Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012648.1 Corchorus olitorius cultivar O-4 contig12681, 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: 30810
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:49 original size:6 final size:6
Alignment explanation
Indices: 38--68 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28 TGATACTTTC
*
38 TTTTTG TTTTTG TTTTTG TTTTTT TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
69 GGCCAGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:2284 original size:31 final size:32
Alignment explanation
Indices: 2259--2338 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 32
2249 AAACCACTTG
* **
2259 AACCCGAGCCCGAAAGAATC-CAAACCTGAAA
1 AACCCGAGCCCGAAAGAAACTCAAACCACAAA
*
2290 AACCCGAGCCCGAAAGAAACTCAAACCCGAAAAA
1 AACCCGAGCCCGAAAGAAACTCAAA-CC-ACAAA
*
2324 AACCCGAACCCGAAA
1 AACCCGAGCCCGAAA
2339 ATACCCGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 19 0.45
32 4 0.10
33 2 0.05
34 17 0.40
ACGTcount: A:0.47, C:0.34, G:0.15, T:0.04
Consensus pattern (32 bp):
AACCCGAGCCCGAAAGAAACTCAAACCACAAA
Found at i:2318 original size:17 final size:17
Alignment explanation
Indices: 2287--2339 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2277 TCCAAACCTG
* *
2287 AAAAACCCGAGCCCGAA
1 AAAAACCCAAACCCGAA
* *
2304 AGAAACTCAAACCCGAA
1 AAAAACCCAAACCCGAA
*
2321 AAAAACCCGAACCCGAA
1 AAAAACCCAAACCCGAA
2338 AA
1 AA
2340 TACCCGAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.53, C:0.32, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAACCCAAACCCGAA
Found at i:2344 original size:16 final size:16
Alignment explanation
Indices: 2259--2347 Score: 72
Period size: 16 Copynumber: 5.5 Consensus size: 16
2249 AAACCACTTG
* *
2259 AACCCGAGCCCGAAAG
1 AACCCGAACCCGAAAA
* * *
2275 AATCCAAACCTG-AAA
1 AACCCGAACCCGAAAA
*
2290 AACCCGAGCCCGAAAGA
1 AACCCGAACCCGAAA-A
* *
2307 AACTCAAACCCGAAAAA
1 AACCCGAACCCG-AAAA
2324 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
*
2340 TACCCGAA
1 AACCCGAA
2348 TTCAATACTA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
15 10 0.18
16 21 0.38
17 21 0.38
18 3 0.05
ACGTcount: A:0.47, C:0.34, G:0.15, T:0.04
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:3154 original size:25 final size:25
Alignment explanation
Indices: 3094--3155 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
3084 TCGAACACGA
3094 ATTAACCTGACATGAAATTGACCCG
1 ATTAACCTGACATGAAATTGACCCG
** * * **
3119 AAAAACTTGACCTGAAATTGATTCG
1 ATTAACCTGACATGAAATTGACCCG
3144 ATTAACCTGACA
1 ATTAACCTGACA
3156 CAAATTTGAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (25 bp):
ATTAACCTGACATGAAATTGACCCG
Found at i:5101 original size:14 final size:14
Alignment explanation
Indices: 5082--5111 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5072 AAGAAGGCCC
5082 GGCAAATACAACAA
1 GGCAAATACAACAA
5096 GGCAAATACAACAA
1 GGCAAATACAACAA
5110 GG
1 GG
5112 GGGTTTGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (14 bp):
GGCAAATACAACAA
Found at i:12109 original size:9 final size:9
Alignment explanation
Indices: 12091--12158 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
12081 CCTACCCCCA
*
12091 AGGAGGAGG
1 AGGAGAAGG
12100 AGGAGAAGG
1 AGGAGAAGG
12109 AGGAGAAGG
1 AGGAGAAGG
*
12118 AGAAGAAGG
1 AGGAGAAGG
*
12127 AGAAGAAGG
1 AGGAGAAGG
12136 AGGAGAAGG
1 AGGAGAAGG
* *
12145 AAGAGAAGA
1 AGGAGAAGG
12154 AGGAG
1 AGGAG
12159 TTGGTGTCTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (9 bp):
AGGAGAAGG
Done.