Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008455.1 Kokia drynarioides strain JFW-HI SEQ_123130, 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: 19202
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7047 original size:23 final size:23
Alignment explanation
Indices: 7017--7093 Score: 79
Period size: 24 Copynumber: 3.4 Consensus size: 23
7007 AAGGTGGAAG
*
7017 TTATGTGGTCATTAATGGCAAAA
1 TTATGTGGTCATTATTGGCAAAA
*
7040 TTATGTGG-CAATTTATTTGCAAAA
1 TTATGTGGTC-A-TTATTGGCAAAA
* *
7064 CTATGTGGCCATTATTGGC-AAA
1 TTATGTGGTCATTATTGGCAAAA
7086 -TATGTGGT
1 TTATGTGGT
7094 GGCTTGTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.15
22 4 0.09
23 16 0.35
24 18 0.39
25 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (23 bp):
TTATGTGGTCATTATTGGCAAAA
Found at i:7512 original size:18 final size:19
Alignment explanation
Indices: 7479--7514 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7469 ATTATTTTGG
7479 ATTTTGTGGATTTTACTTT
1 ATTTTGTGGATTTTACTTT
*
7498 ATTTTG-GGCTTTTACTT
1 ATTTTGTGGATTTTACTT
7515 CATAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.61
Consensus pattern (19 bp):
ATTTTGTGGATTTTACTTT
Found at i:16066 original size:17 final size:17
Alignment explanation
Indices: 16044--16088 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
16034 CCAATAAGTG
*
16044 ACCCAATAACCCTTAAT
1 ACCCAATAACCCTTAAA
16061 ACCCAATAACCCTTAAA
1 ACCCAATAACCCTTAAA
16078 ACCCAA-AACCC
1 ACCCAATAACCC
16089 AAATCAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (17 bp):
ACCCAATAACCCTTAAA
Found at i:16186 original size:29 final size:29
Alignment explanation
Indices: 16139--16208 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
16129 ATTCAGGTTT
* * * *
16139 GACCGTTGATCGACCGTTGATCATTGATC
1 GACCATTGACCGACCGTTGACCATTGACC
*
16168 GACTATTGACCGACCGTTGACCATTGACC
1 GACCATTGACCGACCGTTGACCATTGACC
*
16197 GACCGTTGACCG
1 GACCATTGACCG
16209 TTGATCGATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (29 bp):
GACCATTGACCGACCGTTGACCATTGACC
Found at i:16193 original size:18 final size:18
Alignment explanation
Indices: 16172--16212 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
16162 TTGATCGACT
16172 ATTGACCGACCGTTGACC
1 ATTGACCGACCGTTGACC
16190 ATTGACCGACCGTTGACC
1 ATTGACCGACCGTTGACC
*
16208 GTTGA
1 ATTGA
16213 TCGATAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (18 bp):
ATTGACCGACCGTTGACC
Found at i:17446 original size:6 final size:6
Alignment explanation
Indices: 17426--17455 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
17416 AATTATAGAC
17426 TTTATA TTATATA TTTATA TTTATA TTTAT
1 TTTATA TT-TATA TTTATA TTTATA TTTAT
17456 GAATGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:17452 original size:12 final size:13
Alignment explanation
Indices: 17413--17455 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
17403 GTTATTTTAT
*
17413 TTTA-ATTATAGA
1 TTTATATTATATA
17425 CTTTATATTATATA
1 -TTTATATTATATA
17439 TTTATATT-TATA
1 TTTATATTATATA
17451 TTTAT
1 TTTAT
17456 GAATGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 12 0.43
14 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:18543 original size:18 final size:18
Alignment explanation
Indices: 18520--18568 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
18510 CCCACAACTC
18520 ATTGTACTTTTTGGTTAA
1 ATTGTACTTTTTGGTTAA
**
18538 ATTGTACTTTTTCTTTAA
1 ATTGTACTTTTTGGTTAA
18556 ATTGTACTTTTTG
1 ATTGTACTTTTTG
18569 TCCTTCCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.59
Consensus pattern (18 bp):
ATTGTACTTTTTGGTTAA
Done.