Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014344.1 Kokia drynarioides strain JFW-HI SEQ_129381, 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: 48217
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:4993 original size:17 final size:17
Alignment explanation
Indices: 4955--5017 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
4945 TAAAAAACTC
4955 AAAAATAC-TTTAT-TT
1 AAAAATACTTTTATCTT
*
4970 AATAATACTTTTATCTT
1 AAAAATACTTTTATCTT
* **
4987 AAAAATATTTTTTATCCC
1 AAAAATA-CTTTTATCTT
*
5005 AAAAATATTTTTA
1 AAAAATACTTTTA
5018 AAAAGCAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 7 0.17
16 5 0.12
17 14 0.35
18 14 0.35
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAATACTTTTATCTT
Found at i:7386 original size:12 final size:12
Alignment explanation
Indices: 7369--7403 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
7359 ACTAGACCAA
7369 CAATAATTAAAT
1 CAATAATTAAAT
7381 CAATAATTAAAT
1 CAATAATTAAAT
7393 -AATTAATTAAA
1 CAA-TAATTAAA
7404 AATTCCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 20 0.91
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (12 bp):
CAATAATTAAAT
Found at i:15655 original size:171 final size:171
Alignment explanation
Indices: 15370--15714 Score: 609
Period size: 171 Copynumber: 2.0 Consensus size: 171
15360 GCGCTGCTTA
15370 AAAATAATACTAAACACACCCTAAATCATTACTCTTGTATTATGCATAAAGTTATAAATTTAGCC
1 AAAATAATACTAAACACACCCTAAATCATTACTCTTGTATTATGCATAAAGTTATAAATTTAGCC
* *
15435 CACGCTGGTCAATTGGATAATTTTAGTTGTTATATTTTTTGAATTTCAAAATTTTAGTCTTACTG
66 CACGCTCGTCAATTGGATAATTTTAGTGGTTATATTTTTTGAATTTCAAAATTTTAGTCTTACTG
15500 CATTTTAAATCTATTAACTAATTTTTTGTGAGTAAAATGTG
131 CATTTTAAATCTATTAACTAATTTTTTGTGAGTAAAATGTG
* * *
15541 AAAATAATACTAAACACACCTTAAATCATTATTCTTGTATTATGCATAAAGTTATAGATTTAGCC
1 AAAATAATACTAAACACACCCTAAATCATTACTCTTGTATTATGCATAAAGTTATAAATTTAGCC
* * * *
15606 CATGCTCGTCAATTGGATAATTTTAGTGGTTATTTTTTTTTAATTTCAAAATTTTAGTCTTATTG
66 CACGCTCGTCAATTGGATAATTTTAGTGGTTATATTTTTTGAATTTCAAAATTTTAGTCTTACTG
15671 CATTTTAAATCTATTAACTAATTTTTTGTGAGTAAAATGTG
131 CATTTTAAATCTATTAACTAATTTTTTGTGAGTAAAATGTG
15712 AAA
1 AAA
15715 TTAGCAAACA
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 165 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (171 bp):
AAAATAATACTAAACACACCCTAAATCATTACTCTTGTATTATGCATAAAGTTATAAATTTAGCC
CACGCTCGTCAATTGGATAATTTTAGTGGTTATATTTTTTGAATTTCAAAATTTTAGTCTTACTG
CATTTTAAATCTATTAACTAATTTTTTGTGAGTAAAATGTG
Found at i:26842 original size:17 final size:18
Alignment explanation
Indices: 26817--26853 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
26807 TTTTTTAAAA
26817 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
26835 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
26852 AT
1 AT
26854 ATTTTATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:26847 original size:24 final size:24
Alignment explanation
Indices: 26814--26878 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
26804 TAATTTTTTA
*
26814 AAAATTATAAATATATAAATTATT
1 AAAATAATAAATATATAAATTATT
**
26838 AAAATAATAAA-ATTATATTTTATT
1 AAAATAATAAATA-TATAAATTATT
* *
26862 ACAATAA-AAATAAATAA
1 AAAATAATAAATATATAA
26879 TTTAATTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAATAAATATATAAATTATT
Found at i:31854 original size:20 final size:18
Alignment explanation
Indices: 31829--31867 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
31819 CTATTAAATT
31829 TTATAAATATTGAATTTATA
1 TTATAAA-ATT-AATTTATA
*
31849 TTATAAAATTATTTTATA
1 TTATAAAATTAATTTATA
31867 T
1 T
31868 ATTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATAAAATTAATTTATA
Found at i:40461 original size:17 final size:17
Alignment explanation
Indices: 40439--40477 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
40429 TTAGTACAAG
40439 ATTTATGGATAAACCAC
1 ATTTATGGATAAACCAC
40456 ATTTATGGATAAACCAC
1 ATTTATGGATAAACCAC
40473 ATTTA
1 ATTTA
40478 AAGTCGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (17 bp):
ATTTATGGATAAACCAC
Found at i:40918 original size:31 final size:31
Alignment explanation
Indices: 40883--40941 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
40873 AGCATCTTAG
40883 TGACTTAAATAAAAACTTTAGAATAGTTCAA
1 TGACTTAAATAAAAACTTTAGAATAGTTCAA
* * *
40914 TGACTTAAATGAAAATTTTCGAATAGTT
1 TGACTTAAATAAAAACTTTAGAATAGTT
40942 TAAGGATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTAGAATAGTTCAA
Found at i:44154 original size:71 final size:69
Alignment explanation
Indices: 44033--44171 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 69
44023 TGCTCTCTAT
* * *
44033 TCAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGTGCTTTTTGTTTAGCA-TGTTGTGTGCCC
1 TCAGCACTGTGTGTGCCCTCTGTTTAGCACTGTGTGTGCTTTCTGATTAGCACT-TTGTGTGCCC
44097 TCTGA
65 TCTGA
*
44102 TCAGCACTTTGTGTGCCCTCTGTTATTAGCACT-TCGTGTG-TCTTCTGATTAGCACTTTGTGTG
1 TCAGCACTGTGTGTGCCCTCTG-T-TTAGCACTGT-GTGTGCT-TTCTGATTAGCACTTTGTGTG
44165 CCCTCTG
62 CCCTCTG
44172 TTACCCAGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
69 20 0.33
70 3 0.05
71 37 0.61
72 1 0.02
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (69 bp):
TCAGCACTGTGTGTGCCCTCTGTTTAGCACTGTGTGTGCTTTCTGATTAGCACTTTGTGTGCCCT
CTGA
Found at i:44171 original size:23 final size:23
Alignment explanation
Indices: 44001--44171 Score: 134
Period size: 23 Copynumber: 7.3 Consensus size: 23
43991 ACACTAGCGC
*
44001 GCCCTCT-ATTTAGCACGTTT-CGT
1 GCCCTCTGA-TTAGCAC-TTTGTGT
* *
44024 GCTCTCT-ATTCAGCACTGTGTGT
1 GCCCTCTGATT-AGCACTTTGTGT
* * *
44047 GCTCTCTGTTTAGCACTGTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
** * *
44070 GCTTTTTGTTTAGCA-TGTTGTGT
1 GCCCTCTGATTAGCACT-TTGTGT
*
44093 GCCCTCTGATCAGCACTTTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
*
44116 GCCCTCTGTTATTAGCACTTCGTGT
1 GCCCTCTG--ATTAGCACTTTGTGT
* *
44141 GTCTTCTGATTAGCACTTTGTGT
1 GCCCTCTGATTAGCACTTTGTGT
44164 GCCCTCTG
1 GCCCTCTG
44172 TTACCCAGCA
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.04
23 95 0.78
24 3 0.02
25 19 0.16
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (23 bp):
GCCCTCTGATTAGCACTTTGTGT
Found at i:44577 original size:82 final size:82
Alignment explanation
Indices: 44477--44640 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
44467 GATGAAAATG
* *
44477 TAAAATCTACCATTGAGGTAAGTTGCG-ATATGAGAATTAATGTGTGTTGTGGTGACATTAAGGT
1 TAAAATCTACCATTGAGGTAAGTTG-GAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGT
44541 AAGTTAAATGTTACATGC
65 AAGTTAAATGTTACATGC
*
44559 TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGGCATTAAGGTA
1 TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGTA
44624 AGTTAAATGTTACATGC
66 AGTTAAATGTTACATGC
44641 AAGAAAGGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.01
82 77 0.99
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.33
Consensus pattern (82 bp):
TAAAATCTACCATTGAGGTAAGTTGGAATATGAGAATGAATGTGTGATGTGGTGACATTAAGGTA
AGTTAAATGTTACATGC
Found at i:46335 original size:24 final size:24
Alignment explanation
Indices: 46288--46337 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
46278 GTACTGGAGC
* *
46288 TACTGATGCTATTACAGCAAGTGT
1 TACTGATGCTACTACAACAAGTGT
* *
46312 TACTGATGCTACTATAACATGTGT
1 TACTGATGCTACTACAACAAGTGT
46336 TA
1 TA
46338 GTACTAGTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (24 bp):
TACTGATGCTACTACAACAAGTGT
Done.