Hi, I see repNames like the following rmsk table. Some names are intuitive (like (CATA)n). But others are not (like Charlie2b). Does anybody know where are these unintuitive names come from? What are the canonical sequence for these repeats with unintuitive names?
> head(unique(f$repName),n=100) [1] "L1_Mur2" "(TTTG)n" "Lx9" "RLTR25A" "(TA)n" [6] "L1M2" "B3" "AT_rich" "L1Md_F2" "RLTRETN_Mm" [11] "L1MEf" "RLTR14" "RMER17A" "RLTR13C2" "T-rich" [16] "Lx2" "IAPLTR1a_Mm" "RLTR9C" "ID_B1" "L1Md_A" [21] "(TTC)n" "RLTR1D" "(CA)n" "MER44D" "RLTR13C1" [26] "MER74B" "ID4_" "MLT1A1" "Lx4B" "(TAAG)n" [31] "B4A" "BGLII_B" "(TCTCCC)n" "(TTCTCC)n" "L1_Mur3" [36] "(TTTA)n" "B2_Mm2" "(TTTTTG)n" "B1_Mus1" "(TTCC)n" [41] "Lx7" "L1_Rod" "RLTR45" "RLTR45-int" "PB1D10" [46] "ORR1E" "(CATA)n" "RLTR9B2" "B2_Mm1t" "PB1" [51] "Charlie2b" "(TCTA)n" "(TATG)n" "Lx8" "MTEa" [56] "RSINE1" "(TTTTG)n" "B1F" "L1_Mus3" "MT2_Mm" [61] "(TG)n" "(GAA)n" "L1_Mur1" "RMER4B" "(TC)n" [66] "RLTR10D" "(A)n" "Lx" "(CAAA)n" "MER119" [71] "B1_Mm" "L1Md_T" "(TAAAA)n" "L2a" "(TTG)n" [76] "MTD" "MTC" "U6" "L1M5" "(GAAAA)n" [81] "B1F2" "L1MEg" "Lx5" "L1MB7" "MTEb" [86] "B3A" "RMER15" "RLTR20A" "B1F1" "MLT1A" [91] "(GA)n" "RMER1B" "L1_Mus1" "(CAA)n" "Lx3A" [96] "MLT1B" "MTB" "MLT1C" "L1_Mm" "IAPEY2_LTR" -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
