Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014605.1 Kokia drynarioides strain JFW-HI SEQ_129644, 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: 29624
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:619 original size:42 final size:41
Alignment explanation
Indices: 558--665 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 41
548 TTCTCGAATG
* * * * *
558 AAAAAATTGCAAATTTTTTTGTTGACACTCTATTTTTTACAT
1 AAAAAATTTCAAA-ATTTTTGTTGACACCCCATTTTTCACAT
*** *
600 AAAAAAATTTCAAAATTTTTGCCAACACCCCCTTTTTCACAT
1 -AAAAAATTTCAAAATTTTTGTTGACACCCCATTTTTCACAT
*
642 AAAAAATTTTAAAATTTTT-TTGAC
1 AAAAAATTTCAAAATTTTTGTTGAC
666 GTTGGCCATG
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
40 2 0.04
41 18 0.35
42 20 0.38
43 12 0.23
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.42
Consensus pattern (41 bp):
AAAAAATTTCAAAATTTTTGTTGACACCCCATTTTTCACAT
Found at i:9103 original size:48 final size:47
Alignment explanation
Indices: 9032--9125 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
9022 AAACAGCGCG
9032 TGAGTTTTTTTTATTTAAAAAAAAAAAAATGTAAAAGCTCCCCCATT
1 TGAGTTTTTTTTATTTAAAAAAAAAAAAATGTAAAAGCTCCCCCATT
9079 NTGAG-TTTTTTTATTTAAAAAAAAAAAAATGTAAAAGCTCCCCCATT
1 -TGAGTTTTTTTTATTTAAAAAAAAAAAAATGTAAAAGCTCCCCCATT
9126 GGGTGTGGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 42 0.91
48 4 0.09
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (47 bp):
TGAGTTTTTTTTATTTAAAAAAAAAAAAATGTAAAAGCTCCCCCATT
Found at i:20722 original size:19 final size:19
Alignment explanation
Indices: 20698--20763 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
20688 TAAGTCTAAT
20698 TGTTAATTTAAGTATTAAA
1 TGTTAATTTAAGTATTAAA
* *
20717 TGTTAATTCAA--ATTCAA
1 TGTTAATTTAAGTATTAAA
*
20734 -GTGGAATTTAAGTATTAAA
1 TGT-TAATTTAAGTATTAAA
20753 TGTTAATTTAA
1 TGTTAATTTAA
20764 ATTTAATTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 11 0.30
19 22 0.59
20 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (19 bp):
TGTTAATTTAAGTATTAAA
Found at i:20749 original size:36 final size:36
Alignment explanation
Indices: 20702--20779 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
20692 TCTAATTGTT
20702 AATTTAAGTATTAAATGTTAATTCAAATTCAAGTGG
1 AATTTAAGTATTAAATGTTAATTCAAATTCAAGTGG
* * *
20738 AATTTAAGTATTAAATGTTAATTTAAATTTAATTGG
1 AATTTAAGTATTAAATGTTAATTCAAATTCAAGTGG
20774 AATTTA
1 AATTTA
20780 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.44
Consensus pattern (36 bp):
AATTTAAGTATTAAATGTTAATTCAAATTCAAGTGG
Found at i:21003 original size:20 final size:20
Alignment explanation
Indices: 20978--21024 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20968 AATAATTATT
20978 ATAATTTT-ATATATTTCTTA
1 ATAATTTTAAT-TATTTCTTA
*
20998 ATAATTTTAATTATTTTTTA
1 ATAATTTTAATTATTTCTTA
*
21018 AAAATTT
1 ATAATTT
21025 AGAAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATAATTTTAATTATTTCTTA
Found at i:22186 original size:13 final size:13
Alignment explanation
Indices: 22139--22186 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
22129 CAAATCATAT
22139 CTCCATATTATTC
1 CTCCATATTATTC
* *
22152 CTCCACTACTATTT
1 CTCCA-TATTATTC
**
22166 CTTTATATTATTC
1 CTCCATATTATTC
22179 CTCCATAT
1 CTCCATAT
22187 ATGCTATTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (13 bp):
CTCCATATTATTC
Found at i:22466 original size:85 final size:83
Alignment explanation
Indices: 22377--22645 Score: 206
Period size: 85 Copynumber: 3.1 Consensus size: 83
22367 ATAAAATGTT
22377 AACATAAATAAATTTTTTCAAAATAAATCTTCATAAAAATTTCATTTAAAAAACAGAAAAATAAT
1 AACATAAATAAA-TTTTTCAAAATAAATCTTCATAAAAATTTCATTTAAAAAA-AGAAAAATAAT
22442 TTCTTTTTTAAAATTTTACC
64 TTCTTTTTTAAAATTTTACC
* *** * * * ** ** * **
22462 AACATAATTAAAGGATT-AATATATTAAATTTTAACTTGATTACATAATTTAAACAAAA-AATTA
1 AACATAAATAAATTTTTCAA-A-A-TAAATCTT--CATAAAAATTTCATTTAAA-AAAAGAAAAA
* ** *
22525 TAATTTGTATTGAAATAAAATGTT---
60 TAATTTCT-TT--TTTAAAATTTTACC
*
22549 AACATAAATAAAATTTTTCAAAATAAATCTTCAAAAAAATTTCATTTAAAAAAAAGAAAAATAAT
1 AACATAAAT-AAATTTTTCAAAATAAATCTTCATAAAAATTTCATTT-AAAAAAAGAAAAATAAT
22614 TTCTTTTTTAAAATTTTACC
64 TTCTTTTTTAAAATTTTACC
*
22634 AACATAATTAAA
1 AACATAAATAAA
22646 GGATTAATAT
Statistics
Matches: 130, Mismatches: 38, Indels: 33
0.65 0.19 0.16
Matches are distributed among these distances:
82 8 0.06
83 2 0.02
84 20 0.15
85 33 0.25
86 14 0.11
87 19 0.15
88 21 0.16
89 5 0.04
90 8 0.06
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (83 bp):
AACATAAATAAATTTTTCAAAATAAATCTTCATAAAAATTTCATTTAAAAAAAGAAAAATAATTT
CTTTTTTAAAATTTTACC
Found at i:22622 original size:172 final size:172
Alignment explanation
Indices: 22336--22680 Score: 663
Period size: 172 Copynumber: 2.0 Consensus size: 172
22326 ATAATCTCTC
*
22336 ATTTAAACAAAAAATTATAATTTGTATTGAAATAAAATGTTAACATAAATAAATTTTTTCAAAAT
1 ATTTAAACAAAAAATTATAATTTGTATTGAAATAAAATGTTAACATAAATAAAATTTTTCAAAAT
* *
22401 AAATCTTCATAAAAATTTCATTTAAAAAACAGAAAAATAATTTCTTTTTTAAAATTTTACCAACA
66 AAATCTTCAAAAAAATTTCATTTAAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACA
22466 TAATTAAAGGATTAATATATTAAATTTTAACTTGATTACATA
131 TAATTAAAGGATTAATATATTAAATTTTAACTTGATTACATA
22508 ATTTAAACAAAAAATTATAATTTGTATTGAAATAAAATGTTAACATAAATAAAATTTTTCAAAAT
1 ATTTAAACAAAAAATTATAATTTGTATTGAAATAAAATGTTAACATAAATAAAATTTTTCAAAAT
22573 AAATCTTCAAAAAAATTTCATTTAAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACA
66 AAATCTTCAAAAAAATTTCATTTAAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACA
22638 TAATTAAAGGATTAATATATTAAATTTTAACTTGATTACATA
131 TAATTAAAGGATTAATATATTAAATTTTAACTTGATTACATA
22680 A
1 A
22681 AAAAAAAAAT
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 170 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.38
Consensus pattern (172 bp):
ATTTAAACAAAAAATTATAATTTGTATTGAAATAAAATGTTAACATAAATAAAATTTTTCAAAAT
AAATCTTCAAAAAAATTTCATTTAAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACA
TAATTAAAGGATTAATATATTAAATTTTAACTTGATTACATA
Found at i:22685 original size:85 final size:85
Alignment explanation
Indices: 22424--22688 Score: 227
Period size: 85 Copynumber: 3.1 Consensus size: 85
22414 AATTTCATTT
*
22424 AAAAAACAGAAAAATAATTTCTTTTTTAAAATTTTACCAACATAATTAAAGGATTAATATATTAA
1 AAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACATAATTAAAGGATTAATATATTAA
22489 ATTTTAACTTGATTACATAA
66 ATTTTAACTTGATTACATAA
* ** * ** * * **
22509 TTTAAACAAAA-AATTATAATTTGTATTGAAATAAAATGTT---AACATAAATAAA--ATTTTTC
1 ---AAAAAAAAGAAAAATAATTTCT-TT--TTTAAAATTTTACCAACATAATTAAAGGATTAAT-
* * * **** * **
22568 AAAATAAATCTTCAAAAAAATTTCATTT
59 ATATTAAAT-TTTAACTTGATTACATAA
22596 AAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACATAATTAAAGGATTAATATATTAA
1 AAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACATAATTAAAGGATTAATATATTAA
22661 ATTTTAACTTGATTACATAA
66 ATTTTAACTTGATTACATAA
22681 AAAAAAAA
1 AAAAAAAA
22689 ATAAAGGTGT
Statistics
Matches: 125, Mismatches: 41, Indels: 25
0.65 0.21 0.13
Matches are distributed among these distances:
82 8 0.06
84 9 0.07
85 43 0.34
86 14 0.11
87 35 0.28
88 8 0.06
90 8 0.06
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (85 bp):
AAAAAAAAGAAAAATAATTTCTTTTTTAAAATTTTACCAACATAATTAAAGGATTAATATATTAA
ATTTTAACTTGATTACATAA
Found at i:24216 original size:24 final size:24
Alignment explanation
Indices: 24155--24216 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 24
24145 TTCATTCTAG
* * *
24155 GAAGAAGCTGAAGTGGAGGAAGAA
1 GAAGAACCTGAAGAGGAAGAAGAA
*
24179 GAAGAACGGTCTGAAGAGGAAGTAGAA
1 GAAGAAC---CTGAAGAGGAAGAAGAA
24206 GAAGAACCTGA
1 GAAGAACCTGA
24217 GGTCATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 10 0.32
27 21 0.68
ACGTcount: A:0.45, C:0.08, G:0.37, T:0.10
Consensus pattern (24 bp):
GAAGAACCTGAAGAGGAAGAAGAA
Done.