Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014374.1 Corchorus olitorius cultivar O-4 contig14407, 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: 14155
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2506 original size:6 final size:6
Alignment explanation
Indices: 2495--2524 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2485 ATATTGCGAG
*
2495 GTTCAA GTTCAA GTTCAA GGTCAA GTTCAA
1 GTTCAA GTTCAA GTTCAA GTTCAA GTTCAA
2525 CTTTTGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (6 bp):
GTTCAA
Found at i:2625 original size:27 final size:27
Alignment explanation
Indices: 2589--2644 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2579 CCTTGCTTGT
*
2589 AGATTCTTCTCCAAAATTTGAAGATGC
1 AGATTCTTCTACAAAATTTGAAGATGC
*
2616 AGATTTTTCTACAAAATTTGAAGATGC
1 AGATTCTTCTACAAAATTTGAAGATGC
2643 AG
1 AG
2645 GTGATGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (27 bp):
AGATTCTTCTACAAAATTTGAAGATGC
Found at i:4753 original size:15 final size:15
Alignment explanation
Indices: 4736--4830 Score: 109
Period size: 15 Copynumber: 6.3 Consensus size: 15
4726 TGTAAACCTG
* *
4736 AATTTGCACCTGCTG
1 AATTCGCACCTGCTA
* *
4751 AATTCGAACTTGCTA
1 AATTCGCACCTGCTA
* * *
4766 AATTTGCACCAGCTG
1 AATTCGCACCTGCTA
*
4781 AATTCACACCTGCTA
1 AATTCGCACCTGCTA
*
4796 GATTCGCACCTGCTA
1 AATTCGCACCTGCTA
4811 AATTCGCACCTGCTA
1 AATTCGCACCTGCTA
4826 AATTC
1 AATTC
4831 ACACATTATA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (15 bp):
AATTCGCACCTGCTA
Found at i:4801 original size:45 final size:45
Alignment explanation
Indices: 4733--4834 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
4723 CTCTGTAAAC
** * *
4733 CTGAATTTGCACCTGCTGAATTCGAACTTGCTAAATTTGCACCAG
1 CTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTCGCACCAG
* *
4778 CTGAATTCACACCTGCT-AGATTCGCACCTGCTAAATTCGCACCTG
1 CTGAATTCACACCTGCTGA-ATTCGAACCTGCTAAATTCGCACCAG
*
4823 CTAAATTCACAC
1 CTGAATTCACAC
4835 ATTATAAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28
Consensus pattern (45 bp):
CTGAATTCACACCTGCTGAATTCGAACCTGCTAAATTCGCACCAG
Found at i:8833 original size:13 final size:14
Alignment explanation
Indices: 8807--8835 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8797 TGTACTTACT
8807 ATTAAAAAATATAC
1 ATTAAAAAATATAC
8821 ATTAAAAAA-ATAC
1 ATTAAAAAATATAC
8834 AT
1 AT
8836 GCCAACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAAAAATATAC
Found at i:9187 original size:22 final size:20
Alignment explanation
Indices: 9162--9211 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
9152 TTTTTGGTTG
*
9162 CCTTATTTAGTTTTTTACCTAA
1 CCTTATTTAG-GTTTTA-CTAA
* *
9184 CCTTATTAAGGTTTTAGTAA
1 CCTTATTTAGGTTTTACTAA
9204 CCTTATTT
1 CCTTATTT
9212 TAGAAACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
22 9 0.38
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (20 bp):
CCTTATTTAGGTTTTACTAA
Found at i:9214 original size:14 final size:14
Alignment explanation
Indices: 9195--9224 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9185 CTTATTAAGG
*
9195 TTTTAGTAACCTTA
1 TTTTAGAAACCTTA
9209 TTTTAGAAACCTTA
1 TTTTAGAAACCTTA
9223 TT
1 TT
9225 AAACTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTTAGAAACCTTA
Found at i:10603 original size:107 final size:108
Alignment explanation
Indices: 10488--10692 Score: 340
Period size: 108 Copynumber: 1.9 Consensus size: 108
10478 CCATGGATAA
10488 ATATAAGTATTTAAATTTTATTTATATCATTTT-AAAAAACTTCCCATTTAAAAAAAAACTGTCA
1 ATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTTCCCATTTAAAAAAAAACTGTCA
* *
10552 AAAATTACTCACGTAGTGAGTGTCCTGTGTCTTTTTTTTGTAC
66 AAAATTACTCACGTAATGAGTGTCATGTGTCTTTTTTTTGTAC
* ** *
10595 ATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTTCTCATTTAAAAAGGAATTGTCA
1 ATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTTCCCATTTAAAAAAAAACTGTCA
*
10660 AAAATTACTTACGTAATGAGTGTCATGTGTCTT
66 AAAATTACTCACGTAATGAGTGTCATGTGTCTT
10693 GTAATTTATA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
107 33 0.37
108 57 0.63
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (108 bp):
ATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTTCCCATTTAAAAAAAAACTGTCA
AAAATTACTCACGTAATGAGTGTCATGTGTCTTTTTTTTGTAC
Done.