Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015991.1 Corchorus olitorius cultivar O-4 contig16024, 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: 39748
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:5951 original size:42 final size:42
Alignment explanation
Indices: 5771--5938 Score: 320
Period size: 42 Copynumber: 4.0 Consensus size: 42
5761 CGGAACCACT
5771 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
1 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
5813 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
1 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
5855 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
1 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
*
5897 AGAAATCGTAAGAAACCTGCAAATCCCA-GCAGAAATGGAAA
1 AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
5938 A
1 A
5939 TAAAAGAATA
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 13 0.10
42 112 0.90
ACGTcount: A:0.48, C:0.19, G:0.23, T:0.10
Consensus pattern (42 bp):
AGAAATCGTAAGAAACCTGCAAATCCCAGGCAGAAAGGGAAA
Found at i:6537 original size:17 final size:17
Alignment explanation
Indices: 6515--6555 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6505 GTGCACTTTT
* *
6515 AGCTCGGGCTCGTTTGG
1 AGCTCGAGCTCGATTGG
6532 AGCTCGAGCTCGATTGG
1 AGCTCGAGCTCGATTGG
6549 AGCTCGA
1 AGCTCGA
6556 AATTTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.24
Consensus pattern (17 bp):
AGCTCGAGCTCGATTGG
Found at i:16786 original size:16 final size:16
Alignment explanation
Indices: 16767--16798 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16757 TTTCAGGTTA
16767 AAAAATGCAGAGGTCC
1 AAAAATGCAGAGGTCC
16783 AAAAATGCAGAGGTCC
1 AAAAATGCAGAGGTCC
16799 TCCATTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (16 bp):
AAAAATGCAGAGGTCC
Found at i:18940 original size:11 final size:11
Alignment explanation
Indices: 18924--18958 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
18914 TTGACAGCGC
18924 AACAAAAACAA
1 AACAAAAACAA
*
18935 AACAAAAACGA
1 AACAAAAACAA
18946 AACAAAAACAA
1 AACAAAAACAA
18957 AA
1 AA
18959 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:19159 original size:2 final size:2
Alignment explanation
Indices: 19152--19183 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19142 ACAAACAAAC
19152 AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19184 CTCATAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27781 original size:81 final size:81
Alignment explanation
Indices: 27646--27962 Score: 573
Period size: 81 Copynumber: 3.9 Consensus size: 81
27636 AGAGAGGCAG
*
27646 GGAATCCAATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
1 GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
*
27711 CTGGTGTGATGGGCGA
66 CTGCTGTGATGGGCGA
*
27727 GGAATCCGACGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
1 GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
27792 CTGCTGTGGA-GGGCGA
66 CTGCTGT-GATGGGCGA
*
27808 GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGAGCCAAGGGTGCGGTTGAGGAAGAAGAGA
1 GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
27873 CTGCTGTGATGGGCGA
66 CTGCTGTGATGGGCGA
*
27889 GGAATCCGATGTAGCAGTGAAGAAGACATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
1 GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
27954 CTGCTGTGA
66 CTGCTGTGA
27963 AGAGCGAGAA
Statistics
Matches: 227, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
80 2 0.01
81 223 0.98
82 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.38, T:0.14
Consensus pattern (81 bp):
GGAATCCGATGTAGCAGTGAAGAAGAAATCAAAACGGGCCAAGGGTGCGGTTGAGGAAGAAGAGA
CTGCTGTGATGGGCGA
Found at i:36162 original size:22 final size:21
Alignment explanation
Indices: 36136--36176 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36126 AAATATTATT
*
36136 GGGGAAAGCTTTTGAAAAGGTA
1 GGGG-AAGCTTCTGAAAAGGTA
*
36158 GGGGAATCTTCTGAAAAGG
1 GGGGAAGCTTCTGAAAAGG
36177 ATTTCATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.07, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGAAGCTTCTGAAAAGGTA
Found at i:39553 original size:22 final size:21
Alignment explanation
Indices: 39480--39554 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
39470 GTTTTGTTTA
*
39480 AATTATTATTATTAATTAATTT
1 AATTATTATTTTTAATT-ATTT
* * *
39502 AGTTAATTATTTTTAAATAGTT
1 AATT-ATTATTTTTAATTATTT
*
39524 ATTATATTATTTTTAGATTATTT
1 AAT-TATTATTTTTA-ATTATTT
39547 AATTATTA
1 AATTATTA
39555 AATCATTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 23 0.55
23 19 0.45
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTATTATTTTTAATTATTT
Done.