Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010954.1 Kokia drynarioides strain JFW-HI SEQ_125922, 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: 18504
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:7489 original size:26 final size:26
Alignment explanation
Indices: 7436--7489 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
7426 ATTCTGGGCG
* * *
7436 CAATTCTGGACACGTTCATGTAGTGA
1 CAATTCTAGACACGTTCATGCAGCGA
*
7462 CAATTCTAGACATGTTCATGCAGCGA
1 CAATTCTAGACACGTTCATGCAGCGA
7488 CA
1 CA
7490 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAGCGA
Found at i:7520 original size:37 final size:38
Alignment explanation
Indices: 7479--7576 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
7469 AGACATGTTC
*
7479 ATGCAGCGACATTCCTGGGTGCAA-TTGAAGAATAATT
1 ATGCAACGACATTCCTGGGTGCAATTTGAAGAATAATT
* * * *
7516 ATGCAACGATAGTT-CTGGATGCAATTTGAAGGATATTT
1 ATGCAACGACA-TTCCTGGGTGCAATTTGAAGAATAATT
* * *
7554 ATGTAACGACAGTCTTGGGTGCA
1 ATGCAACGACATTCCTGGGTGCA
7577 TTCCGGAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (38 bp):
ATGCAACGACATTCCTGGGTGCAATTTGAAGAATAATT
Found at i:12680 original size:20 final size:19
Alignment explanation
Indices: 12653--12692 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12643 CAACGAGTTC
12653 ACAAAAAA-CACAAGAAAAA
1 ACAAAAAACCA-AAGAAAAA
12672 ACAAGAAAACCAAAGAAAAA
1 ACAA-AAAACCAAAGAAAAA
12692 A
1 A
12693 TCGTGTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 13 0.68
21 2 0.11
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (19 bp):
ACAAAAAACCAAAGAAAAA
Found at i:16753 original size:87 final size:89
Alignment explanation
Indices: 16615--16788 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 89
16605 TAATGAGTTA
* * * *
16615 TCTTATTAAGTGGGAGGTTTCAAATGTAGAAAAAGATTTGCGGCAGTGCATCTTTTTCTGTTATT
1 TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
16680 CGATCAAC-AAAGAGAATGAGAAC
66 CGATCAACAAAAGAGAATGAGAAC
16703 TCTTATTAAGTGGGAGG-TTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
1 TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
*
16767 CGATCGACAAAAGAGAATGAGA
66 CGATCAACAAAAGAGAATGAGA
16789 CGATGCAGGG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 50 0.62
88 30 0.38
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (89 bp):
TCTTATTAAGTGGGAGGTTTAAAATGCAGAAAAAGATTTGCAGCAGTGCATCATTTTCTGTTATT
CGATCAACAAAAGAGAATGAGAAC
Found at i:17675 original size:3 final size:3
Alignment explanation
Indices: 17667--17724 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
17657 CTGGCTTGTG
* * *
17667 GAA GAA GAA GAA GAA GTA GAA G-A GAA GAA GGA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
17714 AAA G-A GAA GAA
1 GAA GAA GAA GAA
17725 ATGGAGATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:17707 original size:20 final size:20
Alignment explanation
Indices: 17669--17709 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17659 GGCTTGTGGA
**
17669 AGAAGAAGAAGAAGTAGAAG
1 AGAAGAAGAAGAAAAAGAAG
*
17689 AGAAGAAGGAGAAAAAGAAG
1 AGAAGAAGAAGAAAAAGAAG
17709 A
1 A
17710 AGAAAAAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (20 bp):
AGAAGAAGAAGAAAAAGAAG
Found at i:17711 original size:29 final size:29
Alignment explanation
Indices: 17669--17724 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
17659 GGCTTGTGGA
* * *
17669 AGAAGAAGAAGAAGTAGAAGAGAAGAAGG
1 AGAAAAAGAAGAAGAAAAAGAGAAGAAGG
17698 AGAAAAAGAAGAAGAAAAAGAGAAGAA
1 AGAAAAAGAAGAAGAAAAAGAGAAGAA
17725 ATGGAGATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (29 bp):
AGAAAAAGAAGAAGAAAAAGAGAAGAAGG
Done.