Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016582.1 Corchorus olitorius cultivar O-4 contig16615, 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: 17817
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:5680 original size:5 final size:5
Alignment explanation
Indices: 5670--5712 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
5660 TCAAATCATT
* * *
5670 AAAGG AAAGG AAAGG AAATG AAAGG AAAGTG AAGGG AAGGG AA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAG-G AAAGG AAAGG AA
5713 GGGGAGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.05
Consensus pattern (5 bp):
AAAGG
Found at i:6267 original size:5 final size:5
Alignment explanation
Indices: 6257--6291 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
6247 TTTCCTCCCA
*
6257 TTTCC TTTCC TTTCA TTTCC TTTCC TTTCC TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
6292 CTCCCCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:6267 original size:15 final size:15
Alignment explanation
Indices: 6247--6282 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6237 GGGATGCCCT
6247 TTTCCTCCCATTTCC
1 TTTCCTCCCATTTCC
**
6262 TTTCCTTTCATTTCC
1 TTTCCTCCCATTTCC
6277 TTTCCT
1 TTTCCT
6283 TTCCTTTCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTCCTCCCATTTCC
Found at i:9186 original size:21 final size:21
Alignment explanation
Indices: 9157--9196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9147 TGGGATAGCT
9157 CGCGCGCGGGCAAACCAAAGC
1 CGCGCGCGGGCAAACCAAAGC
* *
9178 CGCGTGCGGGCAAGCCAAA
1 CGCGCGCGGGCAAACCAAA
9197 TTTGGACGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.35, G:0.35, T:0.03
Consensus pattern (21 bp):
CGCGCGCGGGCAAACCAAAGC
Found at i:12218 original size:27 final size:27
Alignment explanation
Indices: 12176--12235 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
12166 AAGGTATCTG
*
12176 AGAGAGAAAATTGAGATGAAG-AGAAA
1 AGAGAAAAAATTGAGATGAAGTAGAAA
*
12202 AGAGAAAAGAATTGAGATGGAGTAGAAA
1 AGAGAAAA-AATTGAGATGAAGTAGAAA
*
12230 AAAGAA
1 AGAGAA
12236 TGGGAGAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.24
27 12 0.41
28 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (27 bp):
AGAGAAAAAATTGAGATGAAGTAGAAA
Found at i:12521 original size:40 final size:42
Alignment explanation
Indices: 12476--12561 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
12466 AACCCTAAGC
* * *
12476 AAGAGAAAGA-AAGAAATG-CCCTAAAACTAAGTTAAACCTT
1 AAGAGAAAGATAACAAATGCCCCTAAAACTAAGCTAAACCCT
*
12516 AAGAGAAAGATACCAAATGCCCCTAAAACTAAGCTAAACCCT
1 AAGAGAAAGATAACAAATGCCCCTAAAACTAAGCTAAACCCT
12558 AAGA
1 AAGA
12562 AAAAAGAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 10 0.25
41 6 0.15
42 24 0.60
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.15
Consensus pattern (42 bp):
AAGAGAAAGATAACAAATGCCCCTAAAACTAAGCTAAACCCT
Found at i:14030 original size:20 final size:20
Alignment explanation
Indices: 14005--14045 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13995 CAACCATTCC
14005 TTGATTATTTTGAATTCCAA
1 TTGATTATTTTGAATTCCAA
14025 TTGATTATTTTGAATTCCAA
1 TTGATTATTTTGAATTCCAA
14045 T
1 T
14046 ACACATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTGATTATTTTGAATTCCAA
Found at i:15703 original size:29 final size:30
Alignment explanation
Indices: 15648--15720 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
15638 CAGGAGTTTG
15648 GGAGAGGAACGAAAGAGAGAGGAGGGGAA-A
1 GGAGAGGAA-GAAAGAGAGAGGAGGGGAAGA
** *
15678 GGAGAGGAAGAGGGAGGGAGGAGGGGAAGA
1 GGAGAGGAAGAAAGAGAGAGGAGGGGAAGA
*
15708 GAAAGAGGAAGAA
1 G-GAGAGGAAGAA
15721 GGCTTGACGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.44
30 11 0.31
31 9 0.25
ACGTcount: A:0.45, C:0.01, G:0.53, T:0.00
Consensus pattern (30 bp):
GGAGAGGAAGAAAGAGAGAGGAGGGGAAGA
Done.