Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024469.1 Corchorus olitorius cultivar O-4 contig24502, 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: 23002
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2988 original size:13 final size:13
Alignment explanation
Indices: 2970--2995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2960 TATAATCATT
2970 TAACCAACAAAGC
1 TAACCAACAAAGC
2983 TAACCAACAAAGC
1 TAACCAACAAAGC
2996 AAGAGGACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (13 bp):
TAACCAACAAAGC
Found at i:5822 original size:8 final size:8
Alignment explanation
Indices: 5806--5853 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
5796 ATAAGAATAA
*
5806 TTTTCATT
1 TTTTTATT
5814 TTTTTATT
1 TTTTTATT
5822 TTTTTATTTAT
1 TTTTTA--T-T
5833 TTTTTATT
1 TTTTTATT
5841 TTTTTATT
1 TTTTTATT
5849 TTTTT
1 TTTTT
5854 CCATCAGGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
8 27 0.75
9 1 0.03
10 1 0.03
11 7 0.19
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:5837 original size:19 final size:18
Alignment explanation
Indices: 5812--5853 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
5802 ATAATTTTCA
5812 TTTTTTTATTTTTTTATT
1 TTTTTTTATTTTTTTATT
5830 TATTTTTTATTTTTTTATT
1 T-TTTTTTATTTTTTTATT
5849 TTTTT
1 TTTTT
5854 CCATCAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTTATTTTTTTATT
Found at i:10491 original size:25 final size:25
Alignment explanation
Indices: 10463--10605 Score: 207
Period size: 25 Copynumber: 5.8 Consensus size: 25
10453 AAATCAAACA
10463 GCCACATAGTTGGTCGTGAGATTCG
1 GCCACATAGTTGGTCGTGAGATTCG
10488 GCCACATAGTTGGTCGTGAGATTCG
1 GCCACATAGTTGGTCGTGAGATTCG
* **
10513 GCCACATCGTTGGTCGTGAGAAACG
1 GCCACATAGTTGGTCGTGAGATTCG
* *
10538 GCCACATCGTTGGTCGCGAGATTCG
1 GCCACATAGTTGGTCGTGAGATTCG
*
10563 GCCACATAGTTGGTTGTGAGATTCG
1 GCCACATAGTTGGTCGTGAGATTCG
* *
10588 ACCACAT-GGTGGTCGTGA
1 GCCACATAGTTGGTCGTGA
10606 CAAAAGACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 9 0.08
25 97 0.92
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (25 bp):
GCCACATAGTTGGTCGTGAGATTCG
Found at i:10586 original size:75 final size:74
Alignment explanation
Indices: 10458--10605 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 74
10448 GAGGAAAATC
* * *
10458 AAACAGCCACATAGTTGGTCGTGAGATTCGGCCACATAGTTGGTCGTGAGATTCGGCCACATCGT
1 AAACAGCCACATAGTTGGTCGCGAGATTCGGCCACATAGTTGGTCGTGAGATTCGACCACAT-GG
10523 TGGTCGTGAG
65 TGGTCGTGAG
* * *
10533 AAACGGCCACATCGTTGGTCGCGAGATTCGGCCACATAGTTGGTTGTGAGATTCGACCACATGGT
1 AAACAGCCACATAGTTGGTCGCGAGATTCGGCCACATAGTTGGTCGTGAGATTCGACCACATGGT
10598 GGTCGTGA
66 GGTCGTGA
10606 CAAAAGACCA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 10 0.15
75 57 0.85
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (74 bp):
AAACAGCCACATAGTTGGTCGCGAGATTCGGCCACATAGTTGGTCGTGAGATTCGACCACATGGT
GGTCGTGAG
Found at i:10979 original size:19 final size:18
Alignment explanation
Indices: 10955--10990 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10945 TGAAGACTTA
10955 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
10974 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
10991 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:10997 original size:30 final size:30
Alignment explanation
Indices: 10943--11002 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
10933 GAAGTTCGTC
* *
10943 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
10973 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
11003 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:12293 original size:22 final size:22
Alignment explanation
Indices: 12251--12293 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12241 TTTCTGATTA
**
12251 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
12273 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
12294 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Done.