Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010814.1 Kokia drynarioides strain JFW-HI SEQ_125781, 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: 10216
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Found at i:4405 original size:59 final size:58
Alignment explanation
Indices: 4342--4468 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 58
4332 CTTTGGGGGC
* *
4342 AAAATAGTAATTTTT-AAAAGGTTCGAGGTTGAAAA-TAGAATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGAAAA-GTTCAAGG-T-AAAATTAGAATTTTTAGACATTCGAGGGT
* * * * *
4401 AAAATGGTAATTTTTGGAAATTTCAAGGTAAAATTGGAATTTTTGGATATTCGAGGGT
1 AAAATGGTAATTTTTGAAAAGTTCAAGGTAAAATTAGAATTTTTAGACATTCGAGGGT
4459 AAAATGGTAA
1 AAAATGGTAA
4469 AATTGAAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
57 4 0.07
58 32 0.54
59 20 0.34
60 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAAAAGTTCAAGGTAAAATTAGAATTTTTAGACATTCGAGGGT
Found at i:4414 original size:28 final size:29
Alignment explanation
Indices: 4306--4559 Score: 120
Period size: 29 Copynumber: 8.8 Consensus size: 29
4296 TTTGGATGCC
**
4306 CGAGGGTAAAATGGTAA-TTTTGGATGCTT
1 CGAGGGTAAAATGGTAATTTTTGGA-AATT
* * * * *
4335 TGGGGGCAAAATAGTAATTTTT-AAAAGGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAA--TT
* * * *
4365 CGAGGTTGAAAATAG-AATTTTTAGACATT
1 CGAGGGT-AAAATGGTAATTTTTGGAAATT
4394 CGAGGGTAAAATGGTAATTTTTGGAAATTT
1 CGAGGGTAAAATGGTAATTTTTGGAAA-TT
* *
4424 C-AAGGTAAAATTGG-AATTTTTGGATATT
1 CGAGGGTAAAA-TGGTAATTTTTGGAAATT
**
4452 CGAGGGTAAAATGGTAA-AATT-GAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGAAA-TT
* * *
4480 -TACGGTAAAAAT-GTAATATTTGGAAAATT
1 CGAGGGT-AAAATGGTAATTTTTGG-AAATT
* *
4509 CCA-TGTCAAAAATGG-AA-TTTTGGAAAGTT
1 CGAGGGT--AAAATGGTAATTTTTGGAAA-TT
4538 CGAGGGTAAAAAT-GTAATTTTT
1 CGAGGGT-AAAATGGTAATTTTT
4560 AGTAAGTTCG
Statistics
Matches: 172, Mismatches: 31, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
27 11 0.06
28 28 0.16
29 83 0.48
30 40 0.23
31 10 0.06
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (29 bp):
CGAGGGTAAAATGGTAATTTTTGGAAATT
Found at i:4548 original size:29 final size:29
Alignment explanation
Indices: 4392--4593 Score: 132
Period size: 29 Copynumber: 7.0 Consensus size: 29
4382 TTTTTAGACA
*
4392 TTCGAGGGT-AAAATGGTAATTTTTGGAAAT
1 TTCGAGGGTAAAAATGG-AA-TTTTGGAAAG
* * *
4422 TTC-AAGGTAAAATTGGAATTTTTGGATA-
1 TTCGAGGGTAAAAATGGAA-TTTTGGAAAG
**
4450 TTCGAGGGT-AAAATGGTAAAATT-GAAAG
1 TTCGAGGGTAAAAATGG-AATTTTGGAAAG
* * * *
4478 TT-TACGGTAAAAATGTAATATTTGGAAAA
1 TTCGAGGGTAAAAATGGAAT-TTTGGAAAG
* *
4507 TTCCA-TGTCAAAAATGGAATTTTGGAAAG
1 TTCGAGGGT-AAAAATGGAATTTTGGAAAG
* * *
4536 TTCGAGGGTAAAAATGTAATTTTTAGTAAG
1 TTCGAGGGTAAAAATGGAA-TTTTGGAAAG
*
4566 TTCGA-GGTCAAAAATGGAATTTTAGAAA
1 TTCGAGGGT-AAAAATGGAATTTTGGAAA
4594 AATTCTTGCA
Statistics
Matches: 135, Mismatches: 25, Indels: 25
0.73 0.14 0.14
Matches are distributed among these distances:
27 9 0.07
28 21 0.16
29 61 0.45
30 44 0.33
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGGAATTTTGGAAAG
Found at i:4569 original size:30 final size:30
Alignment explanation
Indices: 4350--4593 Score: 122
Period size: 29 Copynumber: 8.4 Consensus size: 30
4340 GCAAAATAGT
** *
4350 AATTTTTA-AAAGGTTCGAGGTTGAAAATAG
1 AATTTTTAGAAA-GTTCGAGGTCAAAAATGG
*
4380 AATTTTTAGACA-TTCGAGGGT--AAAATGG
1 AATTTTTAGAAAGTTCGA-GGTCAAAAATGG
* * * *
4408 TAATTTTTGGAAATTTCAAGGT-AAAATTGG
1 -AATTTTTAGAAAGTTCGAGGTCAAAAATGG
* *
4438 AATTTTTGGATA-TTCGAGGGT--AAAATGG
1 AATTTTTAGAAAGTTCGA-GGTCAAAAATGG
** * *
4466 TAA-AATT-GAAAGTT-TACGGT-AAAAATGT
1 -AATTTTTAGAAAGTTCGA-GGTCAAAAATGG
* * * * *
4494 AATATTTGGAAAATTCCATGTCAAAAATGG
1 AATTTTTAGAAAGTTCGAGGTCAAAAATGG
* *
4524 AA-TTTTGGAAAGTTCGAGGGT-AAAAATGT
1 AATTTTTAGAAAGTTCGA-GGTCAAAAATGG
*
4553 AATTTTTAGTAAGTTCGAGGTCAAAAATGG
1 AATTTTTAGAAAGTTCGAGGTCAAAAATGG
4583 AA-TTTTAGAAA
1 AATTTTTAGAAA
4594 AATTCTTGCA
Statistics
Matches: 169, Mismatches: 29, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
27 9 0.05
28 29 0.17
29 74 0.44
30 55 0.33
31 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAAGTTCGAGGTCAAAAATGG
Found at i:6466 original size:17 final size:17
Alignment explanation
Indices: 6440--6492 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
6430 TTGAGATATT
6440 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
6456 ATTTAAAATAAACTT-A
1 ATTTAAAATAAATTTAA
*
6472 ATGTTAAAATAAATTCAA
1 AT-TTAAAATAAATTTAA
6490 ATT
1 ATT
6493 CTGTTGGGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 21 0.68
18 3 0.10
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:7620 original size:37 final size:37
Alignment explanation
Indices: 7570--7735 Score: 201
Period size: 37 Copynumber: 4.5 Consensus size: 37
7560 CTTCCACAAA
* *
7570 TTCAGGCTATATGCCTAGTATGCTGTGTGCCGGTATT
1 TTCAGGCTATATGCCTAGTAGGCTGTGTGCCGGTGTT
*
7607 TTCAGGCTATATGCCTAGCAGGCTGTGTGCCGGTGTT
1 TTCAGGCTATATGCCTAGTAGGCTGTGTGCCGGTGTT
* * *
7644 TCCAGGCTATATGCCTAGTAGGTTGTGTGTCGGTGTT
1 TTCAGGCTATATGCCTAGTAGGCTGTGTGCCGGTGTT
* * *
7681 TTCAAGCTATGTGCCTAGTAGGCT-TCATGCCGGTGTAT
1 TTCAGGCTATATGCCTAGTAGGCTGT-GTGCCGGTGT-T
* *
7719 TT-GGGCTTTATGCCTAG
1 TTCAGGCTATATGCCTAG
7736 CAAACTTTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
36 1 0.01
37 106 0.96
38 3 0.03
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (37 bp):
TTCAGGCTATATGCCTAGTAGGCTGTGTGCCGGTGTT
Done.