Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002938.1 Kokia drynarioides strain JFW-HI SEQ_115384, 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: 4133
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Found at i:1558 original size:22 final size:23
Alignment explanation
Indices: 1502--1560 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
1492 ATTTTCAATG
1502 TTAATAAATTATAAAAAATACTAT
1 TTAAT-AATTATAAAAAATACTAT
* **
1526 TTTATTTTTATAATAAAA-A-TAT
1 TTAATAATTATAA-AAAATACTAT
1548 TTAATAATTATAA
1 TTAATAATTATAA
1561 CTATTCTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 13 0.46
23 7 0.25
24 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAATAATTATAAAAAATACTAT
Found at i:2047 original size:20 final size:19
Alignment explanation
Indices: 2005--2052 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1995 AAATTAGTGC
2005 TTTTAAAA-AATTACAAAA
1 TTTTAAAATAATTACAAAA
* *
2023 ATTTAAAATAATCTTCAAAA
1 TTTTAAAATAAT-TACAAAA
2043 TTTTAAAATA
1 TTTTAAAATA
2053 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 15 0.60
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAATAATTACAAAA
Found at i:2062 original size:20 final size:20
Alignment explanation
Indices: 2005--2062 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
1995 AAATTAGTGC
* *
2005 TTTTAAAA-AATTACAAAAA
1 TTTTAAAATATTTATAAAAA
* *
2024 -TTTAAAATAATCT-TCAAAA
1 TTTTAAAAT-ATTTATAAAAA
2043 TTTTAAAATATTTATAAAAA
1 TTTTAAAATATTTATAAAAA
2063 AAATTTTCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 15 0.52
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAATATTTATAAAAA
Found at i:3737 original size:23 final size:23
Alignment explanation
Indices: 3709--3776 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
3699 CCGTGAAGAA
3709 AAAGTTAAAAGCCATTTCTAAAG
1 AAAGTTAAAAGCCATTTCTAAAG
**
3732 AAAGTT----GCC-TTTC-AATCT
1 AAAGTTAAAAGCCATTTCTAA-AG
3750 AAA-TTAAAAGCCATTTCTAAAG
1 AAAGTTAAAAGCCATTTCTAAAG
3772 AAAGT
1 AAAGT
3777 CGCTTTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 16
0.62 0.08 0.30
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 3 0.09
21 3 0.09
22 7 0.21
23 9 0.27
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (23 bp):
AAAGTTAAAAGCCATTTCTAAAG
Found at i:3757 original size:40 final size:40
Alignment explanation
Indices: 3713--3796 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
3703 GAAGAAAAAG
*
3713 TTAAAAGCCATTTCTAAAGAAAGTTGCCTTTCAATCTAAA
1 TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
*
3753 TTAAAAGCCATTTCTAAAGAAAGTCGCTTTTCAATCTAAA
1 TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
3793 TTAA
1 TTAA
3797 CTGAAGAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (40 bp):
TTAAAAGCCATTTCTAAAGAAAGTCGCCTTTCAATCTAAA
Found at i:3948 original size:23 final size:23
Alignment explanation
Indices: 3922--3965 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3912 CTCAAAATAC
*
3922 AAACAGATCCAAACCTAAACCCT
1 AAACAGATCCAAACCCAAACCCT
*
3945 AAACAGATCTAAACCCAAACC
1 AAACAGATCCAAACCCAAACC
3966 AAGTCGGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.34, G:0.05, T:0.11
Consensus pattern (23 bp):
AAACAGATCCAAACCCAAACCCT
Done.