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Table 3 List of clusters of LTRharvest predictions compared to the Drosophila melanogaster annotation

From: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

LTR retrotransposon predictions from LTRharvest and clustering Drosophila melanogaster annotation of LTR retrotransposon families from [26]
cluster # sequences in cluster name of family full-length sequences all sequences
LTRharvest_Dmel0 92 Roo 58 146
LTRharvest_Dmel1 18 opus 16 24
LTRharvest_Dmel2 15 mdg1 13 25
LTRharvest_Dmel3 2 McClintock 2 2
LTRharvest_Dmel4 22 blood 22 22
LTRharvest_Dmel5 26 412 24 31
LTRharvest_Dmel6 50 297,17.6 25 69
LTRharvest_Dmel7 12 Stalker, Stalker2, Stalker4 9 27
LTRharvest_Dmel8 3 rover 3 6
LTRharvest_Dmel9 15 micropia, DM88, invader1 3 63
LTRharvest_Dmel10 3 invader3 3 16
LTRharvest_Dmel11 19 Tirant 15 20
LTRharvest_Dmel12 28 copia 26 30
LTRharvest_Dmel13 9 diver 9 9
LTRharvest_Dmel14 6 Quasimodo 5 14
LTRharvest_Dmel15 5 Transpac 5 5
LTRharvest_Dmel16 3 Idefix 2 7
LTRharvest_Dmel17 12 Burdock 7 13
LTRharvest_Dmel18 3    
LTRharvest_Dmel19 16 blastopia 13 17
LTRharvest_Dmel20 6 springer 5 11
LTRharvest_Dmel21 12 HMS-Beagle 9 13
LTRharvest_Dmel22 3    
LTRharvest_Dmel23 5    
LTRharvest_Dmel24 3 GATE 0 20
LTRharvest_Dmel25 8 mdg3 8 16
LTRharvest_Dmel26 4 invader2 3 10
LTRharvest_Dmel27 2    
LTRharvest_Dmel28 4 3S18 4 6
LTRharvest_Dmel29 2 gypsy5 1 2
LTRharvest_Dmel30 3    
LTRharvest_Dmel31 2    
LTRharvest_Dmel32 2 gypsy, gtwin 3 8
LTRharvest_Dmel33 2 invader4 2 9
LTRharvest_Dmel34 2 Tabor 2 3
LTRharvest_Dmel35 2    
  1. For clustering the program Vmatch was used with the following options: seedlength for minimal length of exact repeats = 50, minimal length of matches = 2500, Xdrop = 9 and matching conditions (dbcluster) that cover at least 80% of the smaller sequence and 28% of the larger sequence.
  2. Of 49 annotated families [26], this Table lists 34 out of 41 families containing at least one full length member and one family (GATE) out of 8 families that are entirely composed of partial elements.