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changeset 11:72aade318318 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749"
author iuc
date Thu, 20 May 2021 12:56:42 +0000
parents bfc70c8cc5ca
children 39b40a9a6296
files macros.xml repeatmasker.xml test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.log test-data/small.fasta.stats test-data/small_dfam.fasta.cat test-data/small_dfam.fasta.log test-data/small_dfam.fasta.stats test-data/small_dfam_rattus.fasta.cat test-data/small_dfam_rattus.fasta.log test-data/small_dfam_rattus.fasta.masked test-data/small_dfam_rattus.fasta.stats test-data/small_dfam_up.fasta.cat test-data/small_dfam_up.fasta.log test-data/small_dfam_up.fasta.stats
diffstat 16 files changed, 527 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu May 20 12:56:42 2021 +0000
@@ -0,0 +1,33 @@
+<macros>
+    <token name="@TOOL_VERSION@">4.1.2-p1</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
+    <xml name="edam_ontology">
+        <edam_topics>                                                                                  
+            <edam_topic>topic_0157</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0237</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="requirements">
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">repeatmasker</requirement>
+    </requirements>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+        <xref type='bio.tools'>repeatmasker</xref>
+      </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{RepeatMasker,
+                    title = {RepeatMasker Open-4.0},
+                    howpublished = {\url{http://www.repeatmasker.org}},
+                    author = {Smit, AFA and Hubley, R and Green, P.},
+                    year = {2013-2015}}
+            </citation>
+        </citations>
+    </xml>
+</macros>
--- a/repeatmasker.xml	Fri Dec 11 22:26:02 2020 +0000
+++ b/repeatmasker.xml	Thu May 20 12:56:42 2021 +0000
@@ -1,11 +1,13 @@
-<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="4.1.1">repeatmasker</requirement>
-  </requirements>
-
-  <command detect_errors="exit_code"><![CDATA[
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
+    <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro='xrefs'/>
+    <expand macro='edam_ontology' />
+    <expand macro='requirements' />
+    <version_command>repeatmasker --version</version_command>
+    <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 &&
 
@@ -97,12 +99,10 @@
           </param>
           <when value="yes">
             <param name="species_list" type="select" label="Species">
-              <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="human" selected="true">Human (Homo sapiens)</option>
+              <option value="rodent">Rodent (Order Rodentia)</option>
+              <option value="mouse">Mouse (Mus musculus)</option>
+              <option value="rattus">Rat (Rattus sp.)</option>
               <option value="danio">Danio (zebra fish)</option>
               <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
               <option value="elegans">Caenorhabditis elegans (nematode)</option>
@@ -219,6 +219,15 @@
       <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>
+    <test expect_num_outputs="4">
+      <param name="input_fasta" value="small.fasta" ftype="fasta" />
+      <param name="source_type" value="dfam" />
+      <param name="species_list" value="rattus" />
+      <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />
+      <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />
+      <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />
+      <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>
+    </test>
   </tests>
   <help><![CDATA[
 RepeatMasker is a program that screens DNA for interspersed repeats and low
@@ -234,13 +243,5 @@
 .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
     ]]>
   </help>
-  <citations>
-    <citation type="bibtex">
-      @misc{RepeatMasker,
-        title = {RepeatMasker Open-4.0},
-        howpublished = {\url{http://www.repeatmasker.org}},
-        author = {Smit, AFA and Hubley, R and Green, P.},
-        year = {2013-2015}}
-    </citation>
-  </citations>
+  <expand macro="citations" />
 </tool>
--- a/test-data/small.fasta.cat	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small.fasta.cat	Thu May 20 12:56:42 2021 +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 4.1.1 , default mode
+RepeatMasker version 4.1.2-p1 , default mode
 run with rmblastn version 2.10.0+
 RM Library: 
--- a/test-data/small.fasta.gff	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small.fasta.gff	Thu May 20 12:56:42 2021 +0000
@@ -1,5 +1,5 @@
 ##gff-version 2
-##date 2020-12-11
+##date 2021-05-20
 ##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.log	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small.fasta.log	Thu May 20 12:56:42 2021 +0000
@@ -1,4 +1,4 @@
-SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
+SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
 
 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
--- a/test-data/small.fasta.stats	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small.fasta.stats	Thu May 20 12:56:42 2021 +0000
@@ -53,8 +53,8 @@
   Runs of >=20 X/Ns in query were excluded in % calcs
 
 
-RepeatMasker version 4.1.1 , default mode
-                                        
+RepeatMasker version 4.1.2-p1 , default mode
+                                     
 run with rmblastn version 2.10.0+
-The query was compared to unclassified sequences in ".../dataset_a9c6a294-8dbb-4a71-ad9c-e36735923fbf.dat"
-
+The query was compared to unclassified sequences in ".../dataset_a3b3078d-de09-4651-9e83-62019a3d45ba.dat"
+FamDB: 
--- a/test-data/small_dfam.fasta.cat	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam.fasta.cat	Thu May 20 12:56:42 2021 +0000
@@ -113,6 +113,6 @@
 ## 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
+RepeatMasker version 4.1.2-p1 , default mode
 run with rmblastn version 2.10.0+
-RM Library: CONS-Dfam_3.2
+RM Library: CONS-Dfam_3.3
--- a/test-data/small_dfam.fasta.log	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam.fasta.log	Thu May 20 12:56:42 2021 +0000
@@ -1,4 +1,4 @@
-SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
+SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
 
 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
--- a/test-data/small_dfam.fasta.stats	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam.fasta.stats	Thu May 20 12:56:42 2021 +0000
@@ -45,7 +45,7 @@
 
 
 The query species was assumed to be human         
-RepeatMasker version 4.1.1 , default mode
-                                        
+RepeatMasker version 4.1.2-p1 , default mode
+                                     
 run with rmblastn version 2.10.0+
-
+FamDB: CONS-Dfam_3.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_dfam_rattus.fasta.cat	Thu May 20 12:56:42 2021 +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 4.1.2-p1 , default mode
+run with rmblastn version 2.10.0+
+RM Library: CONS-Dfam_3.3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_dfam_rattus.fasta.log	Thu May 20 12:56:42 2021 +0000
@@ -0,0 +1,10 @@
+SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
+
+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_rattus.fasta.masked	Thu May 20 12:56:42 2021 +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_rattus.fasta.stats	Thu May 20 12:56:42 2021 +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 rattus        
+RepeatMasker version 4.1.2-p1 , default mode
+                                     
+run with rmblastn version 2.10.0+
+FamDB: CONS-Dfam_3.3
--- a/test-data/small_dfam_up.fasta.cat	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam_up.fasta.cat	Thu May 20 12:56:42 2021 +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 4.1.1 , default mode
+RepeatMasker version 4.1.2-p1 , default mode
 run with rmblastn version 2.10.0+
 RM Library: CONS-_
--- a/test-data/small_dfam_up.fasta.log	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam_up.fasta.log	Thu May 20 12:56:42 2021 +0000
@@ -1,4 +1,4 @@
-SW score	% div.	% del.	% ins.	query sequence	pos in  query: begin	end	(left)	repeat	class/family	pos in repeat: begin	end	(left)	ID
+SW scoret% div.t% del.t% ins.tquery sequencetpos in  query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID
 
 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
--- a/test-data/small_dfam_up.fasta.stats	Fri Dec 11 22:26:02 2020 +0000
+++ b/test-data/small_dfam_up.fasta.stats	Thu May 20 12:56:42 2021 +0000
@@ -47,7 +47,7 @@
 
 
 The query species was assumed to be rodent        
-RepeatMasker version 4.1.1 , default mode
-                                        
+RepeatMasker version 4.1.2-p1 , default mode
+                                     
 run with rmblastn version 2.10.0+
-
+FamDB: CONS-_