Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003568.1 Kokia drynarioides strain JFW-HI SEQ_116433, 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: 8381
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2843 original size:25 final size:25
Alignment explanation
Indices: 2815--2888 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 25
2805 TAAATAAAAT
2815 AAAAGTTATGATAATTATATATTT-
1 AAAAGTTATGATAATTATATATTTA
2839 AAAA---A--ATAATTATA-ATTTA
1 AAAAGTTATGATAATTATATATTTA
* *
2858 ATAGAAGTTGTGATAATTATGTATTTA
1 A-A-AAGTTATGATAATTATATATTTA
2885 AAAA
1 AAAA
2889 TAATTAGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 17
0.67 0.03 0.29
Matches are distributed among these distances:
18 4 0.10
19 10 0.26
20 1 0.03
21 3 0.08
24 4 0.10
25 2 0.05
26 9 0.23
27 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (25 bp):
AAAAGTTATGATAATTATATATTTA
Found at i:2872 original size:45 final size:44
Alignment explanation
Indices: 2812--2902 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
2802 TTTTAAATAA
*
2812 AATAAAAGTTATGATAATTATATATTTAAAAAATAATTATAATTT
1 AATAAAAGTTATGATAATTATATATTT-AAAAATAATTAGAATTT
* * *
2857 AATAGAAGTTGTGATAATTATGTATTTAAAAATAATTAGAATTT
1 AATAAAAGTTATGATAATTATATATTTAAAAATAATTAGAATTT
2901 AA
1 AA
2903 ATTACAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 18 0.43
45 24 0.57
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.41
Consensus pattern (44 bp):
AATAAAAGTTATGATAATTATATATTTAAAAATAATTAGAATTT
Found at i:2902 original size:17 final size:18
Alignment explanation
Indices: 2870--2903 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2860 AGAAGTTGTG
*
2870 ATAATTATGTATTTAAAA
1 ATAATTATGAATTTAAAA
2888 ATAATTA-GAATTTAAA
1 ATAATTATGAATTTAAA
2904 TTACAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATAATTATGAATTTAAAA
Found at i:6163 original size:20 final size:20
Alignment explanation
Indices: 6138--6199 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
6128 ATTGACCGAC
6138 TGTTGACCGTTGACTTTGAT
1 TGTTGACCGTTGACTTTGAT
*
6158 TGTTGACTGTTGACTTTGAT
1 TGTTGACCGTTGACTTTGAT
*
6178 CGTTGACCGTTGACTGTTGAT
1 TGTTGACCGTTGACT-TTGAT
6199 T
1 T
6200 TTTTCGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 32 0.86
21 5 0.14
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.45
Consensus pattern (20 bp):
TGTTGACCGTTGACTTTGAT
Found at i:6169 original size:27 final size:27
Alignment explanation
Indices: 6135--6197 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
6125 GCCATTGACC
* **
6135 GACTGTTGACCGTTGA-CTTTGATTGTT
1 GACTGTTGA-CGTTGATCGTTGACCGTT
*
6162 GACTGTTGACTTTGATCGTTGACCGTT
1 GACTGTTGACGTTGATCGTTGACCGTT
6189 GACTGTTGA
1 GACTGTTGA
6198 TTTTTTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.41
Consensus pattern (27 bp):
GACTGTTGACGTTGATCGTTGACCGTT
Done.