Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000720.1 Kokia drynarioides strain JFW-HI SEQ_111738, 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: 1865
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.29
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--48 Score: 80
Period size: 7 Copynumber: 7.0 Consensus size: 7
1 CCAAACC
1 CCAAACC
8 CCAAACC
1 CCAAACC
15 CCAAACC
1 CCAAACC
22 CCAAACC
1 CCAAACC
*
29 CC-AAGC
1 CCAAACC
35 CCAAACC
1 CCAAACC
42 CCAAACC
1 CCAAACC
49 AACCCTCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.42, C:0.56, G:0.02, T:0.00
Consensus pattern (7 bp):
CCAAACC
Found at i:39 original size:13 final size:13
Alignment explanation
Indices: 4--45 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1 CCA
4 AACCCCAAACCCC
1 AACCCCAAACCCC
17 AAACCCCAAACCCC
1 -AACCCCAAACCCC
*
31 AAGCCCAAACCCC
1 AACCCCAAACCCC
44 AA
1 AA
46 ACCAACCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.43, C:0.55, G:0.02, T:0.00
Consensus pattern (13 bp):
AACCCCAAACCCC
Found at i:39 original size:20 final size:21
Alignment explanation
Indices: 1--48 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
1 CCAAACCCCAAACCCCAAACC
1 CCAAACCCCAAACCCCAAACC
*
22 CCAAACCCC-AAGCCCAAACC
1 CCAAACCCCAAACCCCAAACC
42 CCAAACC
1 CCAAACC
49 AACCCTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.56, G:0.02, T:0.00
Consensus pattern (21 bp):
CCAAACCCCAAACCCCAAACC
Found at i:88 original size:7 final size:7
Alignment explanation
Indices: 2--140 Score: 60
Period size: 7 Copynumber: 20.6 Consensus size: 7
1 C
*
2 CAAACCC
1 CAAACCT
*
9 CAAACCC
1 CAAACCT
*
16 CAAACCC
1 CAAACCT
*
23 CAAACCC
1 CAAACCT
*
30 CAAGCC-
1 CAAACCT
*
36 CAAACCC
1 CAAACCT
43 CAAA-C-
1 CAAACCT
*
48 CAACCCT
1 CAAACCT
55 C-AACCT
1 CAAACCT
61 CTAAACCT
1 C-AAACCT
*
69 TAAACC-
1 CAAACCT
*
75 CACACCT
1 CAAACCT
82 CAAACCT
1 CAAACCT
* *
89 TATA--T
1 CAAACCT
94 CAAACC-
1 CAAACCT
*
100 CAAAACT
1 CAAACCT
107 CAAACCCT
1 CAAA-CCT
*
115 CAAAATCT
1 C-AAACCT
*
123 TAAACCT
1 CAAACCT
*
130 CAAACCA
1 CAAACCT
137 CAAA
1 CAAA
141 TCCAACCCTA
Statistics
Matches: 102, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
5 6 0.06
6 21 0.21
7 62 0.61
8 10 0.10
9 3 0.03
ACGTcount: A:0.44, C:0.44, G:0.01, T:0.12
Consensus pattern (7 bp):
CAAACCT
Done.