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Table 1 RISCI annotates the transposon locus in the main genome or the orthologous locus in the comparative genome into several classes based on specific alignment signatures.

From: RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

Data set   L1HS (Full length) L1HS (Truncated) AluYa5 (all)
Reference genome - Reference human genome   Comparative genomes Comparative genomes Comparative genomes
Class RISCI annotation Chimp Celera HuRef Chimp Celera HuRef Chimp Celera HuRef
Shared ancestry OCCUPIED 1 217 171 274 1227 1174 314 3529 3334
Post insertion changes C_DISRUPTED_M_INTER_RMD 1 7 43 16 8 11 5 9 6
  C_INTER_RMD_M_DISRUPTED 4 12 11 32 13 21 90 22 74
  M_INTRA_RMD 0 0 0 32 7 36 0 0 0
  C_INTRA_RMD 0 15 24 10 3 12 0 0 0
Orthologous locus empty CAN 170 27 25 426 62 76 3132 326 420
  PAC 68 9 10 109 16 22 54 2 4
  PTS 32 3 3 78 12 14 23 2 4
INDELS INDEL_CAN 3 2 7 43 4 6 164 34 79
  INDEL_PAC 6 1 1 14 1 2 7 1 0
  INDEL_PTS 9 5 5 28 6 3 96 24 53
Others TWIN PRIMING 0 0 0 142 17 24 0 0 0
Others FRAGMENTED 0 0 0 14 1 1 6 1 1
NMF NMF 8 4 2 203 44 19 165 106 81
Total   302 302 302 1421 1421 1421 4056 4056 4056