======================================================================
file name: At.fasta.mod             
sequences:             7
total length:  119668634 bp  (119483469 bp excl N/X-runs)
bases masked:   19101270 bp ( 15.96 %)
======================================================================
               			number of      length   percentage
               			elements*    occupied  of sequence
----------------------------------------------------------------------
----------------------------Class I:Results---------------------------
Class I Total:			  9632	   9152543 bp	 7.65 %
----------------------------------------------------------------------
|-Non-LTR:			  1498	    573634 bp	 0.48 %
|  |-SINEs:			   571	     83652 bp	 0.07 %
|  |-LINEs:			   927	    489982 bp	 0.41 %
|
|-LTR
|   |-LTR Non-auto:		  1310	    764240 bp	 0.64 %
|   |  |-LARDs:			   969	    523049 bp	 0.44 %
|   |  |-TRIMs:			    70	     30697 bp	 0.03 %
|   |  |-TR_GAG:		   138	     73236 bp	 0.06 %
|   |  |-BARE-2:		   133	    137258 bp	 0.11 %
|   |
|   |-LTR auto:			  6824	   7814669 bp	 6.53 %
|   | |-LTR/Copia:		  2249	   1903340 bp	 1.59 %
|   |    |-Ale:			  1418	    936368 bp    0.78 %
|   |    |-Alesia:		     0	         0 bp	 0.00 %
|   |    |-Angela:		     0	         0 bp	 0.00 %
|   |    |-Bianca:		   170	    195461 bp	 0.16 %
|   |    |-Bryco:		     0	         0 bp	 0.00 %
|   |    |-Lyco:		     0	         0 bp	 0.00 %
|   |    |-Gymco-I:		     0	         0 bp	 0.00 %
|   |    |-Gymco-II:		     0	         0 bp	 0.00 %
|   |    |-Gymco-III:		     0	         0 bp	 0.00 %
|   |    |-Gymco-IV:		     0	         0 bp	 0.00 %
|   |    |-Ikeros:		     0	         0 bp	 0.00 %
|   |    |-Ivana:		   163	    241161 bp	 0.20 %
|   |    |-Osser:		     0	         0 bp	 0.00 %
|   |    |-SIRE:		    89	    152111 bp	 0.13 %
|   |    |-TAR:			    42	     26617 bp	 0.02 %
|   |    |-Tork:		   268	    250926 bp	 0.21 %
|   |    |-Ty1-outgroup:	     0	         0 bp	 0.00 %
|   | 
|   |---LTR/Gypsy:		  4575	   5911329 bp	 4.94 %
|     |-non-chromovirus    
|     |  |-non-chromo-outgroup:      0	         0 bp	 0.00 %
|     |  |-Phygy:		     0	         0 bp	 0.00 %
|     |  |-Selgy:		     0	         0 bp	 0.00 %
|     |  |-OTA:			     0	         0 bp	 0.00 %
|     |  |-OTA|Athila:		  2274	   3211132 bp	 2.68 %
|     |  |-OTA|TatI:		     0	         0 bp	 0.00 %
|     |  |-OTA|TatII:		     0	         0 bp	 0.00 %
|     |  |-OTA|TatIII:		     0	         0 bp	 0.00 %
|     |  |-OTA|Tat|Ogre:	     0	         0 bp	 0.00 %
|     |  |-OTA|Tat|Retand:	  1185	   1562805 bp	 1.31 %
|     |
|     |-chromovirus
|        |-Chlamyvir:		     0	         0 bp	 0.00 %
|        |-Tcn1:		     0	         0 bp	 0.00 %
|        |-chromo-outgroup:	     0	         0 bp	 0.00 %
|        |-CRM:			   536	    280268 bp	 0.23 %
|        |-Galadriel:		     0	         0 bp	 0.00 %
|        |-Tekay:		   264	    522115 bp	 0.44 %
|        |-Reina:		   216	    222402 bp	 0.19 %
|        |-chromo-unclass:	     0	         0 bp	 0.00 %
|
|-Class I others:		     0	         0 bp	 0.00 %
   |-Penelope:			     0	         0 bp	 0.00 %
   |-DIRS:			     0	         0 bp	 0.00 %
   |-Pararetrovirus:		     0	         0 bp	 0.00 %
-Class I Unknown:		     0	         0 bp	 0.00 %

-----------------------------Class II:Results--------------------------
Class II Total:			 16481	   6741063 bp	 5.63 %
-----------------------------------------------------------------------
-Subclass_1
|  |-TIRs:			  3144	   1781426 bp	 1.49 %
|     |-non-autonomous
|     |  |-MITEs:		  1108	    618730 bp	 0.52 %
|     |-autonomous
|        |-EnSpm_CACTA:		   507	    364577 bp	 0.30 %
|        |-hAT:			   565	    221915 bp	 0.19 %
|        |-Kolobok:		     0	         0 bp	 0.00 %
|        |-Merlin:		     0	         0 bp	 0.00 %
|        |-MuDR_Mutator:	   698	    442149 bp	 0.37 %
|        |-Novosib:		     0	         0 bp	 0.00 %
|        |-P element:		     0	         0 bp	 0.00 %
|        |-PIF_Harbinger:	   266	    134055 bp	 0.11 %
|        |-PiggyBac:		     0	         0 bp	 0.00 %
|        |-Sola1:		     0	         0 bp	 0.00 %
|        |-Sola2:		     0	         0 bp	 0.00 %
|        |-Tc1_Mariner:		     0	         0 bp	 0.00 %
-Subclass_2
   |-RC/Helitron:		 13337	   4959637 bp	 4.14 %
-Class II Unknown:		     0           0 bp    0.00 %
-----------------------------------------------------------------------

-Unclassified:			 10859	   3282898 bp	 2.74 %

-----------------------------------------------------------------------
=======================================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element
                                                      

The query species was assumed to be viridiplantae 
RepeatMasker version 4.1.1 , quick mode
                                          
run with rmblastn version 2.10.0+


Plant TEs classification based on Orozco-Arias et al.,2019
=======================================================================