Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010136.1 Kokia drynarioides strain JFW-HI SEQ_124931, 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: 9353
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Found at i:76 original size:2 final size:2
Alignment explanation
Indices: 69--94 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59 AAGCATCACA
69 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
95 TGTTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:436 original size:17 final size:17
Alignment explanation
Indices: 416--449 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
406 TTTTACATGA
*
416 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
433 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
450 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:2517 original size:42 final size:42
Alignment explanation
Indices: 2451--2569 Score: 157
Period size: 43 Copynumber: 2.8 Consensus size: 42
2441 ATGCCTCTAT
* *
2451 AGAACATGGTTTTTAACGACGCTTTCCCATAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGACGCTTTCCCATAAACGCCGCTAA
** * *
2493 AGAACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCTGCTAA
1 AGAACATGGTCTTTAGCGACGC-TTTCCCATAAACGCCGCTAA
* *
2536 AGAACATGGTCTTTAGTGACGCTTTCCTATAAAC
1 AGAACATGGTCTTTAGCGACGCTTTCCCATAAAC
2570 CCCACTAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 28 0.43
43 37 0.57
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (42 bp):
AGAACATGGTCTTTAGCGACGCTTTCCCATAAACGCCGCTAA
Found at i:3918 original size:22 final size:22
Alignment explanation
Indices: 3890--3939 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
3880 TTTAAAAATC
3890 AAAATAATATATAAA-AATTAAA
1 AAAATAA-ATATAAAGAATTAAA
*
3912 AAAATAAATTTAAAGTAATTAAA
1 AAAATAAATATAAAG-AATTAAA
3935 AAAAT
1 AAAAT
3940 TAAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATAAATATAAAGAATTAAA
Found at i:3981 original size:24 final size:23
Alignment explanation
Indices: 3954--4012 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
3944 ATTTATATTT
*
3954 TTTTTAAAATTTTAG-AATAATA
1 TTTTTAAAATTTTAGAAAAAATA
* *
3976 TATTTTAGAATTTTATAAAAAATA
1 T-TTTTAAAATTTTAGAAAAAATA
*
4000 TTTTTAAACTTTT
1 TTTTTAAAATTTT
4013 TTAAATTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.03
23 22 0.73
24 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTTTAAAATTTTAGAAAAAATA
Found at i:5782 original size:29 final size:28
Alignment explanation
Indices: 5750--5839 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
5740 TCTTGTATAA
5750 TTTTTTATGACTTTATAAAATTTTA-AATT
1 TTTTTTAT-A-TTTATAAAATTTTACAATT
* * *
5779 TTTTTTATATTTCTAAATATATTATAATT
1 TTTTTTATATTTATAAA-ATTTTACAATT
* *
5808 TTTTATAATTTTTATAAAATTTTACAATT
1 TTTT-TTATATTTATAAAATTTTACAATT
5837 TTT
1 TTT
5840 ATATTTTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.14
28 6 0.12
29 28 0.55
30 10 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTTTTATATTTATAAAATTTTACAATT
Found at i:5821 original size:9 final size:9
Alignment explanation
Indices: 5800--5877 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
5790 TCTAAATATA
5800 TTATAATTTT
1 TTATAA-TTT
5810 TTATAATTT
1 TTATAATTT
*
5819 TTATAAAATT
1 TTAT-AATTT
*
5829 TTACAATTT
1 TTATAATTT
*
5838 TTATATTTT
1 TTATAATTT
*
5847 TTCTAA-TT
1 TTATAATTT
5855 TTATTAA-TT
1 TTA-TAATTT
* *
5864 TAATAATAT
1 TTATAATTT
5873 TTATA
1 TTATA
5878 GCTTTTATTG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
8 7 0.13
9 34 0.63
10 13 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:5824 original size:19 final size:19
Alignment explanation
Indices: 5723--5856 Score: 73
Period size: 19 Copynumber: 7.2 Consensus size: 19
5713 AATTTACGAA
5723 TTTTAT-ATTTCTTTAT-AT
1 TTTTATAATTT-TTTATAAT
* *
5741 CTTGTATAATTTTTTATGA-
1 -TTTTATAATTTTTTATAAT
* **
5760 CTTTATAAAATTTTA-AAT
1 TTTTATAATTTTTTATAAT
* * *
5778 TTTTTTTATATTTCTA-AAT
1 TTTTATAAT-TTTTTATAAT
*
5797 ATATTATAATTTTTTATAAT
1 -TTTTATAATTTTTTATAAT
** *
5817 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTATAAT
*
5836 TTTTAT-ATTTTTTCTAAT
1 TTTTATAATTTTTTATAAT
5854 TTT
1 TTT
5857 ATTAATTTAA
Statistics
Matches: 85, Mismatches: 24, Indels: 13
0.70 0.20 0.11
Matches are distributed among these distances:
17 1 0.01
18 27 0.32
19 43 0.51
20 14 0.16
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTATAATTTTTTATAAT
Found at i:8053 original size:20 final size:20
Alignment explanation
Indices: 8004--8054 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
7994 AAATTAACTC
* *
8004 TTTTCATTTTTATAACATTT
1 TTTTAATTTTTATAACATTG
*
8024 TTTTAATTTTTAT-ATATTG
1 TTTTAATTTTTATAACATTG
*
8043 TTTTAACTTTTA
1 TTTTAATTTTTA
8055 AAATTAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAATTTTTATAACATTG
Done.