Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004818.1 Kokia drynarioides strain JFW-HI SEQ_118452, 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: 6798
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Found at i:1903 original size:20 final size:20
Alignment explanation
Indices: 1878--1968 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
1868 ATTATATTGT
1878 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
* * *
1898 TGTTTTGATTTTTTTTTTGC
1 TGTTTTGGTGTTTTTTTTAC
** * *
1918 TGTTTTTATGTTGCTTTTTAT
1 TGTTTTGGTGTT-TTTTTTAC
* *
1939 TGTTTTGGTGCTTCTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
1959 TGTTTTGGTG
1 TGTTTTGGTG
1969 GTTGTTTTCG
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 42 0.75
21 14 0.25
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:2012 original size:11 final size:11
Alignment explanation
Indices: 1998--2024 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1988 TGCCGTTTTT
1998 TTTTTTTGCTA
1 TTTTTTTGCTA
2009 TTTTTTTGCTA
1 TTTTTTTGCTA
2020 TTTTT
1 TTTTT
2025 GTTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCTA
Found at i:2045 original size:56 final size:57
Alignment explanation
Indices: 1979--2087 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 57
1969 GTTGTTTTCG
* **
1979 TGTTGTTTTTGCCGTT-TTTTT-TTTTTGCTATTTTTTTGCTATTTTTGTTGTTTTTAA
1 TGTTGTTTTTGCCGTTATTTTTGCTTTTG-T-TTTGGTTGCTATTTTTGTTGTTTTTAA
* *
2036 TGTTG-TTTTGCTGTTATTTTTGCTTTTGTTTTGGTTGTTATTTTTGTTGTTT
1 TGTTGTTTTTGCCGTTATTTTTGCTTTTGTTTTGGTTGCTATTTTTGTTGTTT
2088 GGATGTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 29 0.64
57 11 0.24
58 5 0.11
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.72
Consensus pattern (57 bp):
TGTTGTTTTTGCCGTTATTTTTGCTTTTGTTTTGGTTGCTATTTTTGTTGTTTTTAA
Found at i:2055 original size:23 final size:24
Alignment explanation
Indices: 2024--2080 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
2014 TTGCTATTTT
*
2024 TGTTGTTTTTAATGTTGTTTT-GC
1 TGTTATTTTTAATGTTGTTTTGGC
** * *
2047 TGTTATTTTTGCTTTTGTTTTGGT
1 TGTTATTTTTAATGTTGTTTTGGC
2071 TGTTATTTTT
1 TGTTATTTTT
2081 GTTGTTTGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (24 bp):
TGTTATTTTTAATGTTGTTTTGGC
Found at i:2080 original size:18 final size:20
Alignment explanation
Indices: 2036--2098 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2026 TTGTTTTTAA
* *
2036 TGTTGTTTTGCTGTTATTTT
1 TGTTGTTTGGATGTTATTTT
*
2056 TGCTTTTGTTTTGGTTGTTATTTT
1 TG---TTG-TTTGGATGTTATTTT
2080 TGTTGTTTGGATGTTATTT
1 TGTTGTTTGGATGTTATTT
2099 GTATGCGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 15 0.42
21 3 0.08
23 3 0.08
24 15 0.42
ACGTcount: A:0.06, C:0.03, G:0.22, T:0.68
Consensus pattern (20 bp):
TGTTGTTTGGATGTTATTTT
Found at i:2267 original size:37 final size:37
Alignment explanation
Indices: 2218--2288 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
2208 TATAAAAAAA
* *
2218 TTTTAATGTATTTTAAAT-TTATTTATTTTTTAATGT
1 TTTTAATGTATTTGAAATATTATATATTTTTTAATGT
*
2254 TTTTAAATGTATTTGATATATTATATATTTTTTAA
1 TTTT-AATGTATTTGAAATATTATATATTTTTTAA
2289 ATTTGATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 4 0.13
37 12 0.40
38 14 0.47
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (37 bp):
TTTTAATGTATTTGAAATATTATATATTTTTTAATGT
Found at i:5468 original size:28 final size:29
Alignment explanation
Indices: 5427--5491 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
5417 TGAAAATGAG
*
5427 ATTTTAGGATACTCGA-GGGCAAAATGGTA
1 ATTTT-GGACACTCGAGGGGCAAAATGGTA
5456 ATTTTGGACACTCGAGGGGCAAAATGGTA
1 ATTTTGGACACTCGAGGGGCAAAATGGTA
*
5485 AGTTTGG
1 ATTTTGG
5492 GAAAGTTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (29 bp):
ATTTTGGACACTCGAGGGGCAAAATGGTA
Found at i:5518 original size:59 final size:57
Alignment explanation
Indices: 5447--5636 Score: 161
Period size: 59 Copynumber: 3.2 Consensus size: 57
5437 ACTCGAGGGC
* * *
5447 AAAATGGTAATTTTGGACACTCGAGGGGCAAAATGGTAAGTTTGGGAAAGTTCGAGGTCA
1 AAAATGG-AATTTTAGACA-TCGAGGGGCAAAATGGTAA-TTTGGAAAAGTTCGGGGTCA
* * * * * * *
5507 AAAACGGAATTTTCAAACATTCAAGGGGCAAAATGATAATTTTGTAAAGTTCGGGGAT-T
1 AAAATGGAATTTT-AGACA-TCGAGGGGCAAAATGGTAATTTGGAAAAGTTCGGGG-TCA
* * *
5566 AAAATGGAATTTTTAGACATACGA-GGGTAAAATGGTAATTTTGAAAAAATT-GGGGTCA
1 AAAATGGAA-TTTTAGACAT-CGAGGGGCAAAATGGTAA-TTTGGAAAAGTTCGGGGTCA
5624 AAAATGGAATTTT
1 AAAATGGAATTTT
5637 TGGCAGTTCG
Statistics
Matches: 104, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
57 5 0.05
58 26 0.25
59 42 0.40
60 31 0.30
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (57 bp):
AAAATGGAATTTTAGACATCGAGGGGCAAAATGGTAATTTGGAAAAGTTCGGGGTCA
Found at i:5694 original size:116 final size:116
Alignment explanation
Indices: 5531--5816 Score: 287
Period size: 117 Copynumber: 2.4 Consensus size: 116
5521 AAACATTCAA
* * * * * *
5531 GGGGCAAAATGATAA-TTTTGTAAAGTTCGGGGATTAAAATGGAATTTTTAGACA-TACGAGGGT
1 GGGGTAAAATG-TAATTTTTGAAAAATTCAGGG-TTAAAATGGAATTTTT-GAAAGTAC-AAGGT
* * * *
5594 -AAAATGGTAATT-TTGAAAAAATTGGGGTCAAAAATGGAATTTTTGG-CAGTTCG
62 AAAAATGGTAATTCTTGAAAAAATCGAGGTCAAAAATGGAA-ATTTGGAAAGTTCG
* *
5647 GGGGTAAAGTGGTAATTTTTGAAAAAATTC-GGGTTAAAATGGAATTTTTGAAAGTTCAAGGTAA
1 GGGGTAAAAT-GTAATTTTTG-AAAAATTCAGGGTTAAAATGGAATTTTTGAAAGTACAAGGTAA
* *
5711 AAATGGTAATTCTTGGAAAAATCGAGGTTAAAAATGGAAATTTGGAAAGTTCG
64 AAATGGTAATTCTTGAAAAAATCGAGGTCAAAAATGGAAATTTGGAAAGTTCG
* * * * *
5764 GTGGTAAAATGTAATTTTTGGAAAGTTCAGTGTTAAAAATGGAATTTTGGAAA
1 GGGGTAAAATGTAATTTTTGAAAAATTCAGGGTT-AAAATGGAATTTTTGAAA
5817 AGTTTAAGGG
Statistics
Matches: 142, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
115 13 0.09
116 60 0.42
117 63 0.44
118 6 0.04
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (116 bp):
GGGGTAAAATGTAATTTTTGAAAAATTCAGGGTTAAAATGGAATTTTTGAAAGTACAAGGTAAAA
ATGGTAATTCTTGAAAAAATCGAGGTCAAAAATGGAAATTTGGAAAGTTCG
Found at i:5721 original size:29 final size:27
Alignment explanation
Indices: 5682--5816 Score: 119
Period size: 29 Copynumber: 4.7 Consensus size: 27
5672 AATTCGGGTT
*
5682 AAAATGGAATTTTTGAAAGTTCAAGGTA
1 AAAATGGAATTTTGGAAAGTTC-AGGTA
**
5710 AAAATGGTAATTCTTGGAAAAATCGAGGTTA
1 AAAATGG-AATT-TTGGAAAGTTC-AGG-TA
* *
5741 AAAATGGAAATTTGGAAAGTTC-GGTGGT
1 AAAATGGAATTTTGGAAAGTTCAGGT--A
*
5769 AAAATGTAATTTTTGGAAAGTTCAGTGTTA
1 AAAATGGAA-TTTTGGAAAGTTCAG-G-TA
5799 AAAATGGAATTTTGGAAA
1 AAAATGGAATTTTGGAAA
5817 AGTTTAAGGG
Statistics
Matches: 86, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 15 0.17
29 34 0.40
30 23 0.27
31 10 0.12
32 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.32
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAAGTTCAGGTA
Found at i:5731 original size:59 final size:58
Alignment explanation
Indices: 5564--5787 Score: 219
Period size: 58 Copynumber: 3.8 Consensus size: 58
5554 AGTTCGGGGA
* * *
5564 TTAAAATGGAATTTTTAGACA-TACGAGGGTAAAATGGTAATTTT-GAAAAAATTGGGG
1 TTAAAATGGAATTTTT-GAAAGTTCGAGGGTAAAATGGTAATTTTGGAAAAAATTCGGG
* ** * * *
5621 TCAAAAATGGAATTTTTGGCAGTTCGGGGGTAAAGTGGTAATTTTTGAAAAAATTCGGG
1 T-TAAAATGGAATTTTTGAAAGTTCGAGGGTAAAATGGTAATTTTGGAAAAAATTCGGG
*
5680 TTAAAATGGAATTTTTGAAAGTTC-AAGGTAAAAATGGTAATTCTTGG-AAAAA-TCGAGG
1 TTAAAATGGAATTTTTGAAAGTTCGAGGGT-AAAATGGTAATT-TTGGAAAAAATTCG-GG
* *
5738 TTAAAAATGGAAATTTGGAAAGTTCG-GTGGTAAAAT-GTAATTTTTGGAAA
1 TT-AAAATGGAATTTTTGAAAGTTCGAG-GGTAAAATGGTAA-TTTTGGAAA
5788 GTTCAGTGTT
Statistics
Matches: 140, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
57 10 0.07
58 82 0.59
59 45 0.32
60 3 0.02
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.32
Consensus pattern (58 bp):
TTAAAATGGAATTTTTGAAAGTTCGAGGGTAAAATGGTAATTTTGGAAAAAATTCGGG
Found at i:5785 original size:58 final size:59
Alignment explanation
Indices: 5591--5816 Score: 232
Period size: 58 Copynumber: 3.9 Consensus size: 59
5581 GACATACGAG
* * * * *
5591 GGTAAAATGGTAA-TTTTGAAAAAATTGGGGTCAAAAATGGAATTTTTGG-CAGTTCGGG
1 GGTAAAATGGTAATTTTTGAAAAAATCGAGGTTAAAAATGGAA-TTTTGGAAAGTTCGGA
* * *
5649 GGTAAAGTGGTAATTTTTGAAAAAATTCG-GGTT-AAAATGGAATTTTTGAAAGTTC-AA
1 GGTAAAATGGTAATTTTTGAAAAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGA
* * * *
5706 GGTAAAAATGGTAATTCTTGGAAAAATCGAGGTTAAAAATGGAAATTTGGAAAGTTCGGT
1 GGT-AAAATGGTAATTTTTGAAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGA
* **
5766 GGTAAAAT-GTAATTTTTGGAAAGTTC-AGTGTTAAAAATGGAATTTTGGAAA
1 GGTAAAATGGTAATTTTTGAAAAAATCGAG-GTTAAAAATGGAATTTTGGAAA
5817 AGTTTAAGGG
Statistics
Matches: 142, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
57 13 0.09
58 85 0.60
59 39 0.27
60 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGAAAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGA
Done.