Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020146.1 Corchorus olitorius cultivar O-4 contig20179, 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: 10736
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--91 Score: 85
Period size: 6 Copynumber: 16.7 Consensus size: 6
* *
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA CACTAAA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA-TATA
50 TATA-A TATA-A TA-ATA -ATA-A TA-ATA TA-ATA -ATATA -ATA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
88 TATA
1 TATA
92 ATAATAAATA
Statistics
Matches: 75, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
4 6 0.08
5 26 0.35
6 39 0.52
7 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:13 original size:8 final size:8
Alignment explanation
Indices: 1--91 Score: 85
Period size: 8 Copynumber: 12.5 Consensus size: 8
1 TATATATA
1 TATATATA
9 TATATATA
1 TATATATA
17 TATATATA
1 TATATATA
25 TATATATA
1 TATATATA
33 TATATATA
1 TATATATA
* *
41 TACACTAAA
1 TATA-TATA
50 TATA-ATA
1 TATATATA
57 TA-ATA-A
1 TATATATA
63 TA-ATA-A
1 TATATATA
69 TA-ATATA
1 TATATATA
76 -ATA-ATA
1 TATATATA
82 TA-ATA-A
1 TATATATA
88 TATA
1 TATA
92 ATAATAAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
6 21 0.29
7 10 0.14
8 35 0.49
9 6 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATATA
Found at i:19 original size:14 final size:13
Alignment explanation
Indices: 1--110 Score: 89
Period size: 12 Copynumber: 9.1 Consensus size: 13
1 TATATATAT-ATA
1 TATATATATAATA
13 TATATATAT-ATA
1 TATATATATAATA
25 TATATATAT-ATA
1 TATATATATAATA
*
37 TATATACACTAA-A
1 TATATATA-TAATA
50 TATA-ATATAATA
1 TATATATATAATA
62 -ATA-ATAATAATA
1 TATATAT-ATAATA
74 TA-ATAATATAATA
1 TATAT-ATATAATA
87 -ATATA-ATAATA
1 TATATATATAATA
* *
98 AATAAATA-AATA
1 TATATATATAATA
110 T
1 T
111 TATTTGAAAC
Statistics
Matches: 84, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
11 14 0.17
12 51 0.61
13 16 0.19
14 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATATAATA
Found at i:64 original size:3 final size:3
Alignment explanation
Indices: 51--98 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
41 TACACTAAAT
51 ATA AT- ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
95 ATA A
1 ATA A
99 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:65 original size:11 final size:11
Alignment explanation
Indices: 51--102 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
41 TACACTAAAT
51 ATAATATAATA
1 ATAATATAATA
62 ATAATAATAAT-
1 ATAAT-ATAATA
73 ATAATA-ATATA
1 ATAATATA-ATA
84 ATAATATAATA
1 ATAATATAATA
95 ATAA-ATAA
1 ATAATATAA
103 ATAAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.19
11 23 0.62
12 6 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAATA
Found at i:105 original size:11 final size:11
Alignment explanation
Indices: 48--106 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
38 ATATACACTA
48 AATATAATATAAT
1 AATA-AATA-AAT
61 AAT-AAT-AAT
1 AATAAATAAAT
70 AATATAATAATAT
1 AATA-AATAA-AT
83 AAT-AATATAAT
1 AATAAATA-AAT
94 AATAAATAAAT
1 AATAAATAAAT
105 AA
1 AA
107 ATATTATTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 6 0.15
11 20 0.50
12 6 0.15
13 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:109 original size:8 final size:8
Alignment explanation
Indices: 51--106 Score: 89
Period size: 8 Copynumber: 7.1 Consensus size: 8
41 TACACTAAAT
51 ATAATATA
1 ATAATATA
59 ATAATAATA
1 ATAAT-ATA
68 ATAATATA
1 ATAATATA
76 ATAATATA
1 ATAATATA
84 ATAATATA
1 ATAATATA
92 ATAATA-A
1 ATAATATA
99 ATAA-ATA
1 ATAATATA
106 A
1 A
107 ATATTATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
6 1 0.02
7 7 0.15
8 30 0.65
9 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATAATATA
Found at i:1546 original size:27 final size:25
Alignment explanation
Indices: 1499--1550 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1489 TTGAGTTGCC
1499 TAAATAAATAATAATATAAATAAAA
1 TAAATAAATAATAATATAAATAAAA
* *
1524 TAAACTAAATAAATATTTTAAATAAAA
1 TAAA-TAAAT-AATAATATAAATAAAA
1551 AATATGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAATAAATAATAATATAAATAAAA
Found at i:2681 original size:17 final size:17
Alignment explanation
Indices: 2659--2693 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2649 CGGTGCATTC
2659 TTTTTAAAATTCCTATT
1 TTTTTAAAATTCCTATT
*
2676 TTTTTAAATTTCCTATT
1 TTTTTAAAATTCCTATT
2693 T
1 T
2694 GAACATCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAAATTCCTATT
Found at i:10662 original size:39 final size:40
Alignment explanation
Indices: 10606--10686 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
10596 TTTAATTCCT
10606 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
10646 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
10685 AT
1 AT
10687 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:10713 original size:25 final size:24
Alignment explanation
Indices: 10677--10723 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
10667 AATACTTACA
10677 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
10701 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
10724 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Done.