Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014457.1 Corchorus olitorius cultivar O-4 contig14490, 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: 7796
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:666 original size:27 final size:27
Alignment explanation
Indices: 627--708 Score: 121
Period size: 27 Copynumber: 3.0 Consensus size: 27
617 GCAGACCATT
*
627 AAACCCTATGGTCCCAACTGCTGGGCC
1 AAACCCTATGGTCCCAGCTGCTGGGCC
*
654 AAACCCTAGGGTCACC-GCTGCTGGGCC
1 AAACCCTATGGTC-CCAGCTGCTGGGCC
*
681 AGACCCTATGGTCCCAGCTGCTGGGCC
1 AAACCCTATGGTCCCAGCTGCTGGGCC
708 A
1 A
709 GGCCCAATCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.04
27 45 0.92
28 2 0.04
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (27 bp):
AAACCCTATGGTCCCAGCTGCTGGGCC
Found at i:3601 original size:21 final size:21
Alignment explanation
Indices: 3575--3731 Score: 199
Period size: 21 Copynumber: 7.5 Consensus size: 21
3565 GTTTAACGTG
*
3575 TTGACTATCAAAATTTGGGGT
1 TTGACTATCAAACTTTGGGGT
* *
3596 TTGACTATCAAATTTTGGGAT
1 TTGACTATCAAACTTTGGGGT
*
3617 TTGACTATCAAATTTTGGGGT
1 TTGACTATCAAACTTTGGGGT
* * *
3638 TTGACTTTCAAACTATGAGGT
1 TTGACTATCAAACTTTGGGGT
3659 TTGACTATCAAACTTTGGGGT
1 TTGACTATCAAACTTTGGGGT
* * * *
3680 TGGACTTTTAAACTTTGAGGT
1 TTGACTATCAAACTTTGGGGT
3701 TTGACTATCACAA-TTTGGGGT
1 TTGACTATCA-AACTTTGGGGT
3722 TTGACTATCA
1 TTGACTATCA
3732 TTCTTTATGA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
21 115 0.98
22 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGACTATCAAACTTTGGGGT
Found at i:3921 original size:16 final size:16
Alignment explanation
Indices: 3900--3933 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3890 TATACTTTTT
3900 TTTAATATTCAATATA
1 TTTAATATTCAATATA
*
3916 TTTAATCTTCAATATA
1 TTTAATATTCAATATA
3932 TT
1 TT
3934 GGATGGTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATATTCAATATA
Found at i:6519 original size:21 final size:21
Alignment explanation
Indices: 6495--6561 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
6485 AATTCTTTGT
6495 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
6516 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
6537 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
6558 AAAT
1 AAAT
6562 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:6541 original size:42 final size:42
Alignment explanation
Indices: 6482--6562 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
6472 GCTAAGTCTT
6482 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
6524 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
6563 CTGATCCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:7607 original size:2 final size:2
Alignment explanation
Indices: 7600--7637 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
7590 GGAACCGAGC
*
7600 AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
7638 AAAGTACGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7702 original size:32 final size:32
Alignment explanation
Indices: 7661--7721 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
7651 TGTAAAACTT
*
7661 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
*
7693 TTGAATCGACCATTATATCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
7722 AAACATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Done.