Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014864.1 Corchorus olitorius cultivar O-4 contig14897, 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: 17012
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:5484 original size:14 final size:14
Alignment explanation
Indices: 5441--5484 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
5431 AATAGGCAAG
5441 CAATCAAAGCAATAA
1 CAATCAAAGCAA-AA
5456 TCAATCAAAGCAAAA
1 -CAATCAAAGCAAAA
5471 CAATGCAAAG-AAAA
1 CAAT-CAAAGCAAAA
5485 TAAATAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 12 0.44
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (14 bp):
CAATCAAAGCAAAA
Found at i:8272 original size:21 final size:20
Alignment explanation
Indices: 8240--8283 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
8230 ATTAAAAAGA
*
8240 AAATCAATTAAACTAAAAAT
1 AAATCAAATAAACTAAAAAT
* *
8260 AAATCAAAATAAATTAAATAT
1 AAATC-AAATAAACTAAAAAT
8281 AAA
1 AAA
8284 CTATAGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATCAAATAAACTAAAAAT
Found at i:10549 original size:15 final size:15
Alignment explanation
Indices: 10519--10560 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
10509 TTACTTTGTT
10519 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
10535 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
10550 TTGTTTTCTGT
1 TTGTTTTCTGT
10561 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:10845 original size:11 final size:11
Alignment explanation
Indices: 10829--10853 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10819 CCCTCTTCTT
10829 AAACTAGAGAA
1 AAACTAGAGAA
10840 AAACTAGAGAA
1 AAACTAGAGAA
10851 AAA
1 AAA
10854 TAAAAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAACTAGAGAA
Found at i:12423 original size:2 final size:2
Alignment explanation
Indices: 12411--12442 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12401 TAATTCAACC
12411 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12443 TACTCCCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12761 original size:31 final size:31
Alignment explanation
Indices: 12700--12761 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
12690 AACAGAGGGA
*
12700 GTATAATATAATATTATATATATTAGATATT
1 GTATAATATAATATTATATATAATAGATATT
* * *
12731 GTATATTATAATGTTTATTTATAATA-ATATT
1 GTATAATATAAT-ATTATATATAATAGATATT
12762 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (31 bp):
GTATAATATAATATTATATATAATAGATATT
Found at i:12774 original size:16 final size:15
Alignment explanation
Indices: 12707--12777 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
12697 GGAGTATAAT
*
12707 ATAATATTATATATA
1 ATAATATTATTTATA
* * * *
12722 TTAGATATTGTATATT
1 ATA-ATATTATTTATA
*
12738 ATAATGTTTATTTATA
1 ATAAT-ATTATTTATA
*
12754 ATAATATTATTTTTA
1 ATAATATTATTTATA
12769 ATTAATATT
1 A-TAATATT
12778 TACATCTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
15 13 0.30
16 30 0.70
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (15 bp):
ATAATATTATTTATA
Found at i:16792 original size:16 final size:16
Alignment explanation
Indices: 16759--16814 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
16749 GGGCGGGTTT
*
16759 GGGTTCGAG-TACTTC
1 GGGTTCGAGTTATTTC
*
16774 GGGTTCGAGTTTTTTC
1 GGGTTCGAGTTATTTC
* *
16790 GGGTTCGGGTTATGTC
1 GGGTTCGAGTTATTTC
16806 GGGTTCGAG
1 GGGTTCGAG
16815 CTCGAGTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 9 0.26
16 25 0.74
ACGTcount: A:0.09, C:0.14, G:0.39, T:0.38
Consensus pattern (16 bp):
GGGTTCGAGTTATTTC
Done.