Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021783.1 Corchorus olitorius cultivar O-4 contig21816, 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: 14731
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1139 original size:11 final size:11
Alignment explanation
Indices: 1115--1149 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1105 TTGACAGTGC
1115 AACAAAAACAA
1 AACAAAAACAA
* *
1126 AACGAAAACGA
1 AACAAAAACAA
1137 AACAAAAACAA
1 AACAAAAACAA
1148 AA
1 AA
1150 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:3993 original size:21 final size:22
Alignment explanation
Indices: 3951--3996 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3941 ACTTGGTGTC
3951 AACTGTCATGAAACCAAAAAAA
1 AACTGTCATGAAACCAAAAAAA
*
3973 AACTGTCATGAAACGAAAAAAA
1 AACTGTCATGAAACCAAAAAAA
3995 AA
1 AA
3997 GTGGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.13
Consensus pattern (22 bp):
AACTGTCATGAAACCAAAAAAA
Found at i:5004 original size:29 final size:30
Alignment explanation
Indices: 4943--5015 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
4933 GTATCCAGGA
**
4943 GGTCCCTGTACTATATGATTTGTGCAATTT
1 GGTCCCTGTACTATATGATTTGTGCAAAAT
**
4973 GGTCCCTGTACTAT-TTTTTTGTGCAAAAT
1 GGTCCCTGTACTATATGATTTGTGCAAAAT
*
5002 GGTCCCTTTACTAT
1 GGTCCCTGTACTAT
5016 CAAAAGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (30 bp):
GGTCCCTGTACTATATGATTTGTGCAAAAT
Found at i:5174 original size:23 final size:22
Alignment explanation
Indices: 5140--5188 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5130 AAAAAAATAA
*
5140 AAAAATCAAAAATGTATTTTTTT
1 AAAAATCAAAAAT-TATTTATTT
5163 AAAAAT-ATAAAATTATTTATTT
1 AAAAATCA-AAAATTATTTATTT
5185 AAAA
1 AAAA
5189 TAAAGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAATCAAAAATTATTTATTT
Found at i:5179 original size:22 final size:21
Alignment explanation
Indices: 5140--5204 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
5130 AAAAAAATAA
5140 AAAAATCAAAAATGTATTTTTTT
1 AAAAAT-AAAAAT-TATTTTTTT
*
5163 AAAAATATAAAATTATTTATTT
1 AAAAATA-AAAATTATTTTTTT
5185 -AAAATAAAGAATT-TTTTTTT
1 AAAAATAAA-AATTATTTTTTT
5205 CTTACGAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 8 0.21
21 10 0.26
22 9 0.24
23 11 0.29
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (21 bp):
AAAAATAAAAATTATTTTTTT
Found at i:6260 original size:21 final size:23
Alignment explanation
Indices: 6235--6285 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
6225 AAAAAATCTT
6235 TATTTTAAATAAATA-A-TTTT-A
1 TATTTTAAA-AAATACATTTTTGA
*
6256 TATTTTGAAAAATACATTTTTGA
1 TATTTTAAAAAATACATTTTTGA
6279 TATTTTA
1 TATTTTA
6286 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 4 0.16
23 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TATTTTAAAAAATACATTTTTGA
Found at i:7355 original size:35 final size:35
Alignment explanation
Indices: 7316--7385 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
7306 GCATGTTGTG
7316 TTCACAATAAATTAAGTATCTTCACTAAGTAGAAA
1 TTCACAATAAATTAAGTATCTTCACTAAGTAGAAA
*
7351 TTCACAATAAATTGAGTATCTTCACTAAGTAGAAA
1 TTCACAATAAATTAAGTATCTTCACTAAGTAGAAA
7386 AATTCAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (35 bp):
TTCACAATAAATTAAGTATCTTCACTAAGTAGAAA
Found at i:12757 original size:18 final size:18
Alignment explanation
Indices: 12717--12758 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12707 TAGGGCTATT
12717 TGATGATGAAAATGAGGA
1 TGATGATGAAAATGAGGA
* *
12735 AGATGATGAAGATG-GTGA
1 TGATGATGAAAATGAG-GA
12753 TGATGA
1 TGATGA
12759 AATTGATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (18 bp):
TGATGATGAAAATGAGGA
Done.