Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008571.1 Kokia drynarioides strain JFW-HI SEQ_123249, 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: 47913
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:2614 original size:7 final size:7
Alignment explanation
Indices: 2602--2630 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2592 TTCAAATCCA
2602 CCACTGC
1 CCACTGC
2609 CCACTGC
1 CCACTGC
2616 CCACTGC
1 CCACTGC
2623 CCACTGC
1 CCACTGC
2630 C
1 C
2631 AAACAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.59, G:0.14, T:0.14
Consensus pattern (7 bp):
CCACTGC
Found at i:11422 original size:87 final size:86
Alignment explanation
Indices: 11273--11489 Score: 234
Period size: 87 Copynumber: 2.5 Consensus size: 86
11263 TTAAGGGTGT
*
11273 AAAAGGCACTCAAACTTTCTCAAAAAAAGCAATTAAGCCCCTCTTTTTTTACACTTATTTGGGTA
1 AAAAGGCACTCAAACTTTCTCAAAAAAAGCAATTAAGCCCCTCTTTTTTTACACTTAATTGGGTA
11338 CTTGAACTTTCAAAATGCATCA
66 CTTGAACTTTCAAAATGCAT-A
* * * * *
11360 AAAGGGCCCTCAAACCTTT-TCAAAAAAAATCAATTAAG-CCCTTTTTTTTTTCA-TTCAATTGG
1 AAAAGGCACTCAAA-CTTTCTC-AAAAAAAGCAATTAAGCCCCTCTTTTTTTACACTT-AATTGG
*
11422 GTACTTGAACTTTTAAAATGCATAA
63 GTACTTGAACTTTCAAAATGCAT-A
** *
11447 AAAAATC-CTCAAAC--T-T-AAAAAAAACAATTAAGCCCCTACTTTT
1 AAAAGGCACTCAAACTTTCTCAAAAAAAGCAATTAAGCCCCT-CTTTT
11490 ATTAAAAAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
81 15 0.13
82 4 0.04
83 6 0.05
85 1 0.01
86 8 0.07
87 59 0.53
88 19 0.17
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (86 bp):
AAAAGGCACTCAAACTTTCTCAAAAAAAGCAATTAAGCCCCTCTTTTTTTACACTTAATTGGGTA
CTTGAACTTTCAAAATGCATA
Found at i:11638 original size:8 final size:8
Alignment explanation
Indices: 11627--11665 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
11617 AAAATCGTAA
11627 AAAATTAT
1 AAAATTAT
11635 AAAATATAT
1 AAAAT-TAT
* *
11644 AAAAATAA
1 AAAATTAT
11652 AAAATTAT
1 AAAATTAT
11660 AAAATT
1 AAAATT
11666 TTATAAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAATTAT
Found at i:11656 original size:54 final size:56
Alignment explanation
Indices: 11594--11720 Score: 163
Period size: 54 Copynumber: 2.3 Consensus size: 56
11584 CATAACAAAT
11594 ATAAAAAATTGTAAAATTTCATAAAAATCGT-AAAAAATTAT--AAAATATATAA-AA
1 ATAAAAAATTGTAAAATTTCAT-AAAATCGTAAAAAAATTATACAAAATATA-AATAA
* * *
11648 ATAAAAAATTATAAAATTTTATAAAGTCGTAAAAAAATTATACAAAATATAAATAA
1 ATAAAAAATTGTAAAATTTCATAAAATCGTAAAAAAATTATACAAAATATAAATAA
*
11704 ATATAAAATTCGTAAAA
1 ATAAAAAATT-GTAAAA
11721 AAAATTTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
53 7 0.11
54 30 0.48
55 2 0.03
56 19 0.30
57 5 0.08
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (56 bp):
ATAAAAAATTGTAAAATTTCATAAAATCGTAAAAAAATTATACAAAATATAAATAA
Found at i:11733 original size:9 final size:9
Alignment explanation
Indices: 11549--11739 Score: 63
Period size: 10 Copynumber: 20.1 Consensus size: 9
11539 AATTTTAATA
11549 AAAAATTATT
1 AAAAATTA-T
*
11559 AAAAATTAGA
1 AAAAATTA-T
**
11569 AAAAAAAAT
1 AAAAATTAT
**
11578 AAAAACCAT
1 AAAAATTAT
11587 AACAAA-TAT
1 AA-AAATTAT
*
11596 AAAAAATTGT
1 -AAAAATTAT
*
11606 AAAATTTCAT
1 AAAAATT-AT
11616 AAAAATCGTA-
1 AAAAAT--TAT
11626 AAAAATTAT
1 AAAAATTAT
11635 -AAAATATAT
1 AAAAAT-TAT
11644 AAAAA-TA-
1 AAAAATTAT
11651 AAAAATTAT
1 AAAAATTAT
*
11660 -AAAATTTT
1 AAAAATTAT
* *
11668 ATAAAGTCGTAA
1 A-AAAAT--TAT
11680 AAAAATTAT
1 AAAAATTAT
11689 ACAAAA-TAT
1 A-AAAATTAT
*
11698 AAATAAATAT
1 AAA-AATTAT
* *
11708 AAAATTCGTAAA
1 AAAAAT--T-AT
11720 AAAAATTTAT
1 AAAAA-TTAT
11730 AAAAATTAT
1 AAAAATTAT
11739 A
1 A
11740 GTACCAAAAG
Statistics
Matches: 136, Mismatches: 23, Indels: 45
0.67 0.11 0.22
Matches are distributed among these distances:
7 5 0.04
8 20 0.15
9 38 0.28
10 57 0.42
11 7 0.05
12 8 0.06
13 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:13030 original size:30 final size:30
Alignment explanation
Indices: 12968--13030 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
12958 TAGCCTATAT
* * *
12968 TTTTATAATTTTTAAAAGATTACATTAAAA
1 TTTTATAATTTTTAAAAGATCAAAGTAAAA
* * *
12998 TTTTATCATTTTTAAGAGATCAAAGTACAA
1 TTTTATAATTTTTAAAAGATCAAAGTAAAA
13028 TTT
1 TTT
13031 AACATTTACT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAGATCAAAGTAAAA
Found at i:18630 original size:18 final size:18
Alignment explanation
Indices: 18607--18649 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
18597 TGTAATATTA
18607 TAAAAATTAAAAGTTAAT
1 TAAAAATTAAAAGTTAAT
* *
18625 TAAAAAGTAAAATTTAAT
1 TAAAAATTAAAAGTTAAT
*
18643 TTAAAAT
1 TAAAAAT
18650 AATATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TAAAAATTAAAAGTTAAT
Found at i:36184 original size:15 final size:16
Alignment explanation
Indices: 36157--36186 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36147 ATTAAAATTG
36157 AATAAATATATATAAT
1 AATAAATATATATAAT
36173 AATAAA-ATATATAA
1 AATAAATATATATAA
36187 AAATTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATATATATAAT
Found at i:36972 original size:23 final size:23
Alignment explanation
Indices: 36956--37077 Score: 115
Period size: 23 Copynumber: 5.4 Consensus size: 23
36946 AATGAATAGA
*
36956 GAAGATTCTCTGTAATGAACAAT
1 GAAGATTCTCTGCAATGAACAAT
*
36979 GAATATTCTCTGCAATGAACAAT
1 GAAGATTCTCTGCAATGAACAAT
* * *
37002 --A-ATTATTTGCAATGAACAGT
1 GAAGATTCTCTGCAATGAACAAT
* * *
37022 GAAGATTTTCTACAATGAACAGT
1 GAAGATTCTCTGCAATGAACAAT
* * * *
37045 GAAGATTCCCTGCAATTAATAGT
1 GAAGATTCTCTGCAATGAACAAT
37068 GAAGATTCTC
1 GAAGATTCTC
37078 AAAATTTAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.20
21 1 0.01
22 1 0.01
23 64 0.78
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (23 bp):
GAAGATTCTCTGCAATGAACAAT
Found at i:41818 original size:16 final size:16
Alignment explanation
Indices: 41797--41829 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41787 TTTTGTCAGC
*
41797 AAAATATTCAAATATT
1 AAAATATTCAAAGATT
41813 AAAATATTCAAAGATT
1 AAAATATTCAAAGATT
41829 A
1 A
41830 TGGTCATCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATATTCAAAGATT
Done.