# HG changeset patch
# User iuc
# Date 1607725562 0
# Node ID bfc70c8cc5ca40a304d19d5f9fae81e4022a04d7
# Parent  438f65cb1d1498973f61bca8d10e906a83854746
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 69abffb867af7c4329eaa513201bd6626ac39cbf"

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
@@ -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[
diff -r 438f65cb1d14 -r bfc70c8cc5ca test-data/Dfam_partial_test.h5
Binary file test-data/Dfam_partial_test.h5 has changed
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
@@ -0,0 +1,1 @@
+Dfam_partial_test.h5 was generated from the test dataset in https://github.com/Dfam-consortium/FamDB/ (commit: 6b28b66)
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
@@ -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: 
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
@@ -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
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
@@ -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"
 
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
@@ -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
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
@@ -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
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
@@ -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
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
@@ -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+
+
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
@@ -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-_
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
@@ -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
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
@@ -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
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
@@ -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+
+
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
@@ -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
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
@@ -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+
-