Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015112.1 Kokia drynarioides strain JFW-HI SEQ_130156, 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: 54462
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:977 original size:3 final size:3
Alignment explanation
Indices: 969--1018 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
959 TTTATCATAC
969 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1017 AT
1 AT
1019 AATAATAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1626 original size:5 final size:5
Alignment explanation
Indices: 1616--1671 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
1606 GTAGAACATT
* * ** * *
1616 ATATG ATATG ATCTG ATATG ATGTG ATATG ATATG ATCCG ATACG TTATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1666 ATATG A
1 ATATG A
1672 ATAGTTATGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (5 bp):
ATATG
Found at i:4576 original size:18 final size:18
Alignment explanation
Indices: 4553--4598 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4543 TCTTTCCCCC
*
4553 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
4571 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
4589 TGCTTT-ATTT
1 TTCTTTCATTT
4599 TTATGCGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.72
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:12770 original size:20 final size:20
Alignment explanation
Indices: 12747--12784 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12737 TTTTATATAA
12747 AAAC-ATAATATACAATATCC
1 AAACAATAATA-ACAATATCC
12767 AAACAATAATAACAATAT
1 AAACAATAATAACAATAT
12785 AATTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACAATAATAACAATATCC
Found at i:16263 original size:7 final size:7
Alignment explanation
Indices: 16251--16282 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
16241 TAGGTCCAAT
16251 GAAACAG
1 GAAACAG
16258 GAAACAG
1 GAAACAG
16265 GAAACAG
1 GAAACAG
16272 GAAACAG
1 GAAACAG
16279 GAAA
1 GAAA
16283 ACCCATGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.28, T:0.00
Consensus pattern (7 bp):
GAAACAG
Found at i:16491 original size:19 final size:20
Alignment explanation
Indices: 16448--16491 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16438 AAGAATGTTA
16448 ATAAAATGTTAGGTATTTTG
1 ATAAAATGTTAGGTATTTTG
*
16468 GTAAAATGTTA-G-ATGTTTG
1 ATAAAATGTTAGGTAT-TTTG
16487 ATAAA
1 ATAAA
16492 TCTATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (20 bp):
ATAAAATGTTAGGTATTTTG
Found at i:16509 original size:20 final size:20
Alignment explanation
Indices: 16484--16526 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
16474 TGTTAGATGT
*
16484 TTGATAAATCT-ATATAAATA
1 TTGATAAAT-TGATAGAAATA
16504 TTGATAAATTGATAGAAATA
1 TTGATAAATTGATAGAAATA
16524 TTG
1 TTG
16527 GTAAGTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TTGATAAATTGATAGAAATA
Found at i:16891 original size:16 final size:17
Alignment explanation
Indices: 16862--16894 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16852 TGATTATGAT
*
16862 TGATATAATTTATTATA
1 TGATATAATATATTATA
16879 TGATA-AATATATTATA
1 TGATATAATATATTATA
16895 ATATTTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TGATATAATATATTATA
Found at i:23789 original size:17 final size:20
Alignment explanation
Indices: 23767--23804 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
23757 AGACTCTCTC
23767 ATTTTC-TC-TCCTTT-TTT
1 ATTTTCTTCTTCCTTTGTTT
23784 ATTTTCTTCTTCCTTTGTTT
1 ATTTTCTTCTTCCTTTGTTT
23804 A
1 A
23805 AGCTTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 6 0.33
20 4 0.22
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTTCTTCTTCCTTTGTTT
Found at i:48573 original size:59 final size:59
Alignment explanation
Indices: 48472--48601 Score: 242
Period size: 59 Copynumber: 2.2 Consensus size: 59
48462 AATAAAGTCA
48472 TAAAGAGAGCTAGTAGACACCTCTAATCTCATATAGAGTTATTTTTGGGGTGTTAGAGAGG
1 TAAAG-GA-CTAGTAGACACCTCTAATCTCATATAGAGTTATTTTTGGGGTGTTAGAGAGG
48533 TAAAGGACTAGTAGACACCTCTAATCTCATATAGAGTTATTTTTGGGGTGTTAGAGAGG
1 TAAAGGACTAGTAGACACCTCTAATCTCATATAGAGTTATTTTTGGGGTGTTAGAGAGG
48592 TAAAGGACTA
1 TAAAGGACTA
48602 AATTGAGAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 62 0.90
60 2 0.03
61 5 0.07
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (59 bp):
TAAAGGACTAGTAGACACCTCTAATCTCATATAGAGTTATTTTTGGGGTGTTAGAGAGG
Found at i:49705 original size:24 final size:26
Alignment explanation
Indices: 49678--49725 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
49668 AGAGAAATGT
49678 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
49702 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
49726 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:51805 original size:19 final size:20
Alignment explanation
Indices: 51776--51830 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
51766 TCAATAGATG
*
51776 TTTACTTGAATAATTAT-TTA
1 TTTA-TTGAATAATTATACTA
51796 TTTATTGAATAATTATGACTA
1 TTTATTGAATAATTAT-ACTA
51817 TTTATT-AATAATTA
1 TTTATTGAATAATTA
51831 ACTGAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.38
20 12 0.38
21 8 0.25
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTATTGAATAATTATACTA
Done.