCCCGAAAATACCCGAACCCGACATAA
Found at i:833 original size:15 final size:16
Alignment explanation
Indices: 719--839 Score: 131
Period size: 16 Copynumber: 7.6 Consensus size: 16
709 CCTACCCGAG
719 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
735 CCCAAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
*
751 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
**
767 CCCGAACCCG-ACTTAA
1 CCCGAACCCGAAAAT-A
*
783 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
799 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
* *
815 CCCGAACTCG-AAGTA
1 CCCGAACCCGAAAATA
830 CCCGAACCCG
1 CCCGAACCCG
840 CCCGAGCCCG
Statistics
Matches: 86, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
15 18 0.21
16 63 0.73
17 5 0.06
ACGTcount: A:0.37, C:0.40, G:0.15, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:5559 original size:3 final size:3
Alignment explanation
Indices: 5551--5580 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5541 ATATATATAT
5551 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5581 TATTGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5707 original size:17 final size:17
Alignment explanation
Indices: 5687--5722 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5677 AGGGTATAGA
5687 TAATTTTAATAGTAGGG
1 TAATTTTAATAGTAGGG
5704 TAATTTTAATAGTAGGG
1 TAATTTTAATAGTAGGG
5721 TA
1 TA
5723 TAGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (17 bp):
TAATTTTAATAGTAGGG
Found at i:5719 original size:40 final size:40
Alignment explanation
Indices: 5664--5745 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
5654 CGTTTGGGAA
5664 TAATTTTAATAGTAGGGTATAGATAATTTTAATAGTAGGG
1 TAATTTTAATAGTAGGGTATAGATAATTTTAATAGTAGGG
5704 TAATTTTAATAGTAGGGTATAGATAATTTTAATAGTAGGG
1 TAATTTTAATAGTAGGGTATAGATAATTTTAATAGTAGGG
5744 TA
1 TA
5746 TAGATGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (40 bp):
TAATTTTAATAGTAGGGTATAGATAATTTTAATAGTAGGG
Found at i:5756 original size:23 final size:23
Alignment explanation
Indices: 5663--5750 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
5653 ACGTTTGGGA
5663 ATAATTTTAATAGTAGGGTATAG
1 ATAATTTTAATAGTAGGGTATAG
5686 ATAATTTTAATAGTA-GG----G
1 ATAATTTTAATAGTAGGGTATAG
5704 -TAATTTTAATAGTAGGGTATAG
1 ATAATTTTAATAGTAGGGTATAG
5726 ATAATTTTAATAGTAGGGTATAG
1 ATAATTTTAATAGTAGGGTATAG
5749 AT
1 AT
5751 GTTTTTCTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
17 14 0.24
18 3 0.05
22 3 0.05
23 39 0.66
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.40
Consensus pattern (23 bp):
ATAATTTTAATAGTAGGGTATAG
Found at i:11581 original size:23 final size:22
Alignment explanation
Indices: 11549--11632 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 22
11539 CATAATTGCT
*
11549 TGGCGCCCGACCACTTCCAAATC
1 TGGCGACCGACCACTTCCAAA-C
* *
11572 TGGCGACCGACCATTTTC--A-
1 TGGCGACCGACCACTTCCAAAC
* * *
11591 TAGCGCCCGACCACTTTCAAACC
1 TGGCGACCGACCACTTCCAAA-C
11614 TGGCGACCGACCACTTCCA
1 TGGCGACCGACCACTTCCA
11633 TAACGCGGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 15 0.31
21 2 0.04
23 31 0.65
ACGTcount: A:0.23, C:0.40, G:0.18, T:0.19
Consensus pattern (22 bp):
TGGCGACCGACCACTTCCAAAC
Done.