Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012146.1 Corchorus olitorius cultivar O-4 contig12179, 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: 21487
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:13207 original size:13 final size:13
Alignment explanation
Indices: 13189--13215 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13179 CTCTATAACC
13189 TCATAAATCATAT
1 TCATAAATCATAT
13202 TCATAAATCATAT
1 TCATAAATCATAT
13215 T
1 T
13216 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:13368 original size:19 final size:19
Alignment explanation
Indices: 13330--13372 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13320 ATGAGTAGTT
* *
13330 TTAAAGTAAAAATGTCATA
1 TTAAAGTAAAAATATAATA
13349 TATAAA-TAAAAATATAATA
1 T-TAAAGTAAAAATATAATA
13368 TTAAA
1 TTAAA
13373 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 13 0.62
20 4 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TTAAAGTAAAAATATAATA
Found at i:15116 original size:12 final size:12
Alignment explanation
Indices: 15099--15142 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
15089 ATAATGAAGA
15099 AAAAATAAAAAG
1 AAAAATAAAAAG
*
15111 AAAAATAAAGA-
1 AAAAATAAAAAG
*
15122 AAAAATTAAAAG
1 AAAAATAAAAAG
15134 AAAAATAAA
1 AAAAATAAA
15143 TCAGAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAAATAAAAAG
Found at i:15121 original size:23 final size:23
Alignment explanation
Indices: 15095--15142 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
15085 GAAGATAATG
15095 AAGAAAAAATAAAAAGAAAAATA
1 AAGAAAAAATAAAAAGAAAAATA
*
15118 AAGAAAAAATTAAAAGAAAAATA
1 AAGAAAAAATAAAAAGAAAAATA
15141 AA
1 AA
15143 TCAGAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (23 bp):
AAGAAAAAATAAAAAGAAAAATA
Found at i:15987 original size:15 final size:15
Alignment explanation
Indices: 15964--15994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15954 CAAGCAATTA
*
15964 CGTTCACATTAACAT
1 CGTTAACATTAACAT
15979 CGTTAACATTAACAT
1 CGTTAACATTAACAT
15994 C
1 C
15995 TCTTGGAGTT
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:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (15 bp):
CGTTAACATTAACAT
Found at i:16945 original size:143 final size:143
Alignment explanation
Indices: 16687--16975 Score: 560
Period size: 143 Copynumber: 2.0 Consensus size: 143
16677 TCTTTGGACT
*
16687 CAAACCTGTTGGATTCAAATGGGTATTTATTTGGAAATGAAATGAAGAACTAAGGTCGTGAGGTA
1 CAAACCTATTGGATTCAAATGGGTATTTATTTGGAAATGAAATGAAGAACTAAGGTCGTGAGGTA
16752 TAAAACCCGACGTCTGTAGCCCAAGGGTTTTACTTAGAGAACTAGGGTTGATTATTAAGTATTAA
66 TAAAACCCGACGTCTGTAGCCCAAGGGTTTTACTTAGAGAACTAGGGTTGATTATTAAGTATTAA
16817 CTTGTGATGAATA
131 CTTGTGATGAATA
16830 CAAACCTATTGGATTCAAATGGGTATTTATTTGGAAATGAAATGAAGAACTAAGGTCGTGAGGTA
1 CAAACCTATTGGATTCAAATGGGTATTTATTTGGAAATGAAATGAAGAACTAAGGTCGTGAGGTA
*
16895 TAAAACCCGACGTCTGTAGCCCAAGGGTTTTACTTAGAGAACTGGGGTTGATTATTAAGTATTAA
66 TAAAACCCGACGTCTGTAGCCCAAGGGTTTTACTTAGAGAACTAGGGTTGATTATTAAGTATTAA
16960 CTTGTGATGAATA
131 CTTGTGATGAATA
16973 CAA
1 CAA
16976 TTTCATTTCC
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 144 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (143 bp):
CAAACCTATTGGATTCAAATGGGTATTTATTTGGAAATGAAATGAAGAACTAAGGTCGTGAGGTA
TAAAACCCGACGTCTGTAGCCCAAGGGTTTTACTTAGAGAACTAGGGTTGATTATTAAGTATTAA
CTTGTGATGAATA
Found at i:19043 original size:51 final size:52
Alignment explanation
Indices: 18942--19043 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
18932 GTTCATCAAA
* **
18942 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
18994 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
19044 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Done.