Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001842.1 Corchorus olitorius cultivar O-4 contig01842, 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, 603
Length: 1005
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:77 original size:27 final size:30
Alignment explanation
Indices: 48--111 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
38 TTATTTTTAT
48 TCTATTTTCTATATTC-T-ATT-TATTTAT
1 TCTATTTTCTATATTCATAATTCTATTTAT
* *
75 TCTATATTCTTTATTCTATAATTCTATTTAT
1 TCTATTTTCTATATTC-ATAATTCTATTTAT
106 TCTATT
1 TCTATT
112 ATATATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.47
29 1 0.03
30 3 0.10
31 12 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.64
Consensus pattern (30 bp):
TCTATTTTCTATATTCATAATTCTATTTAT
Found at i:82 original size:7 final size:7
Alignment explanation
Indices: 45--101 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
35 AATTTATTTT
45 TATTCTA
1 TATTCTA
*
52 TTTTCTA
1 TATTCTA
59 TATTCTA
1 TATTCTA
* *
66 T-TTATT
1 TATTCTA
72 TATTCTA
1 TATTCTA
*
79 TATTCTT
1 TATTCTA
86 TATTCTA
1 TATTCTA
93 TAATTCTA
1 T-ATTCTA
101 T
1 T
102 TTATTCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 4 0.10
7 29 0.73
8 7 0.17
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (7 bp):
TATTCTA
Found at i:94 original size:14 final size:14
Alignment explanation
Indices: 39--110 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
29 ATTCGAAATT
39 TATT-TTTATTCTA
1 TATTCTTTATTCTA
* *
52 TTTTCTATATTCTA
1 TATTCTTTATTCTA
*
66 T-TTATTTATTCTA
1 TATTCTTTATTCTA
79 TATTCTTTATTCTA
1 TATTCTTTATTCTA
93 TAATTCTATTTATTCTA
1 T-ATTC--TTTATTCTA
110 T
1 T
111 TATATATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
13 14 0.29
14 21 0.43
15 4 0.08
17 10 0.20
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTCTTTATTCTA
Found at i:111 original size:22 final size:22
Alignment explanation
Indices: 59--116 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
49 CTATTTTCTA
*
59 TATTCTATTTATTTATTCTATAT
1 TATTCTATTTA-TAATTCTATAT
*
82 TCTT-TATTCTATAATTCTAT-T
1 TATTCTATT-TATAATTCTATAT
103 TATTCTATTATATA
1 TATTCTATT-TATA
117 TAGAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTCTATTTATAATTCTATAT
Found at i:137 original size:14 final size:14
Alignment explanation
Indices: 118--146 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
108 TATTATATAT
118 AGAATATATTTTTG
1 AGAATATATTTTTG
132 AGAATATATTTTTG
1 AGAATATATTTTTG
146 A
1 A
147 TTTTCTATCT
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:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
AGAATATATTTTTG
Found at i:202 original size:12 final size:12
Alignment explanation
Indices: 185--209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
175 TAGAAAATTT
185 TATGAAATTATG
1 TATGAAATTATG
197 TATGAAATTATG
1 TATGAAATTATG
209 T
1 T
210 TTATGAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TATGAAATTATG
Found at i:223 original size:13 final size:13
Alignment explanation
Indices: 183--229 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
173 GATAGAAAAT
183 TTTATGAAATTATG
1 TTTATG-AATTATG
197 --TATGAAATTATG
1 TTTATG-AATTATG
*
209 TTTATGAATTCTG
1 TTTATGAATTATG
222 TTTATGAA
1 TTTATGAA
230 AAAGATCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.40
13 14 0.47
14 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (13 bp):
TTTATGAATTATG
Done.