Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005169.1 Kokia drynarioides strain JFW-HI SEQ_119019, 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: 9809
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:737 original size:4 final size:4
Alignment explanation
Indices: 723--757 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
713 TAGATGGAGT
723 TTAA CTTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA -TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
758 TTAATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:770 original size:14 final size:14
Alignment explanation
Indices: 728--767 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
718 GGAGTTTAAC
728 TTAATTAATTAATT
1 TTAATTAATTAATT
742 AATTAATTAATTAATT
1 --TTAATTAATTAATT
758 TTAATATAAT
1 TTAAT-TAAT
768 AATAAACCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAATTAATTAATT
Found at i:4434 original size:23 final size:23
Alignment explanation
Indices: 4396--4439 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
4386 AAATTTAATT
*
4396 TTTATGTTTTT-GTTTTCAAAAA
1 TTTATGTTTTTATTTTTCAAAAA
4418 TTTAGTGTTTTTATTTTTCAAA
1 TTTA-TGTTTTTATTTTTCAAA
4440 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTATGTTTTTATTTTTCAAAAA
Found at i:5761 original size:13 final size:13
Alignment explanation
Indices: 5739--5802 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
5729 TTTAACATTA
*
5739 CTTTTGAAAAGTG
1 CTTTTAAAAAGTG
5752 CTTTTAAAAAGTG
1 CTTTTAAAAAGTG
** *
5765 -TGGTAGAAAAGTA
1 CTTTTA-AAAAGTG
*
5778 CTTTTAAGAAGTG
1 CTTTTAAAAAGTG
*
5791 CTTTTGAAAAGT
1 CTTTTAAAAAGT
5803 TTGGTTTAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
12 3 0.08
13 33 0.85
14 3 0.08
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (13 bp):
CTTTTAAAAAGTG
Found at i:5799 original size:26 final size:26
Alignment explanation
Indices: 5739--5802 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
5729 TTTAACATTA
*
5739 CTTTTGAAAAGTGCTTTTAAAAAGTG
1 CTTTTGAAAAGTACTTTTAAAAAGTG
* * *
5765 -TGGTAGAAAAGTACTTTTAAGAAGTG
1 CT-TTTGAAAAGTACTTTTAAAAAGTG
5791 CTTTTGAAAAGT
1 CTTTTGAAAAGT
5803 TTGGTTTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
25 1 0.03
26 28 0.93
27 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (26 bp):
CTTTTGAAAAGTACTTTTAAAAAGTG
Found at i:9637 original size:23 final size:23
Alignment explanation
Indices: 9563--9704 Score: 95
Period size: 23 Copynumber: 6.4 Consensus size: 23
9553 TAAACGGAAC
* * *
9563 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
9585 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
9607 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
9633 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
* *
9653 --AC--TGAGCACACAAAATGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
9672 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
9695 AATCAGAGAG
1 AAACAGAGAG
9705 AGCGCTAGTG
Statistics
Matches: 95, Mismatches: 13, Indels: 23
0.73 0.10 0.18
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.19
23 40 0.42
25 13 0.14
26 7 0.07
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Done.