Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013825.1 Kokia drynarioides strain JFW-HI SEQ_128853, 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: 50608
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:17113 original size:15 final size:15
Alignment explanation
Indices: 17084--17122 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
17074 ATTAATATAA
17084 TATTCATATCATATCG
1 TATT-ATATCATATCG
*
17100 TATTATATCGTATCG
1 TATTATATCATATCG
*
17115 TATCATAT
1 TATTATAT
17123 TTTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (15 bp):
TATTATATCATATCG
Found at i:20398 original size:12 final size:12
Alignment explanation
Indices: 20381--20414 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20371 TAAAAAATCA
20381 TTTTAATTATTC
1 TTTTAATTATTC
*
20393 TTTTAATTAATC
1 TTTTAATTATTC
*
20405 TTTGAATTAT
1 TTTTAATTAT
20415 ATCGTTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (12 bp):
TTTTAATTATTC
Found at i:20546 original size:27 final size:28
Alignment explanation
Indices: 20503--20557 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
20493 TAGTTTAATT
**
20503 TTTTTAAATTTAAAACT-TT-AAATATA
1 TTTTTAAAAATAAAACTATTCAAATATA
20529 TTTTTAAAAATAAGAACTATTCAAATATA
1 TTTTTAAAAATAA-AACTATTCAAATATA
20558 AAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 4 0.17
28 2 0.08
29 7 0.29
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
TTTTTAAAAATAAAACTATTCAAATATA
Found at i:22873 original size:13 final size:13
Alignment explanation
Indices: 22855--22881 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22845 GTAATGTTAC
22855 CATTAGGGGGAGT
1 CATTAGGGGGAGT
22868 CATTAGGGGGAGT
1 CATTAGGGGGAGT
22881 C
1 C
22882 TAAAACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (13 bp):
CATTAGGGGGAGT
Found at i:24236 original size:12 final size:12
Alignment explanation
Indices: 24221--24254 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24211 GACATGGTTA
*
24221 TGGTCGTGGACG
1 TGGTCGAGGACG
*
24233 TGGTAGAGGACG
1 TGGTCGAGGACG
24245 TGGTCGAGGA
1 TGGTCGAGGA
24255 TCTACTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.50, T:0.21
Consensus pattern (12 bp):
TGGTCGAGGACG
Found at i:28793 original size:45 final size:45
Alignment explanation
Indices: 28720--28810 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
28710 AAAAATACAC
* *
28720 TCTCTCATTCTCTTGTTCTTTTTATTATTTACTCTCTGCTCTTTA
1 TCTCTCATTCTCTTGTTCTCTTTATTATTTACTCTCTACTCTTTA
* *
28765 TCTCTCATTCTCTTGTTCTCTTTGTTATTTATTCTCTACTCTTTA
1 TCTCTCATTCTCTTGTTCTCTTTATTATTTACTCTCTACTCTTTA
28810 T
1 T
28811 TTTATAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.11, C:0.24, G:0.04, T:0.60
Consensus pattern (45 bp):
TCTCTCATTCTCTTGTTCTCTTTATTATTTACTCTCTACTCTTTA
Found at i:32493 original size:16 final size:17
Alignment explanation
Indices: 32472--32504 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32462 AAAATATATC
*
32472 TAAATTT-AAACTAAAA
1 TAAATTTGAAAATAAAA
32488 TAAATTTGAAAATAAAA
1 TAAATTTGAAAATAAAA
32505 AAACCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAATTTGAAAATAAAA
Found at i:41329 original size:14 final size:14
Alignment explanation
Indices: 41310--41340 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41300 AACATTTTAA
*
41310 TATTTATTAATAAT
1 TATTTATAAATAAT
41324 TATTTATAAATAAT
1 TATTTATAAATAAT
41338 TAT
1 TAT
41341 CATTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTTATAAATAAT
Found at i:42506 original size:21 final size:20
Alignment explanation
Indices: 42476--42516 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
42466 ATCTTAACAA
*
42476 TTTTTAATATTTTTAATCAT
1 TTTTTAATATTTGTAATCAT
42496 TTTTGTAATATTTGTAATCAT
1 TTTT-TAATATTTGTAATCAT
42517 GTATAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTAATATTTGTAATCAT
Found at i:49196 original size:8 final size:8
Alignment explanation
Indices: 49183--49211 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
49173 ACCCAAACAA
49183 AAAAAAAC
1 AAAAAAAC
49191 AAAAAAAC
1 AAAAAAAC
49199 -AAAAAAC
1 AAAAAAAC
49206 AAAAAA
1 AAAAAA
49212 GTCCATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:49291 original size:13 final size:13
Alignment explanation
Indices: 49272--49306 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
49262 GCCCAAATTA
49272 CCAAACCTAATAAC
1 CCAAACCTAAT-AC
49286 CC-AACCTAATAC
1 CCAAACCTAATAC
49298 CCAAACCTA
1 CCAAACCTA
49307 GACCTAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 14 0.70
14 2 0.10
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (13 bp):
CCAAACCTAATAC
Done.