Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020891.1 Corchorus olitorius cultivar O-4 contig20924, 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: 6021
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38 AACAATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5566 original size:2 final size:2
Alignment explanation
Indices: 5561--5803 Score: 294
Period size: 2 Copynumber: 123.0 Consensus size: 2
5551 AAGAAGACGT
* * * * * *
5561 GA GA GA GA -A GA GC GA GA GA GG GA GA GA GA GG GA GG GG GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
5602 GA GA GG GA GA G- GG GG GA GA GG GA GA GA GA GA GA GC GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5643 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5685 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
5727 GA GA GA GC GA GA GA GC GA GA GA GA GA GA GA CA CA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
5769 TA GA GA GA CA GA GA CA GA GA G- GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5804 CCCTAAACGC
Statistics
Matches: 207, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
1 3 0.01
2 204 0.99
ACGTcount: A:0.44, C:0.03, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5819 original size:13 final size:12
Alignment explanation
Indices: 5803--5895 Score: 56
Period size: 13 Copynumber: 7.8 Consensus size: 12
5793 GGAGAGAGAG
5803 ACCCTAAACGCTA
1 ACCCTAAAC-CTA
*
5816 ACCCTAAACCCTG
1 ACCCTAAA-CCTA
* *
5829 ACCATAACCCTAA
1 ACCCTAAACCT-A
5842 ACCCT-AACGCTA
1 ACCCTAAAC-CTA
5854 A----A-ACCTA
1 ACCCTAAACCTA
5861 ACCCTAAA-CTAA
1 ACCCTAAACCT-A
5873 ACCCTAAACCATA
1 ACCCTAAACC-TA
5886 ACCCTAAACC
1 ACCCTAAACC
5896 CTAAACAGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
11 3 0.05
12 17 0.27
13 34 0.55
14 2 0.03
ACGTcount: A:0.42, C:0.40, G:0.03, T:0.15
Consensus pattern (12 bp):
ACCCTAAACCTA
Found at i:5825 original size:7 final size:7
Alignment explanation
Indices: 5803--5901 Score: 88
Period size: 7 Copynumber: 15.3 Consensus size: 7
5793 GGAGAGAGAG
5803 ACCCTAA
1 ACCCTAA
*
5810 ACGCT-A
1 ACCCTAA
5816 ACCCTAA
1 ACCCTAA
*
5823 ACCCT-G
1 ACCCTAA
*
5829 ACCAT-A
1 ACCCTAA
5835 ACCCTAA
1 ACCCTAA
5842 ACCCT-A
1 ACCCTAA
*
5848 ACGCTAA
1 ACCCTAA
*
5855 AACCT-A
1 ACCCTAA
5861 ACCCTAA
1 ACCCTAA
5868 A--CTAA
1 ACCCTAA
5873 ACCCTAA
1 ACCCTAA
*
5880 ACCAT-A
1 ACCCTAA
5886 ACCCTAA
1 ACCCTAA
5893 ACCCTAA
1 ACCCTAA
5900 AC
1 AC
5902 AGAGACAGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.07
6 28 0.38
7 40 0.55
ACGTcount: A:0.42, C:0.39, G:0.03, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:5849 original size:32 final size:32
Alignment explanation
Indices: 5803--5879 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
5793 GGAGAGAGAG
* * *
5803 ACCCTAAACGCTAACCCTAAACCCTGACCATA
1 ACCCTAAACCCTAACCCTAAAACCTAACCATA
* *
5835 ACCCTAAACCCTAACGCTAAAACCTAACCCTA
1 ACCCTAAACCCTAACCCTAAAACCTAACCATA
*
5867 A-ACTAAACCCTAA
1 ACCCTAAACCCTAA
5880 ACCATAACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 11 0.28
32 28 0.72
ACGTcount: A:0.42, C:0.39, G:0.04, T:0.16
Consensus pattern (32 bp):
ACCCTAAACCCTAACCCTAAAACCTAACCATA
Found at i:5875 original size:12 final size:13
Alignment explanation
Indices: 5829--5895 Score: 84
Period size: 13 Copynumber: 5.2 Consensus size: 13
5819 CTAAACCCTG
5829 ACCATAACCCTAA
1 ACCATAACCCTAA
* *
5842 ACCCTAACGCTAAA
1 ACCATAACCCT-AA
5856 ACC-TAACCCTAA
1 ACCATAACCCTAA
*
5868 ACTA-AACCCTAA
1 ACCATAACCCTAA
5880 ACCATAACCCTAA
1 ACCATAACCCTAA
5893 ACC
1 ACC
5896 CTAAACAGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
12 15 0.33
13 26 0.57
14 5 0.11
ACGTcount: A:0.45, C:0.39, G:0.01, T:0.15
Consensus pattern (13 bp):
ACCATAACCCTAA
Found at i:5961 original size:10 final size:10
Alignment explanation
Indices: 5946--5988 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
5936 ACAGAAACAC
5946 AGACAGAGAG
1 AGACAGAGAG
5956 AGACAGAGACAG
1 AGACAGAG--AG
**
5968 AGGGAGAGAG
1 AGACAGAGAG
5978 AGACAGAGAG
1 AGACAGAGAG
5988 A
1 A
5989 CCCCAAACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 19 0.70
12 8 0.30
ACGTcount: A:0.49, C:0.09, G:0.42, T:0.00
Consensus pattern (10 bp):
AGACAGAGAG
Found at i:5967 original size:16 final size:16
Alignment explanation
Indices: 5920--5988 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
5910 AGGGAGAGGG
*
5920 AGAGAGAGATAGAGA-
1 AGAGAGAGACAGAGAC
* * *
5935 A-ACAGAAACACAGAC
1 AGAGAGAGACAGAGAC
5950 AGAGAGAGACAGAGAC
1 AGAGAGAGACAGAGAC
* *
5966 AGAGGGAGAGAGAGAC
1 AGAGAGAGACAGAGAC
5982 AGAGAGA
1 AGAGAGA
5989 CCCCAAACCC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
14 9 0.21
15 2 0.05
16 31 0.74
ACGTcount: A:0.52, C:0.10, G:0.36, T:0.01
Consensus pattern (16 bp):
AGAGAGAGACAGAGAC
Found at i:6003 original size:7 final size:7
Alignment explanation
Indices: 5988--6017 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5978 AGACAGAGAG
*
5988 ACCCCAA
1 ACCCTAA
5995 ACCCTAA
1 ACCCTAA
6002 ACCCTAA
1 ACCCTAA
6009 ACCCTAA
1 ACCCTAA
6016 AC
1 AC
6018 GCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.47, G:0.00, T:0.10
Consensus pattern (7 bp):
ACCCTAA
Done.