Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012456.1 Corchorus olitorius cultivar O-4 contig12489, 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: 10375
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Found at i:5455 original size:34 final size:34
Alignment explanation
Indices: 5412--5483 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
5402 GTCCATGGGT
5412 CTGATCCGACCAGGCCCAAAAAAAGACTTAACTA
1 CTGATCCGACCAGGCCCAAAAAAAGACTTAACTA
5446 CTGATCCGACCAGGCCCAAAAAAAGACTTAACTA
1 CTGATCCGACCAGGCCCAAAAAAAGACTTAACTA
5480 CTGA
1 CTGA
5484 ATTTCCGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.15
Consensus pattern (34 bp):
CTGATCCGACCAGGCCCAAAAAAAGACTTAACTA
Found at i:5570 original size:31 final size:33
Alignment explanation
Indices: 5511--5589 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
5501 ATTAAATAGT
5511 AAATACCTCATATTTATTTATTTTTTGGCCAGA
1 AAATACCTCATATTTATTTATTTTTTGGCCAGA
*
5544 AAATATCTCATATTTA-TTA-TTTTTGGCC---
1 AAATACCTCATATTTATTTATTTTTTGGCCAGA
*
5572 ACATACCTCATATTTATT
1 AAATACCTCATATTTATT
5590 CATGTAACGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.33
29 1 0.02
31 9 0.21
32 3 0.07
33 15 0.36
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.47
Consensus pattern (33 bp):
AAATACCTCATATTTATTTATTTTTTGGCCAGA
Found at i:5587 original size:28 final size:30
Alignment explanation
Indices: 5511--5589 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 30
5501 ATTAAATAGT
5511 AAATACCTCATATTTATTTATTTTTTGGCCAGA
1 AAATACCTCATATTTA-TTATTTTTTGGCC--A
*
5544 AAATATCTCATATTTATTA-TTTTTGGCC-
1 AAATACCTCATATTTATTATTTTTTGGCCA
*
5572 ACATACCTCATATTTATT
1 AAATACCTCATATTTATT
5590 CATGTAACGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.37
31 9 0.21
32 3 0.07
33 15 0.35
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.47
Consensus pattern (30 bp):
AAATACCTCATATTTATTATTTTTTGGCCA
Found at i:5891 original size:131 final size:129
Alignment explanation
Indices: 5737--5998 Score: 368
Period size: 131 Copynumber: 2.0 Consensus size: 129
5727 TTGTTTAAAC
* * * *
5737 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTTAA-TCTAATAT-TCTTATAAC
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTA-ATAAAGTCTAATATCT-TTATAAC
* **
5800 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAAACTT-ATATATTAGAATTTTTTTAAT
64 TATTTTATTTTTACCATTTTACTAATTTAATT---AAAAACTTAATATATTAGAATTTTTAAAAT
5864 ATAT
126 ATAT
* *
5868 TTTTATAATTTTATTCAACTAAAAACTCTATTTCTATTTAATAAAGTCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAGTCTAATATCTTTATAACTA
5933 TTTTATTTTTACCATTTTACTAATTTAATTAAAAACTTAGATATATTAGAATTTTTAAAATATAT
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAACTTA-ATATATTAGAATTTTTAAAATATAT
5998 T
1 T
5999 CTTAAATGAC
Statistics
Matches: 118, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
128 8 0.07
130 27 0.23
131 82 0.69
132 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (129 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAGTCTAATATCTTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAACTTAATATATTAGAATTTTTAAAATATAT
Found at i:7743 original size:31 final size:31
Alignment explanation
Indices: 7705--7766 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
7695 GAGTTTTGTA
* *
7705 AAACTTTTGAATCGCCTATTATACCTTTATT
1 AAACTTTTGAATCGCCTATTACACCCTTATT
7736 AAACTTTTGAATCGCCTATTACACCCTTATT
1 AAACTTTTGAATCGCCTATTACACCCTTATT
7767 TTTCGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTACACCCTTATT
Found at i:7969 original size:92 final size:93
Alignment explanation
Indices: 7802--7985 Score: 298
Period size: 92 Copynumber: 2.0 Consensus size: 93
7792 TTGTTTAAAT
* *
7802 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTTATTAAATCCAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATAACTA
* *
7867 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* *
7895 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTT-TTTAATTAAATCTAATATCCTTATATCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATAACTA
*
7959 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
7986 ATTAAAAAGT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 50 0.60
93 34 0.40
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.53
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCCAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:8726 original size:26 final size:24
Alignment explanation
Indices: 8689--8743 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
8679 GCCTTGAATT
* *
8689 TTTTAATGTTTAATTCTTAAATTTA
1 TTTTAATCTTT-ATTATTAAATTTA
**
8714 TTTTATATCTTTATTATTCGATTTA
1 TTTTA-ATCTTTATTATTAAATTTA
8739 TTTTA
1 TTTTA
8744 CAATCGACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTTAATCTTTATTATTAAATTTA
Done.