Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013835.1 Corchorus olitorius cultivar O-4 contig13868, 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: 10496
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:5277 original size:11 final size:11
Alignment explanation
Indices: 5261--5286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5251 TCCTTACATG
5261 GCATTCATCAT
1 GCATTCATCAT
5272 GCATTCATCAT
1 GCATTCATCAT
5283 GCAT
1 GCAT
5287 GATCACGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (11 bp):
GCATTCATCAT
Found at i:7115 original size:21 final size:21
Alignment explanation
Indices: 7089--7312 Score: 299
Period size: 21 Copynumber: 10.4 Consensus size: 21
7079 TGCTAGGAGT
7089 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
7110 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
7131 TCATTGGAAAAGGTTCCAATTCCAAGC
1 TCATTGGAGAAGG------TTCCAAGC
7158 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
7179 TTATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
7200 TCATTGGAAAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
7221 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
7242 TTATTGGAGAAGATTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
7263 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
**
7284 TCATTGGAGAAGGTTTTAAGC
1 TCATTGGAGAAGGTTCCAAGC
7305 TCATTGGA
1 TCATTGGA
7313 ATTGCCTAAG
Statistics
Matches: 182, Mismatches: 12, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
20 4 0.02
21 159 0.87
27 17 0.09
28 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:8768 original size:28 final size:28
Alignment explanation
Indices: 8728--8812 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
8718 TTCTAATTGA
8728 TTGAATTGATTGATTTGTGTTTTGTGTT
1 TTGAATTGATTGATTTGTGTTTTGTGTT
* **
8756 TTGAATTGATTGATTTGTG-TTTCT-AA
1 TTGAATTGATTGATTTGTGTTTTGTGTT
*
8782 TTGAATTGATTGATTTGT-TAATTGTGTT
1 TTGAATTGATTGATTTGTGT-TTTGTGTT
8810 TTG
1 TTG
8813 TGCAGCAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 18 0.38
27 7 0.15
28 22 0.47
ACGTcount: A:0.19, C:0.01, G:0.22, T:0.58
Consensus pattern (28 bp):
TTGAATTGATTGATTTGTGTTTTGTGTT
Found at i:8774 original size:21 final size:22
Alignment explanation
Indices: 8748--8792 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
8738 TGATTTGTGT
8748 TTTGTGTTT-TGAATTG-ATTGA
1 TTTGTGTTTCT-AATTGAATTGA
8769 TTTGTGTTTCTAATTGAATTGA
1 TTTGTGTTTCTAATTGAATTGA
8791 TT
1 TT
8793 GATTTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.58
Consensus pattern (22 bp):
TTTGTGTTTCTAATTGAATTGA
Found at i:8792 original size:26 final size:28
Alignment explanation
Indices: 8727--8799 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
8717 TTTCTAATTG
* *
8727 ATTGAATTGATTGATTTGTGTTTTGTGT
1 ATTGAATTGATTGATTTGTGTTTTCTGA
*
8755 TTTGAATTGATTGATTTGTG-TTTCT-A
1 ATTGAATTGATTGATTTGTGTTTTCTGA
8781 ATTGAATTGATTGATTTGT
1 ATTGAATTGATTGATTTGT
8800 TAATTGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 18 0.44
27 4 0.10
28 19 0.46
ACGTcount: A:0.21, C:0.01, G:0.22, T:0.56
Consensus pattern (28 bp):
ATTGAATTGATTGATTTGTGTTTTCTGA
Done.