Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005148.1 Kokia drynarioides strain JFW-HI SEQ_118988, 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: 9739
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Found at i:55 original size:3 final size:3
Alignment explanation
Indices: 47--96 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
37 CCTCCCTTTT
* *
47 TTA TTA TTAA TTA TTAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
94 TTA
1 TTA
97 ATGCTATTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:906 original size:18 final size:17
Alignment explanation
Indices: 868--955 Score: 104
Period size: 18 Copynumber: 5.0 Consensus size: 17
858 TTTTACTTAT
* *
868 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
885 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
903 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
920 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
*
938 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
956 GAGTCCGGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
17 23 0.38
18 38 0.62
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:907 original size:35 final size:35
Alignment explanation
Indices: 868--955 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 35
858 TTTTACTTAT
* * *
868 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAA
**
903 TTTAAATTTAAAATAAATTTAAATTTTTAAACAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAA
*
938 TTTAATTTTTAAAATAAA
1 TTTAA-ATTTAAAATAAA
956 GAGTCCGGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 35 0.76
36 11 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAA
Found at i:3615 original size:26 final size:26
Alignment explanation
Indices: 3579--3630 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3569 GATGATGCAT
3579 GGTTACCGGGGAATGTTCATTTTAAA
1 GGTTACCGGGGAATGTTCATTTTAAA
3605 GGTTACCGGGGAATGTTCATTTTAAA
1 GGTTACCGGGGAATGTTCATTTTAAA
3631 TTATTTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (26 bp):
GGTTACCGGGGAATGTTCATTTTAAA
Found at i:5324 original size:28 final size:28
Alignment explanation
Indices: 5287--5773 Score: 175
Period size: 28 Copynumber: 16.8 Consensus size: 28
5277 CGGTCAAACA
*
5287 ATTTTAGTAAATATTTTTAAAAATAGCT
1 ATTTTCGTAAATATTTTTAAAAATAGCT
* *
5315 ACTTTCGTAAATAATTTTT-AAAA-CGTCT
1 ATTTTCGTAAAT-ATTTTTAAAAATAG-CT
5343 ATTTTCGTAAATATTTTTAAAAATA-CTT
1 ATTTTCGTAAATATTTTTAAAAATAGC-T
* * *
5371 ATTTTTGTCAATATTTTTAAAACAT--TT
1 ATTTTCGTAAATATTTTTAAAA-ATAGCT
* *
5398 GTTGTCGTAAATATTTTTAAAAAT-GCTT
1 ATTTTCGTAAATATTTTTAAAAATAGC-T
* *
5426 ATTTTCATAAATATTTTTAAAAA-CGCCTT
1 ATTTTCGTAAATATTTTTAAAAATAG-C-T
** *
5455 AATTTT-AAAAATGTCTATTTTCGTGAAAAAATTTAAAAAC-
1 -ATTTTCGTAAA----TATTTT--T--AAAAA--T---AGCT
* *
5495 ACCTATTCCTGTAAATATTTTTTAAAAATACCT
1 A--T-TTTC-GTAAATA-TTTTTAAAAATAGCT
*
5528 ATTTTCGTAAATAATTTT--AAATACGCCT
1 ATTTTCGTAAATATTTTTAAAAATA-G-CT
* *
5556 ATTTCCGTAAATATATTT-AAAA-AGTCT
1 ATTTTCGTAAATATTTTTAAAAATAG-CT
* *
5583 ATTTTCGTAAATATTTTTAAAAACACCT
1 ATTTTCGTAAATATTTTTAAAAATAGCT
** * *
5611 ATTCCCGTAAATA-TTTTAAAAACACCT
1 ATTTTCGTAAATATTTTTAAAAATAGCT
* * *
5638 -GTTCCAGTAAATATTTTTAAAAA-CGCCT
1 ATTTTC-GTAAATATTTTTAAAAATAG-CT
** * *
5666 ATTCCCATATATATTTTTAAAAAT-GCCT
1 ATTTTCGTAAATATTTTTAAAAATAG-CT
* * *
5694 ATTTCCCTAAATATTTTTAAAAACA-CTT
1 ATTTTCGTAAATATTTTTAAAAATAGC-T
* *
5722 ATTCCTC-TAAATATTTTTTAAAAATATCT
1 ATT-TTCGTAAATA-TTTTTAAAAATAGCT
** *
5751 ATTCCCCTAAATATTTTTAAAAA
1 ATTTTCGTAAATATTTTTAAAAA
5774 CATTTATTCC
Statistics
Matches: 360, Mismatches: 51, Indels: 96
0.71 0.10 0.19
Matches are distributed among these distances:
26 10 0.03
27 68 0.19
28 185 0.51
29 51 0.14
30 9 0.03
31 1 0.00
32 2 0.01
33 7 0.02
35 2 0.01
37 10 0.03
39 2 0.01
40 2 0.01
41 5 0.01
42 3 0.01
44 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (28 bp):
ATTTTCGTAAATATTTTTAAAAATAGCT
Found at i:5409 original size:55 final size:55
Alignment explanation
Indices: 5293--5781 Score: 273
Period size: 55 Copynumber: 8.9 Consensus size: 55
5283 AACAATTTTA
* * *
5293 GTAAATATTTTTAAAAATAGC-TACTTTCGTAAATAATTTTTAAAACGTCTATTTTC
1 GTAAATATTTTTAAAAATA-CTTATTTTCGTAAAT-ATTTTTAAAACATCTATTGTC
* * * *
5349 GTAAATATTTTTAAAAATACTTATTTTTGTCAATATTTTTAAAACATTTGTTGTC
1 GTAAATATTTTTAAAAATACTTATTTTCGTAAATATTTTTAAAACATCTATTGTC
* *
5404 GTAAATATTTTTAAAAATGCTTATTTTCATAAATATTTTTAAAA-A-C----G-C
1 GTAAATATTTTTAAAAATACTTATTTTCGTAAATATTTTTAAAACATCTATTGTC
* * * * * * * *
5452 CT---TAATTTTAAAAAT-GTCTATTTTCGTGAAAAAATTTAAAAACACCTATT-CC
1 GTAAATATTTTTAAAAATACT-TATTTTCGT-AAATATTTTTAAAACATCTATTGTC
* * **
5504 TGTAAATATTTTTTAAAAATACCTATTTTCGTAAATAATTTTAAATACGCCTATT-TCC
1 -GTAAATA-TTTTTAAAAATACTTATTTTCGTAAATATTTTTAAA-ACATCTATTGT-C
* * **
5562 GTAAATATATTTAAAAAGT-C-TATTTTCGTAAATATTTTTAAAAACACCTATTCCC
1 GTAAATATTTTTAAAAA-TACTTATTTTCGTAAATATTTTT-AAAACATCTATTGTC
* * * * ** **
5617 GTAAATA-TTTTAAAAACACCT-GTTCCAGTAAATATTTTTAAAAACGCCTATTCCC
1 GTAAATATTTTTAAAAATACTTATTTTC-GTAAATATTTTT-AAAACATCTATTGTC
* * * * * * *
5672 ATATATATTTTTAAAAATGCCTATTTCCCTAAATATTTTTAAAAACA-CTTATTCCTC
1 GTAAATATTTTTAAAAATACTTATTTTCGTAAATATTTTT-AAAACATC-TATT-GTC
** * *
5729 -TAAATATTTTTTAAAAATA-TCTATTCCCCTAAATATTTTTAAAAACATTTATT
1 GTAAATA-TTTTTAAAAATACT-TATTTTCGTAAATATTTTT-AAAACATCTATT
5782 CCCCTAAAAA
Statistics
Matches: 353, Mismatches: 49, Indels: 61
0.76 0.11 0.13
Matches are distributed among these distances:
44 1 0.00
45 20 0.06
46 11 0.03
47 1 0.00
48 3 0.01
49 1 0.00
52 1 0.00
53 1 0.00
54 13 0.04
55 126 0.36
56 93 0.26
57 81 0.23
58 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (55 bp):
GTAAATATTTTTAAAAATACTTATTTTCGTAAATATTTTTAAAACATCTATTGTC
Found at i:5781 original size:28 final size:28
Alignment explanation
Indices: 5486--5824 Score: 295
Period size: 28 Copynumber: 12.1 Consensus size: 28
5476 CGTGAAAAAA
**
5486 TTTAAAAACACCTATTCCTGTAAATATTT
1 TTTAAAAACACCTATTCCCCTAAATA-TT
* ** * *
5515 TTTAAAAATACCTATTTTCGTAAATAAT
1 TTTAAAAACACCTATTCCCCTAAATATT
* * * * *
5543 TTTAAATACGCCTATTTCCGTAAATATA
1 TTTAAAAACACCTATTCCCCTAAATATT
** ** *
5571 TTTAAAAA-GTCTATTTTCGTAAATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
*
5598 TTTAAAAACACCTATTCCCGTAAATA-T
1 TTTAAAAACACCTATTCCCCTAAATATT
* **
5625 TTTAAAAACACCTGTTCCAGTAAATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
* * *
5653 TTTAAAAACGCCTATTCCCATATATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
** *
5681 TTTAAAAATGCCTATTTCCCTAAATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
* *
5709 TTTAAAAACACTTATTCCTCTAAATATTT
1 TTTAAAAACACCTATTCCCCTAAATA-TT
* *
5738 TTTAAAAATATCTATTCCCCTAAATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
** * *
5766 TTTAAAAACATTTATTCCCCTAAAAAAT
1 TTTAAAAACACCTATTCCCCTAAATATT
** * *
5794 TTTAAAAACGTCTATACCCTTAAATATT
1 TTTAAAAACACCTATTCCCCTAAATATT
5822 TTT
1 TTT
5825 TTTAAAAATG
Statistics
Matches: 258, Mismatches: 49, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
27 49 0.19
28 163 0.63
29 46 0.18
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTAAAAACACCTATTCCCCTAAATATT
Found at i:5900 original size:29 final size:29
Alignment explanation
Indices: 5868--5929 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5858 TAAAAATGGC
5868 ATATCCCTAAAAAACACTTATTACCCTAA
1 ATATCCCTAAAAAACACTTATTACCCTAA
*** * *
5897 ATATTTTTTAAAAACGCTTATTACCCTAA
1 ATATCCCTAAAAAACACTTATTACCCTAA
5926 ATAT
1 ATAT
5930 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (29 bp):
ATATCCCTAAAAAACACTTATTACCCTAA
Found at i:5930 original size:29 final size:29
Alignment explanation
Indices: 5877--5984 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 29
5867 CATATCCCTA
5877 AAAAACACTTATTACCCTAAATATTTTTT
1 AAAAACACTTATTACCCTAAATATTTTTT
*
5906 AAAAACGCTTATTACCCTAAATATTTTTT
1 AAAAACACTTATTACCCTAAATATTTTTT
* * *
5935 AAAAACACCTATT-CTCCTAAATA-CTTTA
1 AAAAACACTTATTAC-CCTAAATATTTTTT
* *
5963 AAAAACGATTTATTCCCCTAAA
1 AAAAAC-ACTTATTACCCTAAA
5985 AAAAATTTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 10 0.14
29 58 0.84
30 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAACACTTATTACCCTAAATATTTTTT
Done.