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Table 4 Features and diversity of TE models found in the galGal4 model based on the REPET and DM annotations (STEP3 + STEP4, Fig. 2) after stack resolving and merging stacked and juxtaposed annotations

From: Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

Names of TE models a b ca d e
CR1 308 LINE 413857 66.4707 11.8457
Ancestral_LTR_group_1 3 LTR 86 0.0138 0.0034
Ancestral_LTR_group_2 1 LTR 22 0.0035 0.0013
Ancestral_LTR_group_3 1 LTR 40 0.0064 0.0012
Ancestral_LTR_group_4 1 LTR 308 0.0495 0.0119
BIRDDAWG 10 LTR 6238 1.0019 0.2525
EAV 1 LTR 191 0.0307 0.0212
EAV-HP 7 LTR 765 0.1229 0.0496
ERV2 2 LTR 426 0.0684 0.0209
ERV7 10 LTR 2885 0.4634 0.1061
ERV11 1 LTR 512 0.0822 0.0168
Kronos 46 LTR 30732 4.9359 0.7377
putative_LTR_group4 2 LTR 835 0.1341 0.0137
putative_LTR_group9 1 LTR 170 0.0273 0.0017
putative_LTR_group12 17 LTR 1797 0.2886 0.05
putative_LTR_group22 3 LTR 1219 0.1958 0.0257
putative_LTR_group28 2 LTR 367 0.0589 0.0116
putative_LTR_group30 13 LTR 3847 0.6179 0.0996
retroCalimero 1 LTR 826 0.1327 0.0540
retroSaturnin 1 LTR 161 0.0259 0.0118
retroTux 2 LTR 2490 0.3999 0.1243
Soprano 19 LTR 3014 0.4841 0.1171
Charlie 3 TIR 37319 5.9939 0.5868
Charlie-Galluhop 5 TIR 67691 10.872 1.0296
Galluhop 2 TIR 4588 0.7369 0.1198
Mariner1_GG 10 TIR 5686 0.9132 0.1491
Hitchcock 4 undefined 27033 4.3418 0.4182
undetermined_group_1 3 undefined 2219 0.3564 0.0773
undetermined_group_2 2 undefined 1030 0.1654 0.0165
undetermined_group_3 2 undefined 174 0.0279 0.0045
undetermined_group_4 4 undefined 2550 0.4096 0.0423
undetermined_group_5 2 undefined 134 0.0215 0.0036
undetermined_group_6 1 undefined 372 0.0597 0.0100
Z_rep 9 undefined 3032 0.487 0.1476
Total 499   622616 100 16.1832b
  1. a, Number of consensus; b, TE types; c, Total number of TE copies; d, Percentage of the total number of TE copies; e, Percentage of chromosome coverage; aPost stack resolving and annotation merging are called copies all complete elements, internally deleted elements; 5' or 3' truncated elements and elements truncated at both ends (i.e. internal regions of a TE devoid of ends). bthis coverage value was more elevated than the 15.7 % indicated in the main text because the coverage corresponding to the small TE copies nested in larger TEs were not removed for these calculations