Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008456.1 Kokia drynarioides strain JFW-HI SEQ_123131, 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: 19201
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:16065 original size:17 final size:17
Alignment explanation
Indices: 16043--16087 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
16033 CCAATAAGTG
*
16043 ACCCAATAACCCTTAAT
1 ACCCAATAACCCTTAAA
16060 ACCCAATAACCCTTAAA
1 ACCCAATAACCCTTAAA
16077 ACCCAA-AACCC
1 ACCCAATAACCC
16088 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:16185 original size:29 final size:29
Alignment explanation
Indices: 16138--16207 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
16128 ATTCAGGTTT
* * * *
16138 GACCGTTGATCGACCGTTGATCATTGATC
1 GACCATTGACCGACCGTTGACCATTGACC
*
16167 GACTATTGACCGACCGTTGACCATTGACC
1 GACCATTGACCGACCGTTGACCATTGACC
*
16196 GACCGTTGACCG
1 GACCATTGACCG
16208 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:16192 original size:18 final size:18
Alignment explanation
Indices: 16171--16211 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
16161 TTGATCGACT
16171 ATTGACCGACCGTTGACC
1 ATTGACCGACCGTTGACC
16189 ATTGACCGACCGTTGACC
1 ATTGACCGACCGTTGACC
*
16207 GTTGA
1 ATTGA
16212 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:17445 original size:6 final size:6
Alignment explanation
Indices: 17425--17454 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
17415 AATTATAGAC
17425 TTTATA TTATATA TTTATA TTTATA TTTAT
1 TTTATA TT-TATA TTTATA TTTATA TTTAT
17455 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:17451 original size:12 final size:13
Alignment explanation
Indices: 17412--17454 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
17402 GTTATTTTAT
*
17412 TTTA-ATTATAGA
1 TTTATATTATATA
17424 CTTTATATTATATA
1 -TTTATATTATATA
17438 TTTATATT-TATA
1 TTTATATTATATA
17450 TTTAT
1 TTTAT
17455 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:18542 original size:18 final size:18
Alignment explanation
Indices: 18519--18567 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
18509 CCCACAACTC
18519 ATTGTACTTTTTGGTTAA
1 ATTGTACTTTTTGGTTAA
**
18537 ATTGTACTTTTTCTTTAA
1 ATTGTACTTTTTGGTTAA
18555 ATTGTACTTTTTG
1 ATTGTACTTTTTG
18568 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.