Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014338.1 Corchorus olitorius cultivar O-4 contig14371, 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: 53726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:863 original size:4 final size:4
Alignment explanation
Indices: 849--880 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
839 ATACTTGTCT
849 TATG TTATG TATG TATG TATG TATG TATG TAT
1 TATG -TATG TATG TATG TATG TATG TATG TAT
881 TTAGGGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:11394 original size:17 final size:17
Alignment explanation
Indices: 11340--11387 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
11330 GATCATCTCC
* **
11340 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
11357 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
11374 AGATCACCGGTGAT
1 AGATCACCAGTGAT
11388 CAAAGATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:26051 original size:19 final size:19
Alignment explanation
Indices: 26027--26065 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26017 ATTATAGGCC
26027 ATGATCTTGAAATCTTGAA
1 ATGATCTTGAAATCTTGAA
26046 ATGATCTTGAAATCTTGAA
1 ATGATCTTGAAATCTTGAA
26065 A
1 A
26066 ATTGCTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATCTTGAAATCTTGAA
Found at i:27761 original size:69 final size:69
Alignment explanation
Indices: 27650--27791 Score: 248
Period size: 69 Copynumber: 2.1 Consensus size: 69
27640 TTAACCAACC
* *
27650 AATTTTAATCTGTTTAATTTTGAAATATGGTACCAGCCAGTTGGAGTTGGTTCTGTATTCCATGT
1 AATTTTAATATGTTTAATTTTGAAATATGGTACCAGCCAGTTGGAGTTGGTTCTGTATTCCATAT
27715 ACAG
66 ACAG
* *
27719 AATTTTAATATGTTTAATTTTGAAATATGGTATCAGCCAGTTGGAGTTGTTTCTGTATTCCATAT
1 AATTTTAATATGTTTAATTTTGAAATATGGTACCAGCCAGTTGGAGTTGGTTCTGTATTCCATAT
27784 ACAG
66 ACAG
27788 AATT
1 AATT
27792 ATCAATAACT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (69 bp):
AATTTTAATATGTTTAATTTTGAAATATGGTACCAGCCAGTTGGAGTTGGTTCTGTATTCCATAT
ACAG
Found at i:27897 original size:26 final size:28
Alignment explanation
Indices: 27863--27914 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
27853 TTGTACCTCC
*
27863 GTTGTG-AAATTGAATTAGGGTTTATCT
1 GTTGTGAAAATTGAATTAGGGGTTATCT
*
27890 GTTG-GAAAATTGATTTAGGGGTTAT
1 GTTGTGAAAATTGAATTAGGGGTTAT
27915 ATTTTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42
Consensus pattern (28 bp):
GTTGTGAAAATTGAATTAGGGGTTATCT
Found at i:32413 original size:7 final size:8
Alignment explanation
Indices: 32397--32423 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
32387 GTTACTTTTA
32397 TTTTCTTT
1 TTTTCTTT
32405 TTTTCTTT
1 TTTTCTTT
32413 TTTTCTTT
1 TTTTCTTT
32421 TTT
1 TTT
32424 GTTCACACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:39008 original size:14 final size:14
Alignment explanation
Indices: 38972--39008 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38962 TATCACACGT
38972 TCCCTCTCTC-CTC
1 TCCCTCTCTCTCTC
*
38985 T-TCTCTCTCTCTC
1 TCCCTCTCTCTCTC
38998 TCCCTCTCTCT
1 TCCCTCTCTCT
39009 TCAGAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 7 0.35
13 5 0.25
14 8 0.40
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (14 bp):
TCCCTCTCTCTCTC
Found at i:40598 original size:47 final size:47
Alignment explanation
Indices: 40529--40622 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
40519 TATCCCATGT
40529 TTTGTAGTAAAATTCCACTTGAATAATGGTGAGACCAGTCTGCTGGA
1 TTTGTAGTAAAATTCCACTTGAATAATGGTGAGACCAGTCTGCTGGA
*
40576 TTTGTAGTAAAATTCCACTTGAATAATGGTGGGACCAGTCTGCTGGA
1 TTTGTAGTAAAATTCCACTTGAATAATGGTGAGACCAGTCTGCTGGA
40623 CCAATCATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (47 bp):
TTTGTAGTAAAATTCCACTTGAATAATGGTGAGACCAGTCTGCTGGA
Found at i:45012 original size:19 final size:19
Alignment explanation
Indices: 44988--45024 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44978 TTTTGTCACA
*
44988 TTTAAATTGATAGTTTTTT
1 TTTAAATGGATAGTTTTTT
*
45007 TTTAAATGGGTAGTTTTT
1 TTTAAATGGATAGTTTTT
45025 ATCTTCACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (19 bp):
TTTAAATGGATAGTTTTTT
Found at i:47004 original size:14 final size:14
Alignment explanation
Indices: 46985--47013 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46975 TTAAATTGTA
46985 ATTTCTAATAAAAT
1 ATTTCTAATAAAAT
46999 ATTTCTAATAAAAT
1 ATTTCTAATAAAAT
47013 A
1 A
47014 AAAATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTCTAATAAAAT
Found at i:52425 original size:13 final size:13
Alignment explanation
Indices: 52393--52426 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
52383 TAATAATAAG
*
52393 AATTATCAAAAAT
1 AATTATTAAAAAT
52406 AATTATTAAAAAT
1 AATTATTAAAAAT
52419 AATTATTA
1 AATTATTA
52427 TAATTTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTATTAAAAAT
Found at i:52671 original size:2 final size:2
Alignment explanation
Indices: 52664--52704 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
52654 TTGGAAGGTG
* *
52664 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52705 GATAATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Done.