Mercurial > repos > bgruening > repeat_masker
changeset 10:bfc70c8cc5ca draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"
author | iuc |
---|---|
date | Fri, 11 Dec 2020 22:26:02 +0000 |
parents | 438f65cb1d14 |
children | 72aade318318 |
files | repeatmasker.xml test-data/Dfam_partial_test.h5 test-data/README.md test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.stats 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 test-data/small_repbase.fasta.log test-data/small_repbase.fasta.stats |
diffstat | 16 files changed, 1006 insertions(+), 152 deletions(-) [+] |
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--- a/repeatmasker.xml Tue Aug 18 05:39:55 2020 -0400 +++ b/repeatmasker.xml Fri Dec 11 22:26:02 2020 +0000 @@ -1,31 +1,36 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01"> +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01"> <description>screen DNA sequences for interspersed repeats and low complexity regions</description> <requirements> - <requirement type="package" version="4.0.9_p2">repeatmasker</requirement> + <requirement type="package" version="4.1.1">repeatmasker</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ RM_PATH=\$(which RepeatMasker) && if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && + RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && - mkdir lib && - export REPEATMASKER_LIB_DIR=\$(pwd)/lib && - for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && - #if $repeat_source.source_type == "repbase": - cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' && + #if $repeat_source.source_type == "dfam_up": + mkdir lib/ && + ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 && + RM_LIB_PATH=\$(pwd)/lib && #end if + ln -s '${input_fasta}' rm_input.fasta && + RepeatMasker -dir \$(pwd) + -libdir \$RM_LIB_PATH #if $repeat_source.source_type == "library": -lib '${repeat_source.repeat_lib}' -cutoff '${repeat_source.cutoff}' - #else if $repeat_source.source_type == "repbase": + #else if $repeat_source.source_type == "dfam": #if $repeat_source.species_source.species_from_list == 'yes': - $repeat_source.species_source.species_list + -species $repeat_source.species_source.species_list #else -species '${repeat_source.species_source.species_name}' #end if + #else if $repeat_source.source_type == "dfam_up": + -species '${repeat_source.species_name}' #end if -parallel \${GALAXY_SLOTS:-1} ${gff} @@ -79,13 +84,12 @@ <inputs> <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" /> <conditional name="repeat_source"> - <param label="Repeat library source" name="source_type" type="select"> - <option selected="true" value="repbase">RepBase</option> + <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."> + <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option> + <option value="dfam_up">DFam (full/specific version)</option> <option value="library">Custom library of repeats</option> </param> - <when value="repbase"> - <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" /> - <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase --> + <when value="dfam"> <conditional name="species_source"> <param label="Select species name from a list?" name="species_from_list" type="select"> <option value="yes" selected="true">Yes</option> @@ -93,40 +97,26 @@ </param> <when value="yes"> <param name="species_list" type="select" label="Species"> - <option value="-species anopheles" selected="true">anopheles</option> - <option value="-species arabidopsis">arabidopsis</option> - <option value="-species artiodactyl">artiodactyl</option> - <option value="-species aspergillus">aspergillus</option> - <option value="-species carnivore">carnivore</option> - <option value="-species cat">cat</option> - <option value="-species chicken">chicken</option> - <option value="-species 'ciona intestinalis'">ciona intestinalis</option> - <option value="-species 'ciona savignyi'">ciona savignyi</option> - <option value="-species cow">cow</option> - <option value="-species danio">danio</option> - <option value="-species diatoaea">diatomea</option> - <option value="-species dog">dog</option> - <option value="-species drosophila">drosophila</option> - <option value="-species elegans">elegans</option> - <option value="-species fugu">fugu</option> - <option value="-species fungi" selected="true">fungi</option> - <option value="-species human">human</option> - <option value="-species maize">maize</option> - <option value="-species mammal">mammal</option> - <option value="-species mouse">mouse</option> - <option value="-species pig">pig</option> - <option value="-species rat">rat</option> - <option value="-species rice">rice</option> - <option value="-species rodentia">rodentia</option> - <option value="-species ruminantia">ruminantia</option> - <option value="-species wheat">wheat</option> + <option value="vertebrate">Vertebrate (other than below)</option> + <option value="mammal">Mammal (other than below)</option> + <option value="human" selected="true">Human</option> + <option value="rodent">Rodent</option> + <option value="mouse">Mouse</option> + <option value="rat">Rat</option> + <option value="danio">Danio (zebra fish)</option> + <option value="drosophila">Fruit fly (Drosophila melanogaster)</option> + <option value="elegans">Caenorhabditis elegans (nematode)</option> </param> </when> <when value="no"> - <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" /> + <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" /> </when> </conditional> </when> + <when value="dfam_up"> + <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" /> + <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" /> + </when> <when value="library"> <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" /> <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" /> @@ -199,7 +189,6 @@ <param name="input_fasta" value="small.fasta" ftype="fasta" /> <param name="source_type" value="library" /> <param name="gff" value="-gff" /> - <!-- <param name="show" value="yes" /> --> <param name="keep_alignments" value="-ali" /> <param name="poly" value="-poly" /> <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> @@ -213,14 +202,22 @@ </test> <test expect_num_outputs="4"> <param name="input_fasta" value="small.fasta" ftype="fasta" /> - <param name="source_type" value="repbase" /> - <param name="repbase_file" value="fake_repbase.embl" /> - <param name="repbase_file_name" value="fake.embl" /> - <param name="species_list" value="anopheles" /> - <output name="output_masked_genome" file="small.fasta.masked" /> - <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> - <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" /> - <output name="output_log" file="small_repbase.fasta.log" lines_diff="2"/> + <param name="source_type" value="dfam" /> + <param name="species_list" value="human" /> + <output name="output_masked_genome" file="small_dfam.fasta.masked" /> + <output name="output_table" file="small_dfam.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small_dfam.fasta.cat" lines_diff="2" /> + <output name="output_log" file="small_dfam.fasta.log" lines_diff="2"/> + </test> + <test expect_num_outputs="4"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="dfam_up" /> + <param name="dfam_lib" value="Dfam_partial_test.h5" ftype="h5" /> + <param name="species_name" value="rodent" /> + <output name="output_masked_genome" file="small_dfam_up.fasta.masked" /> + <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" /> + <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/> </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README.md Fri Dec 11 22:26:02 2020 +0000 @@ -0,0 +1,1 @@ +Dfam_partial_test.h5 was generated from the test dataset in https://github.com/Dfam-consortium/FamDB/ (commit: 6b28b66)
--- 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 @@ -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:
--- 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 @@ -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
--- 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 @@ -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"
--- /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 @@ -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
--- /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 @@ -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
--- /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 @@ -0,0 +1,286 @@ +>scaffold_1 +TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC +CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC +ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA +CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC +AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA +CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT +AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC +CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA +ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC +GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG +GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC +AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC +TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC +ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT +CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC +CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA +CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT +TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA +AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG +ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA +GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT +CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT +GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT +ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG +TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT +CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG +TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC +CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA +GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA +AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC +AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT +CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG +TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC +TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC +ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG +TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA +TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT +TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC +TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC +TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG +TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT +GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC +CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT +TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA +GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG +GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA +AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT +TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA +AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC +TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT +CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG +AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG +AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA +CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT +CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG +CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG +TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG +CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT +GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA +GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC +TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG +GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT +CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA +AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT +CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA +GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA +TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC +AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA +GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG +CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA +TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT +GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG +TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA +TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA +AACCTAAATCAGATCAGTATTTCTTATGACCCCCCTCCCCTACCACCCAT +CTTTAAAACAGCTCCAGTTCTCCTCAATCCCCCTGTACTTAGGTAGTTTT +TTTCTAGCGTCTTGGAGAAGTTGCCTCAGTTCTTCTGTGGATTTTAGGCT +GTCTCTGTGTCTTCTGTCTCCTCATGTATTCTCAGACTGACTCCATGATG +TTGAGATCAGGGCTCTGTGGTGGGGGGGTCAGACCATCTGTTGCGGGACT +CCTTGTTCTTCTTGTCTCTGAGGATAGTTCTTTATGATGCTGACTGTGTG +ATTGGACTCATTGTCCTGCTGCAGAATTAATCTGGGACTGATCAGACATC +TCCCTGATTGTACTGACAAAGGATAAGAGCAAAAACCTGTAGACTGCCTA +AAACTTCTGCACAGTACTGCACAATACTGTATGTATGTGTGATAATACTC +AGAAGTGATATAGAGTGGTTCAGGAGAAGCCTTAACTTACTTGTTCTTCT +TTTCCCTATGATGCAATTTCTCTCCAAGCAAACAGTACATAATGAAATAT +GTCTAAGAAAACACTAGCTGTTTGTCTTTTTGAAACACATTTAATAATTC +AGATTTAGCCACAAATTAAAAATGAGCTTATACTTTGAACTTGCCCATTG +GTTTTGATGTATGAAGCTGACAGATTTAGTCCACTGCATACTGCACTTTT +TTGGATAGTGAAATAAATTAATTTATTATGCAGCATTTAAGCATATTGCT +GTTATCTAGAATTTTATATATTAATAGGTATATATTATATTAACTCTTCA +TTTGCTTAAATTTGGCCTGTATATTCCTCCATTTTATACAACCTTTAGAA +AACACTGGAGTGAACAAAAATGTGAGGTTCAAAAGTGAGAGGAAAGAAAA +ATCAGTGTGTGCAGCAAGACTGTAAGAGTCCCTGAACAAAAGTGTTGATT +TATTGTTGGCTGTGAAAGTTTTTGCTGCAGGGGTTTTTGTAAACAGTGAC +TCTTCTTTATGTCTTTGTTTCTATCTTTTTGTGTTTTCTTTTTTCATCTT +ATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NATACTCATGCTTCTCTTTTACTCTAATGGAAAACATAGAATTGAGGTGC +AGTATCACTGAGAACAGCCAATGCTGATACTGTCATTTGTTATAGGATGT +TTACTTAAGAAATGATTGTGGCCTTATTTGCCAAAGACGATTAGGCCCTG +AGCCATTTGTACAGCCAATGTGACACCTCCGTAACCATAAGAAAAATTAT +GCTTCCACAAACAGAAAGAGAGACAAATACAGACAGTGAAAGCAAAACTA +TGAGAGAAGGGATAGCCATCTCAGCATTCAGCCAGTGTGTCACATGTCCA +GAGGGCTGCAATATGAAGCCAATAAACTGAGAGAAAGGTGTGATTCCAGA +GGGCTTTCCGGACTTTAAACTTTTCTCATTTTCACCTTCAGCTCGTTGTG +AAGCCTTCAATTGTTCCTTGGTCACATGAAGCCCCCTGTGTGTAAAATTG +ACATTCAGCTTATTACTCTCATCTACATCTCTAAAGTTGCACATGACTGC +CAGTAGAGGGTGCTCATGATTTGAGACAAGTAACTTTTCTGTGCTTGTGT +CAACAGTTAAAAATTCCCTATGGATACTTGAAAGAAATGCACCAGTGTTT +AAATTTAGACTCAGTCCAAGTAGGCTTTGCCATTTGCTTTACTGTTGTAA +TCAAATCAGTGCTCACAGTACATCAGTGGCAAAAGCAATTAGCTTAATTG +AGTTAGTAGGGAGTGAAAAGATAGATCACTATTTCCTGGCAGCGATATAT +TTTTCTCAGTTAACCTTCTCACAGAAAATTAGTTAGATGAGTTTCTTATC +TCATTAGAACCATTGTTGTTTATTATTTAAACCTGACCTTTATCCAGAGA +ATGTTTTTCACAGTAAGCATGTGTTTCACTCCAGCTCATACAGACACACC +TTGTGGCCAGTCAGGGAATGTGCATTAAAACTAATGTTCTCTCTGGTAGA +GCCATTCTGCCTATTCTGTTATTCACCAAAACTTTCCTGCCCAGATTTTT +CCATCTAGTCAGGGGACTTTTTCCTCAGCTGAACTGTCAGTAGCCAGCTG +CTCTGACCTTTACTCACCTCAGAGATTACTCATTCAAGTTATTTTACCAA +TGATGGAATAAAGTGAATACACACATCGTGACTTCATCATACTTTCCCTC +CTTTACCGTACTTTCCTAACATCAGTTAGCAAATTATACACTTAAATATG +CTAAAATAGAGATTTGTTTCAAATTGAAGAGCAACACAGGACACATTTGC +TTACACAAGTGACTCTATCTTATTTTTTAAGTGGCTGTCATCCTCAATAT +CATCAATATTTTAGGCATGTGAATGTAGGNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATTATTATGATAAAG +CTACACATTATACTGCAATTCCGGGCCAACACTATTGTTTCGCCCTTACA +GTACAGGACTGTACATATCACTGTCACTACAAATTGTTTCAGTGAGGCTC +AGATTACAGCTCATCTTGCTTAGTCATTACGGCTCAGACCACCAGACAAT +GTCTTTACGTCAGAGAAAGTCTGAGTGAGAGCTGTCCTTAAAACCAAGTC +CCATGAGGCAAGTAAAGAGGTGACTCGCTGAGAGGATCAGGGAGAGGNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNGGTGCTGCATTGAGTCGAGAGGTGTGAGGATGTTCGATAAGCCA +TTATCACTCTGCTCGGAGGACGTCAGGCCCTATCCTTTTTTCTTTGAGTC +ACCACTTTCTCACCACAGCCATCCTTCTTCCTTTGTCTGTTTAATCTTTT +GCAGCCAAACATTTGGTATGCAAACTATAGGAAGATATGGTCTGACACCG +ACTGATGTGATGCTAATGCCTTCTCTGTTTTATCCAATGACTCCTCATTT +ATCAGGACCAATCCAGCTATTGTGTGCTATTGGCCCAACACAGCATTAAA +CATGGTGACCAGAATAGCCACAGCAAAATAAATAACGGGCCTCTGTGACT +ATTGTATGTGCATTTCTTACAGCTGTCATTTTTCTTTTCTGTTAGCTTTC +ATTCTACTGTGCGTGCTCTCTATCTGCCTACGTTGTATCTGTGCCTTTTG +TTAAATTCATTCAGCCTTTTATCTGTCTTGAATTTCTTTCTCTGTGTCCT +CCTTTCCCTCTCTGTCTCAGCAGATCCGTCCCTTGTTTTTGCAGGAGAAG +CGCTCTGCGTCATGCAAGGTCCATCTTCTGCGACGCACCATCAGCGTTCC +AGTGGAAACACAGTTTCCAGAACTCCATAGCCAGCTGTCCACTGAGAGCG +GTGAGTAGCCTGAGGACATGCCTCTGCTGTGATTAGCATGCATCATTATT +TCCATACACACACTGGAAATCTTTTAATCGTTTTTCTTGACACAATTTAA +TTAATTTAAATAATTAATAACATTGAAATCAACTGTTAAACACTTGTTCA +ACATGGTTGTGGACAAAATCATCATAATGACTGTGGAGACTAAGGAGAAA +CAATGCTTTGTTAAAATCTTTGCTCTGGTTTTGGCTTTTTCTATATTCTA +TTTGTGTGTGCAGTGCTGCTAAACATCATCTTAGTCAGAGTCAAACTTGA +GCACTCATGCAGATGCTTGTTCTATTCAGTGGTCAAATGGGCAGTGTAGC +TTAGGAGAAGCACTTCTTTCCGCTCCTCAGTGACATAACCAGTCACACAC +TCACACAGGCAAGTGAGCCTTTTAAAATTGCTGATACTATTTTTTTCTAC +TTCATATCCACTAGATGGAGAGCTTGGTGCTTTGTAGCACTCCAGTGTAC +TTGGAATGTTTCATCATAACCACTAAGGCAGACATTGATAAAGGCTTCGG +TCTCTTTCAAACTGCAGGTGTCATGTTGCACTCTCCCTATTGCTTTTATG +AAAATGTAGTGCCGGTAATATAACACAGTTACTCTCTGCATATATCACTA +TGTACACTTACTTCTATGGAAAAGATGGAGCGCCACAGTGAAAACTGTTT +TGAGTCTGTGAGGGGAAAACACAGCATCAGTCACAGTGAAACACTAGGTG +GCACTCAGGTTTGACATTCAAGCATTTGTATCCCACAGTTACTGTTGCTG +GGTTGTTGGCTGGCATGCAACTTAATATGATCTATCTTTAAATCAGTGTG +TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNGTTCTGAGGTGGCATTGCCCTCAGGTATATATCCCTCAGG +CAGTGTTACTGGACAGCATATAGATTGTAATGTTGTGTAAGCAGTGTTGT +GTAAGCTTTTTTAACCAAAATGCTCTCATGTTTCTTTGTTACCACAGTGG +TTTTAGTGATGTTTTGTGCTGTGAACAGAATCATGATTTCTGCAGACACT +CCACATCTGTTTAAACAGTGATTTTCACATCTGTCTGTAACTGAGTCAGT +CAGTTTGTGGTTGGATTGATGTGTAGTGGGATCTACAGATCATCAACCCT +CGGGGAAGCCATTTAGTTCTGTGTTAAATAAAAATACAACTTTTGAGCAC +TGTTTTTTCATATTTTTCTTCATCCCTTAGTTGATATTAAAGGTGCTATA +TGTAGATTTTTGCTATCACTACATAGCCAATGTTAGGATTAAGAACCCCA +GCAACCCGAATGTTAACTCGTACTTTGCTTCTATTTCTATTACATATTTT +CTTCTATGGAAGTTAGGATGTTAACCAGCTAACCCCAGGTCATCTCATAA +TACCACTTGGCAATAGTCAGTCACTGTTGCATTCAGTCTGCCCCTCCAGC +ATGAAAGGATGAAGAAGTACCGCTACCCAGAAGGCGTAGTCTAACCCCTT +GTCTTGTAAACACAGCAATGGCTGAAGCTCTTGGTAAGTAAACAGCTGTT +AATGTCAGTGTTGGCTACATAGCTAAAACTTACACATAGCACCGTTAAAA +AAATAAATGGTAAGTTTTTGTCCTTTTAGTTAAAGCATGTAAATGTCAGT +TAAAACAATTTAGAAAATTTCTCATTCAAATAGTCATTTTATTTTGTGTG +CTATAAATACCTTCAGTTTTTTTTCTTGTACTTTATTTTAAACTCTTGTC +TTTCTCTTATGCCCCTTATCTACCAGGAGAGGTCACACTCTTGTTGATAG +CATGATAAGGAAATGAGCAGAGATGTCCTTATTTCTCCTCAAAGTTATTC +CCTGCATAGCACATATTTGACTTTAAAAATACAAAGACTACAGGTGCTAA +ATCACACACACAACACCCAAAAGAATAGAGGACTTTTAAATATGTGCATC +CCATTTTCTAATCTATATTCACCACTGATACAAGTGATGACACGGTGATG +AGAAAATAACGTAACATACATTATTATACAAGATTGGTATGATTGCTGTA +GGTTGGTTTTGTTTATCTGAGAAGGGACAGAGGCTAAAAGAATAAACAAA +GTCTGCCAGCTACTTCACTAATTACAGAGTACCCCTGCAACTCTGCCAAT +GACATTCTGAAACTTTTCCATGACTATTATGTAAGATAATTTTTGAATCA +CTGATTCAGATTTCCATAGCCAAGATACACTATTCTGCATGTTGGCTAGA +ATACATTACAATACATTAATATATTACTGTAGTGGTTATTATGTCAGCCA +TTTAAACATAATTTCATACTTTCAGCTGTTCGCAGGGCAAACTTTTTATT +TTTGTCACCTGAATCCAGTTGCATTTGGATTTGAATTCAGTGGTGACTGC +CAATGAAAAATAACTCACAGGGGCACTTAGAGATCTGAGGCGGCATTGAC +TGAACATCGAAGGGCTACTATTACAGAAATGCAAGTGGAAAAAGAATCTG +ATATGATACTTGCCAGTATGAAAAGCATAATTAGGACTTTAAATGCATGT +TTTAAATGTTTTTGTGAACCATAATTTCAGTGTAAAAGTTCCAGTTATAT +TTTAAAAGGAACTCCAAATATCCAGTGGTAGCATCAAGGTAACCTGAGAT +AAGTGAAAAGTAATTCTAAATTAATCAGTATGTTGAAATATCAGACATTT +GTGTGCATTATTGTTAGTGTGACCATGGTGGGATACTTCAAACACACTTG +TTCATTGGCAAAATAATTGTCACATGAATTAACACAAGTGACACTTTCAG +TATCATACTGACAGAATGTTTGTTGTTAACTTTATCCCTGAAAACAAACA +CTAATACATGTTCTTGTCGCCCCTTCAGTGCCTAACCTTTAAAATTGTGC +TTGTGAGTGTGTGTATGTGAGCGCACCTGTATGGTTTTCAAATAATGTTC +CACATCACAACACTACAAACACTCACATGGTCTATGTTTTACTAAATTAT +TCATTGGCGTAGGCCCCACCTGCTCTTGTCCTTGTGTGACACAGGCTCTA +AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC +AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG +AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC +ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT +AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA +AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT +ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT +TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT +ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA +TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA +TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT +GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA +ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA +TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG +GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT +TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT +ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA +TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG +AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA +AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC +GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT +TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG +ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG +ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA +CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA +CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT +TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG +GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG +GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC +CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA +AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC +TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG +TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC +AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC +AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT +TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA +TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC +ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA +GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG +GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT +GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC +AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA +ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC +TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT +AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT +CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC +TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT +TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT +TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA +GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG +AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG +ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT +TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA +CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA +AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG +CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA +AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA +CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG +AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC +TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC +CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC +TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT +TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC +TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA +GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT +AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA +TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT +ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG +CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA +TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC +TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC +CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT +TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC +AAGCACCCATGCCTAAATCA
--- /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 @@ -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+ +
--- /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 @@ -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-_
--- /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 @@ -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
--- /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 @@ -0,0 +1,286 @@ +>scaffold_1 +TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC +CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC +ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA +CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC +AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA +CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT +AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC +CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA +ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC +GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG +GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC +AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC +TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC +ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT +CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC +CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA +CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT +TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA +AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG +ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA +GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT +CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT +GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT +ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG +TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT +CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG +TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC +CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA +GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA +AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC +AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT +CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG +TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC +TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC +ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG +TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA +TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT +TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC +TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC +TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG +TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT +GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC +CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT +TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA +GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG +GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA +AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT +TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA +AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC +TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT +CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG +AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG +AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA +CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT +CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG +CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG +TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG +CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT +GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA +GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC +TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG +GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT +CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA +AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT +CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA +GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA +TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC +AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA +GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG +CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA +TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT +GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG +TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA +TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA +AACCTAAATCAGATCAGTATTTCTTATGACCCCCCTCCCCTACCACCCAT +CTTTAAAACAGCTCCAGTTCTCCTCAATCCCCCTGTACTTAGGTAGTTTT +TTTCTAGCGTCTTGGAGAAGTTGCCTCAGTTCTTCTGTGGATTTTAGGCT +GTCTCTGTGTCTTCTGTCTCCTCATGTATTCTCAGACTGACTCCATGATG +TTGAGATCAGGGCTCTGTGGTGGGGGGGTCAGACCATCTGTTGCGGGACT +CCTTGTTCTTCTTGTCTCTGAGGATAGTTCTTTATGATGCTGACTGTGTG +ATTGGACTCATTGTCCTGCTGCAGAATTAATCTGGGACTGATCAGACATC +TCCCTGATTGTACTGACAAAGGATAAGAGCAAAAACCTGTAGACTGCCTA +AAACTTCTGCACAGTACTGCACAATACTGTATGTATGTGTGATAATACTC +AGAAGTGATATAGAGTGGTTCAGGAGAAGCCTTAACTTACTTGTTCTTCT +TTTCCCTATGATGCAATTTCTCTCCAAGCAAACAGTACATAATGAAATAT +GTCTAAGAAAACACTAGCTGTTTGTCTTTTTGAAACACATTTAATAATTC +AGATTTAGCCACAAATTAAAAATGAGCTTATACTTTGAACTTGCCCATTG +GTTTTGATGTATGAAGCTGACAGATTTAGTCCACTGCATACTGCACTTTT +TTGGATAGTGAAATAAATTAATTTATTATGCAGCATTTAAGCATATTGCT +GTTATCTAGAATTTTATATATTAATAGGTATATATTATATTAACTCTTCA +TTTGCTTAAATTTGGCCTGTATATTCCTCCATTTTATACAACCTTTAGAA +AACACTGGAGTGAACAAAAATGTGAGGTTCAAAAGTGAGAGGAAAGAAAA +ATCAGTGTGTGCAGCAAGACTGTAAGAGTCCCTGAACAAAAGTGTTGATT +TATTGTTGGCTGTGAAAGTTTTTGCTGCAGGGGTTTTTGTAAACAGTGAC +TCTTCTTTATGTCTTTGTTTCTATCTTTTTGTGTTTTCTTTTTTCATCTT +ATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NATACTCATGCTTCTCTTTTACTCTAATGGAAAACATAGAATTGAGGTGC +AGTATCACTGAGAACAGCCAATGCTGATACTGTCATTTGTTATAGGATGT +TTACTTAAGAAATGATTGTGGCCTTATTTGCCAAAGACGATTAGGCCCTG +AGCCATTTGTACAGCCAATGTGACACCTCCGTAACCATAAGAAAAATTAT +GCTTCCACAAACAGAAAGAGAGACAAATACAGACAGTGAAAGCAAAACTA +TGAGAGAAGGGATAGCCATCTCAGCATTCAGCCAGTGTGTCACATGTCCA +GAGGGCTGCAATATGAAGCCAATAAACTGAGAGAAAGGTGTGATTCCAGA +GGGCTTTCCGGACTTTAAACTTTTCTCATTTTCACCTTCAGCTCGTTGTG +AAGCCTTCAATTGTTCCTTGGTCACATGAAGCCCCCTGTGTGTAAAATTG +ACATTCAGCTTATTACTCTCATCTACATCTCTAAAGTTGCACATGACTGC +CAGTAGAGGGTGCTCATGATTTGAGACAAGTAACTTTTCTGTGCTTGTGT +CAACAGTTAAAAATTCCCTATGGATACTTGAAAGAAATGCACCAGTGTTT +AAATTTAGACTCAGTCCAAGTAGGCTTTGCCATTTGCTTTACTGTTGTAA +TCAAATCAGTGCTCACAGTACATCAGTGGCAAAAGCAATTAGCTTAATTG +AGTTAGTAGGGAGTGAAAAGATAGATCACTATTTCCTGGCAGCGATATAT +TTTTCTCAGTTAACCTTCTCACAGAAAATTAGTTAGATGAGTTTCTTATC +TCATTAGAACCATTGTTGTTTATTATTTAAACCTGACCTTTATCCAGAGA +ATGTTTTTCACAGTAAGCATGTGTTTCACTCCAGCTCATACAGACACACC +TTGTGGCCAGTCAGGGAATGTGCATTAAAACTAATGTTCTCTCTGGTAGA +GCCATTCTGCCTATTCTGTTATTCACCAAAACTTTCCTGCCCAGATTTTT +CCATCTAGTCAGGGGACTTTTTCCTCAGCTGAACTGTCAGTAGCCAGCTG +CTCTGACCTTTACTCACCTCAGAGATTACTCATTCAAGTTATTTTACCAA +TGATGGAATAAAGTGAATACACACATCGTGACTTCATCATACTTTCCCTC +CTTTACCGTACTTTCCTAACATCAGTTAGCAAATTATACACTTAAATATG +CTAAAATAGAGATTTGTTTCAAATTGAAGAGCAACACAGGACACATTTGC +TTACACAAGTGACTCTATCTTATTTTTTAAGTGGCTGTCATCCTCAATAT +CATCAATATTTTAGGCATGTGAATGTAGGNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATTATTATGATAAAG +CTACACATTATACTGCAATTCCGGGCCAACACTATTGTTTCGCCCTTACA +GTACAGGACTGTACATATCACTGTCACTACAAATTGTTTCAGTGAGGCTC +AGATTACAGCTCATCTTGCTTAGTCATTACGGCTCAGACCACCAGACAAT +GTCTTTACGTCAGAGAAAGTCTGAGTGAGAGCTGTCCTTAAAACCAAGTC +CCATGAGGCAAGTAAAGAGGTGACTCGCTGAGAGGATCAGGGAGAGGNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNGGTGCTGCATTGAGTCGAGAGGTGTGAGGATGTTCGATAAGCCA +TTATCACTCTGCTCGGAGGACGTCAGGCCCTATCCTTTTTTCTTTGAGTC +ACCACTTTCTCACCACAGCCATCCTTCTTCCTTTGTCTGTTTAATCTTTT +GCAGCCAAACATTTGGTATGCAAACTATAGGAAGATATGGTCTGACACCG +ACTGATGTGATGCTAATGCCTTCTCTGTTTTATCCAATGACTCCTCATTT +ATCAGGACCAATCCAGCTATTGTGTGCTATTGGCCCAACACAGCATTAAA +CATGGTGACCAGAATAGCCACAGCAAAATAAATAACGGGCCTCTGTGACT +ATTGTATGTGCATTTCTTACAGCTGTCATTTTTCTTTTCTGTTAGCTTTC +ATTCTACTGTGCGTGCTCTCTATCTGCCTACGTTGTATCTGTGCCTTTTG +TTAAATTCATTCAGCCTTTTATCTGTCTTGAATTTCTTTCTCTGTGTCCT +CCTTTCCCTCTCTGTCTCAGCAGATCCGTCCCTTGTTTTTGCAGGAGAAG +CGCTCTGCGTCATGCAAGGTCCATCTTCTGCGACGCACCATCAGCGTTCC +AGTGGAAACACAGTTTCCAGAACTCCATAGCCAGCTGTCCACTGAGAGCG +GTGAGTAGCCTGAGGACATGCCTCTGCTGTGATTAGCATGCATCATTATT +TCCATACACACACTGGAAATCTTTTAATCGTTTTTCTTGACACAATTTAA +TTAATTTAAATAATTAATAACATTGAAATCAACTGTTAAACACTTGTTCA +ACATGGTTGTGGACAAAATCATCATAATGACTGTGGAGACTAAGGAGAAA +CAATGCTTTGTTAAAATCTTTGCTCTGGTTTTGGCTTTTTCTATATTCTA +TTTGTGTGTGCAGTGCTGCTAAACATCATCTTAGTCAGAGTCAAACTTGA +GCACTCATGCAGATGCTTGTTCTATTCAGTGGTCAAATGGGCAGTGTAGC +TTAGGAGAAGCACTTCTTTCCGCTCCTCAGTGACATAACCAGTCACACAC +TCACACAGGCAAGTGAGCCTTTTAAAATTGCTGATACTATTTTTTTCTAC +TTCATATCCACTAGATGGAGAGCTTGGTGCTTTGTAGCACTCCAGTGTAC +TTGGAATGTTTCATCATAACCACTAAGGCAGACATTGATAAAGGCTTCGG +TCTCTTTCAAACTGCAGGTGTCATGTTGCACTCTCCCTATTGCTTTTATG +AAAATGTAGTGCCGGTAATATAACACAGTTACTCTCTGCATATATCACTA +TGTACACTTACTTCTATGGAAAAGATGGAGCGCCACAGTGAAAACTGTTT +TGAGTCTGTGAGGGGAAAACACAGCATCAGTCACAGTGAAACACTAGGTG +GCACTCAGGTTTGACATTCAAGCATTTGTATCCCACAGTTACTGTTGCTG +GGTTGTTGGCTGGCATGCAACTTAATATGATCTATCTTTAAATCAGTGTG +TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCACAACATTATT +TTGTCTACACCCTGCATACAGCACAGTATATTAAATTTAGGTTTTATTAA +GTTAAGTAATGTTCTGAGGTGGCATTGCCCTCAGGTATATATCCCTCAGG +CAGTGTTACTGGACAGCATATAGATTGTAATGTTGTGTAAGCAGTGTTGT +GTAAGCTTTTTTAACCAAAATGCTCTCATGTTTCTTTGTTACCACAGTGG +TTTTAGTGATGTTTTGTGCTGTGAACAGAATCATGATTTCTGCAGACACT +CCACATCTGTTTAAACAGTGATTTTCACATCTGTCTGTAACTGAGTCAGT +CAGTTTGTGGTTGGATTGATGTGTAGTGGGATCTACAGATCATCAACCCT +CGGGGAAGCCATTTAGTTCTGTGTTAAATAAAAATACAACTTTTGAGCAC +TGTTTTTTCATATTTTTCTTCATCCCTTAGTTGATATTAAAGGTGCTATA +TGTAGATTTTTGCTATCACTACATAGCCAATGTTAGGATTAAGAACCCCA +GCAACCCGAATGTTAACTCGTACTTTGCTTCTATTTCTATTACATATTTT +CTTCTATGGAAGTTAGGATGTTAACCAGCTAACCCCAGGTCATCTCATAA +TACCACTTGGCAATAGTCAGTCACTGTTGCATTCAGTCTGCCCCTCCAGC +ATGAAAGGATGAAGAAGTACCGCTACCCAGAAGGCGTAGTCTAACCCCTT +GTCTTGTAAACACAGCAATGGCTGAAGCTCTTGGTAAGTAAACAGCTGTT +AATGTCAGTGTTGGCTACATAGCTAAAACTTACACATAGCACCGTTAAAA +AAATAAATGGTAAGTTTTTGTCCTTTTAGTTAAAGCATGTAAATGTCAGT +TAAAACAATTTAGAAAATTTCTCATTCAAATAGTCATTTTATTTTGTGTG +CTATAAATACCTTCAGTTTTTTTTCTTGTACTTTATTTTAAACTCTTGTC +TTTCTCTTATGCCCCTTATCTACCAGGAGAGGTCACACTCTTGTTGATAG +CATGATAAGGAAATGAGCAGAGATGTCCTTATTTCTCCTCAAAGTTATTC +CCTGCATAGCACATATTTGACTTTAAAAATACAAAGACTACAGGTGCTAA +ATCACACACACAACACCCAAAAGAATAGAGGACTTTTAAATATGTGCATC +CCATTTTCTAATCTATATTCACCACTGATACAAGTGATGACACGGTGATG +AGAAAATAACGTAACATACATTATTATACAAGATTGGTATGATTGCTGTA +GGTTGGTTTTGTTTATCTGAGAAGGGACAGAGGCTAAAAGAATAAACAAA +GTCTGCCAGCTACTTCACTAATTACAGAGTACCCCTGCAACTCTGCCAAT +GACATTCTGAAACTTTTCCATGACTATTATGTAAGATAATTTTTGAATCA +CTGATTCAGATTTCCATAGCCAAGATACACTATTCTGCATGTTGGCTAGA +ATACATTACAATACATTAATATATTACTGTAGTGGTTATTATGTCAGCCA +TTTAAACATAATTTCATACTTTCAGCTGTTCGCAGGGCAAACTTTTTATT +TTTGTCACCTGAATCCAGTTGCATTTGGATTTGAATTCAGTGGTGACTGC +CAATGAAAAATAACTCACAGGGGCACTTAGAGATCTGAGGCGGCATTGAC +TGAACATCGAAGGGCTACTATTACAGAAATGCAAGTGGAAAAAGAATCTG +ATATGATACTTGCCAGTATGAAAAGCATAATTAGGACTTTAAATGCATGT +TTTAAATGTTTTTGTGAACCATAATTTCAGTGTAAAAGTTCCAGTTATAT +TTTAAAAGGAACTCCAAATATCCAGTGGTAGCATCAAGGTAACCTGAGAT +AAGTGAAAAGTAATTCTAAATTAATCAGTATGTTGAAATATCAGACATTT +GTGTGCATTATTGTTAGTGTGACCATGGTGGGATACTTCAAACACACTTG +TTCATTGGCAAAATAATTGTCACATGAATTAACACAAGTGACACTTTCAG +TATCATACTGACAGAATGTTTGTTGTTAACTTTATCCCTGAAAACAAACA +CTAATACATGTTCTTGTCGCCCCTTCAGTGCCTAACCTTTAAAATTGTGC +TTGTGAGTGTGTGTATGTGAGCGCACCTGTATGGTTTTCAAATAATGTTC +CACATCACAACACTACAAACACTCACATGGTCTATGTTTTACTAAATTAT +TCATTGGCGTAGGCCCCACCTGCTCTTGTCCTTGTGTGACACAGGCTCTA +AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC +AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG +AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC +ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT +AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA +AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT +ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT +TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT +ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA +TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA +TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT +GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA +ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA +TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG +GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT +TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT +ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA +TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG +AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA +AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC +GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT +TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG +ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG +ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA +CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA +CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT +TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG +GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG +GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC +CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA +AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC +TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG +TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC +AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC +AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT +TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA +TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC +ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA +GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG +GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT +GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC +AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA +ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC +TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT +AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT +CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC +TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT +TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT +TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA +GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG +AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG +ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT +TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA +CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA +AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG +CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA +AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA +CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG +AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC +TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC +CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC +TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT +TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC +TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA +GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT +AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA +TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT +ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG +CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA +TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC +TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC +CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT +TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC +AAGCACCCATGCCTAAATCA
--- /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 @@ -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+ +
--- 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 @@ -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
--- 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 @@ -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+ -