Mercurial > repos > bgruening > repeat_masker

diff test-data/small_repbase.fasta.stats @ 4:04f5c3d7448e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
author iuc
date Fri, 04 May 2018 07:59:50 -0400
parents
children 438f65cb1d14
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_repbase.fasta.stats	Fri May 04 07:59:50 2018 -0400
@@ -0,0 +1,60 @@
+==================================================
+file name: rm_input.fasta           
+sequences:             1
+total length:      14220 bp  (14220 bp excl N/X-runs) 
+GC level:         39.94 %
+bases masked:        378 bp ( 2.66 %)
+==================================================
+               number of      length   percentage
+               elements*    occupied  of sequence
+--------------------------------------------------
+Retroelements            0            0 bp    0.00 %
+   SINEs:                0            0 bp    0.00 %
+   Penelope              0            0 bp    0.00 %
+   LINEs:                0            0 bp    0.00 %
+    CRE/SLACS            0            0 bp    0.00 %
+     L2/CR1/Rex          0            0 bp    0.00 %
+     R1/LOA/Jockey       0            0 bp    0.00 %
+     R2/R4/NeSL          0            0 bp    0.00 %
+     RTE/Bov-B           0            0 bp    0.00 %
+     L1/CIN4             0            0 bp    0.00 %
+   LTR elements:         0            0 bp    0.00 %
+     BEL/Pao             0            0 bp    0.00 %
+     Ty1/Copia           0            0 bp    0.00 %
+     Gypsy/DIRS1         0            0 bp    0.00 %
+       Retroviral        0            0 bp    0.00 %
+
+DNA transposons          0            0 bp    0.00 %
+   hobo-Activator        0            0 bp    0.00 %
+   Tc1-IS630-Pogo        0            0 bp    0.00 %
+   En-Spm                0            0 bp    0.00 %
+   MuDR-IS905            0            0 bp    0.00 %
+   PiggyBac              0            0 bp    0.00 %
+   Tourist/Harbinger     0            0 bp    0.00 %
+   Other (Mirage,        0            0 bp    0.00 %
+    P-element, Transib)
+
+Rolling-circles          0            0 bp    0.00 %
+
+Unclassified:            0            0 bp    0.00 %
+
+Total interspersed repeats:           0 bp    0.00 %
+
+
+Small RNA:               0            0 bp    0.00 %
+
+Satellites:              0            0 bp    0.00 %
+Simple repeats:          7          378 bp    2.66 %
+Low complexity:          0            0 bp    0.00 %
+==================================================
+
+* most repeats fragmented by insertions or deletions
+  have been counted as one element
+  Runs of >=20 X/Ns in query were excluded in % calcs
+
+
+The query species was assumed to be anopheles genus
+RepeatMasker Combined Database: Dfam_Consensus-20170127
+                          
+run with rmblastn version 2.2.27+
+