Mercurial > repos > bgruening > repeat_masker

annotate test-data/small.fasta.stats @ 9:438f65cb1d14 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
author iuc
date Tue, 18 Aug 2020 05:39:55 -0400
parents 04f5c3d7448e
children bfc70c8cc5ca
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bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
1 ==================================================
9
438f65cb1d14 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
iuc
parents: 4
diff changeset
2 file name: rm_input.fasta
3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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3 sequences: 1
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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4 total length: 14220 bp (14220 bp excl N/X-runs)
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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5 GC level: 39.94 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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6 bases masked: 378 bp ( 2.66 %)
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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7 ==================================================
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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8 number of length percentage
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
diff changeset
9 elements* occupied of sequence
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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10 --------------------------------------------------
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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11 SINEs: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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12 ALUs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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13 MIRs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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14
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
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15 LINEs: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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16 LINE1 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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17 LINE2 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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18 L3/CR1 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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19
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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20 LTR elements: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
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21 ERVL 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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22 ERVL-MaLRs 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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23 ERV_classI 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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24 ERV_classII 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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25
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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26 DNA elements: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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27 hAT-Charlie 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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28 TcMar-Tigger 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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29
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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30 Unclassified: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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31
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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32 Total interspersed repeats: 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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33
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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34
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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35 Small RNA: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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36
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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37 Satellites: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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38 Simple repeats: 8 378 bp 2.66 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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39 Low complexity: 0 0 bp 0.00 %
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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40 ==================================================
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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41
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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42 * most repeats fragmented by insertions or deletions
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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43 have been counted as one element
4
04f5c3d7448e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
iuc
parents: 3
diff changeset
44 Runs of >=20 X/Ns in query were excluded in % calcs
04f5c3d7448e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86
iuc
parents: 3
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45
3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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46
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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47 The query species was assumed to be homo
9
438f65cb1d14 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
iuc
parents: 4
diff changeset
48 RepeatMasker Combined Database: Dfam-Dfam_3.0
438f65cb1d14 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
iuc
parents: 4
diff changeset
49
438f65cb1d14 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
iuc
parents: 4
diff changeset
50 run with rmblastn version 2.9.0+
438f65cb1d14 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab"
iuc
parents: 4
diff changeset
51 The query was compared to unclassified sequences in ".../dataset_257a7a8f-7065-486a-ae21-53e1fceff0f8.dat"
3
bdfc22c1c3e3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
iuc
parents:
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52