Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003666.1 Kokia drynarioides strain JFW-HI SEQ_116579, 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: 12016
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:967 original size:18 final size:17
Alignment explanation
Indices: 946--985 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
936 TAAAAAATCA
946 TAAAAGTTA-TAAAATTTT
1 TAAAA-TTATTAAAA-TTT
964 TAAAATTATTAAAATTT
1 TAAAATTATTAAAATTT
981 TAAAA
1 TAAAA
986 ATGAAAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAAATTATTAAAATTT
Found at i:986 original size:18 final size:18
Alignment explanation
Indices: 927--987 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
917 ATTTCTCATA
**
927 AAAAATTATTAAAAAATCAT
1 AAAAATTATT--AAAATTTT
*
947 AAAAGTTA-TAAAATTTT
1 AAAAATTATTAAAATTTT
*
964 TAAAATTATTAAAATTTT
1 AAAAATTATTAAAATTTT
982 AAAAAT
1 AAAAAT
988 GAAAATTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 1 0.03
20 7 0.21
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAAATTATTAAAATTTT
Found at i:5582 original size:21 final size:21
Alignment explanation
Indices: 5559--5598 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
5549 TTTTGGTGCT
5559 TTTTTTTACTG-TTTGGTTGA
1 TTTTTTTACTGTTTTGGTTGA
5579 TTTTTTTACTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
5599 GTATTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (21 bp):
TTTTTTTACTGTTTTGGTTGA
Found at i:5605 original size:20 final size:20
Alignment explanation
Indices: 5562--5605 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5552 TGGTGCTTTT
* *
5562 TTTTACTGTTTGGTTGATTT
1 TTTTACTGTTTGGTTGAGTA
5582 TTTTACTGTTTTGGTTG-GTA
1 TTTTACTG-TTTGGTTGAGTA
5602 TTTT
1 TTTT
5606 GGTGCTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (20 bp):
TTTTACTGTTTGGTTGAGTA
Found at i:5605 original size:21 final size:20
Alignment explanation
Indices: 5561--5605 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
5551 TTGGTGCTTT
*
5561 TTTTTACTGTTTGGTTGATT
1 TTTTTACTGTTTGGTTGATA
*
5581 TTTTTACTGTTTTGGTTGGTA
1 TTTTTACTG-TTTGGTTGATA
5602 TTTT
1 TTTT
5606 GGTGCTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (20 bp):
TTTTTACTGTTTGGTTGATA
Found at i:5646 original size:21 final size:21
Alignment explanation
Indices: 5622--5687 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
5612 GTTATTTTTG
5622 TTGTTATTTTTGTTGCTATTT
1 TTGTTATTTTTGTTGCTATTT
* * *
5643 TTGTTGTTTTTGTTGTTGTTT
1 TTGTTATTTTTGTTGCTATTT
**
5664 TACTGTTATTTTTACTGCTATTT
1 T--TGTTATTTTTGTTGCTATTT
5687 T
1 T
5688 GGTTGTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.70
Consensus pattern (21 bp):
TTGTTATTTTTGTTGCTATTT
Found at i:5646 original size:24 final size:24
Alignment explanation
Indices: 5614--5699 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
5604 TTGGTGCTGT
5614 TATTTTTGTTGTTATTTTTGTTGC
1 TATTTTTGTTGTTATTTTTGTTGC
5638 TATTTTTGTTG---TTTTTGTTG-
1 TATTTTTGTTGTTATTTTTGTTGC
** **
5658 T-TGTTTTACTGTTATTTTTACTGC
1 TAT-TTTTGTTGTTATTTTTGTTGC
*
5682 TATTTTGGTTGTTATTTT
1 TATTTTTGTTGTTATTTT
5700 GTTTGTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.02
20 7 0.14
21 9 0.18
23 7 0.14
24 24 0.49
25 1 0.02
ACGTcount: A:0.09, C:0.05, G:0.16, T:0.70
Consensus pattern (24 bp):
TATTTTTGTTGTTATTTTTGTTGC
Found at i:5664 original size:12 final size:12
Alignment explanation
Indices: 5611--5662 Score: 79
Period size: 12 Copynumber: 4.3 Consensus size: 12
5601 ATTTTGGTGC
5611 TGTTATTTTTGT
1 TGTTATTTTTGT
5623 TGTTATTTTTGT
1 TGTTATTTTTGT
*
5635 TGCTATTTTTGT
1 TGTTATTTTTGT
5647 TGTT-TTTGTTGT
1 TGTTATTT-TTGT
5659 TGTT
1 TGTT
5663 TTACTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 3 0.08
12 34 0.92
ACGTcount: A:0.06, C:0.02, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:5676 original size:44 final size:44
Alignment explanation
Indices: 5623--5721 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
5613 TTATTTTTGT
** * * * *
5623 TGTTATTTTTGTTGCTATTTTTGTTGTTTTTGTTG-TTGTTTTAC
1 TGTTATTTTTACTGCTATTTTGGTTGTTATT-TTGTTTGTTTAAA
5667 TGTTATTTTTACTGCTATTTTGGTTGTTATTTTGTTTGTTTAAA
1 TGTTATTTTTACTGCTATTTTGGTTGTTATTTTGTTTGTTTAAA
5711 TGTTATTTTTA
1 TGTTATTTTTA
5722 TGCGTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.12, C:0.04, G:0.16, T:0.68
Consensus pattern (44 bp):
TGTTATTTTTACTGCTATTTTGGTTGTTATTTTGTTTGTTTAAA
Found at i:5697 original size:12 final size:12
Alignment explanation
Indices: 5590--5706 Score: 71
Period size: 12 Copynumber: 9.9 Consensus size: 12
5580 TTTTTTACTG
*
5590 TTTTGGTTGGTA
1 TTTTGGTTGTTA
5602 TTTTGGTGCTGTTA
1 TTTTGGT--TGTTA
*
5616 TTTTTGTTGTTA
1 TTTTGGTTGTTA
* *
5628 TTTTTGTTGCTA
1 TTTTGGTTGTTA
*
5640 TTTTTGTTG-T-
1 TTTTGGTTGTTA
*
5650 TTTT-GTTGTTG
1 TTTTGGTTGTTA
**
5661 TTTT-ACTGTTA
1 TTTTGGTTGTTA
*** *
5672 TTTTTACTGCTA
1 TTTTGGTTGTTA
5684 TTTTGGTTGTTA
1 TTTTGGTTGTTA
*
5696 TTTTGTTTGTT
1 TTTTGGTTGTT
5707 TAAATGTTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
9 4 0.05
10 5 0.06
11 13 0.15
12 56 0.64
14 10 0.11
ACGTcount: A:0.08, C:0.04, G:0.21, T:0.68
Consensus pattern (12 bp):
TTTTGGTTGTTA
Found at i:5907 original size:39 final size:39
Alignment explanation
Indices: 5837--5920 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
5827 TATAAAGAAT
* * *
5837 TTTTAATTTATTTTAAATTTGTTTATTTTTTA-ATGTTTG
1 TTTTAATGTATTTTAAATTTATTTATATTTTATAT-TTTG
* *
5876 TTTTAATGT-TTTTAAGTTTATTTGATATTTTATATTTTT
1 TTTTAATGTATTTTAAATTTATTT-ATATTTTATATTTTG
5915 TTTTAA
1 TTTTAA
5921 ATTTGTTGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
38 12 0.32
39 24 0.63
40 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (39 bp):
TTTTAATGTATTTTAAATTTATTTATATTTTATATTTTG
Done.