Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001291.1 Kokia drynarioides strain JFW-HI SEQ_112686, 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: 18120
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11150 original size:14 final size:14
Alignment explanation
Indices: 11133--11180 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
11123 ATTAAATATT
*
11133 TTTTATTATATTTA
1 TTTTATTATAATTA
*
11147 TTTTAATATAATTA
1 TTTTATTATAATTA
*
11161 TTCTTATTTTTAATTA
1 TT-TTA-TTATAATTA
11177 TTTT
1 TTTT
11181 TTAATTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 14 0.50
15 5 0.18
16 9 0.32
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTATAATTA
Found at i:15786 original size:18 final size:18
Alignment explanation
Indices: 15756--15812 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
15746 TTAATAATGC
15756 TTTTAT-CTCAAAAGTGTT
1 TTTTATCCT-AAAAGTGTT
* *
15774 TTTTGTCCTAAAAGTGCT
1 TTTTATCCTAAAAGTGTT
15792 TTTTATCCTAAAAGTGCTT
1 TTTTATCCTAAAAGTG-TT
15811 TT
1 TT
15813 GAGAAGCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (18 bp):
TTTTATCCTAAAAGTGTT
Found at i:15794 original size:17 final size:18
Alignment explanation
Indices: 15765--15812 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
15755 CTTTTATCTC
*
15765 AAAAGTGTTTTTTGTCCT
1 AAAAGTGCTTTTTGTCCT
*
15783 AAAAGTGCTTTTTATCCT
1 AAAAGTGCTTTTTGTCCT
15801 AAAAGTGCTTTT
1 AAAAGTGCTTTT
15813 GAGAAGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (18 bp):
AAAAGTGCTTTTTGTCCT
Found at i:16712 original size:14 final size:15
Alignment explanation
Indices: 16683--16716 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
16673 TAAATAATTT
16683 TTTTATTTTTTAAAA
1 TTTTATTTTTTAAAA
*
16698 TTTTA-TTTTTGAAA
1 TTTTATTTTTTAAAA
16712 TTTTA
1 TTTTA
16717 AGAATTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:17026 original size:11 final size:11
Alignment explanation
Indices: 17012--17103 Score: 62
Period size: 11 Copynumber: 8.1 Consensus size: 11
17002 AACTAAACCC
17012 ATTTTAAATTT
1 ATTTTAAATTT
*
17023 ATTTTAAGATTA
1 ATTTTAA-ATTT
* **
17035 AATTT-GTTTT
1 ATTTTAAATTT
*
17045 AAATTTAAATTT
1 -ATTTTAAATTT
17057 ATTTTAAATTT
1 ATTTTAAATTT
*
17068 AAATTT-AATTT
1 -ATTTTAAATTT
*
17079 AAGTTTAAATTT
1 -ATTTTAAATTT
17091 ATTTTTAAATTT
1 A-TTTTAAATTT
17103 A
1 A
17104 AAATTATTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.03
11 33 0.52
12 29 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:17037 original size:17 final size:17
Alignment explanation
Indices: 17014--17123 Score: 150
Period size: 17 Copynumber: 6.4 Consensus size: 17
17004 CTAAACCCAT
17014 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
17032 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
17048 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
17065 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
17082 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
17100 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
17117 TTTAAAT
1 TTTAAAT
17124 ACATAAAAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
16 1 0.01
17 66 0.81
18 14 0.17
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:17051 original size:6 final size:6
Alignment explanation
Indices: 17042--17123 Score: 82
Period size: 6 Copynumber: 14.2 Consensus size: 6
17032 TTAAATTTGT
* *
17042 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
17088 TTTATT TTTAAA TTTAAA ATT--A TTATAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
17124 ACATAAAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
4 2 0.03
5 10 0.16
6 46 0.75
7 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:17068 original size:23 final size:23
Alignment explanation
Indices: 17042--17103 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
17032 TTAAATTTGT
*
17042 TTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAAATTTAGTTTAAA
17065 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
**
17088 TTTATTTTTAAATTTA
1 TTTAAATTTAAATTTA
17104 AAATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.15
23 24 0.71
24 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:17862 original size:12 final size:12
Alignment explanation
Indices: 17845--17885 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
17835 TTAATAAATA
17845 ATAATAATTATT
1 ATAATAATTATT
17857 ATAATAA-TATT
1 ATAATAATTATT
17868 ATTAATAATT-TT
1 A-TAATAATTATT
17880 -TAATAA
1 ATAATAA
17886 AAGAAAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.22
11 5 0.19
12 15 0.56
13 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:17862 original size:15 final size:15
Alignment explanation
Indices: 17841--17876 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
17831 GCTTTTAATA
17841 AATAATAATAATTATT
1 AATAATAAT-ATTATT
17857 -ATAATAATATTATT
1 AATAATAATATTATT
17871 AATAAT
1 AATAAT
17877 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAATAATATTATT
Done.