Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021900.1 Corchorus olitorius cultivar O-4 contig21933, 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: 12873
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3832 original size:29 final size:32
Alignment explanation
Indices: 3794--3864 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
3784 CTTGCTCAAT
*
3794 TTGAGTCTAAAAC-TT-T-AAAATGC-ACCAAA
1 TTGAGCCTAAAACGTTATCAAAAT-CAACCAAA
*
3823 TTGAGCCT-AAACGTTATCAAAATCAACCAAT
1 TTGAGCCTAAAACGTTATCAAAATCAACCAAA
3854 TTGAGCCTAAA
1 TTGAGCCTAAA
3865 TTAGACGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 4 0.11
29 9 0.26
30 2 0.06
31 18 0.51
32 2 0.06
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (32 bp):
TTGAGCCTAAAACGTTATCAAAATCAACCAAA
Found at i:8019 original size:21 final size:21
Alignment explanation
Indices: 7991--8080 Score: 87
Period size: 21 Copynumber: 4.3 Consensus size: 21
7981 ATGGCAAAAG
7991 TGATGATGATGAAGAATATTA
1 TGATGATGATGAAGAATATTA
* * * *
8012 TTATGATGATGATGATTATGA
1 TGATGATGATGAAGAATATTA
8033 TGATGATGATGACGAGGAATATTA
1 TGATGATGATGA--A-GAATATTA
*
8057 TGATGACG--G-AGAATATTA
1 TGATGATGATGAAGAATATTA
8075 TGATGA
1 TGATGA
8081 GAAAGATGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 14 0.25
19 1 0.02
21 28 0.49
22 1 0.02
24 13 0.23
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (21 bp):
TGATGATGATGAAGAATATTA
Found at i:8029 original size:15 final size:15
Alignment explanation
Indices: 8011--8042 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8001 GAAGAATATT
8011 ATTATGATGATGATG
1 ATTATGATGATGATG
8026 ATTATGATGATGATG
1 ATTATGATGATGATG
8041 AT
1 AT
8043 GACGAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
ATTATGATGATGATG
Found at i:8059 original size:18 final size:18
Alignment explanation
Indices: 8038--8080 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
8028 TATGATGATG
8038 ATGATGAC-GAGGAATATT
1 ATGATGACGGA-GAATATT
8056 ATGATGACGGAGAATATT
1 ATGATGACGGAGAATATT
8074 ATGATGA
1 ATGATGA
8081 GAAAGATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (18 bp):
ATGATGACGGAGAATATT
Found at i:8062 original size:3 final size:3
Alignment explanation
Indices: 7991--8044 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
7981 ATGGCAAAAG
* * * *
7991 TGA TGA TGA TGA AGAA T-A TTA TTA TGA TGA TGA TGA TTA TGA TGA
1 TGA TGA TGA TGA TG-A TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
8036 TGA TGA TGA
1 TGA TGA TGA
8045 CGAGGAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
2 2 0.05
3 41 0.93
4 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:8110 original size:18 final size:18
Alignment explanation
Indices: 8089--8129 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
8079 GAGAAAGATG
8089 AGAAAAATGAAAAAGAAA
1 AGAAAAATGAAAAAGAAA
** *
8107 AGAAAGCTGAGAAAGAAA
1 AGAAAAATGAAAAAGAAA
8125 AGAAA
1 AGAAA
8130 TAAGCGGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (18 bp):
AGAAAAATGAAAAAGAAA
Done.