Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023358.1 Corchorus olitorius cultivar O-4 contig23391, 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: 10969
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:57 original size:33 final size:32
Alignment explanation
Indices: 12--150 Score: 152
Period size: 33 Copynumber: 4.2 Consensus size: 32
2 GATGTTGTAA
* *
12 GTGATGATACTAAACCTAATTTGAGTATTGTTT
1 GTGATGACACTAAACCT-ATTTGAGTGTTGTTT
* * *
45 GTGATGACACTAAATCTGTTTTAGATGTTGTTT
1 GTGATGACACTAAACCTATTTGAG-TGTTGTTT
* *
78 GCGATGATACTAAACCTAATTTGAGTGTTGTTT
1 GTGATGACACTAAACCT-ATTTGAGTGTTGTTT
* * *
111 GTGATGACACTAAATCTGTTTTAGGTGTTGTTT
1 GTGATGACACTAAACCTATTTGA-GTGTTGTTT
144 GTGATGA
1 GTGATGA
151 AACAAATTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
32 9 0.10
33 74 0.84
34 5 0.06
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (32 bp):
GTGATGACACTAAACCTATTTGAGTGTTGTTT
Found at i:109 original size:66 final size:66
Alignment explanation
Indices: 14--150 Score: 247
Period size: 66 Copynumber: 2.1 Consensus size: 66
4 TGTTGTAAGT
14 GATGATACTAAACCTAATTTGAGTATTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
1 GATGATACTAAACCTAATTTGAGTATTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
79 C
66 C
* *
80 GATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTG
1 GATGATACTAAACCTAATTTGAGTATTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
*
145 T
66 C
146 GATGA
1 GATGA
151 AACAAATTCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (66 bp):
GATGATACTAAACCTAATTTGAGTATTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
C
Found at i:162 original size:33 final size:32
Alignment explanation
Indices: 12--201 Score: 150
Period size: 33 Copynumber: 5.8 Consensus size: 32
2 GATGTTGTAA
* * ** *
12 GTGATGATACTAAACCTAATTTGAGTATTGTTT
1 GTGATGAAACTAAATCTGTTTTG-GTGTTGTTT
* *
45 GTGATGACACTAAATCTGTTTTAGATGTTGTTT
1 GTGATGAAACTAAATCTGTTTT-GGTGTTGTTT
* * * **
78 GCGATGATACTAAACCTAATTTGAGTGTTGTTT
1 GTGATGAAACTAAATCTGTTTTG-GTGTTGTTT
*
111 GTGATGACACTAAATCTGTTTTAGGTGTTGTTT
1 GTGATGAAACTAAATCTGTTTT-GGTGTTGTTT
* **
144 GTGATGAAAC-AAATTCTGTTTTGGATGCTAATT
1 GTGATGAAACTAAA-TCTGTTTTGG-TGTTGTTT
*
177 GTGATGAAAAC-AAATCTATTTTGGT
1 GTGATG-AAACTAAATCTGTTTTGGT
202 TGATCATAGC
Statistics
Matches: 129, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
32 7 0.05
33 113 0.88
34 9 0.07
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (32 bp):
GTGATGAAACTAAATCTGTTTTGGTGTTGTTT
Found at i:179 original size:66 final size:66
Alignment explanation
Indices: 14--183 Score: 182
Period size: 66 Copynumber: 2.6 Consensus size: 66
4 TGTTGTAAGT
* ** **
14 GATGATACTAAACCTAATTTGAGTATTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
1 GATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
79 C
66 C
* * ** *
80 GATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGGTGTTGTTTG
1 GATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
*
145 T
66 C
* **
146 GATGAAAC-AAATTCTGTTTTG-GATGCTAATTGTGATGA
1 GATGAAACTAAA-CCTAATTTGAG-TGCTAATTGTGATGA
184 AAACAAATCT
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 4 0.04
66 88 0.96
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (66 bp):
GATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGACACTAAATCTGTTTTAGATGTTGTTTG
C
Found at i:1969 original size:21 final size:21
Alignment explanation
Indices: 1943--2034 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
1933 TGCTAGTAGA
1943 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
1964 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
1985 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
2006 TCATTGGAGAATGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
2027 TCATTGGA
1 TCATTGGA
2035 ATTGCCTAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 2 0.03
21 66 0.97
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:2969 original size:21 final size:21
Alignment explanation
Indices: 2945--3057 Score: 192
Period size: 21 Copynumber: 5.4 Consensus size: 21
2935 TGTCAGGAGA
2945 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
2966 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
2987 TCATTGGAGAAGGTTCCAAGG
1 TCATTGGAGAAGGTTCCAAGC
3008 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
3029 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
3050 TCATTGGA
1 TCATTGGA
3058 ATTGCCTAAG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
20 2 0.02
21 86 0.98
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:8242 original size:20 final size:21
Alignment explanation
Indices: 8214--8256 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
8204 ATCTTGAAGA
*
8214 ATTTAAAG-CTATCGGAGATC
1 ATTTAAAGCCCATCGGAGATC
* *
8234 ATTTGAAGCCCATTGGAGATC
1 ATTTAAAGCCCATCGGAGATC
8255 AT
1 AT
8257 CAACAAAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (21 bp):
ATTTAAAGCCCATCGGAGATC
Done.