| Previous changeset 9:438f65cb1d14 (2020-08-18) Next changeset 11:72aade318318 (2021-05-20) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf" |
|
modified:
repeatmasker.xml test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.stats |
|
added:
test-data/Dfam_partial_test.h5 test-data/README.md test-data/small_dfam.fasta.cat test-data/small_dfam.fasta.log test-data/small_dfam.fasta.masked test-data/small_dfam.fasta.stats test-data/small_dfam_up.fasta.cat test-data/small_dfam_up.fasta.log test-data/small_dfam_up.fasta.masked test-data/small_dfam_up.fasta.stats |
|
removed:
test-data/small_repbase.fasta.log test-data/small_repbase.fasta.stats |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca repeatmasker.xml --- a/repeatmasker.xml Tue Aug 18 05:39:55 2020 -0400 +++ b/repeatmasker.xml Fri Dec 11 22:26:02 2020 +0000 |
| [ |
| b'@@ -1,31 +1,36 @@\n-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01">\n+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">\n <description>screen DNA sequences for interspersed repeats and low complexity regions</description>\n \n <requirements>\n- <requirement type="package" version="4.0.9_p2">repeatmasker</requirement>\n+ <requirement type="package" version="4.1.1">repeatmasker</requirement>\n </requirements>\n \n <command detect_errors="exit_code"><![CDATA[\n RM_PATH=\\$(which RepeatMasker) &&\n if [ -z "\\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\\$PATH)" >&2 ; exit 1 ; fi &&\n+\n RM_LIB_PATH=\\$(dirname \\$RM_PATH)/../share/RepeatMasker/Libraries &&\n- mkdir lib &&\n- export REPEATMASKER_LIB_DIR=\\$(pwd)/lib &&\n- for file in \\$(ls \\$RM_LIB_PATH) ; do ln -s \\$RM_LIB_PATH/\\$file lib/\\$file ; done &&\n- #if $repeat_source.source_type == "repbase":\n- cp \'${repeat_source.repbase_file}\' \'lib/${repeat_source.repbase_file_name}\' &&\n+ #if $repeat_source.source_type == "dfam_up":\n+ mkdir lib/ &&\n+ ln -s \'${repeat_source.dfam_lib}\' lib/RepeatMaskerLib.h5 &&\n+ RM_LIB_PATH=\\$(pwd)/lib &&\n #end if\n+\n ln -s \'${input_fasta}\' rm_input.fasta &&\n+\n RepeatMasker -dir \\$(pwd)\n+ -libdir \\$RM_LIB_PATH\n #if $repeat_source.source_type == "library":\n -lib \'${repeat_source.repeat_lib}\'\n -cutoff \'${repeat_source.cutoff}\'\n- #else if $repeat_source.source_type == "repbase":\n+ #else if $repeat_source.source_type == "dfam":\n #if $repeat_source.species_source.species_from_list == \'yes\':\n- $repeat_source.species_source.species_list\n+ -species $repeat_source.species_source.species_list\n #else\n -species \'${repeat_source.species_source.species_name}\'\n #end if\n+ #else if $repeat_source.source_type == "dfam_up":\n+ -species \'${repeat_source.species_name}\'\n #end if\n -parallel \\${GALAXY_SLOTS:-1}\n ${gff}\n@@ -79,13 +84,12 @@\n <inputs>\n <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />\n <conditional name="repeat_source">\n- <param label="Repeat library source" name="source_type" type="select">\n- <option selected="true" value="repbase">RepBase</option>\n+ <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose \'Custom library of repeats\' and select a fasta version of this non-free database.">\n+ <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option>\n+ <option value="dfam_up">DFam (full/specific version)</option>\n <option value="library">Custom library of repeats</option>\n </param>\n- <when value="repbase">\n- <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" />\n- <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase -->\n+ <when value="dfam">\n <conditional name="species_source">\n <param label="Select species name from a list?" name="species_from_list" type="select">\n <option value="yes" selected="true">Yes</option>\n@@ -93,40 +97,26 @@\n </param>\n <when value="yes">\n <param name="species_list" type="select" label="Species">\n- <option value="-species anopheles" selected="true">anopheles</option>\n- <option value="-species arabidopsis">arabidopsis</option>\n- <option value="-species artiodactyl">artiodactyl</option>\n- <option value="-species aspergillus">aspergillus</option>\n- <option value="-species carnivore">carnivore</option>\n- <option value="-species cat">cat</option>\n- <option value="-species chicken">chicken</option>\n- <option value="-species \'ciona intestinalis\'">ciona intestinalis<'..b' <option value="-species wheat">wheat</option>\n+ <option value="vertebrate">Vertebrate (other than below)</option>\n+ <option value="mammal">Mammal (other than below)</option>\n+ <option value="human" selected="true">Human</option>\n+ <option value="rodent">Rodent</option>\n+ <option value="mouse">Mouse</option>\n+ <option value="rat">Rat</option>\n+ <option value="danio">Danio (zebra fish)</option>\n+ <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>\n+ <option value="elegans">Caenorhabditis elegans (nematode)</option>\n </param>\n </when>\n <when value="no">\n- <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" />\n+ <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />\n </when>\n </conditional>\n </when>\n+ <when value="dfam_up">\n+ <param name="dfam_lib" type="data" format="h5" label="DFam library" help="The full DFam library can be downloaded from https://www.dfam.org/releases/current/families/Dfam.h5.gz" />\n+ <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />\n+ </when>\n <when value="library">\n <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" />\n <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />\n@@ -199,7 +189,6 @@\n <param name="input_fasta" value="small.fasta" ftype="fasta" />\n <param name="source_type" value="library" />\n <param name="gff" value="-gff" />\n- <!-- <param name="show" value="yes" /> -->\n <param name="keep_alignments" value="-ali" />\n <param name="poly" value="-poly" />\n <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />\n@@ -213,14 +202,22 @@\n </test>\n <test expect_num_outputs="4">\n <param name="input_fasta" value="small.fasta" ftype="fasta" />\n- <param name="source_type" value="repbase" />\n- <param name="repbase_file" value="fake_repbase.embl" />\n- <param name="repbase_file_name" value="fake.embl" />\n- <param name="species_list" value="anopheles" />\n- <output name="output_masked_genome" file="small.fasta.masked" />\n- <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />\n- <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />\n- <output name="output_log" file="small_repbase.fasta.log" lines_diff="2"/>\n+ <param name="source_type" value="dfam" />\n+ <param name="species_list" value="human" />\n+ <output name="output_masked_genome" file="small_dfam.fasta.masked" />\n+ <output name="output_table" file="small_dfam.fasta.stats" lines_diff="2" />\n+ <output name="output_repeat_catalog" file="small_dfam.fasta.cat" lines_diff="2" />\n+ <output name="output_log" file="small_dfam.fasta.log" lines_diff="2"/>\n+ </test>\n+ <test expect_num_outputs="4">\n+ <param name="input_fasta" value="small.fasta" ftype="fasta" />\n+ <param name="source_type" value="dfam_up" />\n+ <param name="dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />\n+ <param name="species_name" value="rodent" />\n+ <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />\n+ <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />\n+ <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />\n+ <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>\n </test>\n </tests>\n <help><![CDATA[\n' |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/Dfam_partial_test.h5 |
| b |
| Binary file test-data/Dfam_partial_test.h5 has changed |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README.md Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +Dfam_partial_test.h5 was generated from the test dataset in https://github.com/Dfam-consortium/FamDB/ (commit: 6b28b66) |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small.fasta.cat --- a/test-data/small.fasta.cat Tue Aug 18 05:39:55 2020 -0400 +++ b/test-data/small.fasta.cat Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -98,6 +98,6 @@ ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version open-4.0.9 , default mode -run with rmblastn version 2.9.0+ -RepeatMasker Combined Database: Dfam-Dfam_3.0 +RepeatMasker version 4.1.1 , default mode +run with rmblastn version 2.10.0+ +RM Library: |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small.fasta.gff --- a/test-data/small.fasta.gff Tue Aug 18 05:39:55 2020 -0400 +++ b/test-data/small.fasta.gff Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -1,5 +1,5 @@ ##gff-version 2 -##date 2020-08-18 +##date 2020-12-11 ##sequence-region rm_input.fasta scaffold_1 RepeatMasker similarity 613 632 0.0 + . Target "Motif:(GT)n" 1 20 scaffold_1 RepeatMasker similarity 780 824 18.3 + . Target "Motif:(ATAATA)n" 1 45 |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small.fasta.stats --- a/test-data/small.fasta.stats Tue Aug 18 05:39:55 2020 -0400 +++ b/test-data/small.fasta.stats Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -8,35 +8,44 @@ number of length percentage elements* occupied of sequence -------------------------------------------------- -SINEs: 0 0 bp 0.00 % - ALUs 0 0 bp 0.00 % - MIRs 0 0 bp 0.00 % - -LINEs: 0 0 bp 0.00 % - LINE1 0 0 bp 0.00 % - LINE2 0 0 bp 0.00 % - L3/CR1 0 0 bp 0.00 % +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 % -LTR elements: 0 0 bp 0.00 % - ERVL 0 0 bp 0.00 % - ERVL-MaLRs 0 0 bp 0.00 % - ERV_classI 0 0 bp 0.00 % - ERV_classII 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) -DNA elements: 0 0 bp 0.00 % - hAT-Charlie 0 0 bp 0.00 % - TcMar-Tigger 0 0 bp 0.00 % +Rolling-circles 0 0 bp 0.00 % -Unclassified: 0 0 bp 0.00 % +Unclassified: 0 0 bp 0.00 % -Total interspersed repeats: 0 bp 0.00 % +Total interspersed repeats: 0 bp 0.00 % -Small RNA: 0 0 bp 0.00 % +Small RNA: 0 0 bp 0.00 % -Satellites: 0 0 bp 0.00 % -Simple repeats: 8 378 bp 2.66 % -Low complexity: 0 0 bp 0.00 % +Satellites: 0 0 bp 0.00 % +Simple repeats: 8 378 bp 2.66 % +Low complexity: 0 0 bp 0.00 % ================================================== * most repeats fragmented by insertions or deletions @@ -44,9 +53,8 @@ Runs of >=20 X/Ns in query were excluded in % calcs -The query species was assumed to be homo -RepeatMasker Combined Database: Dfam-Dfam_3.0 - -run with rmblastn version 2.9.0+ -The query was compared to unclassified sequences in ".../dataset_257a7a8f-7065-486a-ae21-53e1fceff0f8.dat" +RepeatMasker version 4.1.1 , default mode + +run with rmblastn version 2.10.0+ +The query was compared to unclassified sequences in ".../dataset_a9c6a294-8dbb-4a71-ad9c-e36735923fbf.dat" |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam.fasta.cat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam.fasta.cat Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,118 @@ +18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 + + scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632 + + (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 + +Matrix = Unknown +Transitions / transversions = 1.00 (0/0) +Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) + +16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 + + scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824 + v - v - i v vv i + (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45 + +Matrix = Unknown +Transitions / transversions = 0.40 (2/5) +Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) + +12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 + + scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274 + - i v v iv -i vv v + (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46 + +Matrix = Unknown +Transitions / transversions = 0.50 (3/6) +Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) + +15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 + + scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898 + v i i - vv vv i - - - + (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 + + scaffold_1 4899 -CTC 4901 + - + (TC)n#Simple_ 51 TCTC 54 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) + +13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 + + scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278 + v i - v -i - i v - v v + (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47 + + scaffold_1 6279 AAATAA 6284 + - + (TAATTAA)n#Si 48 -AATAA 52 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) + +15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 + + scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597 + v i i viv i vi v -v i - + (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48 + + scaffold_1 6598 GACAGAGAG 6606 + v + (GACA)n#Simpl 49 GACAGACAG 57 + +Matrix = Unknown +Transitions / transversions = 0.86 (6/7) +Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) + +180 25.44 1.41 5.88 scaffold_1 8140 8210 (5941) C AmnL2-1#LINE/L2 (11) 2602 2535 m_b1s601i0 + + scaffold_1 8140 ACAACATTATTTTGTCTA-CACCCTGCATACAGCACAGTATATTAAATTT 8188 + v v - ii i v i- v vii --- +C AmnL2-1#LINE/ 2602 ACAACTTTATTTTGTATAGCGTCTTTCATACAA-ACTGTATCCCAAA--- 2557 + + scaffold_1 8189 AGGTTTTATTAAGTTAAGTAAT 8210 + v i ivi i +C AmnL2-1#LINE/ 2556 ACGCTTTACAGAGTTAAATAAT 2535 + +Matrix = 25p39g.matrix +Kimura (with divCpGMod) = 29.45 +Transitions / transversions = 1.43 (10/7) +Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) + +67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 + + scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 + i i - + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 + + scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050 + + (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 + +Matrix = Unknown +Transitions / transversions = 1.00 (2/0) +Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) + +19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 + + scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113 + v v i - i v + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 + +Matrix = Unknown +Transitions / transversions = 0.67 (2/3) +Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) + +## Total Sequences: 1 +## Total Length: 14220 +## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 +## Total NonSub ( excluding all non ACGT bases ):14220 +RepeatMasker version 4.1.1 , default mode +run with rmblastn version 2.10.0+ +RM Library: CONS-Dfam_3.2 |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam.fasta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam.fasta.log Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,11 @@ +SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID + +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 +16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 +12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 +15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 +13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 +15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 +180 25.4 1.4 5.9 scaffold_1 8140 8210 (6010) C AmnL2-1 LINE/L2 (11) 2602 2535 7 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 8 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 8 |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam.fasta.masked --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam.fasta.masked Fri Dec 11 22:26:02 2020 +0000 |
| b |
| b'@@ -0,0 +1,286 @@\n+>scaffold_1\n+TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC\n+CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC\n+ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA\n+CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC\n+AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA\n+CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT\n+AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC\n+CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA\n+ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC\n+GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG\n+GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC\n+AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC\n+TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC\n+ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT\n+CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC\n+CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA\n+CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT\n+TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA\n+AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG\n+ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA\n+GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT\n+CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT\n+GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT\n+ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG\n+TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT\n+CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG\n+TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC\n+CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA\n+GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA\n+AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC\n+AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT\n+CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG\n+TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC\n+TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC\n+ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG\n+TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA\n+TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT\n+TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC\n+TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC\n+TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG\n+TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT\n+GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC\n+CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT\n+TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA\n+GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG\n+GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA\n+AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT\n+TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA\n+AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC\n+TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT\n+CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG\n+AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG\n+AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA\n+CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT\n+CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG\n+CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG\n+TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG\n+CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT\n+GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA\n+GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC\n+TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG\n+GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT\n+CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA\n+AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT\n+CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA\n+GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA\n+TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC\n+AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA\n+GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG\n+CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA\n+TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT\n+GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG\n+TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA\n+TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA\n+AACCTAAATCAGATC'..b'TGTCCTTGTGTGACACAGGCTCTA\n+AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC\n+AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG\n+AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC\n+ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT\n+AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA\n+AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT\n+ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT\n+TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT\n+ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA\n+TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA\n+TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT\n+GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA\n+ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA\n+TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG\n+GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT\n+TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT\n+ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA\n+TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG\n+AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA\n+AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC\n+GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT\n+TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG\n+ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG\n+ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA\n+CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA\n+CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT\n+TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG\n+GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG\n+GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC\n+CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA\n+AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC\n+TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG\n+TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC\n+AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC\n+AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT\n+TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA\n+TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC\n+ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA\n+GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG\n+GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT\n+GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC\n+AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA\n+ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC\n+TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT\n+AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT\n+CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC\n+TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT\n+TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT\n+TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA\n+GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG\n+AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG\n+ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT\n+TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA\n+CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA\n+AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG\n+CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA\n+AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA\n+CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG\n+AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC\n+TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC\n+CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC\n+TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT\n+TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC\n+TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA\n+GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT\n+AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA\n+TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT\n+ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG\n+CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA\n+TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC\n+TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC\n+CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT\n+TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC\n+AAGCACCCATGCCTAAATCA\n' |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam.fasta.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam.fasta.stats Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,51 @@ +================================================== +file name: rm_input.fasta +sequences: 1 +total length: 14220 bp (14220 bp excl N/X-runs) +GC level: 39.94 % +bases masked: 449 bp ( 3.16 %) +================================================== + number of length percentage + elements* occupied of sequence +-------------------------------------------------- +SINEs: 0 0 bp 0.00 % + ALUs 0 0 bp 0.00 % + MIRs 0 0 bp 0.00 % + +LINEs: 1 71 bp 0.50 % + LINE1 0 0 bp 0.00 % + LINE2 1 71 bp 0.50 % + L3/CR1 0 0 bp 0.00 % + +LTR elements: 0 0 bp 0.00 % + ERVL 0 0 bp 0.00 % + ERVL-MaLRs 0 0 bp 0.00 % + ERV_classI 0 0 bp 0.00 % + ERV_classII 0 0 bp 0.00 % + +DNA elements: 0 0 bp 0.00 % + hAT-Charlie 0 0 bp 0.00 % + TcMar-Tigger 0 0 bp 0.00 % + +Unclassified: 0 0 bp 0.00 % + +Total interspersed repeats: 71 bp 0.50 % + + +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 human +RepeatMasker version 4.1.1 , default mode + +run with rmblastn version 2.10.0+ + |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam_up.fasta.cat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_up.fasta.cat Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,103 @@ +18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 + + scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632 + + (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 + +Matrix = Unknown +Transitions / transversions = 1.00 (0/0) +Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) + +16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 + + scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824 + v - v - i v vv i + (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45 + +Matrix = Unknown +Transitions / transversions = 0.40 (2/5) +Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) + +12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 + + scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274 + - i v v iv -i vv v + (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46 + +Matrix = Unknown +Transitions / transversions = 0.50 (3/6) +Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) + +15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 + + scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898 + v i i - vv vv i - - - + (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 + + scaffold_1 4899 -CTC 4901 + - + (TC)n#Simple_ 51 TCTC 54 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) + +13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 + + scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278 + v i - v -i - i v - v v + (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47 + + scaffold_1 6279 AAATAA 6284 + - + (TAATTAA)n#Si 48 -AATAA 52 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) + +15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 + + scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597 + v i i viv i vi v -v i - + (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48 + + scaffold_1 6598 GACAGAGAG 6606 + v + (GACA)n#Simpl 49 GACAGACAG 57 + +Matrix = Unknown +Transitions / transversions = 0.86 (6/7) +Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) + +67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 + + scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 + i i - + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 + + scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050 + + (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 + +Matrix = Unknown +Transitions / transversions = 1.00 (2/0) +Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) + +19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 + + scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113 + v v i - i v + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 + +Matrix = Unknown +Transitions / transversions = 0.67 (2/3) +Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) + +## Total Sequences: 1 +## Total Length: 14220 +## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 +## Total NonSub ( excluding all non ACGT bases ):14220 +RepeatMasker version 4.1.1 , default mode +run with rmblastn version 2.10.0+ +RM Library: CONS-_ |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam_up.fasta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_up.fasta.log Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID + +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 +16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 +12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 +15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 +13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 +15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 7 |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam_up.fasta.masked --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_up.fasta.masked Fri Dec 11 22:26:02 2020 +0000 |
| b |
| b'@@ -0,0 +1,286 @@\n+>scaffold_1\n+TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC\n+CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC\n+ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA\n+CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC\n+AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA\n+CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT\n+AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC\n+CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA\n+ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC\n+GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG\n+GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC\n+AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC\n+TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC\n+ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT\n+CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC\n+CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA\n+CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT\n+TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA\n+AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG\n+ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA\n+GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT\n+CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT\n+GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT\n+ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG\n+TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT\n+CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG\n+TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC\n+CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA\n+GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA\n+AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC\n+AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT\n+CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG\n+TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC\n+TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC\n+ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG\n+TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA\n+TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT\n+TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC\n+TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC\n+TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG\n+TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT\n+GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC\n+CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT\n+TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA\n+GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG\n+GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA\n+AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT\n+TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA\n+AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC\n+TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT\n+CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG\n+AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG\n+AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA\n+CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT\n+CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG\n+CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG\n+TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG\n+CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT\n+GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA\n+GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC\n+TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG\n+GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT\n+CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA\n+AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT\n+CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA\n+GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA\n+TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC\n+AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA\n+GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG\n+CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA\n+TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT\n+GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG\n+TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA\n+TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA\n+AACCTAAATCAGATC'..b'TGTCCTTGTGTGACACAGGCTCTA\n+AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC\n+AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG\n+AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC\n+ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT\n+AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA\n+AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT\n+ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT\n+TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT\n+ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA\n+TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA\n+TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT\n+GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA\n+ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA\n+TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG\n+GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT\n+TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT\n+ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA\n+TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG\n+AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA\n+AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC\n+GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT\n+TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG\n+ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG\n+ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA\n+CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA\n+CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT\n+TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG\n+GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG\n+GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC\n+CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA\n+AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC\n+TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG\n+TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC\n+AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC\n+AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT\n+TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA\n+TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC\n+ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA\n+GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG\n+GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT\n+GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC\n+AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA\n+ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC\n+TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT\n+AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT\n+CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC\n+TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT\n+TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT\n+TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA\n+GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG\n+AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG\n+ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT\n+TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA\n+CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA\n+AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG\n+CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA\n+AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA\n+CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG\n+AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC\n+TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC\n+CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC\n+TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT\n+TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC\n+TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA\n+GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT\n+AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA\n+TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT\n+ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG\n+CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA\n+TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC\n+TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC\n+CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT\n+TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC\n+AAGCACCCATGCCTAAATCA\n' |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_dfam_up.fasta.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_up.fasta.stats Fri Dec 11 22:26:02 2020 +0000 |
| b |
| @@ -0,0 +1,53 @@ +================================================== +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 +-------------------------------------------------- +SINEs: 0 0 bp 0.00 % + Alu/B1 0 0 bp 0.00 % + B2-B4 0 0 bp 0.00 % + IDs 0 0 bp 0.00 % + MIRs 0 0 bp 0.00 % + +LINEs: 0 0 bp 0.00 % + LINE1 0 0 bp 0.00 % + LINE2 0 0 bp 0.00 % + L3/CR1 0 0 bp 0.00 % + +LTR elements: 0 0 bp 0.00 % + ERVL 0 0 bp 0.00 % + ERVL-MaLRs 0 0 bp 0.00 % + ERV_classI 0 0 bp 0.00 % + ERV_classII 0 0 bp 0.00 % + +DNA elements: 0 0bp 0.00 % + hAT-Charlie 0 0 bp 0.00 % + TcMar-Tigger 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 rodent +RepeatMasker version 4.1.1 , default mode + +run with rmblastn version 2.10.0+ + |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_repbase.fasta.log --- a/test-data/small_repbase.fasta.log Tue Aug 18 05:39:55 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID - -18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 -16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 -12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 -15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 -13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 -15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 -67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 -19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 7 |
| b |
| diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/small_repbase.fasta.stats --- a/test-data/small_repbase.fasta.stats Tue Aug 18 05:39:55 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,60 +0,0 @@ -================================================== -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-Dfam_3.0 - -run with rmblastn version 2.9.0+ - |