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Table 4 Assignment of TSDs flanking transposed a Tos17 in ttm2 and ttm5 to the genome of the original line, Nipponbare

From: Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

Detected by

Line

Chromosome

bPosition of junction for

Size of TSD

TSD for

Direction

Confirmed by PCR/Sequencing

Tos17 tail

Tos17 head

Tos17 tail

Tos17head

TIF

RelocaTE

ttm2

chr04

30 259 052

30 259 056

5

GTTTC

GTTTC

Forward

Yes

TIF

RelocaTE

ttm2

chr05

1 925 905

1 925 909

5

CTATC

CTATC

Forward

Yes

TIF

RelocaTE

ttm2

chr10

22 134 718

22 134 714

5

CTTGC

CTTGC

Reverse

Yes

TIF

RelocaTE

ttm2

chr10

22 531 003

22 531 007

5

ACTTT

ACTTT

Forward

Yes

TIF

 

ttm5

chr01

34 453 645

34 453 641

5

CTTTG

CTTTG

Reverse

Yes

TIF

RelocaTE

ttm5

chr02

1 004 769

1 004 765

5

ATACC

ATACC

Reverse

Yes

TIF

RelocaTE

ttm5

chr02

31 596 628

31 596 632

5

CTAAT

CTAAT

Forward

Yes

TIF

RelocaTE

ttm5

chr03

741 226

741 222

5

GCTGC

GCTGC

Reverse

Yes

TIF

RelocaTE

ttm5

chr03

8 304 678

8 304 674

5

GAATA

GAATA

Reverse

Yes

TIF

 

ttm5

chr06

24 967 881

24 967 877

5

TGCAT

TGCAT

Reverse

Yes

TIF

 

ttm5

chr07

20 064 391

20 064 395

5

CTTAT

CTTAT

Forward

cYes

20 080 552

20 080 556

TIF

RelocaTE

ttm5

chr09

12 970 618

12 970 614

5

CATGC

CATGC

Reverse

Yes

 

RelocaTE

ttm5

chr10

14 739 090

14 739 094

5

 

GAACT

Forward

No

TIF

 

ttm5

chr10

19 069 885

19 069 889

5

ACTTG

ACTTG

Forward

Yes

TIF

RelocaTE

ttm5

chr10

21 583 054

21 583 058

5

CTTAT

CTTAT

Forward

Yes

TIF

RelocaTE

ttm5

chr12

2 155 899

2 155 895

5

GGAAC

GGAAC

Reverse

Yes

  1. aOriginal Tos17s are located from 26 694 799 to 26 698 904 at chromosome 7 and from 15 415 378 to 15 419 573 at chromosome 10.
  2. bpositions of 1st base of flanking sequences to the tail and head sequence of Tos17.
  3. cTSD on chromosome 7 in ttm5 is located within one of two very similar sequences; thus, it was difficult to determine its position conclusively from the short read sequences.