Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024118.1 Corchorus olitorius cultivar O-4 contig24151, 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: 20184
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:6661 original size:17 final size:17
Alignment explanation
Indices: 6641--6699 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
6631 GCAAAATTAC
6641 AAAAACACAAAAACAAA
1 AAAAACACAAAAACAAA
*
6658 AAAAAAAC-AAAACAAA
1 AAAAACACAAAAACAAA
*
6674 AACAAA-ATACAAAACAAA
1 AA-AAACACA-AAAACAAA
6692 ACAAAACA
1 A-AAAACA
6700 AAACTAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.31
17 10 0.29
18 12 0.34
19 2 0.06
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (17 bp):
AAAAACACAAAAACAAA
Found at i:6665 original size:11 final size:11
Alignment explanation
Indices: 6649--6702 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
6639 ACAAAAACAC
6649 AAAAACAAAAA
1 AAAAACAAAAA
*
6660 AAAAACAAAAC
1 AAAAACAAAAA
6671 AAAAACAAAATA
1 AAAAACAAAA-A
*
6683 CAAAAC-AAAA
1 AAAAACAAAAA
*
6693 CAAAACAAAA
1 AAAAACAAAA
6703 CTAAAGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 7 0.18
11 26 0.68
12 5 0.13
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:6672 original size:22 final size:23
Alignment explanation
Indices: 6647--6707 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
6637 TTACAAAAAC
6647 ACAAAAACAAAA-AAAAAACAAA
1 ACAAAAACAAAATAAAAAACAAA
*
6669 ACAAAAACAAAATACAAAACAAA
1 ACAAAAACAAAATAAAAAACAAA
6692 AC-AAAACAAAACTAAA
1 ACAAAAACAAAA-TAAA
6708 GGAAAGTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 21 0.60
23 14 0.40
ACGTcount: A:0.80, C:0.16, G:0.00, T:0.03
Consensus pattern (23 bp):
ACAAAAACAAAATAAAAAACAAA
Found at i:6679 original size:28 final size:29
Alignment explanation
Indices: 6642--6703 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
6632 CAAAATTACA
6642 AAAACACAAAA-ACAAAAAAAAAACAAAAC
1 AAAACACAAAATAC-AAAAAAAAACAAAAC
*
6671 AAAA-ACAAAATACAAAACAAAACAAAAC
1 AAAACACAAAATACAAAAAAAAACAAAAC
6699 AAAAC
1 AAAAC
6704 TAAAGGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.02
Consensus pattern (29 bp):
AAAACACAAAATACAAAAAAAAACAAAAC
Found at i:6723 original size:5 final size:5
Alignment explanation
Indices: 6650--6703 Score: 63
Period size: 5 Copynumber: 10.0 Consensus size: 5
6640 CAAAAACACA
*
6650 AAAAC AAAAAA AAAAC AAAAC AAAAAC AAAATAC AAAAC AAAAC AAAAC
1 AAAAC -AAAAC AAAAC AAAAC -AAAAC -AAA-AC AAAAC AAAAC AAAAC
6699 AAAAC
1 AAAAC
6704 TAAAGGAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 26 0.59
6 16 0.36
7 2 0.05
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (5 bp):
AAAAC
Found at i:9093 original size:36 final size:35
Alignment explanation
Indices: 9053--9129 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
9043 GTAACAAGGA
9053 ATCAATGATGAGAGTTTTTGTGTATGGCGCTTTTGT
1 ATCAAT-ATGAGAGTTTTTGTGTATGGCGCTTTTGT
*
9089 ATCAATTTGAGAGTTTTTGTGTATGGCGCTTTTGT
1 ATCAATATGAGAGTTTTTGTGTATGGCGCTTTTGT
9124 ATCAAT
1 ATCAAT
9130 TTTAGGGAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 34 0.85
36 6 0.15
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (35 bp):
ATCAATATGAGAGTTTTTGTGTATGGCGCTTTTGT
Found at i:9101 original size:35 final size:35
Alignment explanation
Indices: 9061--9131 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
9051 GAATCAATGA
9061 TGAGAGTTTTTGTGTATGGCGCTTTTGTATCAATT
1 TGAGAGTTTTTGTGTATGGCGCTTTTGTATCAATT
9096 TGAGAGTTTTTGTGTATGGCGCTTTTGTATCAATT
1 TGAGAGTTTTTGTGTATGGCGCTTTTGTATCAATT
9131 T
1 T
9132 TAGGGAGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.49
Consensus pattern (35 bp):
TGAGAGTTTTTGTGTATGGCGCTTTTGTATCAATT
Found at i:15933 original size:44 final size:42
Alignment explanation
Indices: 15883--15967 Score: 152
Period size: 44 Copynumber: 2.0 Consensus size: 42
15873 ATCTAGACTT
15883 TCCAATTTTGGCAAGAGAGTACGTAATAATTAATATATGCCTTC
1 TCCAATTTTGGCAAGAGAGTACGTAATAA-T-ATATATGCCTTC
15927 TCCAATTTTGGCAAGAGAGTACGTAATAATATATATGCCTT
1 TCCAATTTTGGCAAGAGAGTACGTAATAATATATATGCCTT
15968 ACCTAATCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 11 0.27
43 1 0.02
44 29 0.71
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (42 bp):
TCCAATTTTGGCAAGAGAGTACGTAATAATATATATGCCTTC
Done.