Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004808.1 Kokia drynarioides strain JFW-HI SEQ_118436, 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: 6096
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:4820 original size:18 final size:16
Alignment explanation
Indices: 4791--4836 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
4781 ATTATAATTG
4791 TTAAAA-TAAAAAAAT
1 TTAAAATTAAAAAAAT
4806 TATGAAAATTAAAAAAAT
1 T-T-AAAATTAAAAAAAT
4824 TTAAAATTCAAAA
1 TTAAAATT-AAAA
4837 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 7 0.26
17 9 0.33
18 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
TTAAAATTAAAAAAAT
Found at i:4821 original size:40 final size:39
Alignment explanation
Indices: 4793--4874 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
4783 TATAATTGTT
4793 AAAATAAAAAA-ATTATGAAAATTAAAAAAATTTAAAATTC
1 AAAATAAAAAATATT-TGAAAA-TAAAAAAATTTAAAATTC
* *
4833 AAAATAAAAAATATTTTAAAATAAAAAATTTTAAAAATTC
1 AAAATAAAAAATATTTGAAAATAAAAAAATTT-AAAATTC
4873 AA
1 AA
4875 TGTTACCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 10 0.26
40 25 0.66
41 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (39 bp):
AAAATAAAAAATATTTGAAAATAAAAAAATTTAAAATTC
Found at i:4836 original size:23 final size:24
Alignment explanation
Indices: 4810--4854 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4800 AAAAATTATG
4810 AAAATTAAAAAA-A-TTTAAAATTC
1 AAAA-TAAAAAATATTTTAAAATTC
4833 AAAATAAAAAATATTTTAAAAT
1 AAAATAAAAAATATTTTAAAAT
4855 AAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATAAAAAATATTTTAAAATTC
Found at i:4860 original size:24 final size:22
Alignment explanation
Indices: 4810--4861 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
4800 AAAAATTATG
* *
4810 AAAATTAAAAAAATTTAAAATT
1 AAAAATAAAAAAATTTAAAATA
*
4832 CAAAATAAAAAATATTTTAAAATA
1 AAAAATAAAAAA-A-TTTAAAATA
4856 AAAAAT
1 AAAAAT
4862 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 13 0.54
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATAAAAAAATTTAAAATA
Found at i:4869 original size:16 final size:17
Alignment explanation
Indices: 4833--4870 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4823 TTTAAAATTC
*
4833 AAAATAAAAAATATTTT
1 AAAATAAAAAATATTTA
4850 AAAATAAAAAAT-TTTA
1 AAAATAAAAAATATTTA
4866 AAAAT
1 AAAAT
4871 TCAATGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAAAAAATATTTA
Found at i:5478 original size:5 final size:6
Alignment explanation
Indices: 5461--5485 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5451 GTTTTTAAAA
5461 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5486 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:6022 original size:4 final size:4
Alignment explanation
Indices: 6013--6096 Score: 168
Period size: 4 Copynumber: 21.0 Consensus size: 4
6003 CATTTAGCCC
6013 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
6061 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG CGTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 80 1.00
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (4 bp):
CGTG
Done.