Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024761.1 Corchorus olitorius cultivar O-4 contig24794, 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: 25406
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:885 original size:35 final size:36
Alignment explanation
Indices: 846--916 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
836 CATTCTCAAC
846 ACCACCATTTGAACCAGTTTTTCCTA-CCCTCCAAT
1 ACCACCATTTGAACCAGTTTTTCCTACCCCTCCAAT
881 ACCACCATTTGAACCAGTTTTTCCTACCCCTCCAAT
1 ACCACCATTTGAACCAGTTTTTCCTACCCCTCCAAT
917 GAAACCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 26 0.74
36 9 0.26
ACGTcount: A:0.25, C:0.38, G:0.06, T:0.31
Consensus pattern (36 bp):
ACCACCATTTGAACCAGTTTTTCCTACCCCTCCAAT
Found at i:924 original size:36 final size:35
Alignment explanation
Indices: 849--924 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 35
839 TCTCAACACC
*
849 ACCATTTGAACCAGTTTTTCCTACCCTCCAATACC
1 ACCATTTGAACCAGTTTTTCCTACCCTCCAATACA
884 ACCATTTGAACCAGTTTTTCCTACCCCTCCAATGA-A
1 ACCATTTGAACCAGTTTTTCCTA-CCCTCCAAT-ACA
920 ACCAT
1 ACCAT
925 CACCAACTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
35 23 0.61
36 14 0.37
37 1 0.03
ACGTcount: A:0.28, C:0.36, G:0.07, T:0.30
Consensus pattern (35 bp):
ACCATTTGAACCAGTTTTTCCTACCCTCCAATACA
Found at i:4089 original size:30 final size:30
Alignment explanation
Indices: 4053--4121 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
4043 GGCCGATAGC
*
4053 TCTTATCCTTAGGATGCTATGTGCTTTGCA
1 TCTTATCATTAGGATGCTATGTGCTTTGCA
* * *
4083 TCTTATCATTTGGGTGCTATGTGTTTTGCA
1 TCTTATCATTAGGATGCTATGTGCTTTGCA
*
4113 TTTTATCAT
1 TCTTATCAT
4122 GACATTTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (30 bp):
TCTTATCATTAGGATGCTATGTGCTTTGCA
Found at i:6022 original size:21 final size:21
Alignment explanation
Indices: 5998--6037 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5988 ACTGCCTATC
5998 TGGGTGATCAGACAAACCACA
1 TGGGTGATCAGACAAACCACA
**
6019 TGGGTTTTCAGACAAACCA
1 TGGGTGATCAGACAAACCA
6038 TGTGGGCGCC
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:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
TGGGTGATCAGACAAACCACA
Found at i:18263 original size:2 final size:2
Alignment explanation
Indices: 18256--18280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18246 TGAATTGTAC
18256 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18281 TGATAATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18608 original size:14 final size:14
Alignment explanation
Indices: 18589--18628 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18579 GATTAGAATT
18589 AAGATTATTCATAA
1 AAGATTATTCATAA
18603 AAGATTATT-AT--
1 AAGATTATTCATAA
18614 AA-ATTATTCATAA
1 AAGATTATTCATAA
18627 AA
1 AA
18629 TATTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.26
11 4 0.17
13 4 0.17
14 9 0.39
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (14 bp):
AAGATTATTCATAA
Found at i:22225 original size:47 final size:46
Alignment explanation
Indices: 22135--22225 Score: 103
Period size: 47 Copynumber: 1.9 Consensus size: 46
22125 TCCTGCATGT
** * * *
22135 ACAATGATATATATAAATATAATTTGGTTTAGCTTTGTCTATGAAGA
1 ACAATGATATATATAAATATAATTT-GTAAAGATTGGTATATGAAGA
22182 ACAATGATATATATAAATATAATTT-TAAATGATATGGTATATGA
1 ACAATGATATATATAAATATAATTTGTAAA-GAT-TGGTATATGA
22226 CAATGAGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.05
46 2 0.05
47 33 0.89
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (46 bp):
ACAATGATATATATAAATATAATTTGTAAAGATTGGTATATGAAGA
Found at i:23671 original size:48 final size:46
Alignment explanation
Indices: 23596--23730 Score: 166
Period size: 48 Copynumber: 2.9 Consensus size: 46
23586 GAGCGTGCCA
* * *
23596 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAA-AAAAAG
23643 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAAAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAAAAAAG
* *
23691 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAA
23731 GTAAAGAATT
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
46 7 0.09
47 15 0.19
48 47 0.59
49 9 0.11
50 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (46 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAAAAAAG
Done.