Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019732.1 Corchorus olitorius cultivar O-4 contig19765, 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: 17040
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37 TAGGAAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6489 original size:33 final size:33
Alignment explanation
Indices: 6447--6540 Score: 128
Period size: 33 Copynumber: 3.0 Consensus size: 33
6437 GGCCCCTCGT
6447 CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
1 CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
6480 CCTCTTCCTCCTCTAAAGCCTCCAT------CA
1 CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
* *
6507 CCTCTTCCTCCTCTAAAGCCACCACCACCACCA
1 CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
6540 C
1 C
6541 GGCCTGCACA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 25 0.47
33 28 0.53
ACGTcount: A:0.21, C:0.52, G:0.03, T:0.23
Consensus pattern (33 bp):
CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
Found at i:6508 original size:27 final size:27
Alignment explanation
Indices: 6447--6535 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 27
6437 GGCCCCTCGT
6447 CCTCTTCCTCCTCTAAAGCCTCCATCACCACCA
1 CCTCTTCCTCCTCTAAAGCCTCCAT------CA
6480 CCTCTTCCTCCTCTAAAGCCTCCATCA
1 CCTCTTCCTCCTCTAAAGCCTCCATCA
* *
6507 CCTCTTCCTCCTCTAAAGCCACCACCA
1 CCTCTTCCTCCTCTAAAGCCTCCATCA
6534 CC
1 CC
6536 ACCACGGCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 29 0.54
33 25 0.46
ACGTcount: A:0.20, C:0.52, G:0.03, T:0.25
Consensus pattern (27 bp):
CCTCTTCCTCCTCTAAAGCCTCCATCA
Found at i:13612 original size:6 final size:6
Alignment explanation
Indices: 13601--13641 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
13591 TTGCGATTAC
*
13601 ATCTAT ATCTAT ATTTAT AT-T-T ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
13642 TAAAAAGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
4 3 0.10
5 7 0.23
6 21 0.68
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATCTAT
Found at i:16811 original size:60 final size:60
Alignment explanation
Indices: 16693--16811 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 60
16683 GCTAATTGCT
** * * * *
16693 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAAGGTCTGAGCTGTCAATTTGGC
* *
16753 CAAATAAGGGTCTAACGTTATAAAAAAAATGCTCAAATAAAGGTCTG-GC-GTCAGTTTGG
1 CAAATAAGGGCCTAACGTTAT--AAAAAATGCTCAAATAAAGGTCTGAGCTGTCAATTTGG
16812 ATGATAGGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
60 27 0.55
61 1 0.02
62 21 0.43
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATAAAAAATGCTCAAATAAAGGTCTGAGCTGTCAATTTGGC
Found at i:16877 original size:31 final size:30
Alignment explanation
Indices: 16836--16993 Score: 103
Period size: 31 Copynumber: 5.2 Consensus size: 30
16826 TTTTCGACGC
*
16836 TAGGCTCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
** *
16867 TAGGCCCTTATTTG-GCCAAATT--AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGCAAACG-T
* *
16896 CAGACCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
* * **
16927 TTGGCCCTTACTTG-GCCAAATTG-AAA-GAT
1 TAGGCCCTTATTTGAG-CATTTTGCAAACG-T
* *
16956 CAGGCCCTTATTTGAGCATTTTAACAAACGT
1 TAGGCCCTTATTTGAGCATTTT-GCAAACGT
16987 TAGGCCC
1 TAGGCCC
16994 AGGAGCGGAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
28 5 0.05
29 36 0.39
30 5 0.05
31 42 0.45
32 5 0.05
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTGCAAACGT
Found at i:16935 original size:60 final size:60
Alignment explanation
Indices: 16842--16993 Score: 250
Period size: 60 Copynumber: 2.5 Consensus size: 60
16832 ACGCTAGGCT
*
16842 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTACTTGGCCAAATTAAAAGATCAGACC
* * *
16902 CTTATTTGAGCATTTTGGCAAACGTTTGGCCCTTACTTGGCCAAATTGAAAGATCAGGCC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTACTTGGCCAAATTAAAAGATCAGACC
**
16962 CTTATTTGAGCATTTTAACAAACGTTAGGCCC
1 CTTATTTGAGCATTTTGGCAAACGTTAGGCCC
16994 AGGAGCGGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (60 bp):
CTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTACTTGGCCAAATTAAAAGATCAGACC
Done.