Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013360.1 Kokia drynarioides strain JFW-HI SEQ_128383, 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: 6480
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Found at i:4902 original size:21 final size:21
Alignment explanation
Indices: 4878--4988 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
4868 ACCAACACCC
*
4878 AAACAACAA-AAATAATAGCAA
1 AAACAACAATAAA-AATAACAA
4899 AAACAACAATAAAAATAACAA
1 AAACAACAATAAAAATAACAA
*
4920 AAA-AAGCAGTAAAAATAACTGGAAA
1 AAACAA-CAATAAAAATAAC----AA
* *
4945 AATAGAAGCAA-AAATAACAACAA
1 AA-ACAA-CAATAAA-AATAACAA
*
4968 AAACAACAGTAAAAATAACAA
1 AAACAACAATAAAAATAACAA
4989 CATAAACAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.03
21 40 0.55
22 9 0.12
23 4 0.05
25 4 0.05
26 4 0.05
27 10 0.14
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (21 bp):
AAACAACAATAAAAATAACAA
Found at i:4924 original size:24 final size:24
Alignment explanation
Indices: 4885--4997 Score: 99
Period size: 24 Copynumber: 4.8 Consensus size: 24
4875 CCCAAACAAC
* * *
4885 AAAAATAATAGCAAAAACAACAAT
1 AAAAATAACAACAAAAACAACAGT
*
4909 AAAAATAAC-A-AAAAA-AGCAGT
1 AAAAATAACAACAAAAACAACAGT
*** * *
4930 AAAAATAACTGGAAAAATAGA-AGC
1 AAAAATAACAACAAAAACA-ACAGT
4954 AAAAATAACAACAAAAACAACAGT
1 AAAAATAACAACAAAAACAACAGT
*
4978 AAAAATAACAACATAAACAA
1 AAAAATAACAACAAAAACAA
4998 TATACTAACA
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
21 13 0.18
22 5 0.07
23 6 0.08
24 47 0.66
ACGTcount: A:0.70, C:0.12, G:0.07, T:0.11
Consensus pattern (24 bp):
AAAAATAACAACAAAAACAACAGT
Found at i:4968 original size:12 final size:12
Alignment explanation
Indices: 4879--4990 Score: 61
Period size: 12 Copynumber: 9.6 Consensus size: 12
4869 CCAACACCCA
4879 AACAACAAAAAT
1 AACAACAAAAAT
* * *
4891 AATAGCAAAAAC
1 AACAACAAAAAT
*
4903 AACAATAAAAAT
1 AACAACAAAAAT
4915 AAC-A-AAAAA-
1 AACAACAAAAAT
* **
4924 AGCAGTAAAAAT
1 AACAACAAAAAT
***
4936 AACTGGAAAAAT
1 AACAACAAAAAT
*
4948 AGA-AGCAAAAAT
1 A-ACAACAAAAAT
*
4960 AACAACAAAAAC
1 AACAACAAAAAT
**
4972 AACAGTAAAAAT
1 AACAACAAAAAT
4984 AACAACA
1 AACAACA
4991 TAAACAATAT
Statistics
Matches: 74, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
9 2 0.03
10 5 0.07
11 7 0.09
12 59 0.80
13 1 0.01
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5319 original size:21 final size:21
Alignment explanation
Indices: 5295--5336 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5285 TGAAAGAGAA
5295 AGGAAATGATAAGGGGAAACT
1 AGGAAATGATAAGGGGAAACT
5316 AGGAAATGATAAGGGGAAACT
1 AGGAAATGATAAGGGGAAACT
5337 GCCCTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.33, T:0.14
Consensus pattern (21 bp):
AGGAAATGATAAGGGGAAACT
Found at i:5767 original size:31 final size:31
Alignment explanation
Indices: 5732--5799 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5722 TTTAGTGTCC
**
5732 AAACTTGACACGTTTTCCTAATTTGGTACTT
1 AAACTTGACACGTTTTCCTAACCTGGTACTT
* *
5763 AAACTTGACACTTTTTCTTAACCTGGTACTT
1 AAACTTGACACGTTTTCCTAACCTGGTACTT
5794 AAACTT
1 AAACTT
5800 TTTGAGGTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (31 bp):
AAACTTGACACGTTTTCCTAACCTGGTACTT
Done.