Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017251.1 Corchorus olitorius cultivar O-4 contig17284, 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: 17975
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:92 original size:41 final size:41
Alignment explanation
Indices: 23--118 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
13 GTTTTCACCT
* *
23 TAGTCCCTTGATTTAGTATCTCATTTACT-TTCTGATGCAATC
1 TAGTCCC-TGATTTAGGATCTCAGTTACTATT-TGATGCAATC
* * * *
65 TAGTCCCTGATTTAGGATTTTAGTTACTATTTGATTCACTC
1 TAGTCCCTGATTTAGGATCTCAGTTACTATTTGATGCAATC
*
106 TAGTCCTTGATTT
1 TAGTCCCTGATTT
119 TAGAAATTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 37 0.80
42 9 0.20
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.47
Consensus pattern (41 bp):
TAGTCCCTGATTTAGGATCTCAGTTACTATTTGATGCAATC
Found at i:1943 original size:28 final size:28
Alignment explanation
Indices: 1911--1964 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1901 CTAAAACCTA
*
1911 ATGGGAACTTTTCCAATTTGAAAACTGG
1 ATGGGAACTTTCCCAATTTGAAAACTGG
1939 ATGGGAACTTTCCCAATTTGAAAACT
1 ATGGGAACTTTCCCAATTTGAAAACT
1965 TGAAAAGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (28 bp):
ATGGGAACTTTCCCAATTTGAAAACTGG
Found at i:1984 original size:38 final size:38
Alignment explanation
Indices: 1927--2014 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 38
1917 ACTTTTCCAA
1927 TTTG-AAAAC-TGGATGGGAACTTTCCCAATTTGAAAA-C
1 TTTGAAAAACTTGG-TGGGAACTTTCCCAATTT-AAAAGC
1964 -TTGAAAAGACTTGGTGGGAACTTTCCCAATTTAAAAGC
1 TTTGAAAA-ACTTGGTGGGAACTTTCCCAATTTAAAAGC
2002 TTTGAAAAACTTG
1 TTTGAAAAACTTG
2015 AAGGAAATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
36 3 0.07
37 7 0.15
38 26 0.57
39 10 0.22
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (38 bp):
TTTGAAAAACTTGGTGGGAACTTTCCCAATTTAAAAGC
Found at i:12391 original size:34 final size:36
Alignment explanation
Indices: 12353--12436 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 36
12343 AAAAAAAATA
*
12353 TTTTCTGCGTTTTTAATCT-AAAAAAATA-ATTCTG
1 TTTTCTGCGTTTTTAATCTAAAAAAAAAAGATTCTG
* *
12387 TTTTCTACGTTTTT--TCTAAAAAAAAAAGATTTTG
1 TTTTCTGCGTTTTTAATCTAAAAAAAAAAGATTCTG
*
12421 -ATTCTGCGTTTTTAAT
1 TTTTCTGCGTTTTTAAT
12437 TTTTTTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
32 3 0.07
33 19 0.46
34 18 0.44
35 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.49
Consensus pattern (36 bp):
TTTTCTGCGTTTTTAATCTAAAAAAAAAAGATTCTG
Found at i:17105 original size:29 final size:29
Alignment explanation
Indices: 17072--17136 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17062 TTTTTAATCT
17072 AAAAAAAAAAAGATTTTGCGTTTTTCTAA
1 AAAAAAAAAAAGATTTTGCGTTTTTCTAA
* *
17101 AAAAAAAATAAGTTTTTGCGTTTTTCTAA
1 AAAAAAAAAAAGATTTTGCGTTTTTCTAA
17130 AAAAAAA
1 AAAAAAA
17137 TAATTTGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (29 bp):
AAAAAAAAAAAGATTTTGCGTTTTTCTAA
Found at i:17137 original size:28 final size:28
Alignment explanation
Indices: 17069--17139 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
17059 GCGTTTTTAA
17069 TCTAAAAAAAAA-AAGATTTTGCGTTTT
1 TCTAAAAAAAAATAAGATTTTGCGTTTT
*
17096 TCTAAAAAAAAAATAAGTTTTTGCGTTTT
1 TCT-AAAAAAAAATAAGATTTTGCGTTTT
17125 TCTAAAAAAAAATAA
1 TCTAAAAAAAAATAA
17140 TTTGCGTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 3 0.07
28 21 0.51
29 17 0.41
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.35
Consensus pattern (28 bp):
TCTAAAAAAAAATAAGATTTTGCGTTTT
Done.