Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024493.1 Corchorus olitorius cultivar O-4 contig24526, 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: 13150
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3734 original size:25 final size:25
Alignment explanation
Indices: 3706--3755 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3696 CTTGGTCCTT
*
3706 GGTTTGGATTTGGGCCTTAGTTTTA
1 GGTTAGGATTTGGGCCTTAGTTTTA
* *
3731 GGTTAGGGTTTGGGCTTTAGTTTTA
1 GGTTAGGATTTGGGCCTTAGTTTTA
3756 AATCACACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.48
Consensus pattern (25 bp):
GGTTAGGATTTGGGCCTTAGTTTTA
Found at i:4595 original size:62 final size:62
Alignment explanation
Indices: 4477--4595 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
4467 TTTTAAATTG
* * **
4477 GGAAAGTTCCCATCCAGTTTTCAAAGTATTCAATTTAAGTTTTTCAAAAGTTTTCAATTTAC
1 GGAAAGTTCCCATCAAGTTTTCAAAATATTCAATTTAAGTTTTTCAAAAGCATTCAATTTAC
* *
4539 GGAAAGTTCCCATCAAGTTTTCAAAATGTTCAATTTAGGTCTTTTCAAAA-CATTCAA
1 GGAAAGTTCCCATCAAGTTTTCAAAATATTCAATTTAAGT-TTTTCAAAAGCATTCAA
4596 CCAGCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 41 0.82
63 9 0.18
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38
Consensus pattern (62 bp):
GGAAAGTTCCCATCAAGTTTTCAAAATATTCAATTTAAGTTTTTCAAAAGCATTCAATTTAC
Found at i:5495 original size:29 final size:29
Alignment explanation
Indices: 5438--5495 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5428 AAGTTCGTAT
* *
5438 TTGAAGACTTATTGAAGATAATTTGAAGA
1 TTGAAGACTTATTGAAGATAATCTCAAGA
*
5467 TTGAAGAC-TATTGAAGAATTATCTCAAGA
1 TTGAAGACTTATTGAAG-ATAATCTCAAGA
5496 GGAAAGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
TTGAAGACTTATTGAAGATAATCTCAAGA
Found at i:7029 original size:6 final size:6
Alignment explanation
Indices: 7018--7046 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
7008 TTGTGTATTA
7018 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
7047 CTATTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:8918 original size:15 final size:16
Alignment explanation
Indices: 8900--8932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8890 GAAAGAAAGA
8900 AATTAAAC-AGAAAAC
1 AATTAAACTAGAAAAC
*
8915 AATTATACTAGAAAAC
1 AATTAAACTAGAAAAC
8931 AA
1 AA
8933 AGCAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AATTAAACTAGAAAAC
Found at i:9750 original size:9 final size:10
Alignment explanation
Indices: 9719--9752 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
9709 TAAAGAGAAT
9719 TATGTGAAGG
1 TATGTGAAGG
9729 TATGTGAAGG
1 TATGTGAAGG
9739 TATGTG-AGG
1 TATGTGAAGG
9748 TATGT
1 TATGT
9753 TACAGGAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:12372 original size:20 final size:21
Alignment explanation
Indices: 12330--12372 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12320 TCCTTTGTTG
12330 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
12351 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
12371 AT
1 AT
12373 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:12734 original size:21 final size:21
Alignment explanation
Indices: 12708--12862 Score: 217
Period size: 21 Copynumber: 7.4 Consensus size: 21
12698 TGCTAGAAGT
12708 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
12729 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
12750 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
12771 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
12792 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
12813 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
* *
12834 TCATTAGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
12855 TCATTGGA
1 TCATTGGA
12863 ATTGCCTAAG
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
20 2 0.02
21 125 0.98
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.