Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000497.1 Kokia drynarioides strain JFW-HI SEQ_111373, 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: 26072
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5162 original size:68 final size:67
Alignment explanation
Indices: 5088--5222 Score: 252
Period size: 68 Copynumber: 2.0 Consensus size: 67
5078 ATAGGAGGCT
*
5088 TGAATTGAATGATTCTTTTGGCAACGAGAAGATTGGGTGGCTGTTGTGGTTTGGGTTGGGAAGAT
1 TGAATTGAATGATTCTTTTGGCAACGAGAAGATTGGGTGGCTGTTGTGATTTGGGTTGGGAAGAT
5153 GA
66 GA
5155 NTGAATTGAATGATTCTTTTGGCAACGAGAAGATTGGGTGGCTGTTGTGATTTGGGTTGGGAAGA
1 -TGAATTGAATGATTCTTTTGGCAACGAGAAGATTGGGTGGCTGTTGTGATTTGGGTTGGGAAGA
5220 TGA
65 TGA
5223 GAGAAAAGAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.23, C:0.06, G:0.36, T:0.34
Consensus pattern (67 bp):
TGAATTGAATGATTCTTTTGGCAACGAGAAGATTGGGTGGCTGTTGTGATTTGGGTTGGGAAGAT
GA
Found at i:5615 original size:3 final size:3
Alignment explanation
Indices: 5607--5641 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5597 AAATTAAAAT
5607 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5642 TGATGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5708 original size:30 final size:32
Alignment explanation
Indices: 5674--5755 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 32
5664 ATTGGAAATT
5674 AAAATTATTTAATAATTTTATTAT-TTC-AAA
1 AAAATTATTTAATAATTTTATTATATTCTAAA
* *
5704 AAAATAATTTAA-AAATTT-TTATATTCTAAA
1 AAAATTATTTAATAATTTTATTATATTCTAAA
*
5734 AAAATGATTTTTAATAATTTTA
1 AAAAT--TATTTAATAATTTTA
5756 AAATCATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.10
29 8 0.20
30 19 0.46
32 5 0.12
33 5 0.12
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (32 bp):
AAAATTATTTAATAATTTTATTATATTCTAAA
Found at i:6428 original size:16 final size:17
Alignment explanation
Indices: 6407--6441 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6397 AAAAAGTAGA
*
6407 TTATTT-AATAATATTT
1 TTATTTCAAAAATATTT
6423 TTATTTCAAAAATATTT
1 TTATTTCAAAAATATTT
6440 TT
1 TT
6442 TTATCGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTTCAAAAATATTT
Found at i:9546 original size:20 final size:20
Alignment explanation
Indices: 9518--9555 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
9508 CTACATATCT
9518 AAATCAAATTATATAAAATTA
1 AAATCAAA-TATATAAAATTA
*
9539 AAAT-AAATATATTAAAT
1 AAATCAAATATATAAAAT
9556 ACACTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.56
20 3 0.19
21 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATCAAATATATAAAATTA
Found at i:9692 original size:2 final size:2
Alignment explanation
Indices: 9687--9716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9677 TTAAGTGTTA
9687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9717 GAAGGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10037 original size:19 final size:20
Alignment explanation
Indices: 10015--10062 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
10005 TTTATTGCTT
*
10015 ATATATTTTA-ATATTTAAA
1 ATATATTTTACATATTCAAA
*
10034 ATATAGTTTACATATTCAAA
1 ATATATTTTACATATTCAAA
*
10054 TTATATTTT
1 ATATATTTT
10063 TAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATTTTACATATTCAAA
Found at i:15782 original size:19 final size:19
Alignment explanation
Indices: 15739--15784 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
15729 TGGAAAAATA
*
15739 ATTTTTAAAAAATAAATTG
1 ATTTATAAAAAATAAATTG
* *
15758 ATTTTATAAAAAATAATTTT
1 A-TTTATAAAAAATAAATTG
15778 ATTTATA
1 ATTTATA
15785 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTATAAAAAATAAATTG
Found at i:16304 original size:34 final size:38
Alignment explanation
Indices: 16265--16342 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 38
16255 GTACTATAGA
*
16265 ATATTTATTATT-AAATGTT-TATAAA-TTGTAAT-AT
1 ATATTTATTATTCAAATATTATATAAATTTGTAATAAT
*
16299 ATATTTATTATTCAAATATTAATATAAATTTTTAATAAT
1 ATATTTATTATTCAAATATT-ATATAAATTTGTAATAAT
16338 ATATT
1 ATATT
16343 AATAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 12 0.32
35 6 0.16
37 6 0.16
38 6 0.16
39 7 0.19
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (38 bp):
ATATTTATTATTCAAATATTATATAAATTTGTAATAAT
Found at i:18150 original size:46 final size:47
Alignment explanation
Indices: 18067--18155 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 47
18057 ACTTCATATC
* * * *
18067 TTTCTATATTATTCTTGTCATCTCGGGTGACCTGACAACGATGACTT
1 TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATGACTT
* * *
18114 TTTCTAT-TTATACTTATCTTCCCGGGTGGCCCGACAATGATG
1 TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATG
18156 GTTACTCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
46 28 0.80
47 7 0.20
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (47 bp):
TTTCTATATTATACTTATCATCCCGGGTGACCCGACAACGATGACTT
Found at i:24420 original size:19 final size:18
Alignment explanation
Indices: 24381--24436 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
24371 AAATTAATAA
*
24381 TCAAAATAATTTTCAAAAAT
1 TCAAAA-AATTTT-TAAAAT
*
24401 TGAAAACAATTTTTAAAAT
1 TCAAAA-AATTTTTAAAAT
*
24420 TCAAAATATTTTTAAAA
1 TCAAAAAATTTTTAAAA
24437 ATTCTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
20 11 0.35
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (18 bp):
TCAAAAAATTTTTAAAAT
Found at i:24437 original size:19 final size:19
Alignment explanation
Indices: 24381--24445 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
24371 AAATTAATAA
*
24381 TCAAAATAATTTTCAAAAAT
1 TCAAAAT-ATTTTTAAAAAT
* *
24401 TGAAAACAATTTTT-AAAAT
1 TCAAAA-TATTTTTAAAAAT
24420 TCAAAATATTTTTAAAAAT
1 TCAAAATATTTTTAAAAAT
*
24439 TCTAAAT
1 TCAAAAT
24446 TTTGTATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 6 0.16
19 21 0.57
20 10 0.27
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATATTTTTAAAAAT
Done.