Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013617.1 Kokia drynarioides strain JFW-HI SEQ_128645, 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: 5096
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:53 original size:26 final size:26
Alignment explanation
Indices: 24--84 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
14 GACATTTTTT
24 TCTAATTTGATAGTAAACTTTTTTGG
1 TCTAATTTGATAGTAAACTTTTTTGG
50 TCTAATTTGATAGTAAACTTTTTTGG
1 TCTAATTTGATAGTAAACTTTTTTGG
76 TCTAATTTG
1 TCTAATTTG
85 GAGTCCAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (26 bp):
TCTAATTTGATAGTAAACTTTTTTGG
Found at i:398 original size:4 final size:4
Alignment explanation
Indices: 389--434 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
379 TACTTTTAGT
* * * *
389 TTAA TTAA TTAA TTAA TTAA TTAA TTAT TTAT TTAT TTTA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
435 TAAAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (4 bp):
TTAA
Found at i:4452 original size:12 final size:12
Alignment explanation
Indices: 4437--4462 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4427 ATACACTTAA
4437 AAATATTAAAAC
1 AAATATTAAAAC
4449 AAATATTAAAAC
1 AAATATTAAAAC
4461 AA
1 AA
4463 TAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:4659 original size:12 final size:12
Alignment explanation
Indices: 4642--4753 Score: 64
Period size: 12 Copynumber: 8.9 Consensus size: 12
4632 ACAACACCCA
4642 AACAACAAAAAT
1 AACAACAAAAAT
*
4654 AACAACAAAAAC
1 AACAACAAAAAT
*
4666 AACAATAAAAAT
1 AACAACAAAAAT
*
4678 AAAAAAACAGTAAAAAT
1 --AACAAC---AAAAAT
****
4695 AATTGGAAAAAT
1 AACAACAAAAAT
*
4707 AGA-AGCAAAAAT
1 A-ACAACAAAAAT
* *
4719 AACAACAATAAC
1 AACAACAAAAAT
*
4731 AACAGCAAAAAT
1 AACAACAAAAAT
4743 AACAACAAAAA
1 AACAACAAAAA
4754 CAGTATACTA
Statistics
Matches: 75, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
11 1 0.01
12 61 0.81
13 1 0.01
14 4 0.05
15 2 0.03
17 6 0.08
ACGTcount: A:0.71, C:0.13, G:0.05, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:4686 original size:17 final size:18
Alignment explanation
Indices: 4645--4696 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
4635 ACACCCAAAC
* * *
4645 AACAAAAATAACAACAAA
1 AACAACAATAAAAATAAA
4663 AACAACAATAAAAATAAA
1 AACAACAATAAAAATAAA
*
4681 AA-AACAGTAAAAATAA
1 AACAACAATAAAAATAA
4697 TTGGAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.10
Consensus pattern (18 bp):
AACAACAATAAAAATAAA
Found at i:4737 original size:24 final size:24
Alignment explanation
Indices: 4710--4755 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4700 GAAAAATAGA
*
4710 AGCAAAAATAACAACAATAACAAC
1 AGCAAAAATAACAACAAAAACAAC
4734 AGCAAAAATAACAACAAAAACA
1 AGCAAAAATAACAACAAAAACA
4756 GTATACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.07
Consensus pattern (24 bp):
AGCAAAAATAACAACAAAAACAAC
Done.