Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020022.1 Corchorus olitorius cultivar O-4 contig20055, 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: 33480
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:131 original size:16 final size:16
Alignment explanation
Indices: 112--148 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
102 TGCCTCAGGT
*
112 TCGGGTATTTTCGGGC
1 TCGGGTAATTTCGGGC
*
128 TCGGGTAATTTCGGGT
1 TCGGGTAATTTCGGGC
144 TCGGG
1 TCGGG
149 CTCGGGCGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.16, G:0.41, T:0.35
Consensus pattern (16 bp):
TCGGGTAATTTCGGGC
Found at i:6467 original size:21 final size:21
Alignment explanation
Indices: 6441--6485 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
6431 CAAATAACTG
6441 TATGTAATGTGCCATCTGGTT
1 TATGTAATGTGCCATCTGGTT
6462 TATGTAATGTGCCATCTGGTT
1 TATGTAATGTGCCATCTGGTT
6483 TAT
1 TAT
6486 TAACGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.44
Consensus pattern (21 bp):
TATGTAATGTGCCATCTGGTT
Found at i:10413 original size:31 final size:31
Alignment explanation
Indices: 10378--10476 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 31
10368 CGTTTCACGA
* *
10378 AGGGACTAACTTGATCATTTTTCAATAGTAG
1 AGGGACTAAATTGATCATTTTTCAATAATAG
* * ** *
10409 AGGGATTAAATT-AACAGATTTC-ATAATTG
1 AGGGACTAAATTGATCATTTTTCAATAATAG
* * * *
10438 AGGGACTAAAATGATCTTTTTTCAATACTAC
1 AGGGACTAAATTGATCATTTTTCAATAATAG
10469 AGGGACTA
1 AGGGACTA
10477 TTTAGGTACT
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
29 15 0.30
30 13 0.26
31 22 0.44
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (31 bp):
AGGGACTAAATTGATCATTTTTCAATAATAG
Found at i:10872 original size:17 final size:17
Alignment explanation
Indices: 10828--10875 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
10818 ATATTACATG
*
10828 ACTAGTAATGGTTTAGA
1 ACTAGTAATGTTTTAGA
* **
10845 ACTAGTCATGTTTTATT
1 ACTAGTAATGTTTTAGA
10862 ACTAGTAATGTTTT
1 ACTAGTAATGTTTT
10876 TCAAATCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (17 bp):
ACTAGTAATGTTTTAGA
Found at i:13738 original size:17 final size:16
Alignment explanation
Indices: 13716--13757 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
13706 TTCTTCCTTT
13716 TTTTTCTTTTCTTATTC
1 TTTTTCTTTTCTT-TTC
* *
13733 TTTTTCATTTCTTTTG
1 TTTTTCTTTTCTTTTC
13749 TTTTT-TTTT
1 TTTTTCTTTT
13758 GTAATTTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 3 0.14
16 7 0.32
17 12 0.55
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTC
Found at i:13865 original size:22 final size:23
Alignment explanation
Indices: 13798--13866 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 23
13788 TTGAGCCCAA
13798 CTGCTGC-CAGGCCCGCGCATGGC
1 CTGCTGCGCAGGCCCGCGCA-GGC
* * **
13821 CCGC-GCGCTGGCCCAAG-AGGC
1 CTGCTGCGCAGGCCCGCGCAGGC
13842 CTGCTGCGCAGGCCCGCGCA-GC
1 CTGCTGCGCAGGCCCGCGCAGGC
13864 CTG
1 CTG
13867 GGCTGGCGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
21 6 0.17
22 18 0.51
23 11 0.31
ACGTcount: A:0.10, C:0.43, G:0.36, T:0.10
Consensus pattern (23 bp):
CTGCTGCGCAGGCCCGCGCAGGC
Found at i:16180 original size:31 final size:31
Alignment explanation
Indices: 16100--16187 Score: 117
Period size: 29 Copynumber: 2.9 Consensus size: 31
16090 GTCCTTGTAG
* *
16100 TATTGAAAAAAGATCATTTTAGTCCCTCAAT
1 TATTGAAAAATGATCAATTTAGTCCCTCAAT
** *
16131 TA-TGAAATCTG-TCAATTTAGTCCCTCTAT
1 TATTGAAAAATGATCAATTTAGTCCCTCAAT
16160 TATTGAAAAATGATCAATTTAGTCCCTC
1 TATTGAAAAATGATCAATTTAGTCCCTC
16188 CGTGAAACGG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 18 0.38
30 13 0.27
31 17 0.35
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (31 bp):
TATTGAAAAATGATCAATTTAGTCCCTCAAT
Found at i:28087 original size:1 final size:1
Alignment explanation
Indices: 28081--28109 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
28071 GAATATCTGC
28081 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28110 CTTCTGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33440 original size:2 final size:2
Alignment explanation
Indices: 33435--33480 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
33425 AAAAGAAAAA
33435 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33477 AG AG
1 AG AG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.