Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018217.1 Corchorus olitorius cultivar O-4 contig18250, 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: 5653
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Found at i:5415 original size:4 final size:4
Alignment explanation
Indices: 5408--5626 Score: 65
Period size: 4 Copynumber: 54.5 Consensus size: 4
5398 AAAGATTTTT
* * **
5408 TTTA TTTA TTTA -CTA TTTA TATT- TTTA TTTA TTAA TTTA ACTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * **
5454 TCTA TTTA TTTA -CTA TTTA TCCT- TTTA TTTA TTAA TTTA GCTA -TTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * ** **
5500 TCTA GTTA TTTA CTATTA TCTA CTTTT TTTA CCTA ACTA TTTA TCTTA
1 TTTA TTTA TTTA -T-TTA TTTA -TTTA TTTA TTTA TTTA TTTA T-TTA
* * ** * * * *
5548 -TTA TCTA TATA CCTA TTTA TCTTT TTTA TTTA TCTA TTATT TTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TT-TA TTTA TTTA
* *
5597 TTTA TCTA TTTA TTTA TTTA TTTA TCTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
5627 ACTTTTTTTA
Statistics
Matches: 151, Mismatches: 49, Indels: 30
0.66 0.21 0.13
Matches are distributed among these distances:
3 14 0.09
4 118 0.78
5 16 0.11
6 3 0.02
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.63
Consensus pattern (4 bp):
TTTA
Found at i:5439 original size:27 final size:27
Alignment explanation
Indices: 5402--5465 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
5392 GACCAAAAAG
*
5402 ATTTTT-TTTATTTATTT-ACTATTTAT
1 ATTTTTATTTATTAATTTAACTA-TTAT
5428 ATTTTTATTTATTAATTTAACTATTAT
1 ATTTTTATTTATTAATTTAACTATTAT
* *
5455 CTATTTATTTA
1 ATTTTTATTTA
5466 CTATTTATCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 23 0.70
28 4 0.12
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTATTTATTAATTTAACTATTAT
Found at i:5454 original size:19 final size:18
Alignment explanation
Indices: 5432--5470 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5422 ATTTATATTT
*
5432 TTATTTATTAATTTAACTA
1 TTATCTATTAATTT-ACTA
*
5451 TTATCTATTTATTTACTA
1 TTATCTATTAATTTACTA
5469 TT
1 TT
5471 TATCCTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATCTATTAATTTACTA
Found at i:5480 original size:46 final size:46
Alignment explanation
Indices: 5410--5530 Score: 181
Period size: 46 Copynumber: 2.6 Consensus size: 46
5400 AGATTTTTTT
*
5410 TATTTATTTACTATTTATATTTTTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* *
5456 TATTTATTTACTATTTATCCTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
* *
5502 TAGTTATTTACTATTATCTACTTTT-TTTA
1 TATTTATTTACTATT-TATACTTTTATTTA
5531 CCTAACTATT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 61 0.90
47 7 0.10
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (46 bp):
TATTTATTTACTATTTATACTTTTATTTATTAATTTAACTATTATC
Found at i:5636 original size:20 final size:19
Alignment explanation
Indices: 5564--5636 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 19
5554 ATATACCTAT
5564 TTATCTTTTTTATTTATCTA
1 TTAT-TTTTTTATTTATCTA
5584 TTATTTTTACTTATTTATCTA
1 TTATTTTT--TTATTTATCTA
*
5605 TTTATTTATTTATTTATCTA
1 -TTATTTTTTTATTTATCTA
5625 TTACTTTTTTTA
1 TTA-TTTTTTTA
5637 ATATTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.15
20 22 0.47
21 11 0.23
22 7 0.15
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTTTTATTTATCTA
Done.