Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007634.1 Kokia drynarioides strain JFW-HI SEQ_122265, 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: 2329
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Found at i:1923 original size:26 final size:26
Alignment explanation
Indices: 1879--1948 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
1869 TTTATAAATA
* *
1879 TTAATTTTT-GTTGATTTTGATTAAT
1 TTAATTTTTAATTAATTTTGATTAAT
* *
1904 TTAATTATTTAATT-ATTTTGTTTATT
1 TTAATT-TTTAATTAATTTTGATTAAT
*
1930 TTAATTTTTGATTAATTTT
1 TTAATTTTTAATTAATTTT
1949 TTATTAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 12 0.32
26 24 0.63
27 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (26 bp):
TTAATTTTTAATTAATTTTGATTAAT
Found at i:2037 original size:30 final size:31
Alignment explanation
Indices: 2001--2070 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
1991 TTATCTTTTA
* *
2001 TTTTTTTTGATTGT-TATGTTTATTTTTATG
1 TTTTTTTTGATTATGTAGGTTTATTTTTATG
*
2031 TTTTTTTTG-TTATGTAGGTTTTTTTTTATG
1 TTTTTTTTGATTATGTAGGTTTATTTTTATG
*
2061 TTTTGTTTGA
1 TTTTTTTTGA
2071 AATGTATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.73
Consensus pattern (31 bp):
TTTTTTTTGATTATGTAGGTTTATTTTTATG
Found at i:2041 original size:26 final size:28
Alignment explanation
Indices: 1990--2045 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1980 GTTTAAAGAT
*
1990 TTTATCTTTTATTTTTTTTGATTGTTATG
1 TTTATCTTTTATGTTTTTT-ATTGTTATG
2019 TTTAT-TTTTATGTTTTTT-TTGTTATG
1 TTTATCTTTTATGTTTTTTATTGTTATG
2045 T
1 T
2046 AGGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.35
28 12 0.46
29 5 0.19
ACGTcount: A:0.12, C:0.02, G:0.11, T:0.75
Consensus pattern (28 bp):
TTTATCTTTTATGTTTTTTATTGTTATG
Found at i:2045 original size:14 final size:14
Alignment explanation
Indices: 2011--2099 Score: 67
Period size: 13 Copynumber: 6.0 Consensus size: 14
2001 TTTTTTTTGA
*
2011 TTGTTATG-TTTAT
1 TTGTTATGTTTTTT
2024 TT-TTATGTTTTTT
1 TTGTTATGTTTTTT
2037 TTGTTATGTAGGTTTTT
1 TTGTTATGT---TTTTT
*
2054 TT-TTATGTTTTGT
1 TTGTTATGTTTTTT
2067 TTGAAATGTATGTTTTTT
1 TTG---T-TATGTTTTTT
2085 ATTGTTATGTTTTTT
1 -TTGTTATGTTTTTT
2100 AATATGCATA
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
12 5 0.08
13 14 0.23
14 6 0.10
15 10 0.16
16 7 0.11
17 8 0.13
18 9 0.15
19 3 0.05
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (14 bp):
TTGTTATGTTTTTT
Found at i:2052 original size:26 final size:27
Alignment explanation
Indices: 1996--2053 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
1986 AGATTTTATC
* **
1996 TTTTATTTTTTTTGATTGTTATGTTTAT
1 TTTTATGTTTTTT-ATTGTTATGTAGAT
*
2024 TTTTATGTTTTTT-TTGTTATGTAGGT
1 TTTTATGTTTTTTATTGTTATGTAGAT
2050 TTTT
1 TTTT
2054 TTTTATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.12, C:0.00, G:0.14, T:0.74
Consensus pattern (27 bp):
TTTTATGTTTTTTATTGTTATGTAGAT
Found at i:2076 original size:30 final size:30
Alignment explanation
Indices: 2018--2084 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2008 TGATTGTTAT
* * **
2018 GTTTATTTTTATGTTTTTTTTGTTATGTAG
1 GTTTTTTTTTATGTTTTGTTTGAAATGTAG
*
2048 GTTTTTTTTTATGTTTTGTTTGAAATGTAT
1 GTTTTTTTTTATGTTTTGTTTGAAATGTAG
2078 GTTTTTT
1 GTTTTTT
2085 ATTGTTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.70
Consensus pattern (30 bp):
GTTTTTTTTTATGTTTTGTTTGAAATGTAG
Done.