Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011130.1 Kokia drynarioides strain JFW-HI SEQ_126103, 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: 11250
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Found at i:355 original size:17 final size:16
Alignment explanation
Indices: 332--395 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
322 TTTTAATTGA
332 AAATAAATTTAAATTT
1 AAATAAATTTAAATTT
* **
348 AAAGTAAATTCAAACTCA
1 AAA-TAAATTTAAA-TTT
*
366 AAATGAATTTAAATTT
1 AAATAAATTTAAATTT
382 AGAATAAATTTAAA
1 A-AATAAATTTAAA
396 CTTATTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 5 0.14
17 28 0.76
18 4 0.11
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (16 bp):
AAATAAATTTAAATTT
Found at i:369 original size:34 final size:34
Alignment explanation
Indices: 331--397 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
321 TTTTTAATTG
331 AAAATAAATTTAAATTTA-AAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAGAA-TAAATTCAAACTC
* *
365 AAAATGAATTTAAATTTAGAATAAATTTAAACT
1 AAAATAAATTTAAATTTAGAATAAATTCAAACT
398 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAGAATAAATTCAAACTC
Found at i:5990 original size:25 final size:25
Alignment explanation
Indices: 5913--5996 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 25
5903 ACCAAAGTAC
*
5913 TAACAGAGAGCACACCCAATGCT-A
1 TAACAGAGAGCACACACAATGCTAA
*
5937 -AATAGAGAGCACACA-AAGTGCTAA
1 TAACAGAGAGCACACACAA-TGCTAA
5961 T--CAGAGAGCACACACAATGCTAA
1 TAACAGAGAGCACACACAATGCTAA
5984 TAACAGAGAGCAC
1 TAACAGAGAGCAC
5997 GAGACGTGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 2 0.04
23 36 0.71
24 3 0.06
25 10 0.20
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (25 bp):
TAACAGAGAGCACACACAATGCTAA
Found at i:6006 original size:25 final size:25
Alignment explanation
Indices: 5913--6017 Score: 98
Period size: 23 Copynumber: 4.4 Consensus size: 25
5903 ACCAAAGTAC
* *
5913 TAACAGAGAGCACACCCAATGCT-A
1 TAACAGAGAGCACACACAGTGCTAA
* *
5937 -AATAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
5961 T--CAGAGAGCACACACAATGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
5984 TAACAGAGAGCACGAGAC-GTGCT-A
1 TAACAGAGAGCAC-ACACAGTGCTAA
6008 -AACAGAGAGC
1 TAACAGAGAGC
6018 GCACTAGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
23 48 0.72
24 2 0.03
25 14 0.21
26 3 0.04
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:6008 original size:48 final size:45
Alignment explanation
Indices: 5892--5996 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 45
5882 TATACAAAAC
* * *
5892 AAACAGAGAGTAC-CAAAGTACTAACAGAGAGCACACCCAATGCT
1 AAACAGAGAGCACACAAAGTGCTAACAGAGAGCACACACAATGCT
*
5936 AAATAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATGCT
1 AAACAGAGAGCACACAAAGTGCTAA-CAGAGAGCACACACAATGCT
5982 AATAACAGAGAGCAC
1 -A-AACAGAGAGCAC
5997 GAGACGTGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 11 0.21
45 10 0.19
46 19 0.37
47 1 0.02
48 11 0.21
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (45 bp):
AAACAGAGAGCACACAAAGTGCTAACAGAGAGCACACACAATGCT
Found at i:6011 original size:23 final size:22
Alignment explanation
Indices: 5892--6017 Score: 76
Period size: 23 Copynumber: 5.5 Consensus size: 22
5882 TATACAAAAC
* *
5892 AAACAGAGAGTACCAAA-GTACT
1 AAACAGAGAGCA-CAAACGTGCT
** *
5914 -AACAGAGAGCACACCCAATGCT
1 AAACAGAGAGCACAAAC-GTGCT
* *
5936 AAATAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACA-AACGTGCT
* * *
5959 AATCAGAGAGCACACACAATGCT
1 AAACAGAGAGCACAAAC-GTGCT
*
5982 AATAACAGAGAGCACGAGACGTGCT
1 -A-AACAGAGAGCAC-AAACGTGCT
6007 AAACAGAGAGC
1 AAACAGAGAGC
6018 GCACTAGTGT
Statistics
Matches: 78, Mismatches: 18, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.03
21 10 0.13
22 4 0.05
23 42 0.54
24 2 0.03
25 15 0.19
26 3 0.04
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.11
Consensus pattern (22 bp):
AAACAGAGAGCACAAACGTGCT
Found at i:6014 original size:48 final size:46
Alignment explanation
Indices: 5892--6017 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 46
5882 TATACAAAAC
* * *
5892 AAACAGAGAGTAC-CAAAGTACT-AACAGAGAGCACACCCAATGCT
1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACACAATGCT
* *
5936 AAATAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATGCT
1 AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACACAATGCT
* *
5982 AATAACAGAGAGCACGA-GACGTGCTAAACAGAGAGC
1 -A-AACAGAGAGCAC-ACAAAGTGCTAAACAGAGAGC
6018 GCACTAGTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.16
45 8 0.12
46 20 0.29
47 1 0.01
48 27 0.40
49 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.11
Consensus pattern (46 bp):
AAACAGAGAGCACACAAAGTGCTAAACAGAGAGCACACACAATGCT
Found at i:8312 original size:19 final size:21
Alignment explanation
Indices: 8263--8313 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
8253 GATTGAGAGC
8263 TAAAT-TTAATTAAAAAATAA
1 TAAATATTAATTAAAAAATAA
*
8283 AAAATTAATTAATT-AAAAAT-A
1 TAAA-T-ATTAATTAAAAAATAA
8304 TAAATATTAA
1 TAAATATTAA
8314 AGACTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 5 0.19
22 6 0.23
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATTAATTAAAAAATAA
Found at i:10401 original size:20 final size:20
Alignment explanation
Indices: 10378--10415 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10368 TAACTATAAA
*
10378 AATTAATTGTTAATTTTATC
1 AATTAATTATTAATTTTATC
10398 AATTAATTATTAATTTTA
1 AATTAATTATTAATTTTA
10416 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAATTATTAATTTTATC
Done.