Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013297.1 Corchorus olitorius cultivar O-4 contig13330, 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: 34328
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:349 original size:14 final size:16
Alignment explanation
Indices: 325--366 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
315 GTTGAAAGAT
* *
325 TAAGCACTGAAT-TTT
1 TAAGTACTGAATATTG
340 TAA-TACTGAATATTG
1 TAAGTACTGAATATTG
355 TAAGTACTGAAT
1 TAAGTACTGAAT
367 CCAAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 8 0.35
16 8 0.35
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (16 bp):
TAAGTACTGAATATTG
Found at i:4336 original size:25 final size:25
Alignment explanation
Indices: 4264--4338 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
4254 TCCTCACTAT
4264 TAAATTTACAATTTTTATTAAATAA
1 TAAATTTACAATTTTTATTAAATAA
* * *
4289 AAAAATTA-ACATTTAGTCA-TAAATAA
1 TAAATTTACA-ATTT--TTATTAAATAA
4315 TAAATTTACAATTTTTATTAAATA
1 TAAATTTACAATTTTTATTAAATA
4339 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
24 3 0.08
25 16 0.41
26 17 0.44
27 3 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (25 bp):
TAAATTTACAATTTTTATTAAATAA
Found at i:18750 original size:2 final size:2
Alignment explanation
Indices: 18743--18776 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18733 CAAATCATGA
* *
18743 AT AT AT AT GT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18777 GTAATCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22641 original size:20 final size:20
Alignment explanation
Indices: 22618--22664 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
22608 GAAACATTCA
22618 AAGCGAGGCGAGGGAGGAAG
1 AAGCGAGGCGAGGGAGGAAG
* *
22638 AAGCGAGGCGATGGAGGGAG
1 AAGCGAGGCGAGGGAGGAAG
22658 AAGCGAG
1 AAGCGAG
22665 AAGAAATCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.53, T:0.02
Consensus pattern (20 bp):
AAGCGAGGCGAGGGAGGAAG
Found at i:23035 original size:18 final size:18
Alignment explanation
Indices: 23012--23047 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23002 TTTGGAAGGG
*
23012 AAATTAGACCCACACAAA
1 AAATTAAACCCACACAAA
23030 AAATTAAACCCACACAAA
1 AAATTAAACCCACACAAA
23048 TAAAGATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.28, G:0.03, T:0.11
Consensus pattern (18 bp):
AAATTAAACCCACACAAA
Found at i:23343 original size:2 final size:2
Alignment explanation
Indices: 23336--23362 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23326 TCTAATGATA
23336 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23363 GTCAAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32991 original size:2 final size:2
Alignment explanation
Indices: 32984--33020 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
32974 TTGAGTCAAG
32984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33021 AATAGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.