Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016966.1 Corchorus olitorius cultivar O-4 contig16999, 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: 13730
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:261 original size:51 final size:49
Alignment explanation
Indices: 160--261 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 49
150 GTTCTTCATA
**
160 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACATTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACA-TCTTACAGTGT
*
210 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACA-CTGTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACATCT-TACA-GTGT
261 T
1 T
262 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
49 2 0.04
50 7 0.16
51 35 0.78
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (49 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACATCTTACAGTGT
Found at i:2445 original size:2 final size:2
Alignment explanation
Indices: 2438--2473 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2428 TCACTAAAGT
2438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2474 ATCAAAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3317 original size:6 final size:6
Alignment explanation
Indices: 3306--3339 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3296 AAAAGATAAA
3306 ATTGGT ATTGGT ATTGGT ATTGGT ATTGGT ATTG
1 ATTGGT ATTGGT ATTGGT ATTGGT ATTGGT ATTG
3340 TAGATATCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
ATTGGT
Found at i:4529 original size:13 final size:13
Alignment explanation
Indices: 4511--4538 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4501 TTTCTAATAT
4511 ATATAGATTAGTA
1 ATATAGATTAGTA
4524 ATATAGATTAGTA
1 ATATAGATTAGTA
4537 AT
1 AT
4539 TAACTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATATAGATTAGTA
Found at i:8337 original size:13 final size:13
Alignment explanation
Indices: 8314--8346 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
8304 CCAAAACCCG
8314 TTCCT-AAAGTCA
1 TTCCTAAAAGTCA
8326 TTCCTAAAAGTCA
1 TTCCTAAAAGTCA
8339 TTCCTAAA
1 TTCCTAAA
8347 CCTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (13 bp):
TTCCTAAAAGTCA
Found at i:8927 original size:175 final size:175
Alignment explanation
Indices: 8636--8987 Score: 555
Period size: 175 Copynumber: 2.0 Consensus size: 175
8626 AGTTGATGGG
* *
8636 TAATGTCTTATACGACGTAGATTGGTGTTTGTTACTTGATGTGAGTTTGTATTGCCATGTGAAAA
1 TAATGTCTTATACGACGTAGATTAGTGTTTGTTACTTGATATGAGTTTGTATTGCCATGTGAAAA
*
8701 TTGATTTTGTGTTGAATATAAGAATGAGGGATGTGAATGCATAGATCTATAAATTAGGGGGATAG
66 TTGATTTTGTGTTGAATATAAGAATGAGGGATGTGAATGCATAGATCTATAAATGAGGGGGATAG
* *
8766 AATTGAAAAAAT-GAGAAGTTTAGGGACCTAATTGCAAAAAAATTA
131 AATTGAAAAAATCGA-AAGTTCAGGGACCTAATTGCAAAAAAAATA
* *
8811 TAATGTCTTATA-GAATGTAGATTAGTGTTTGTTGCTTGATATGAGTTTGTATTGCCATGTGAAA
1 TAATGTCTTATACG-ACGTAGATTAGTGTTTGTTACTTGATATGAGTTTGTATTGCCATGTGAAA
* * *
8875 ATTGATTTTGTGTTGAATATATGAATGAGGGATGTGAATGCATATATCTATAAATGAGGTGGATA
65 ATTGATTTTGTGTTGAATATAAGAATGAGGGATGTGAATGCATAGATCTATAAATGAGGGGGATA
** *
8940 GAATTGAAAATTTCTAAAGTTCAGGGACCTAATTGCAAAAAAAATA
130 GAATTGAAAAAATCGAAAGTTCAGGGACCTAATTGCAAAAAAAATA
8986 TA
1 TA
8988 CGGTTAGATT
Statistics
Matches: 162, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 1 0.01
175 160 0.99
176 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (175 bp):
TAATGTCTTATACGACGTAGATTAGTGTTTGTTACTTGATATGAGTTTGTATTGCCATGTGAAAA
TTGATTTTGTGTTGAATATAAGAATGAGGGATGTGAATGCATAGATCTATAAATGAGGGGGATAG
AATTGAAAAAATCGAAAGTTCAGGGACCTAATTGCAAAAAAAATA
Found at i:9755 original size:15 final size:15
Alignment explanation
Indices: 9732--9762 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9722 AAGATGAGGT
*
9732 AGAGGATGAAGGTGA
1 AGAGAATGAAGGTGA
9747 AGAGAATGAAGGTGA
1 AGAGAATGAAGGTGA
9762 A
1 A
9763 CACAAGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (15 bp):
AGAGAATGAAGGTGA
Found at i:12520 original size:15 final size:15
Alignment explanation
Indices: 12497--12527 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12487 AAGATGAGGT
*
12497 AGAGGATGAAGGTGA
1 AGAGAATGAAGGTGA
12512 AGAGAATGAAGGTGA
1 AGAGAATGAAGGTGA
12527 A
1 A
12528 CACTAGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (15 bp):
AGAGAATGAAGGTGA
Found at i:12635 original size:25 final size:27
Alignment explanation
Indices: 12575--12637 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
12565 ACTCTAATTA
* *
12575 TTTGGGGAAACTCTAATTCCTTTATTTT
1 TTTGAGGAAACTCTAATTCCTTCA-TTT
*
12603 TTTTAGGAAACTCTAATT-CTTCA-TT
1 TTTGAGGAAACTCTAATTCCTTCATTT
12628 TTTGAGGAAA
1 TTTGAGGAAA
12638 GGAAACTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 11 0.35
27 4 0.13
28 16 0.52
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (27 bp):
TTTGAGGAAACTCTAATTCCTTCATTT
Found at i:12844 original size:13 final size:13
Alignment explanation
Indices: 12814--12845 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
12804 TCATTCCTAA
12814 ATTTTGGAATGAC
1 ATTTTGGAATGAC
12827 A-TTTGGAATGAC
1 ATTTTGGAATGAC
12839 ATTTTGG
1 ATTTTGG
12846 GAACAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (13 bp):
ATTTTGGAATGAC
Done.