Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022402.1 Corchorus olitorius cultivar O-4 contig22435, 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: 17152
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--172 Score: 293
Period size: 7 Copynumber: 25.3 Consensus size: 7
1 ACCCTAA
1 ACCCTAA
8 ACCCTAA
1 ACCCTAA
15 ACCCT-A
1 ACCCTAA
21 ACCCTAA
1 ACCCTAA
28 ACCCTAA
1 ACCCTAA
35 ACCCTAA
1 ACCCTAA
42 ACCCTAA
1 ACCCTAA
49 ACCCTAA
1 ACCCTAA
56 ACCCT-A
1 ACCCTAA
62 ACCCTAA
1 ACCCTAA
69 ACCCT-A
1 ACCCTAA
75 ACCCTAA
1 ACCCTAA
82 ACCCTAA
1 ACCCTAA
89 ACCCTAA
1 ACCCTAA
96 ACCCTAA
1 ACCCTAA
103 ACCCTAA
1 ACCCTAA
110 ACCCTAA
1 ACCCTAA
117 ACCCT-A
1 ACCCTAA
123 ACCCTAAA
1 ACCCT-AA
131 ACCCTAA
1 ACCCTAA
138 ACCCTAA
1 ACCCTAA
145 ACCCT-A
1 ACCCTAA
151 ACCCTAA
1 ACCCTAA
158 ACCCT-A
1 ACCCTAA
164 ACCCTAA
1 ACCCTAA
171 AC
1 AC
173 AGAACAACAA
Statistics
Matches: 158, Mismatches: 0, Indels: 14
0.92 0.00 0.08
Matches are distributed among these distances:
6 36 0.23
7 116 0.73
8 6 0.04
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:58 original size:41 final size:41
Alignment explanation
Indices: 1--172 Score: 289
Period size: 41 Copynumber: 4.2 Consensus size: 41
1 ACCCTAAACCCTAAACCCT-AACCCTAAACCCTAAACCCTAA
1 ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT-A
42 ACCCTAAACCCTAAACCCT-AACCCTAAACCCT-AACCCTAA
1 ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT-A
82 ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
1 ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
123 ACCCTAAAACCCTAAACCCTAAACCCT-AACCCTAAACCCTA
1 ACCCT-AAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
164 ACCCTAAAC
1 ACCCTAAAC
173 AGAACAACAA
Statistics
Matches: 128, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
40 31 0.24
41 70 0.55
42 27 0.21
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (41 bp):
ACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
Found at i:8188 original size:28 final size:28
Alignment explanation
Indices: 8157--8218 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
8147 CATATGTGGC
8157 TTTTTAAAATAT-TTTTTATTATTTTTAA
1 TTTTTAAAATATATTTTTATT-TTTTTAA
*
8185 TTTTTTAAATATATTTTTATTTTTTTAA
1 TTTTTAAAATATATTTTTATTTTTTTAA
8213 TATTTT
1 T-TTTT
8219 TAAACCGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTTTAAAATATATTTTTATTTTTTTAA
Found at i:8189 original size:29 final size:30
Alignment explanation
Indices: 8157--8222 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
8147 CATATGTGGC
8157 TTTTTAAAATAT-TTTTTATTATTTTTAAT-
1 TTTTTAAAATATATTTTTATT-TTTTTAATA
8186 TTTTT-AAATATATTTTTATTTTTTTAATA
1 TTTTTAAAATATATTTTTATTTTTTTAATA
8215 TTTTTAAA
1 TTTTTAAA
8223 CCGGCTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 14 0.41
29 18 0.53
30 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTTAAAATATATTTTTATTTTTTTAATA
Found at i:8201 original size:19 final size:17
Alignment explanation
Indices: 8167--8221 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
8157 TTTTTAAAAT
*
8167 ATTTTTTATTATTTTTA
1 ATTTTTTAATATTTTTA
8184 ATTTTTTAAATATATTTTTA
1 ATTTTTT--A-ATATTTTTA
*
8204 TTTTTTTAATATTTTTA
1 ATTTTTTAATATTTTTA
8221 A
1 A
8222 ACCGGCTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 16 0.50
18 1 0.03
19 1 0.03
20 14 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTAATATTTTTA
Found at i:8279 original size:31 final size:31
Alignment explanation
Indices: 8236--8298 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
8226 GCTCAAATAG
8236 GTACCAAACGTTTCGAAA-TTGAATCAATTTA
1 GTACCAAACGTTTC-AAAGTTGAATCAATTTA
* *
8267 GTACTAAACGTTTCAAAGTTGGATCAATTTA
1 GTACCAAACGTTTCAAAGTTGAATCAATTTA
8298 G
1 G
8299 ATTTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (31 bp):
GTACCAAACGTTTCAAAGTTGAATCAATTTA
Found at i:16084 original size:25 final size:25
Alignment explanation
Indices: 16056--16112 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
16046 CACCAATTAA
16056 AATTTAAAGTTAAATAAAAGTATTG
1 AATTTAAAGTTAAATAAAAGTATTG
*
16081 AATTAAAAGTTAAATAAAAGTATTG
1 AATTTAAAGTTAAATAAAAGTATTG
16106 AATTTAA
1 AATTTAA
16113 TTCATCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (25 bp):
AATTTAAAGTTAAATAAAAGTATTG
Found at i:16089 original size:14 final size:14
Alignment explanation
Indices: 16070--16109 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
16060 TAAAGTTAAA
16070 TAAAAGTATTGAAT
1 TAAAAGTATTGAAT
*
16084 TAAAAG--TT-AAA
1 TAAAAGTATTGAAT
16095 TAAAAGTATTGAAT
1 TAAAAGTATTGAAT
16109 T
1 T
16110 TAATTCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 2 0.10
14 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (14 bp):
TAAAAGTATTGAAT
Found at i:16650 original size:18 final size:18
Alignment explanation
Indices: 16627--16661 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16617 TAATTAGTAT
16627 AGATATAAATAAATATAA
1 AGATATAAATAAATATAA
* *
16645 AGATATATATATATATA
1 AGATATAAATAAATATA
16662 TACTAGTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AGATATAAATAAATATAA
Done.