Table 1

Variation in the 5' and 3' ends of R1 and R2 elements

Major copy type: mean divergence* (maximum)

Atypical sequences: number (divergence)



5' end

3' end

Variant copies

Variant 5' ends


R1 elements

D. simulans R1A

0.000 (0.000)

0.002 (0.003)

4 (0.01-0.03)

D. sechellia R1A

<0.001 (0.003)

<0.001 (0.002)

D. melanogaster R1A

0.001 (0.008)

0.003 (0.015)

2 (0.07)

D. yakuba R1A

0.001 (0.005)

0.000 (0.000)

1 (0.02)

D. erecta R1A

0.002 (0.005)

0.001 (0.007)

D. ananassae R1A

0.013 (0.043)

<0.001 (0.003)

1 (0.08-0.11)

D. ananassae R1B

0.000 (0.000)

0.002 (0.005)

3 (0.15-0.22)

D. pseudoobscura R1A

0.000 (0.000)

0.002 (0.010)

1 (0.04)

D. persimilis R1A

ND

0.000 (0.000)

1 (0.02)

D. willistoni R1A

0.002 (0.005)

0.001 (0.003)

D. mojavensis R1A

0.000 (0.000)

0.000 (0.000)

D. virilis R1B

0.001 (0.008)

<0.001 (0.003)

6 (0.01-0.05)

D. grimshawi R1B1

0.000 (0.000)

0.001 (0.005)

D. grimshawi R1B2

0.000 (0.000)

0.000 (0.000)

R2 elements

D. simulans R2

0.001 (0.008)

0.000 (0.000)

D. sechellia R2

0.000 (0.000)

<0.001 (0.003)

D. melanogaster R2

0.002 (0.005)

0.001 (0.015)

6 (0.02-0.05)

D. yakuba R2

0.002 (0.013)

0.006 (0.018)

D. ananassae R2

0.004 (0.008)

0.001 (0.005)

D. persimilis R2

ND

ND

D. pseudoobscura R2

ND

0.005 (0.010)

D. willistoni R2 sub1

0.001 (0.003)

0.002 (0.008)

D. willistoni R2 sub2§

0.003 (0.006)

0.015 (0.028)


*Average nucleotide divergence from the consensus. The maximum divergence observed is shown in parentheses. Divergence detected at both the 5' and 3' ends except for the insertion in D. yakuba, where divergence was detected only at the 3' end. The number of distinct 5' ends excludes the majority (consensus) sequence used in the previous columns. The divergence of additional 5' ends is calculated from the consensus. §There may be only two copies of this lineage. ND indicates that these numbers were not included because sequencing reads with variant sequences had poor quality scores.

Stage and Eickbush Genome Biology 2009 10:R49   doi:10.1186/gb-2009-10-5-r49

Open Data