Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004424.1 Kokia drynarioides strain JFW-HI SEQ_117810, 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: 41451
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1690 original size:20 final size:20
Alignment explanation
Indices: 1665--1734 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1655 AACCTTACAG
* *
1665 GTATCGGTAGAATGTAAGTT
1 GTATCGGTAGAACGCAAGTT
1685 GTATCGGTAGAACGCAAGTT
1 GTATCGGTAGAACGCAAGTT
1705 GTATCGGTAGAACGCAAGTT
1 GTATCGGTAGAACGCAAGTT
1725 GTATCGGTAG
1 GTATCGGTAG
1735 TCTTGACCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (20 bp):
GTATCGGTAGAACGCAAGTT
Found at i:5946 original size:18 final size:18
Alignment explanation
Indices: 5925--5971 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
5915 AATTATAAAA
5925 AAAATTAAAATGATTTTT
1 AAAATTAAAATGATTTTT
* *
5943 AAAATTTTAAATTATTTTT
1 AAAA-TTAAAATGATTTTT
*
5962 AAAAATAAAA
1 AAAATTAAAA
5972 ATATTTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATTAAAATGATTTTT
Found at i:5976 original size:18 final size:18
Alignment explanation
Indices: 5924--5984 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
5914 AAATTATAAA
5924 AAAAATTAAAATGATTTTT
1 AAAAATTAAAAT-ATTTTT
* *
5943 AAAATTTTAAATTATTTTT
1 AAAA-ATTAAAATATTTTT
* *
5962 AAAAATAAAAATATTTAT
1 AAAAATTAAAATATTTTT
5980 AAAAA
1 AAAAA
5985 ATTCAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 15 0.43
19 14 0.40
20 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAATATTTTT
Found at i:21147 original size:20 final size:20
Alignment explanation
Indices: 21099--21144 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
21089 AATTCACAAA
*
21099 TTTTAATAATTATTTGCAACT
1 TTTTAATAATT-TTTCCAACT
21120 TTTTAATAATTTTTCCAA-T
1 TTTTAATAATTTTTCCAACT
21139 TTTTAA
1 TTTTAA
21145 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 6 0.25
21 11 0.46
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTAATAATTTTTCCAACT
Found at i:28073 original size:6 final size:6
Alignment explanation
Indices: 28064--28089 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28054 AGAAGAAGAA
28064 GACGGC GACGGC GACGGC GACGGC GA
1 GACGGC GACGGC GACGGC GACGGC GA
28090 TGATGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.50, T:0.00
Consensus pattern (6 bp):
GACGGC
Found at i:29887 original size:22 final size:22
Alignment explanation
Indices: 29807--29887 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 22
29797 AATTGCTTAA
*
29807 AAAATATT-TAAAATTTATTATT
1 AAAATATTATAATA-TTATTATT
* * * * **
29829 CATATATTAAAATATTAATAAC
1 AAAATATTATAATATTATTATT
* * *
29851 AAATTATTTTTATATTATTATT
1 AAAATATTATAATATTATTATT
29873 AAAATATTATAATAT
1 AAAATATTATAATAT
29888 CAACTAATTT
Statistics
Matches: 39, Mismatches: 19, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
22 36 0.92
23 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATTATAATATTATTATT
Found at i:30033 original size:13 final size:13
Alignment explanation
Indices: 30012--30060 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
30002 TACACCAATC
30012 TTTTCAAAAGTA-T
1 TTTTCAAAA-TACT
*
30025 TTTTTAAAATTACT
1 TTTTCAAAA-TACT
30039 TTTTCAAAATACT
1 TTTTCAAAATACT
*
30052 TTTTTAAAA
1 TTTTCAAAA
30061 AAACTTCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTTCAAAATACT
Found at i:30041 original size:14 final size:13
Alignment explanation
Indices: 30024--30060 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
30014 TTCAAAAGTA
30024 TTTTTTAAAATTAC
1 TTTTTTAAAA-TAC
*
30038 TTTTTCAAAATAC
1 TTTTTTAAAATAC
30051 TTTTTTAAAA
1 TTTTTTAAAA
30061 AAACTTCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTTTAAAATAC
Found at i:30061 original size:14 final size:14
Alignment explanation
Indices: 30024--30066 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
30014 TTCAAAAGTA
*
30024 TTTTTTAAAATTAC
1 TTTTTTAAAAATAC
*
30038 -TTTTTCAAAATAC
1 TTTTTTAAAAATAC
*
30051 TTTTTTAAAAAAAC
1 TTTTTTAAAAATAC
30065 TT
1 TT
30067 CTCAAAAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTTTAAAAATAC
Found at i:30066 original size:27 final size:27
Alignment explanation
Indices: 30012--30074 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
30002 TACACCAATC
**
30012 TTTTCAAAAGTATTTTTTAAAATTACT
1 TTTTCAAAAGTATTTTTTAAAAAAACT
30039 TTTTCAAAA-TACTTTTTTAAAAAAAC-
1 TTTTCAAAAGTA-TTTTTTAAAAAAACT
*
30065 TTCTCAAAAG
1 TTTTCAAAAG
30075 CAATGCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (27 bp):
TTTTCAAAAGTATTTTTTAAAAAAACT
Found at i:33558 original size:5 final size:5
Alignment explanation
Indices: 33548--33580 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
33538 TAAGACCCTG
*
33548 TTTGC TTTGC TTTGC TTTGC TTCGC TTTGC TTT
1 TTTGC TTTGC TTTGC TTTGC TTTGC TTTGC TTT
33581 ACATTTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.18, T:0.61
Consensus pattern (5 bp):
TTTGC
Found at i:34822 original size:21 final size:20
Alignment explanation
Indices: 34798--34837 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34788 AAAATTTTAA
*
34798 AAATCATATTTTTTATAAAGT
1 AAATCATA-TTATTATAAAGT
*
34819 AAATTATATTATTATAAAG
1 AAATCATATTATTATAAAG
34838 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATCATATTATTATAAAGT
Done.