# HG changeset patch
# User artbio
# Date 1505856195 14400
# Node ID 15e3e29f310e58b1084273d7318084b4c00ea3ad
# Parent  51b4590a972dd7cf9c4e2265b8139fc91c4929d8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b

diff -r 51b4590a972d -r 15e3e29f310e RepEnrich.py
--- a/RepEnrich.py	Mon Sep 18 17:22:07 2017 -0400
+++ b/RepEnrich.py	Tue Sep 19 17:23:15 2017 -0400
@@ -431,34 +431,34 @@
 if allcountmethod == "TRUE":
     fout1 = open(outputfolder + os.path.sep + outputfile_prefix
                  + '_total_counts.txt', 'w')
-    for key in reptotalcounts.keys():
+    for key in sorted(reptotalcounts.keys()):
         fout1.write(str(key) + '\t' + repeatclass[key] + '\t' +
                     repeatfamily[key] + '\t' + str(reptotalcounts[key])
                     + '\n')
     fout2 = open(outputfolder + os.path.sep + outputfile_prefix
                  + '_class_total_counts.txt', 'w')
-    for key in classtotalcounts.keys():
+    for key in sorted(classtotalcounts.keys()):
         fout2.write(str(key) + '\t' + str(classtotalcounts[key]) + '\n')
     fout3 = open(outputfolder + os.path.sep + outputfile_prefix
                  + '_family_total_counts.txt', 'w')
-    for key in familytotalcounts.keys():
+    for key in sorted(familytotalcounts.keys()):
         fout3.write(str(key) + '\t' + str(familytotalcounts[key]) + '\n')
     fout4 = open(outputfolder + os.path.sep + outputfile_prefix +
                  '_unique_counts.txt', 'w')
-    for key in repcounts2.keys():
+    for key in sorted(repcounts2.keys()):
         fout4.write(str(key) + '\t' + repeatclass[key] + '\t' +
                     repeatfamily[key] + '\t' + str(repcounts2[key]) + '\n')
         fout5 = open(outputfolder + os.path.sep + outputfile_prefix
                      + '_class_fraction_counts.txt', 'w')
-    for key in classfractionalcounts.keys():
+    for key in sorted(classfractionalcounts.keys()):
         fout5.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
     fout6 = open(outputfolder + os.path.sep + outputfile_prefix +
                  '_family_fraction_counts.txt', 'w')
-    for key in familyfractionalcounts.keys():
+    for key in sorted(familyfractionalcounts.keys()):
         fout6.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
     fout7 = open(outputfolder + os.path.sep + outputfile_prefix
                  + '_fraction_counts.txt', 'w')
-    for key in fractionalcounts.keys():
+    for key in sorted(fractionalcounts.keys()):
         fout7.write(str(key) + '\t' + repeatclass[key] + '\t' +
                     repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
                     + '\n')
@@ -472,15 +472,15 @@
 else:
     fout1 = open(outputfolder + os.path.sep + outputfile_prefix +
                  '_class_fraction_counts.txt', 'w')
-    for key in classfractionalcounts.keys():
+    for key in sorted(classfractionalcounts.keys()):
         fout1.write(str(key) + '\t' + str(classfractionalcounts[key]) + '\n')
     fout2 = open(outputfolder + os.path.sep + outputfile_prefix +
                  '_family_fraction_counts.txt', 'w')
-    for key in familyfractionalcounts.keys():
+    for key in sorted(familyfractionalcounts.keys()):
         fout2.write(str(key) + '\t' + str(familyfractionalcounts[key]) + '\n')
     fout3 = open(outputfolder + os.path.sep + outputfile_prefix +
                  '_fraction_counts.txt', 'w')
-    for key in fractionalcounts.keys():
+    for key in sorted(fractionalcounts.keys()):
         fout3.write(str(key) + '\t' + repeatclass[key] + '\t' +
                     repeatfamily[key] + '\t' + str(int(fractionalcounts[key]))
                     + '\n')
diff -r 51b4590a972d -r 15e3e29f310e edgeR_repenrich.R
--- a/edgeR_repenrich.R	Mon Sep 18 17:22:07 2017 -0400
+++ b/edgeR_repenrich.R	Tue Sep 19 17:23:15 2017 -0400
@@ -101,10 +101,10 @@
 filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error")
 sizes <- c()
 for (file in filesi) {
-    sizes <- c(sizes, read.delim(file, header=FALSE)[1,1])
+    sizes <- c(sizes, read.delim(file, header=TRUE)[1,1])
     }
 for (file in filesj) {
-    sizes <- c(sizes, read.delim(file, header=FALSE)[1,1])
+    sizes <- c(sizes, read.delim(file, header=TRUE)[1,1])
     }
 
 # build a meta data object
diff -r 51b4590a972d -r 15e3e29f310e edger-repenrich.xml
--- a/edger-repenrich.xml	Mon Sep 18 17:22:07 2017 -0400
+++ b/edger-repenrich.xml	Tue Sep 19 17:23:15 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.1">
+<tool id="edger-repenrich" name="edgeR-repenrich" version="1.4.2">
     <description>Determines differentially expressed features from RepEnrich counts</description>
     <requirements>
         <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
diff -r 51b4590a972d -r 15e3e29f310e repenrich.xml
--- a/repenrich.xml	Mon Sep 18 17:22:07 2017 -0400
+++ b/repenrich.xml	Tue Sep 19 17:23:15 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="repenrich" name="RepEnrich" version="1.4.1">
+<tool id="repenrich" name="RepEnrich" version="1.4.2">
     <description>Repeat Element Profiling</description>
     <requirements>
         <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -24,12 +24,14 @@
             bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
             TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
             NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
-            echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb &&
+            echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
+            echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
         #else:
             bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
             TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
             NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
-            echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb &&
+            echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
+            echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
         #end if
         samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam &&
         samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
@@ -65,14 +67,10 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb">
-        </data>
-        <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular">
-        </data>
-        <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular">
-        </data>
-        <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular">
-        </data>
+        <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" />
+        <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular" />
+        <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular" />
+        <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" />
    </outputs>
 
     <tests>
diff -r 51b4590a972d -r 15e3e29f310e test-data/353_fraction_counts.tab
--- a/test-data/353_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/353_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,210 +1,210 @@
-LSU-rRNA_Dme	rRNA	rRNA	3078755
-FW3_DM	LINE	Jockey	913
-DMTOM1_LTR	LTR	Gypsy	1012
-R1_DM	LINE	R1	5407
-TAHRE	LINE	Jockey	3914
-G4_DM	LINE	Jockey	3407
-BS	LINE	Jockey	5001
-Stalker2_I-int	LTR	Gypsy	12474
-Stalker3_LTR	LTR	Gypsy	439
-TABOR_I-int	LTR	Gypsy	3081
-G7_DM	LINE	Jockey	98
-BEL_I-int	LTR	Pao	21860
-Gypsy6_I-int	LTR	Gypsy	6746
+5S_DM	RNA	RNA	10392
 ACCORD_I-int	LTR	Gypsy	2165
-DM412B_LTR	LTR	Gypsy	2910
-G2_DM	LINE	Jockey	1132
-SSU-rRNA_Hsa	rRNA	rRNA	172100
-TART_B1	LINE	Jockey	21513
-S2_DM	DNA	TcMar-Tc1	733
-LOOPER1_DM	DNA	PiggyBac	589
-HOBO	DNA	hAT-hobo	4404
+ACCORD_LTR	LTR	Gypsy	220
+ACCORD2_I-int	LTR	Gypsy	2458
+ACCORD2_LTR	LTR	Gypsy	192
+ALA_DM	Unknown	Unknown	6
 ARS406_DM	Unknown	Unknown	719
-G6_DM	LINE	Jockey	3473
-DOC2_DM	LINE	Jockey	4538
 Baggins1	LINE	LOA	3893
-NINJA_LTR	LTR	Pao	406
-TRANSIB2	DNA	CMC-Transib	3076
-Gypsy5_LTR	LTR	Gypsy	451
-MDG3_LTR	LTR	Gypsy	848
-Gypsy12A_LTR	LTR	Gypsy	2242
-Gypsy_LTR	LTR	Gypsy	917
-TIRANT_LTR	LTR	Gypsy	1279
-I_DM	LINE	I	7013
-DIVER2_I-int	LTR	Pao	5627
-P-1_DY	DNA	P	2
-Invader2_I-int	LTR	Gypsy	5510
-DOC6_DM	LINE	Jockey	1240
-BURDOCK_LTR	LTR	Gypsy	370
-SSU-rRNA_Dme	rRNA	rRNA	4153
-MAX_LTR	LTR	Pao	753
-STALKER4_LTR	LTR	Gypsy	1210
-XDMR_DM	Unknown	Unknown	4328
 BARI_DM	DNA	TcMar-Tc1	902
-Transib-N1_DM	DNA	CMC-Transib	371
-Gypsy5_I-int	LTR	Gypsy	2186
-XDMR	Unknown	Unknown	1440
-ACCORD2_LTR	LTR	Gypsy	192
-POGON1	DNA	TcMar-Pogo	403
+BARI1	DNA	TcMar-Tc1	322
+BATUMI_I-int	LTR	Pao	4789
+BATUMI_LTR	LTR	Pao	403
+BEL_I-int	LTR	Pao	21860
+BEL_LTR	LTR	Pao	858
+Bica_I-int	LTR	Gypsy	1390
+Bica_LTR	LTR	Gypsy	125
+BLASTOPIA_I-int	LTR	Gypsy	9540
+BLASTOPIA_LTR	LTR	Gypsy	478
+BLOOD_I-int	LTR	Gypsy	17222
+BLOOD_LTR	LTR	Gypsy	746
+BS	LINE	Jockey	5001
+BS2	LINE	Jockey	4991
+BS3_DM	LINE	Jockey	877
 BS4_DM	LINE	Jockey	21
-ALA_DM	Unknown	Unknown	6
-Gypsy1-I_DM	LTR	Gypsy	6297
-ACCORD_LTR	LTR	Gypsy	220
 BURDOCK_I-int	LTR	Gypsy	3332
-ZAM_I-int	LTR	Gypsy	4426
-Invader5_I-int	LTR	Gypsy	335
-G3_DM	LINE	Jockey	556
-ROOA_I-int	LTR	Pao	4589
-Gypsy1-LTR_DM	LTR	Gypsy	795
+BURDOCK_LTR	LTR	Gypsy	370
+Chimpo_I-int	LTR	Gypsy	1060
+Chimpo_LTR	LTR	Gypsy	120
+Chouto_I-int	LTR	Gypsy	1304
+Chouto_LTR	LTR	Gypsy	281
+CIRCE	LTR	Gypsy	3323
+Copia_I-int	LTR	Copia	26733
+Copia_LTR	LTR	Copia	1129
+Copia1-I_DM	LTR	Copia	3518
+Copia1-LTR_DM	LTR	Copia	566
+Copia2_I-int	LTR	Copia	3455
+Copia2_LTR_DM	LTR	Copia	486
+DIVER_I-int	LTR	Pao	15627
+DIVER_LTR	LTR	Pao	429
+DIVER2_I-int	LTR	Pao	5627
+DIVER2_LTR	LTR	Pao	535
 DM1731_I-int	LTR	Copia	4881
-ROO_I-int	LTR	Pao	28034
+DM1731_LTR	LTR	Copia	440
+DM176_I-int	LTR	Gypsy	2813
+DM176_LTR	LTR	Gypsy	872
+DM297_I-int	LTR	Gypsy	11530
+DM297_LTR	LTR	Gypsy	1478
 DM412	LTR	Gypsy	23566
-PROTOP	DNA	P	4353
-TART-A	LINE	Jockey	3408
-ROO_LTR	LTR	Pao	1851
-DIVER_LTR	LTR	Pao	429
-Gypsy3_I-int	LTR	Gypsy	2753
-BATUMI_LTR	LTR	Pao	403
-IDEFIX_LTR	LTR	Gypsy	1844
-G5_DM	LINE	Jockey	2551
-HETA	LINE	Jockey	24397
-Gypsy11_I-int	LTR	Gypsy	560
-R1-2_DM	LINE	R1	177
-Gypsy11_LTR	LTR	Gypsy	149
-HELENA_RT	LINE	Jockey	627
-FTZ_DM	Unknown	Unknown	0
-MICROPIA_I-int	LTR	Gypsy	10355
-Invader4_I-int	LTR	Gypsy	1219
-PLACW_DM	DNA	P	127
-BLOOD_LTR	LTR	Gypsy	746
-R2_DM	LINE	R2	8407
-Copia1-I_DM	LTR	Copia	3518
-Gypsy4_I-int	LTR	Gypsy	10056
-Chouto_LTR	LTR	Gypsy	281
-BATUMI_I-int	LTR	Pao	4789
-DNAREP1_DM	RC	Helitron	63954
+DM412B_LTR	LTR	Gypsy	2910
+DMCR1A	LINE	CR1	17957
+DMLTR5	LTR	Gypsy	160
+DMRP1	Unknown	Unknown	227
+DMRPR	Unknown	Unknown	187
+DMRT1A	LINE	R1	3540
 DMRT1B	LINE	R1	7119
 DMRT1C	LINE	R1	2087
-TLD2	LTR	Gypsy	17
-DMRT1A	LINE	R1	3540
-DM1731_LTR	LTR	Copia	440
-LSU-rRNA_Cel	rRNA	rRNA	326925
-Copia_LTR	LTR	Copia	1129
+DMTOM1_LTR	LTR	Gypsy	1012
+DNAREP1_DM	RC	Helitron	63954
+DOC	LINE	Jockey	16414
+DOC2_DM	LINE	Jockey	4538
+DOC3_DM	LINE	Jockey	10659
+DOC4_DM	LINE	Jockey	830
+DOC5_DM	LINE	Jockey	2183
+DOC6_DM	LINE	Jockey	1240
+FB4_DM	DNA	TcMar-Tc1	6939
+FROGGER_I-int	LTR	Copia	1361
+FROGGER_LTR	LTR	Copia	54
+FTZ_DM	Unknown	Unknown	0
+FUSHI_DM	Unknown	Unknown	0
+FW2_DM	LINE	Jockey	13847
+FW3_DM	LINE	Jockey	913
+G_DM	LINE	Jockey	8035
+G2_DM	LINE	Jockey	1132
+G3_DM	LINE	Jockey	556
+G4_DM	LINE	Jockey	3407
+G5_DM	LINE	Jockey	2551
+G5A_DM	LINE	Jockey	1595
+G6_DM	LINE	Jockey	3473
+G7_DM	LINE	Jockey	98
+GTWIN_I-int	LTR	Gypsy	5054
+GTWIN_LTR	LTR	Gypsy	467
+Gypsy_I-int	LTR	Gypsy	5634
+Gypsy_LTR	LTR	Gypsy	917
+Gypsy1-I_DM	LTR	Gypsy	6297
+Gypsy1-LTR_DM	LTR	Gypsy	795
+Gypsy10_I-int	LTR	Gypsy	1930
+Gypsy10_LTR	LTR	Gypsy	368
+Gypsy11_I-int	LTR	Gypsy	560
+Gypsy11_LTR	LTR	Gypsy	149
+Gypsy12_I-int	LTR	Gypsy	9627
+Gypsy12_LTR	LTR	Gypsy	5934
+Gypsy12A_LTR	LTR	Gypsy	2242
+Gypsy2_I-int	LTR	Gypsy	3453
+Gypsy2_LTR	LTR	Gypsy	485
+Gypsy2-I_DM	LTR	Gypsy	3896
+Gypsy2-LTR_DM	LTR	Gypsy	690
+Gypsy3_I-int	LTR	Gypsy	2753
+Gypsy3_LTR	LTR	Gypsy	447
+Gypsy4_I-int	LTR	Gypsy	10056
+Gypsy4_LTR	LTR	Gypsy	194
+Gypsy5_I-int	LTR	Gypsy	2186
+Gypsy5_LTR	LTR	Gypsy	451
+Gypsy6_I-int	LTR	Gypsy	6746
 Gypsy6_LTR	LTR	Gypsy	484
-Gypsy12_I-int	LTR	Gypsy	9627
-BLASTOPIA_LTR	LTR	Gypsy	478
-Bica_LTR	LTR	Gypsy	125
+Gypsy6A_LTR	LTR	Gypsy	573
+Gypsy7_I-int	LTR	Gypsy	1009
+Gypsy7_LTR	LTR	Gypsy	87
+Gypsy8_I-int	LTR	Gypsy	4083
 Gypsy8_LTR	LTR	Gypsy	1241
-NINJA_I-int	LTR	Pao	4503
-PROTOP_B	DNA	P	8285
-PROTOP_A	DNA	P	3384
+Gypsy9_I-int	LTR	Gypsy	474
+Gypsy9_LTR	LTR	Gypsy	42
+HELENA_RT	LINE	Jockey	627
+Helitron1_DM	RC	Helitron	6
+HETA	LINE	Jockey	24397
+HMSBEAGLE_I-int	LTR	Gypsy	5908
+HOBO	DNA	hAT-hobo	4404
+I_DM	LINE	I	7013
+IDEFIX_I-int	LTR	Gypsy	5547
+IDEFIX_LTR	LTR	Gypsy	1844
+Invader1_I-int	LTR	Gypsy	1672
+Invader1_LTR	LTR	Gypsy	1931
+Invader2_I-int	LTR	Gypsy	5510
+Invader2_LTR	LTR	Gypsy	472
+Invader3_I-int	LTR	Gypsy	3722
 Invader3_LTR	LTR	Gypsy	608
-Chimpo_LTR	LTR	Gypsy	120
-Invader2_LTR	LTR	Gypsy	472
-BLASTOPIA_I-int	LTR	Gypsy	9540
-FROGGER_LTR	LTR	Copia	54
+Invader4_I-int	LTR	Gypsy	1219
+Invader4_LTR	LTR	Gypsy	1228
+Invader5_I-int	LTR	Gypsy	335
+Invader5_LTR	LTR	Gypsy	64
+Invader6_I-int	LTR	Gypsy	6701
+Invader6_LTR	LTR	Gypsy	588
+IVK_DM	LINE	I	2921
+Jockey2	LINE	Jockey	1588
+LINEJ1_DM	LINE	Jockey	6329
+LmeSINE1c	SINE	tRNA-Deu-L2	1414
+LOOPER1_DM	DNA	PiggyBac	589
+LSU-rRNA_Cel	rRNA	rRNA	326925
+LSU-rRNA_Dme	rRNA	rRNA	3078755
+LSU-rRNA_Hsa	rRNA	rRNA	0
+M4DM	DNA	CMC-Transib	1650
+Mariner2_DM	DNA	TcMar-Tc1	1591
+MAX_I-int	LTR	Pao	9201
+MAX_LTR	LTR	Pao	753
+MDG1_I-int	LTR	Gypsy	13740
+MDG1_LTR	LTR	Gypsy	582
+MDG3_I-int	LTR	Gypsy	4971
+MDG3_LTR	LTR	Gypsy	848
+MICROPIA_I-int	LTR	Gypsy	10355
+MICROPIA_LTR	LTR	Gypsy	863
+MINOS	DNA	TcMar-Tc1	226
+MuDR-1_DEl	DNA	MULE-NOF	9
+NINJA_I-int	LTR	Pao	4503
+NINJA_LTR	LTR	Pao	406
+NOF_FB	DNA	MULE-NOF	960
 NOMAD_I-int	LTR	Gypsy	11594
+NOMAD_LTR	LTR	Gypsy	822
+NTS_DM	Other	Other	36205
+P-1_DY	DNA	P	2
+PLACW_DM	DNA	P	127
+POGO	DNA	TcMar-Pogo	2492
+POGON1	DNA	TcMar-Pogo	403
+PROTOP	DNA	P	4353
+PROTOP_A	DNA	P	3384
+PROTOP_B	DNA	P	8285
+QUASIMODO_I-int	LTR	Gypsy	13018
 QUASIMODO_LTR	LTR	Gypsy	1174
-TABOR_LTR	LTR	Gypsy	273
-Stalker2_LTR	LTR	Gypsy	672
-MICROPIA_LTR	LTR	Gypsy	863
-Gypsy9_I-int	LTR	Gypsy	474
-STALKER4_I-int	LTR	Gypsy	5741
-TRANSIB1	DNA	CMC-Transib	2116
-DOC	LINE	Jockey	16414
-TRANSIB3	DNA	CMC-Transib	1132
-Copia_I-int	LTR	Copia	26733
-TRANSIB4	DNA	CMC-Transib	571
-Gypsy10_LTR	LTR	Gypsy	368
-Invader3_I-int	LTR	Gypsy	3722
-Invader1_I-int	LTR	Gypsy	1672
-BS3_DM	LINE	Jockey	877
-Gypsy2-LTR_DM	LTR	Gypsy	690
-LSU-rRNA_Hsa	rRNA	rRNA	0
-NOMAD_LTR	LTR	Gypsy	822
-Helitron1_DM	RC	Helitron	6
-LINEJ1_DM	LINE	Jockey	6329
-Invader4_LTR	LTR	Gypsy	1228
-MDG3_I-int	LTR	Gypsy	4971
-LmeSINE1c	SINE	tRNA-Deu-L2	1414
+QUASIMODO2-I_DM	LTR	Gypsy	2225
+QUASIMODO2-LTR_DM	LTR	Gypsy	200
+R1_DM	LINE	R1	5407
+R1-2_DM	LINE	R1	177
+R2_DM	LINE	R2	8407
+ROO_I-int	LTR	Pao	28034
+ROO_LTR	LTR	Pao	1851
+ROOA_I-int	LTR	Pao	4589
+ROOA_LTR	LTR	Pao	483
+ROVER-I_DM	LTR	Gypsy	5589
 ROVER-LTR_DM	LTR	Gypsy	415
 S_DM	DNA	TcMar-Tc1	3476
-Invader6_I-int	LTR	Gypsy	6701
-ROVER-I_DM	LTR	Gypsy	5589
-QUASIMODO_I-int	LTR	Gypsy	13018
-Chouto_I-int	LTR	Gypsy	1304
-NTS_DM	Other	Other	36205
-Gypsy3_LTR	LTR	Gypsy	447
+S2_DM	DNA	TcMar-Tc1	733
 SSU-rRNA_Cel	rRNA	rRNA	2183
-MINOS	DNA	TcMar-Tc1	226
-DOC4_DM	LINE	Jockey	830
-ZAM_LTR	LTR	Gypsy	225
-QUASIMODO2-LTR_DM	LTR	Gypsy	200
-Gypsy2-I_DM	LTR	Gypsy	3896
-TRANSPAC_I-int	LTR	Gypsy	14982
-Bica_I-int	LTR	Gypsy	1390
-BS2	LINE	Jockey	4991
-BLOOD_I-int	LTR	Gypsy	17222
-DMCR1A	LINE	CR1	17957
-QUASIMODO2-I_DM	LTR	Gypsy	2225
-HMSBEAGLE_I-int	LTR	Gypsy	5908
-DMLTR5	LTR	Gypsy	160
-Gypsy7_LTR	LTR	Gypsy	87
-G5A_DM	LINE	Jockey	1595
-MDG1_I-int	LTR	Gypsy	13740
-Gypsy2_I-int	LTR	Gypsy	3453
-BARI1	DNA	TcMar-Tc1	322
-Invader5_LTR	LTR	Gypsy	64
-DM176_LTR	LTR	Gypsy	872
-DOC3_DM	LINE	Jockey	10659
-Copia1-LTR_DM	LTR	Copia	566
-TOM_I-int	LTR	Gypsy	2311
-NOF_FB	DNA	MULE-NOF	960
-Chimpo_I-int	LTR	Gypsy	1060
-DIVER_I-int	LTR	Pao	15627
+SSU-rRNA_Dme	rRNA	rRNA	4153
+SSU-rRNA_Hsa	rRNA	rRNA	172100
+Stalker2_I-int	LTR	Gypsy	12474
+Stalker2_LTR	LTR	Gypsy	672
+Stalker3_LTR	LTR	Gypsy	439
+STALKER4_I-int	LTR	Gypsy	5741
+STALKER4_LTR	LTR	Gypsy	1210
+TABOR_I-int	LTR	Gypsy	3081
+TABOR_LTR	LTR	Gypsy	273
+TAHRE	LINE	Jockey	3914
+TART_B1	LINE	Jockey	21513
+TART-A	LINE	Jockey	3408
+TC1_DM	DNA	TcMar-Tc1	1960
+TC1-2_DM	DNA	TcMar-Tc1	3948
 TIRANT_I-int	LTR	Gypsy	8559
-Gypsy2_LTR	LTR	Gypsy	485
-FB4_DM	DNA	TcMar-Tc1	6939
-GTWIN_LTR	LTR	Gypsy	467
-Invader6_LTR	LTR	Gypsy	588
-Gypsy8_I-int	LTR	Gypsy	4083
-G_DM	LINE	Jockey	8035
-TRANSPAC_LTR	LTR	Gypsy	555
-FUSHI_DM	Unknown	Unknown	0
+TIRANT_LTR	LTR	Gypsy	1279
+TLD2	LTR	Gypsy	17
+TOM_I-int	LTR	Gypsy	2311
+Transib-N1_DM	DNA	CMC-Transib	371
+TRANSIB1	DNA	CMC-Transib	2116
+TRANSIB2	DNA	CMC-Transib	3076
+TRANSIB3	DNA	CMC-Transib	1132
+TRANSIB4	DNA	CMC-Transib	571
 Transib5	DNA	CMC-Transib	965
-MuDR-1_DEl	DNA	MULE-NOF	9
-Mariner2_DM	DNA	TcMar-Tc1	1591
-DOC5_DM	LINE	Jockey	2183
-TC1_DM	DNA	TcMar-Tc1	1960
-Gypsy9_LTR	LTR	Gypsy	42
-DMRP1	Unknown	Unknown	227
-Gypsy10_I-int	LTR	Gypsy	1930
-Gypsy4_LTR	LTR	Gypsy	194
-DM297_LTR	LTR	Gypsy	1478
-ACCORD2_I-int	LTR	Gypsy	2458
-Invader1_LTR	LTR	Gypsy	1931
-BEL_LTR	LTR	Pao	858
-IVK_DM	LINE	I	2921
-M4DM	DNA	CMC-Transib	1650
-FW2_DM	LINE	Jockey	13847
-Copia2_I-int	LTR	Copia	3455
-MDG1_LTR	LTR	Gypsy	582
-Gypsy12_LTR	LTR	Gypsy	5934
-Gypsy7_I-int	LTR	Gypsy	1009
-FROGGER_I-int	LTR	Copia	1361
-Gypsy_I-int	LTR	Gypsy	5634
-5S_DM	RNA	RNA	10392
-GTWIN_I-int	LTR	Gypsy	5054
-CIRCE	LTR	Gypsy	3323
-DIVER2_LTR	LTR	Pao	535
-POGO	DNA	TcMar-Pogo	2492
-Gypsy6A_LTR	LTR	Gypsy	573
-MAX_I-int	LTR	Pao	9201
-ROOA_LTR	LTR	Pao	483
-DM176_I-int	LTR	Gypsy	2813
-Copia2_LTR_DM	LTR	Copia	486
-DM297_I-int	LTR	Gypsy	11530
-IDEFIX_I-int	LTR	Gypsy	5547
-Jockey2	LINE	Jockey	1588
-TC1-2_DM	DNA	TcMar-Tc1	3948
-DMRPR	Unknown	Unknown	187
+TRANSPAC_I-int	LTR	Gypsy	14982
+TRANSPAC_LTR	LTR	Gypsy	555
+XDMR	Unknown	Unknown	1440
+XDMR_DM	Unknown	Unknown	4328
+ZAM_I-int	LTR	Gypsy	4426
+ZAM_LTR	LTR	Gypsy	225
diff -r 51b4590a972d -r 15e3e29f310e test-data/354_fraction_counts.tab
--- a/test-data/354_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/354_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,210 +1,210 @@
-LSU-rRNA_Dme	rRNA	rRNA	3659329
-FW3_DM	LINE	Jockey	831
-DMTOM1_LTR	LTR	Gypsy	1004
-R1_DM	LINE	R1	7343
-TAHRE	LINE	Jockey	4560
-G4_DM	LINE	Jockey	3668
-BS	LINE	Jockey	7296
-Stalker2_I-int	LTR	Gypsy	12252
-Stalker3_LTR	LTR	Gypsy	593
-TABOR_I-int	LTR	Gypsy	3947
-G7_DM	LINE	Jockey	162
-BEL_I-int	LTR	Pao	23757
-Gypsy6_I-int	LTR	Gypsy	7489
+5S_DM	RNA	RNA	6317
 ACCORD_I-int	LTR	Gypsy	2723
-DM412B_LTR	LTR	Gypsy	3078
-G2_DM	LINE	Jockey	1328
-SSU-rRNA_Hsa	rRNA	rRNA	318045
-TART_B1	LINE	Jockey	25248
-S2_DM	DNA	TcMar-Tc1	765
-LOOPER1_DM	DNA	PiggyBac	821
-HOBO	DNA	hAT-hobo	5031
+ACCORD_LTR	LTR	Gypsy	295
+ACCORD2_I-int	LTR	Gypsy	2934
+ACCORD2_LTR	LTR	Gypsy	235
+ALA_DM	Unknown	Unknown	5
 ARS406_DM	Unknown	Unknown	563
-G6_DM	LINE	Jockey	4827
-DOC2_DM	LINE	Jockey	4438
 Baggins1	LINE	LOA	5136
-NINJA_LTR	LTR	Pao	491
-TRANSIB2	DNA	CMC-Transib	3197
-Gypsy5_LTR	LTR	Gypsy	651
-MDG3_LTR	LTR	Gypsy	1037
-Gypsy12A_LTR	LTR	Gypsy	3059
-Gypsy_LTR	LTR	Gypsy	1306
-TIRANT_LTR	LTR	Gypsy	1371
-I_DM	LINE	I	7987
-DIVER2_I-int	LTR	Pao	6679
-P-1_DY	DNA	P	8
-Invader2_I-int	LTR	Gypsy	6823
-DOC6_DM	LINE	Jockey	1259
-BURDOCK_LTR	LTR	Gypsy	287
-SSU-rRNA_Dme	rRNA	rRNA	7113
-MAX_LTR	LTR	Pao	1017
-STALKER4_LTR	LTR	Gypsy	1292
-XDMR_DM	Unknown	Unknown	3317
 BARI_DM	DNA	TcMar-Tc1	990
-Transib-N1_DM	DNA	CMC-Transib	308
-Gypsy5_I-int	LTR	Gypsy	2448
-XDMR	Unknown	Unknown	1249
-ACCORD2_LTR	LTR	Gypsy	235
-POGON1	DNA	TcMar-Pogo	331
+BARI1	DNA	TcMar-Tc1	395
+BATUMI_I-int	LTR	Pao	6395
+BATUMI_LTR	LTR	Pao	554
+BEL_I-int	LTR	Pao	23757
+BEL_LTR	LTR	Pao	875
+Bica_I-int	LTR	Gypsy	1852
+Bica_LTR	LTR	Gypsy	140
+BLASTOPIA_I-int	LTR	Gypsy	10309
+BLASTOPIA_LTR	LTR	Gypsy	550
+BLOOD_I-int	LTR	Gypsy	22330
+BLOOD_LTR	LTR	Gypsy	748
+BS	LINE	Jockey	7296
+BS2	LINE	Jockey	5595
+BS3_DM	LINE	Jockey	1252
 BS4_DM	LINE	Jockey	34
-ALA_DM	Unknown	Unknown	5
-Gypsy1-I_DM	LTR	Gypsy	8160
-ACCORD_LTR	LTR	Gypsy	295
 BURDOCK_I-int	LTR	Gypsy	3119
-ZAM_I-int	LTR	Gypsy	5129
-Invader5_I-int	LTR	Gypsy	416
-G3_DM	LINE	Jockey	797
-ROOA_I-int	LTR	Pao	4985
-Gypsy1-LTR_DM	LTR	Gypsy	1042
+BURDOCK_LTR	LTR	Gypsy	287
+Chimpo_I-int	LTR	Gypsy	1288
+Chimpo_LTR	LTR	Gypsy	94
+Chouto_I-int	LTR	Gypsy	1690
+Chouto_LTR	LTR	Gypsy	299
+CIRCE	LTR	Gypsy	3767
+Copia_I-int	LTR	Copia	27612
+Copia_LTR	LTR	Copia	1408
+Copia1-I_DM	LTR	Copia	3588
+Copia1-LTR_DM	LTR	Copia	771
+Copia2_I-int	LTR	Copia	4218
+Copia2_LTR_DM	LTR	Copia	891
+DIVER_I-int	LTR	Pao	13178
+DIVER_LTR	LTR	Pao	469
+DIVER2_I-int	LTR	Pao	6679
+DIVER2_LTR	LTR	Pao	793
 DM1731_I-int	LTR	Copia	5180
-ROO_I-int	LTR	Pao	31793
+DM1731_LTR	LTR	Copia	577
+DM176_I-int	LTR	Gypsy	3627
+DM176_LTR	LTR	Gypsy	899
+DM297_I-int	LTR	Gypsy	11837
+DM297_LTR	LTR	Gypsy	1489
 DM412	LTR	Gypsy	24086
-PROTOP	DNA	P	4942
-TART-A	LINE	Jockey	3697
-ROO_LTR	LTR	Pao	1639
-DIVER_LTR	LTR	Pao	469
-Gypsy3_I-int	LTR	Gypsy	3399
-BATUMI_LTR	LTR	Pao	554
-IDEFIX_LTR	LTR	Gypsy	2191
-G5_DM	LINE	Jockey	2601
-HETA	LINE	Jockey	23025
-Gypsy11_I-int	LTR	Gypsy	671
-R1-2_DM	LINE	R1	267
-Gypsy11_LTR	LTR	Gypsy	134
-HELENA_RT	LINE	Jockey	653
-FTZ_DM	Unknown	Unknown	0
-MICROPIA_I-int	LTR	Gypsy	10149
-Invader4_I-int	LTR	Gypsy	1439
-PLACW_DM	DNA	P	149
-BLOOD_LTR	LTR	Gypsy	748
-R2_DM	LINE	R2	15327
-Copia1-I_DM	LTR	Copia	3588
-Gypsy4_I-int	LTR	Gypsy	12113
-Chouto_LTR	LTR	Gypsy	299
-BATUMI_I-int	LTR	Pao	6395
-DNAREP1_DM	RC	Helitron	67821
+DM412B_LTR	LTR	Gypsy	3078
+DMCR1A	LINE	CR1	20380
+DMLTR5	LTR	Gypsy	161
+DMRP1	Unknown	Unknown	262
+DMRPR	Unknown	Unknown	128
+DMRT1A	LINE	R1	4456
 DMRT1B	LINE	R1	9706
 DMRT1C	LINE	R1	2530
-TLD2	LTR	Gypsy	65
-DMRT1A	LINE	R1	4456
-DM1731_LTR	LTR	Copia	577
-LSU-rRNA_Cel	rRNA	rRNA	520168
-Copia_LTR	LTR	Copia	1408
+DMTOM1_LTR	LTR	Gypsy	1004
+DNAREP1_DM	RC	Helitron	67821
+DOC	LINE	Jockey	17883
+DOC2_DM	LINE	Jockey	4438
+DOC3_DM	LINE	Jockey	11941
+DOC4_DM	LINE	Jockey	813
+DOC5_DM	LINE	Jockey	3037
+DOC6_DM	LINE	Jockey	1259
+FB4_DM	DNA	TcMar-Tc1	7149
+FROGGER_I-int	LTR	Copia	1611
+FROGGER_LTR	LTR	Copia	41
+FTZ_DM	Unknown	Unknown	0
+FUSHI_DM	Unknown	Unknown	0
+FW2_DM	LINE	Jockey	14234
+FW3_DM	LINE	Jockey	831
+G_DM	LINE	Jockey	8905
+G2_DM	LINE	Jockey	1328
+G3_DM	LINE	Jockey	797
+G4_DM	LINE	Jockey	3668
+G5_DM	LINE	Jockey	2601
+G5A_DM	LINE	Jockey	1804
+G6_DM	LINE	Jockey	4827
+G7_DM	LINE	Jockey	162
+GTWIN_I-int	LTR	Gypsy	5448
+GTWIN_LTR	LTR	Gypsy	598
+Gypsy_I-int	LTR	Gypsy	6822
+Gypsy_LTR	LTR	Gypsy	1306
+Gypsy1-I_DM	LTR	Gypsy	8160
+Gypsy1-LTR_DM	LTR	Gypsy	1042
+Gypsy10_I-int	LTR	Gypsy	2258
+Gypsy10_LTR	LTR	Gypsy	314
+Gypsy11_I-int	LTR	Gypsy	671
+Gypsy11_LTR	LTR	Gypsy	134
+Gypsy12_I-int	LTR	Gypsy	9778
+Gypsy12_LTR	LTR	Gypsy	6292
+Gypsy12A_LTR	LTR	Gypsy	3059
+Gypsy2_I-int	LTR	Gypsy	3190
+Gypsy2_LTR	LTR	Gypsy	479
+Gypsy2-I_DM	LTR	Gypsy	4606
+Gypsy2-LTR_DM	LTR	Gypsy	966
+Gypsy3_I-int	LTR	Gypsy	3399
+Gypsy3_LTR	LTR	Gypsy	566
+Gypsy4_I-int	LTR	Gypsy	12113
+Gypsy4_LTR	LTR	Gypsy	274
+Gypsy5_I-int	LTR	Gypsy	2448
+Gypsy5_LTR	LTR	Gypsy	651
+Gypsy6_I-int	LTR	Gypsy	7489
 Gypsy6_LTR	LTR	Gypsy	428
-Gypsy12_I-int	LTR	Gypsy	9778
-BLASTOPIA_LTR	LTR	Gypsy	550
-Bica_LTR	LTR	Gypsy	140
+Gypsy6A_LTR	LTR	Gypsy	617
+Gypsy7_I-int	LTR	Gypsy	1256
+Gypsy7_LTR	LTR	Gypsy	112
+Gypsy8_I-int	LTR	Gypsy	4809
 Gypsy8_LTR	LTR	Gypsy	1311
-NINJA_I-int	LTR	Pao	5274
-PROTOP_B	DNA	P	8690
-PROTOP_A	DNA	P	3533
+Gypsy9_I-int	LTR	Gypsy	504
+Gypsy9_LTR	LTR	Gypsy	51
+HELENA_RT	LINE	Jockey	653
+Helitron1_DM	RC	Helitron	3
+HETA	LINE	Jockey	23025
+HMSBEAGLE_I-int	LTR	Gypsy	7239
+HOBO	DNA	hAT-hobo	5031
+I_DM	LINE	I	7987
+IDEFIX_I-int	LTR	Gypsy	6193
+IDEFIX_LTR	LTR	Gypsy	2191
+Invader1_I-int	LTR	Gypsy	1832
+Invader1_LTR	LTR	Gypsy	3346
+Invader2_I-int	LTR	Gypsy	6823
+Invader2_LTR	LTR	Gypsy	492
+Invader3_I-int	LTR	Gypsy	4667
 Invader3_LTR	LTR	Gypsy	657
-Chimpo_LTR	LTR	Gypsy	94
-Invader2_LTR	LTR	Gypsy	492
-BLASTOPIA_I-int	LTR	Gypsy	10309
-FROGGER_LTR	LTR	Copia	41
+Invader4_I-int	LTR	Gypsy	1439
+Invader4_LTR	LTR	Gypsy	1420
+Invader5_I-int	LTR	Gypsy	416
+Invader5_LTR	LTR	Gypsy	69
+Invader6_I-int	LTR	Gypsy	6931
+Invader6_LTR	LTR	Gypsy	649
+IVK_DM	LINE	I	3349
+Jockey2	LINE	Jockey	1770
+LINEJ1_DM	LINE	Jockey	7025
+LmeSINE1c	SINE	tRNA-Deu-L2	599
+LOOPER1_DM	DNA	PiggyBac	821
+LSU-rRNA_Cel	rRNA	rRNA	520168
+LSU-rRNA_Dme	rRNA	rRNA	3659329
+LSU-rRNA_Hsa	rRNA	rRNA	5
+M4DM	DNA	CMC-Transib	1727
+Mariner2_DM	DNA	TcMar-Tc1	2011
+MAX_I-int	LTR	Pao	12395
+MAX_LTR	LTR	Pao	1017
+MDG1_I-int	LTR	Gypsy	16315
+MDG1_LTR	LTR	Gypsy	690
+MDG3_I-int	LTR	Gypsy	5392
+MDG3_LTR	LTR	Gypsy	1037
+MICROPIA_I-int	LTR	Gypsy	10149
+MICROPIA_LTR	LTR	Gypsy	797
+MINOS	DNA	TcMar-Tc1	173
+MuDR-1_DEl	DNA	MULE-NOF	6
+NINJA_I-int	LTR	Pao	5274
+NINJA_LTR	LTR	Pao	491
+NOF_FB	DNA	MULE-NOF	1272
 NOMAD_I-int	LTR	Gypsy	16469
+NOMAD_LTR	LTR	Gypsy	619
+NTS_DM	Other	Other	65954
+P-1_DY	DNA	P	8
+PLACW_DM	DNA	P	149
+POGO	DNA	TcMar-Pogo	2427
+POGON1	DNA	TcMar-Pogo	331
+PROTOP	DNA	P	4942
+PROTOP_A	DNA	P	3533
+PROTOP_B	DNA	P	8690
+QUASIMODO_I-int	LTR	Gypsy	14906
 QUASIMODO_LTR	LTR	Gypsy	1332
-TABOR_LTR	LTR	Gypsy	384
-Stalker2_LTR	LTR	Gypsy	726
-MICROPIA_LTR	LTR	Gypsy	797
-Gypsy9_I-int	LTR	Gypsy	504
-STALKER4_I-int	LTR	Gypsy	6207
-TRANSIB1	DNA	CMC-Transib	2082
-DOC	LINE	Jockey	17883
-TRANSIB3	DNA	CMC-Transib	1184
-Copia_I-int	LTR	Copia	27612
-TRANSIB4	DNA	CMC-Transib	635
-Gypsy10_LTR	LTR	Gypsy	314
-Invader3_I-int	LTR	Gypsy	4667
-Invader1_I-int	LTR	Gypsy	1832
-BS3_DM	LINE	Jockey	1252
-Gypsy2-LTR_DM	LTR	Gypsy	966
-LSU-rRNA_Hsa	rRNA	rRNA	5
-NOMAD_LTR	LTR	Gypsy	619
-Helitron1_DM	RC	Helitron	3
-LINEJ1_DM	LINE	Jockey	7025
-Invader4_LTR	LTR	Gypsy	1420
-MDG3_I-int	LTR	Gypsy	5392
-LmeSINE1c	SINE	tRNA-Deu-L2	599
+QUASIMODO2-I_DM	LTR	Gypsy	2717
+QUASIMODO2-LTR_DM	LTR	Gypsy	313
+R1_DM	LINE	R1	7343
+R1-2_DM	LINE	R1	267
+R2_DM	LINE	R2	15327
+ROO_I-int	LTR	Pao	31793
+ROO_LTR	LTR	Pao	1639
+ROOA_I-int	LTR	Pao	4985
+ROOA_LTR	LTR	Pao	400
+ROVER-I_DM	LTR	Gypsy	6513
 ROVER-LTR_DM	LTR	Gypsy	564
 S_DM	DNA	TcMar-Tc1	3612
-Invader6_I-int	LTR	Gypsy	6931
-ROVER-I_DM	LTR	Gypsy	6513
-QUASIMODO_I-int	LTR	Gypsy	14906
-Chouto_I-int	LTR	Gypsy	1690
-NTS_DM	Other	Other	65954
-Gypsy3_LTR	LTR	Gypsy	566
+S2_DM	DNA	TcMar-Tc1	765
 SSU-rRNA_Cel	rRNA	rRNA	3463
-MINOS	DNA	TcMar-Tc1	173
-DOC4_DM	LINE	Jockey	813
-ZAM_LTR	LTR	Gypsy	259
-QUASIMODO2-LTR_DM	LTR	Gypsy	313
-Gypsy2-I_DM	LTR	Gypsy	4606
-TRANSPAC_I-int	LTR	Gypsy	9674
-Bica_I-int	LTR	Gypsy	1852
-BS2	LINE	Jockey	5595
-BLOOD_I-int	LTR	Gypsy	22330
-DMCR1A	LINE	CR1	20380
-QUASIMODO2-I_DM	LTR	Gypsy	2717
-HMSBEAGLE_I-int	LTR	Gypsy	7239
-DMLTR5	LTR	Gypsy	161
-Gypsy7_LTR	LTR	Gypsy	112
-G5A_DM	LINE	Jockey	1804
-MDG1_I-int	LTR	Gypsy	16315
-Gypsy2_I-int	LTR	Gypsy	3190
-BARI1	DNA	TcMar-Tc1	395
-Invader5_LTR	LTR	Gypsy	69
-DM176_LTR	LTR	Gypsy	899
-DOC3_DM	LINE	Jockey	11941
-Copia1-LTR_DM	LTR	Copia	771
-TOM_I-int	LTR	Gypsy	2563
-NOF_FB	DNA	MULE-NOF	1272
-Chimpo_I-int	LTR	Gypsy	1288
-DIVER_I-int	LTR	Pao	13178
+SSU-rRNA_Dme	rRNA	rRNA	7113
+SSU-rRNA_Hsa	rRNA	rRNA	318045
+Stalker2_I-int	LTR	Gypsy	12252
+Stalker2_LTR	LTR	Gypsy	726
+Stalker3_LTR	LTR	Gypsy	593
+STALKER4_I-int	LTR	Gypsy	6207
+STALKER4_LTR	LTR	Gypsy	1292
+TABOR_I-int	LTR	Gypsy	3947
+TABOR_LTR	LTR	Gypsy	384
+TAHRE	LINE	Jockey	4560
+TART_B1	LINE	Jockey	25248
+TART-A	LINE	Jockey	3697
+TC1_DM	DNA	TcMar-Tc1	1840
+TC1-2_DM	DNA	TcMar-Tc1	3807
 TIRANT_I-int	LTR	Gypsy	10917
-Gypsy2_LTR	LTR	Gypsy	479
-FB4_DM	DNA	TcMar-Tc1	7149
-GTWIN_LTR	LTR	Gypsy	598
-Invader6_LTR	LTR	Gypsy	649
-Gypsy8_I-int	LTR	Gypsy	4809
-G_DM	LINE	Jockey	8905
-TRANSPAC_LTR	LTR	Gypsy	538
-FUSHI_DM	Unknown	Unknown	0
+TIRANT_LTR	LTR	Gypsy	1371
+TLD2	LTR	Gypsy	65
+TOM_I-int	LTR	Gypsy	2563
+Transib-N1_DM	DNA	CMC-Transib	308
+TRANSIB1	DNA	CMC-Transib	2082
+TRANSIB2	DNA	CMC-Transib	3197
+TRANSIB3	DNA	CMC-Transib	1184
+TRANSIB4	DNA	CMC-Transib	635
 Transib5	DNA	CMC-Transib	1123
-MuDR-1_DEl	DNA	MULE-NOF	6
-Mariner2_DM	DNA	TcMar-Tc1	2011
-DOC5_DM	LINE	Jockey	3037
-TC1_DM	DNA	TcMar-Tc1	1840
-Gypsy9_LTR	LTR	Gypsy	51
-DMRP1	Unknown	Unknown	262
-Gypsy10_I-int	LTR	Gypsy	2258
-Gypsy4_LTR	LTR	Gypsy	274
-DM297_LTR	LTR	Gypsy	1489
-ACCORD2_I-int	LTR	Gypsy	2934
-Invader1_LTR	LTR	Gypsy	3346
-BEL_LTR	LTR	Pao	875
-IVK_DM	LINE	I	3349
-M4DM	DNA	CMC-Transib	1727
-FW2_DM	LINE	Jockey	14234
-Copia2_I-int	LTR	Copia	4218
-MDG1_LTR	LTR	Gypsy	690
-Gypsy12_LTR	LTR	Gypsy	6292
-Gypsy7_I-int	LTR	Gypsy	1256
-FROGGER_I-int	LTR	Copia	1611
-Gypsy_I-int	LTR	Gypsy	6822
-5S_DM	RNA	RNA	6317
-GTWIN_I-int	LTR	Gypsy	5448
-CIRCE	LTR	Gypsy	3767
-DIVER2_LTR	LTR	Pao	793
-POGO	DNA	TcMar-Pogo	2427
-Gypsy6A_LTR	LTR	Gypsy	617
-MAX_I-int	LTR	Pao	12395
-ROOA_LTR	LTR	Pao	400
-DM176_I-int	LTR	Gypsy	3627
-Copia2_LTR_DM	LTR	Copia	891
-DM297_I-int	LTR	Gypsy	11837
-IDEFIX_I-int	LTR	Gypsy	6193
-Jockey2	LINE	Jockey	1770
-TC1-2_DM	DNA	TcMar-Tc1	3807
-DMRPR	Unknown	Unknown	128
+TRANSPAC_I-int	LTR	Gypsy	9674
+TRANSPAC_LTR	LTR	Gypsy	538
+XDMR	Unknown	Unknown	1249
+XDMR_DM	Unknown	Unknown	3317
+ZAM_I-int	LTR	Gypsy	5129
+ZAM_LTR	LTR	Gypsy	259
diff -r 51b4590a972d -r 15e3e29f310e test-data/355_fraction_counts.tab
--- a/test-data/355_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/355_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,210 +1,210 @@
-LSU-rRNA_Dme	rRNA	rRNA	4126525
-FW3_DM	LINE	Jockey	376
-DMTOM1_LTR	LTR	Gypsy	458
-R1_DM	LINE	R1	6019
-TAHRE	LINE	Jockey	1417
-G4_DM	LINE	Jockey	1225
-BS	LINE	Jockey	4135
-Stalker2_I-int	LTR	Gypsy	4814
-Stalker3_LTR	LTR	Gypsy	235
-TABOR_I-int	LTR	Gypsy	3691
-G7_DM	LINE	Jockey	418
-BEL_I-int	LTR	Pao	15192
-Gypsy6_I-int	LTR	Gypsy	3763
+5S_DM	RNA	RNA	4146
 ACCORD_I-int	LTR	Gypsy	2031
-DM412B_LTR	LTR	Gypsy	3001
-G2_DM	LINE	Jockey	764
-SSU-rRNA_Hsa	rRNA	rRNA	301813
-TART_B1	LINE	Jockey	5089
-S2_DM	DNA	TcMar-Tc1	205
-LOOPER1_DM	DNA	PiggyBac	31
-HOBO	DNA	hAT-hobo	2119
+ACCORD_LTR	LTR	Gypsy	344
+ACCORD2_I-int	LTR	Gypsy	1200
+ACCORD2_LTR	LTR	Gypsy	76
+ALA_DM	Unknown	Unknown	0
 ARS406_DM	Unknown	Unknown	230
-G6_DM	LINE	Jockey	786
-DOC2_DM	LINE	Jockey	2052
 Baggins1	LINE	LOA	1832
-NINJA_LTR	LTR	Pao	114
-TRANSIB2	DNA	CMC-Transib	1484
-Gypsy5_LTR	LTR	Gypsy	326
-MDG3_LTR	LTR	Gypsy	454
-Gypsy12A_LTR	LTR	Gypsy	1077
-Gypsy_LTR	LTR	Gypsy	1737
-TIRANT_LTR	LTR	Gypsy	1596
-I_DM	LINE	I	11149
-DIVER2_I-int	LTR	Pao	2668
-P-1_DY	DNA	P	4
-Invader2_I-int	LTR	Gypsy	3157
-DOC6_DM	LINE	Jockey	768
-BURDOCK_LTR	LTR	Gypsy	193
-SSU-rRNA_Dme	rRNA	rRNA	3822
-MAX_LTR	LTR	Pao	343
-STALKER4_LTR	LTR	Gypsy	803
-XDMR_DM	Unknown	Unknown	1587
 BARI_DM	DNA	TcMar-Tc1	522
-Transib-N1_DM	DNA	CMC-Transib	130
-Gypsy5_I-int	LTR	Gypsy	1036
-XDMR	Unknown	Unknown	903
-ACCORD2_LTR	LTR	Gypsy	76
-POGON1	DNA	TcMar-Pogo	256
+BARI1	DNA	TcMar-Tc1	125
+BATUMI_I-int	LTR	Pao	1842
+BATUMI_LTR	LTR	Pao	169
+BEL_I-int	LTR	Pao	15192
+BEL_LTR	LTR	Pao	605
+Bica_I-int	LTR	Gypsy	618
+Bica_LTR	LTR	Gypsy	67
+BLASTOPIA_I-int	LTR	Gypsy	12045
+BLASTOPIA_LTR	LTR	Gypsy	919
+BLOOD_I-int	LTR	Gypsy	13280
+BLOOD_LTR	LTR	Gypsy	542
+BS	LINE	Jockey	4135
+BS2	LINE	Jockey	2086
+BS3_DM	LINE	Jockey	453
 BS4_DM	LINE	Jockey	23
-ALA_DM	Unknown	Unknown	0
-Gypsy1-I_DM	LTR	Gypsy	22753
-ACCORD_LTR	LTR	Gypsy	344
 BURDOCK_I-int	LTR	Gypsy	2232
-ZAM_I-int	LTR	Gypsy	2892
-Invader5_I-int	LTR	Gypsy	117
-G3_DM	LINE	Jockey	250
-ROOA_I-int	LTR	Pao	2579
-Gypsy1-LTR_DM	LTR	Gypsy	576
+BURDOCK_LTR	LTR	Gypsy	193
+Chimpo_I-int	LTR	Gypsy	370
+Chimpo_LTR	LTR	Gypsy	33
+Chouto_I-int	LTR	Gypsy	518
+Chouto_LTR	LTR	Gypsy	159
+CIRCE	LTR	Gypsy	1570
+Copia_I-int	LTR	Copia	87220
+Copia_LTR	LTR	Copia	3075
+Copia1-I_DM	LTR	Copia	1946
+Copia1-LTR_DM	LTR	Copia	389
+Copia2_I-int	LTR	Copia	1892
+Copia2_LTR_DM	LTR	Copia	460
+DIVER_I-int	LTR	Pao	11751
+DIVER_LTR	LTR	Pao	328
+DIVER2_I-int	LTR	Pao	2668
+DIVER2_LTR	LTR	Pao	240
 DM1731_I-int	LTR	Copia	6873
-ROO_I-int	LTR	Pao	22941
+DM1731_LTR	LTR	Copia	321
+DM176_I-int	LTR	Gypsy	2298
+DM176_LTR	LTR	Gypsy	330
+DM297_I-int	LTR	Gypsy	42705
+DM297_LTR	LTR	Gypsy	2516
 DM412	LTR	Gypsy	23508
-PROTOP	DNA	P	2059
-TART-A	LINE	Jockey	1825
-ROO_LTR	LTR	Pao	1453
-DIVER_LTR	LTR	Pao	328
-Gypsy3_I-int	LTR	Gypsy	2258
-BATUMI_LTR	LTR	Pao	169
-IDEFIX_LTR	LTR	Gypsy	1012
-G5_DM	LINE	Jockey	1300
-HETA	LINE	Jockey	10327
-Gypsy11_I-int	LTR	Gypsy	168
-R1-2_DM	LINE	R1	68
-Gypsy11_LTR	LTR	Gypsy	48
-HELENA_RT	LINE	Jockey	416
-FTZ_DM	Unknown	Unknown	0
-MICROPIA_I-int	LTR	Gypsy	3327
-Invader4_I-int	LTR	Gypsy	1180
-PLACW_DM	DNA	P	204
-BLOOD_LTR	LTR	Gypsy	542
-R2_DM	LINE	R2	15128
-Copia1-I_DM	LTR	Copia	1946
-Gypsy4_I-int	LTR	Gypsy	5348
-Chouto_LTR	LTR	Gypsy	159
-BATUMI_I-int	LTR	Pao	1842
-DNAREP1_DM	RC	Helitron	36953
+DM412B_LTR	LTR	Gypsy	3001
+DMCR1A	LINE	CR1	8072
+DMLTR5	LTR	Gypsy	94
+DMRP1	Unknown	Unknown	144
+DMRPR	Unknown	Unknown	136
+DMRT1A	LINE	R1	1235
 DMRT1B	LINE	R1	4115
 DMRT1C	LINE	R1	670
-TLD2	LTR	Gypsy	1
-DMRT1A	LINE	R1	1235
-DM1731_LTR	LTR	Copia	321
-LSU-rRNA_Cel	rRNA	rRNA	251671
-Copia_LTR	LTR	Copia	3075
+DMTOM1_LTR	LTR	Gypsy	458
+DNAREP1_DM	RC	Helitron	36953
+DOC	LINE	Jockey	21700
+DOC2_DM	LINE	Jockey	2052
+DOC3_DM	LINE	Jockey	5205
+DOC4_DM	LINE	Jockey	658
+DOC5_DM	LINE	Jockey	752
+DOC6_DM	LINE	Jockey	768
+FB4_DM	DNA	TcMar-Tc1	3348
+FROGGER_I-int	LTR	Copia	546
+FROGGER_LTR	LTR	Copia	57
+FTZ_DM	Unknown	Unknown	0
+FUSHI_DM	Unknown	Unknown	0
+FW2_DM	LINE	Jockey	8864
+FW3_DM	LINE	Jockey	376
+G_DM	LINE	Jockey	4582
+G2_DM	LINE	Jockey	764
+G3_DM	LINE	Jockey	250
+G4_DM	LINE	Jockey	1225
+G5_DM	LINE	Jockey	1300
+G5A_DM	LINE	Jockey	582
+G6_DM	LINE	Jockey	786
+G7_DM	LINE	Jockey	418
+GTWIN_I-int	LTR	Gypsy	2930
+GTWIN_LTR	LTR	Gypsy	938
+Gypsy_I-int	LTR	Gypsy	11161
+Gypsy_LTR	LTR	Gypsy	1737
+Gypsy1-I_DM	LTR	Gypsy	22753
+Gypsy1-LTR_DM	LTR	Gypsy	576
+Gypsy10_I-int	LTR	Gypsy	927
+Gypsy10_LTR	LTR	Gypsy	162
+Gypsy11_I-int	LTR	Gypsy	168
+Gypsy11_LTR	LTR	Gypsy	48
+Gypsy12_I-int	LTR	Gypsy	2466
+Gypsy12_LTR	LTR	Gypsy	2680
+Gypsy12A_LTR	LTR	Gypsy	1077
+Gypsy2_I-int	LTR	Gypsy	1552
+Gypsy2_LTR	LTR	Gypsy	250
+Gypsy2-I_DM	LTR	Gypsy	2658
+Gypsy2-LTR_DM	LTR	Gypsy	385
+Gypsy3_I-int	LTR	Gypsy	2258
+Gypsy3_LTR	LTR	Gypsy	212
+Gypsy4_I-int	LTR	Gypsy	5348
+Gypsy4_LTR	LTR	Gypsy	218
+Gypsy5_I-int	LTR	Gypsy	1036
+Gypsy5_LTR	LTR	Gypsy	326
+Gypsy6_I-int	LTR	Gypsy	3763
 Gypsy6_LTR	LTR	Gypsy	760
-Gypsy12_I-int	LTR	Gypsy	2466
-BLASTOPIA_LTR	LTR	Gypsy	919
-Bica_LTR	LTR	Gypsy	67
+Gypsy6A_LTR	LTR	Gypsy	219
+Gypsy7_I-int	LTR	Gypsy	742
+Gypsy7_LTR	LTR	Gypsy	39
+Gypsy8_I-int	LTR	Gypsy	1247
 Gypsy8_LTR	LTR	Gypsy	486
-NINJA_I-int	LTR	Pao	1146
-PROTOP_B	DNA	P	4300
-PROTOP_A	DNA	P	1988
+Gypsy9_I-int	LTR	Gypsy	188
+Gypsy9_LTR	LTR	Gypsy	8
+HELENA_RT	LINE	Jockey	416
+Helitron1_DM	RC	Helitron	0
+HETA	LINE	Jockey	10327
+HMSBEAGLE_I-int	LTR	Gypsy	4079
+HOBO	DNA	hAT-hobo	2119
+I_DM	LINE	I	11149
+IDEFIX_I-int	LTR	Gypsy	3286
+IDEFIX_LTR	LTR	Gypsy	1012
+Invader1_I-int	LTR	Gypsy	1768
+Invader1_LTR	LTR	Gypsy	1903
+Invader2_I-int	LTR	Gypsy	3157
+Invader2_LTR	LTR	Gypsy	213
+Invader3_I-int	LTR	Gypsy	2022
 Invader3_LTR	LTR	Gypsy	227
-Chimpo_LTR	LTR	Gypsy	33
-Invader2_LTR	LTR	Gypsy	213
-BLASTOPIA_I-int	LTR	Gypsy	12045
-FROGGER_LTR	LTR	Copia	57
+Invader4_I-int	LTR	Gypsy	1180
+Invader4_LTR	LTR	Gypsy	679
+Invader5_I-int	LTR	Gypsy	117
+Invader5_LTR	LTR	Gypsy	23
+Invader6_I-int	LTR	Gypsy	3298
+Invader6_LTR	LTR	Gypsy	146
+IVK_DM	LINE	I	1769
+Jockey2	LINE	Jockey	760
+LINEJ1_DM	LINE	Jockey	15939
+LmeSINE1c	SINE	tRNA-Deu-L2	653
+LOOPER1_DM	DNA	PiggyBac	31
+LSU-rRNA_Cel	rRNA	rRNA	251671
+LSU-rRNA_Dme	rRNA	rRNA	4126525
+LSU-rRNA_Hsa	rRNA	rRNA	11
+M4DM	DNA	CMC-Transib	918
+Mariner2_DM	DNA	TcMar-Tc1	926
+MAX_I-int	LTR	Pao	3905
+MAX_LTR	LTR	Pao	343
+MDG1_I-int	LTR	Gypsy	8043
+MDG1_LTR	LTR	Gypsy	281
+MDG3_I-int	LTR	Gypsy	3770
+MDG3_LTR	LTR	Gypsy	454
+MICROPIA_I-int	LTR	Gypsy	3327
+MICROPIA_LTR	LTR	Gypsy	149
+MINOS	DNA	TcMar-Tc1	93
+MuDR-1_DEl	DNA	MULE-NOF	4
+NINJA_I-int	LTR	Pao	1146
+NINJA_LTR	LTR	Pao	114
+NOF_FB	DNA	MULE-NOF	63
 NOMAD_I-int	LTR	Gypsy	8154
+NOMAD_LTR	LTR	Gypsy	277
+NTS_DM	Other	Other	21753
+P-1_DY	DNA	P	4
+PLACW_DM	DNA	P	204
+POGO	DNA	TcMar-Pogo	1032
+POGON1	DNA	TcMar-Pogo	256
+PROTOP	DNA	P	2059
+PROTOP_A	DNA	P	1988
+PROTOP_B	DNA	P	4300
+QUASIMODO_I-int	LTR	Gypsy	8000
 QUASIMODO_LTR	LTR	Gypsy	528
-TABOR_LTR	LTR	Gypsy	88
-Stalker2_LTR	LTR	Gypsy	356
-MICROPIA_LTR	LTR	Gypsy	149
-Gypsy9_I-int	LTR	Gypsy	188
-STALKER4_I-int	LTR	Gypsy	3132
-TRANSIB1	DNA	CMC-Transib	289
-DOC	LINE	Jockey	21700
-TRANSIB3	DNA	CMC-Transib	741
-Copia_I-int	LTR	Copia	87220
-TRANSIB4	DNA	CMC-Transib	153
-Gypsy10_LTR	LTR	Gypsy	162
-Invader3_I-int	LTR	Gypsy	2022
-Invader1_I-int	LTR	Gypsy	1768
-BS3_DM	LINE	Jockey	453
-Gypsy2-LTR_DM	LTR	Gypsy	385
-LSU-rRNA_Hsa	rRNA	rRNA	11
-NOMAD_LTR	LTR	Gypsy	277
-Helitron1_DM	RC	Helitron	0
-LINEJ1_DM	LINE	Jockey	15939
-Invader4_LTR	LTR	Gypsy	679
-MDG3_I-int	LTR	Gypsy	3770
-LmeSINE1c	SINE	tRNA-Deu-L2	653
+QUASIMODO2-I_DM	LTR	Gypsy	1811
+QUASIMODO2-LTR_DM	LTR	Gypsy	105
+R1_DM	LINE	R1	6019
+R1-2_DM	LINE	R1	68
+R2_DM	LINE	R2	15128
+ROO_I-int	LTR	Pao	22941
+ROO_LTR	LTR	Pao	1453
+ROOA_I-int	LTR	Pao	2579
+ROOA_LTR	LTR	Pao	276
+ROVER-I_DM	LTR	Gypsy	3069
 ROVER-LTR_DM	LTR	Gypsy	168
 S_DM	DNA	TcMar-Tc1	2041
-Invader6_I-int	LTR	Gypsy	3298
-ROVER-I_DM	LTR	Gypsy	3069
-QUASIMODO_I-int	LTR	Gypsy	8000
-Chouto_I-int	LTR	Gypsy	518
-NTS_DM	Other	Other	21753
-Gypsy3_LTR	LTR	Gypsy	212
+S2_DM	DNA	TcMar-Tc1	205
 SSU-rRNA_Cel	rRNA	rRNA	1817
-MINOS	DNA	TcMar-Tc1	93
-DOC4_DM	LINE	Jockey	658
-ZAM_LTR	LTR	Gypsy	118
-QUASIMODO2-LTR_DM	LTR	Gypsy	105
-Gypsy2-I_DM	LTR	Gypsy	2658
-TRANSPAC_I-int	LTR	Gypsy	16760
-Bica_I-int	LTR	Gypsy	618
-BS2	LINE	Jockey	2086
-BLOOD_I-int	LTR	Gypsy	13280
-DMCR1A	LINE	CR1	8072
-QUASIMODO2-I_DM	LTR	Gypsy	1811
-HMSBEAGLE_I-int	LTR	Gypsy	4079
-DMLTR5	LTR	Gypsy	94
-Gypsy7_LTR	LTR	Gypsy	39
-G5A_DM	LINE	Jockey	582
-MDG1_I-int	LTR	Gypsy	8043
-Gypsy2_I-int	LTR	Gypsy	1552
-BARI1	DNA	TcMar-Tc1	125
-Invader5_LTR	LTR	Gypsy	23
-DM176_LTR	LTR	Gypsy	330
-DOC3_DM	LINE	Jockey	5205
-Copia1-LTR_DM	LTR	Copia	389
-TOM_I-int	LTR	Gypsy	3390
-NOF_FB	DNA	MULE-NOF	63
-Chimpo_I-int	LTR	Gypsy	370
-DIVER_I-int	LTR	Pao	11751
+SSU-rRNA_Dme	rRNA	rRNA	3822
+SSU-rRNA_Hsa	rRNA	rRNA	301813
+Stalker2_I-int	LTR	Gypsy	4814
+Stalker2_LTR	LTR	Gypsy	356
+Stalker3_LTR	LTR	Gypsy	235
+STALKER4_I-int	LTR	Gypsy	3132
+STALKER4_LTR	LTR	Gypsy	803
+TABOR_I-int	LTR	Gypsy	3691
+TABOR_LTR	LTR	Gypsy	88
+TAHRE	LINE	Jockey	1417
+TART_B1	LINE	Jockey	5089
+TART-A	LINE	Jockey	1825
+TC1_DM	DNA	TcMar-Tc1	1485
+TC1-2_DM	DNA	TcMar-Tc1	2287
 TIRANT_I-int	LTR	Gypsy	12728
-Gypsy2_LTR	LTR	Gypsy	250
-FB4_DM	DNA	TcMar-Tc1	3348
-GTWIN_LTR	LTR	Gypsy	938
-Invader6_LTR	LTR	Gypsy	146
-Gypsy8_I-int	LTR	Gypsy	1247
-G_DM	LINE	Jockey	4582
-TRANSPAC_LTR	LTR	Gypsy	979
-FUSHI_DM	Unknown	Unknown	0
+TIRANT_LTR	LTR	Gypsy	1596
+TLD2	LTR	Gypsy	1
+TOM_I-int	LTR	Gypsy	3390
+Transib-N1_DM	DNA	CMC-Transib	130
+TRANSIB1	DNA	CMC-Transib	289
+TRANSIB2	DNA	CMC-Transib	1484
+TRANSIB3	DNA	CMC-Transib	741
+TRANSIB4	DNA	CMC-Transib	153
 Transib5	DNA	CMC-Transib	328
-MuDR-1_DEl	DNA	MULE-NOF	4
-Mariner2_DM	DNA	TcMar-Tc1	926
-DOC5_DM	LINE	Jockey	752
-TC1_DM	DNA	TcMar-Tc1	1485
-Gypsy9_LTR	LTR	Gypsy	8
-DMRP1	Unknown	Unknown	144
-Gypsy10_I-int	LTR	Gypsy	927
-Gypsy4_LTR	LTR	Gypsy	218
-DM297_LTR	LTR	Gypsy	2516
-ACCORD2_I-int	LTR	Gypsy	1200
-Invader1_LTR	LTR	Gypsy	1903
-BEL_LTR	LTR	Pao	605
-IVK_DM	LINE	I	1769
-M4DM	DNA	CMC-Transib	918
-FW2_DM	LINE	Jockey	8864
-Copia2_I-int	LTR	Copia	1892
-MDG1_LTR	LTR	Gypsy	281
-Gypsy12_LTR	LTR	Gypsy	2680
-Gypsy7_I-int	LTR	Gypsy	742
-FROGGER_I-int	LTR	Copia	546
-Gypsy_I-int	LTR	Gypsy	11161
-5S_DM	RNA	RNA	4146
-GTWIN_I-int	LTR	Gypsy	2930
-CIRCE	LTR	Gypsy	1570
-DIVER2_LTR	LTR	Pao	240
-POGO	DNA	TcMar-Pogo	1032
-Gypsy6A_LTR	LTR	Gypsy	219
-MAX_I-int	LTR	Pao	3905
-ROOA_LTR	LTR	Pao	276
-DM176_I-int	LTR	Gypsy	2298
-Copia2_LTR_DM	LTR	Copia	460
-DM297_I-int	LTR	Gypsy	42705
-IDEFIX_I-int	LTR	Gypsy	3286
-Jockey2	LINE	Jockey	760
-TC1-2_DM	DNA	TcMar-Tc1	2287
-DMRPR	Unknown	Unknown	136
+TRANSPAC_I-int	LTR	Gypsy	16760
+TRANSPAC_LTR	LTR	Gypsy	979
+XDMR	Unknown	Unknown	903
+XDMR_DM	Unknown	Unknown	1587
+ZAM_I-int	LTR	Gypsy	2892
+ZAM_LTR	LTR	Gypsy	118
diff -r 51b4590a972d -r 15e3e29f310e test-data/356_fraction_counts.tab
--- a/test-data/356_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/356_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,210 +1,210 @@
-LSU-rRNA_Dme	rRNA	rRNA	5583038
-FW3_DM	LINE	Jockey	647
-DMTOM1_LTR	LTR	Gypsy	1403
-R1_DM	LINE	R1	15424
-TAHRE	LINE	Jockey	3806
-G4_DM	LINE	Jockey	2223
-BS	LINE	Jockey	5200
-Stalker2_I-int	LTR	Gypsy	10966
-Stalker3_LTR	LTR	Gypsy	543
-TABOR_I-int	LTR	Gypsy	5504
-G7_DM	LINE	Jockey	1949
-BEL_I-int	LTR	Pao	29338
-Gypsy6_I-int	LTR	Gypsy	11381
+5S_DM	RNA	RNA	6331
 ACCORD_I-int	LTR	Gypsy	4103
-DM412B_LTR	LTR	Gypsy	5607
-G2_DM	LINE	Jockey	1235
-SSU-rRNA_Hsa	rRNA	rRNA	563673
-TART_B1	LINE	Jockey	13382
-S2_DM	DNA	TcMar-Tc1	716
-LOOPER1_DM	DNA	PiggyBac	220
-HOBO	DNA	hAT-hobo	4375
+ACCORD_LTR	LTR	Gypsy	790
+ACCORD2_I-int	LTR	Gypsy	2286
+ACCORD2_LTR	LTR	Gypsy	213
+ALA_DM	Unknown	Unknown	9
 ARS406_DM	Unknown	Unknown	755
-G6_DM	LINE	Jockey	2874
-DOC2_DM	LINE	Jockey	4511
 Baggins1	LINE	LOA	5500
-NINJA_LTR	LTR	Pao	297
-TRANSIB2	DNA	CMC-Transib	3357
-Gypsy5_LTR	LTR	Gypsy	502
-MDG3_LTR	LTR	Gypsy	926
-Gypsy12A_LTR	LTR	Gypsy	2436
-Gypsy_LTR	LTR	Gypsy	3771
-TIRANT_LTR	LTR	Gypsy	3225
-I_DM	LINE	I	11479
-DIVER2_I-int	LTR	Pao	6446
-P-1_DY	DNA	P	13
-Invader2_I-int	LTR	Gypsy	5970
-DOC6_DM	LINE	Jockey	1718
-BURDOCK_LTR	LTR	Gypsy	543
-SSU-rRNA_Dme	rRNA	rRNA	9958
-MAX_LTR	LTR	Pao	958
-STALKER4_LTR	LTR	Gypsy	2040
-XDMR_DM	Unknown	Unknown	4049
 BARI_DM	DNA	TcMar-Tc1	1117
-Transib-N1_DM	DNA	CMC-Transib	366
-Gypsy5_I-int	LTR	Gypsy	2834
-XDMR	Unknown	Unknown	1771
-ACCORD2_LTR	LTR	Gypsy	213
-POGON1	DNA	TcMar-Pogo	641
+BARI1	DNA	TcMar-Tc1	370
+BATUMI_I-int	LTR	Pao	4723
+BATUMI_LTR	LTR	Pao	348
+BEL_I-int	LTR	Pao	29338
+BEL_LTR	LTR	Pao	927
+Bica_I-int	LTR	Gypsy	1561
+Bica_LTR	LTR	Gypsy	123
+BLASTOPIA_I-int	LTR	Gypsy	13780
+BLASTOPIA_LTR	LTR	Gypsy	1038
+BLOOD_I-int	LTR	Gypsy	27362
+BLOOD_LTR	LTR	Gypsy	1269
+BS	LINE	Jockey	5200
+BS2	LINE	Jockey	5214
+BS3_DM	LINE	Jockey	851
 BS4_DM	LINE	Jockey	8
-ALA_DM	Unknown	Unknown	9
-Gypsy1-I_DM	LTR	Gypsy	36962
-ACCORD_LTR	LTR	Gypsy	790
 BURDOCK_I-int	LTR	Gypsy	5190
-ZAM_I-int	LTR	Gypsy	6896
-Invader5_I-int	LTR	Gypsy	191
-G3_DM	LINE	Jockey	480
-ROOA_I-int	LTR	Pao	4103
-Gypsy1-LTR_DM	LTR	Gypsy	1432
+BURDOCK_LTR	LTR	Gypsy	543
+Chimpo_I-int	LTR	Gypsy	1366
+Chimpo_LTR	LTR	Gypsy	107
+Chouto_I-int	LTR	Gypsy	1231
+Chouto_LTR	LTR	Gypsy	162
+CIRCE	LTR	Gypsy	3676
+Copia_I-int	LTR	Copia	50888
+Copia_LTR	LTR	Copia	2612
+Copia1-I_DM	LTR	Copia	4100
+Copia1-LTR_DM	LTR	Copia	600
+Copia2_I-int	LTR	Copia	3614
+Copia2_LTR_DM	LTR	Copia	747
+DIVER_I-int	LTR	Pao	24742
+DIVER_LTR	LTR	Pao	547
+DIVER2_I-int	LTR	Pao	6446
+DIVER2_LTR	LTR	Pao	648
 DM1731_I-int	LTR	Copia	18829
-ROO_I-int	LTR	Pao	34023
+DM1731_LTR	LTR	Copia	1274
+DM176_I-int	LTR	Gypsy	4726
+DM176_LTR	LTR	Gypsy	560
+DM297_I-int	LTR	Gypsy	82387
+DM297_LTR	LTR	Gypsy	6128
 DM412	LTR	Gypsy	43689
-PROTOP	DNA	P	4775
-TART-A	LINE	Jockey	5092
-ROO_LTR	LTR	Pao	2219
-DIVER_LTR	LTR	Pao	547
-Gypsy3_I-int	LTR	Gypsy	5766
-BATUMI_LTR	LTR	Pao	348
-IDEFIX_LTR	LTR	Gypsy	2538
-G5_DM	LINE	Jockey	2714
-HETA	LINE	Jockey	22459
-Gypsy11_I-int	LTR	Gypsy	487
-R1-2_DM	LINE	R1	184
-Gypsy11_LTR	LTR	Gypsy	159
-HELENA_RT	LINE	Jockey	934
-FTZ_DM	Unknown	Unknown	0
-MICROPIA_I-int	LTR	Gypsy	6941
-Invader4_I-int	LTR	Gypsy	1888
-PLACW_DM	DNA	P	277
-BLOOD_LTR	LTR	Gypsy	1269
-R2_DM	LINE	R2	54042
-Copia1-I_DM	LTR	Copia	4100
-Gypsy4_I-int	LTR	Gypsy	13114
-Chouto_LTR	LTR	Gypsy	162
-BATUMI_I-int	LTR	Pao	4723
-DNAREP1_DM	RC	Helitron	76851
+DM412B_LTR	LTR	Gypsy	5607
+DMCR1A	LINE	CR1	17489
+DMLTR5	LTR	Gypsy	189
+DMRP1	Unknown	Unknown	295
+DMRPR	Unknown	Unknown	221
+DMRT1A	LINE	R1	3797
 DMRT1B	LINE	R1	9003
 DMRT1C	LINE	R1	1907
-TLD2	LTR	Gypsy	33
-DMRT1A	LINE	R1	3797
-DM1731_LTR	LTR	Copia	1274
-LSU-rRNA_Cel	rRNA	rRNA	363697
-Copia_LTR	LTR	Copia	2612
+DMTOM1_LTR	LTR	Gypsy	1403
+DNAREP1_DM	RC	Helitron	76851
+DOC	LINE	Jockey	29082
+DOC2_DM	LINE	Jockey	4511
+DOC3_DM	LINE	Jockey	11067
+DOC4_DM	LINE	Jockey	1030
+DOC5_DM	LINE	Jockey	1793
+DOC6_DM	LINE	Jockey	1718
+FB4_DM	DNA	TcMar-Tc1	7840
+FROGGER_I-int	LTR	Copia	1075
+FROGGER_LTR	LTR	Copia	85
+FTZ_DM	Unknown	Unknown	0
+FUSHI_DM	Unknown	Unknown	0
+FW2_DM	LINE	Jockey	17723
+FW3_DM	LINE	Jockey	647
+G_DM	LINE	Jockey	10948
+G2_DM	LINE	Jockey	1235
+G3_DM	LINE	Jockey	480
+G4_DM	LINE	Jockey	2223
+G5_DM	LINE	Jockey	2714
+G5A_DM	LINE	Jockey	1578
+G6_DM	LINE	Jockey	2874
+G7_DM	LINE	Jockey	1949
+GTWIN_I-int	LTR	Gypsy	7568
+GTWIN_LTR	LTR	Gypsy	2533
+Gypsy_I-int	LTR	Gypsy	24082
+Gypsy_LTR	LTR	Gypsy	3771
+Gypsy1-I_DM	LTR	Gypsy	36962
+Gypsy1-LTR_DM	LTR	Gypsy	1432
+Gypsy10_I-int	LTR	Gypsy	2236
+Gypsy10_LTR	LTR	Gypsy	363
+Gypsy11_I-int	LTR	Gypsy	487
+Gypsy11_LTR	LTR	Gypsy	159
+Gypsy12_I-int	LTR	Gypsy	5002
+Gypsy12_LTR	LTR	Gypsy	7572
+Gypsy12A_LTR	LTR	Gypsy	2436
+Gypsy2_I-int	LTR	Gypsy	4226
+Gypsy2_LTR	LTR	Gypsy	869
+Gypsy2-I_DM	LTR	Gypsy	7374
+Gypsy2-LTR_DM	LTR	Gypsy	1155
+Gypsy3_I-int	LTR	Gypsy	5766
+Gypsy3_LTR	LTR	Gypsy	681
+Gypsy4_I-int	LTR	Gypsy	13114
+Gypsy4_LTR	LTR	Gypsy	390
+Gypsy5_I-int	LTR	Gypsy	2834
+Gypsy5_LTR	LTR	Gypsy	502
+Gypsy6_I-int	LTR	Gypsy	11381
 Gypsy6_LTR	LTR	Gypsy	1423
-Gypsy12_I-int	LTR	Gypsy	5002
-BLASTOPIA_LTR	LTR	Gypsy	1038
-Bica_LTR	LTR	Gypsy	123
+Gypsy6A_LTR	LTR	Gypsy	793
+Gypsy7_I-int	LTR	Gypsy	1162
+Gypsy7_LTR	LTR	Gypsy	80
+Gypsy8_I-int	LTR	Gypsy	4176
 Gypsy8_LTR	LTR	Gypsy	1467
-NINJA_I-int	LTR	Pao	3676
-PROTOP_B	DNA	P	9371
-PROTOP_A	DNA	P	4465
+Gypsy9_I-int	LTR	Gypsy	429
+Gypsy9_LTR	LTR	Gypsy	62
+HELENA_RT	LINE	Jockey	934
+Helitron1_DM	RC	Helitron	0
+HETA	LINE	Jockey	22459
+HMSBEAGLE_I-int	LTR	Gypsy	7863
+HOBO	DNA	hAT-hobo	4375
+I_DM	LINE	I	11479
+IDEFIX_I-int	LTR	Gypsy	7222
+IDEFIX_LTR	LTR	Gypsy	2538
+Invader1_I-int	LTR	Gypsy	2993
+Invader1_LTR	LTR	Gypsy	2525
+Invader2_I-int	LTR	Gypsy	5970
+Invader2_LTR	LTR	Gypsy	417
+Invader3_I-int	LTR	Gypsy	4411
 Invader3_LTR	LTR	Gypsy	506
-Chimpo_LTR	LTR	Gypsy	107
-Invader2_LTR	LTR	Gypsy	417
-BLASTOPIA_I-int	LTR	Gypsy	13780
-FROGGER_LTR	LTR	Copia	85
+Invader4_I-int	LTR	Gypsy	1888
+Invader4_LTR	LTR	Gypsy	1624
+Invader5_I-int	LTR	Gypsy	191
+Invader5_LTR	LTR	Gypsy	47
+Invader6_I-int	LTR	Gypsy	6566
+Invader6_LTR	LTR	Gypsy	312
+IVK_DM	LINE	I	3025
+Jockey2	LINE	Jockey	1823
+LINEJ1_DM	LINE	Jockey	24891
+LmeSINE1c	SINE	tRNA-Deu-L2	627
+LOOPER1_DM	DNA	PiggyBac	220
+LSU-rRNA_Cel	rRNA	rRNA	363697
+LSU-rRNA_Dme	rRNA	rRNA	5583038
+LSU-rRNA_Hsa	rRNA	rRNA	15
+M4DM	DNA	CMC-Transib	1880
+Mariner2_DM	DNA	TcMar-Tc1	1096
+MAX_I-int	LTR	Pao	8914
+MAX_LTR	LTR	Pao	958
+MDG1_I-int	LTR	Gypsy	16306
+MDG1_LTR	LTR	Gypsy	650
+MDG3_I-int	LTR	Gypsy	7857
+MDG3_LTR	LTR	Gypsy	926
+MICROPIA_I-int	LTR	Gypsy	6941
+MICROPIA_LTR	LTR	Gypsy	460
+MINOS	DNA	TcMar-Tc1	273
+MuDR-1_DEl	DNA	MULE-NOF	32
+NINJA_I-int	LTR	Pao	3676
+NINJA_LTR	LTR	Pao	297
+NOF_FB	DNA	MULE-NOF	228
 NOMAD_I-int	LTR	Gypsy	11614
+NOMAD_LTR	LTR	Gypsy	757
+NTS_DM	Other	Other	56043
+P-1_DY	DNA	P	13
+PLACW_DM	DNA	P	277
+POGO	DNA	TcMar-Pogo	2909
+POGON1	DNA	TcMar-Pogo	641
+PROTOP	DNA	P	4775
+PROTOP_A	DNA	P	4465
+PROTOP_B	DNA	P	9371
+QUASIMODO_I-int	LTR	Gypsy	17910
 QUASIMODO_LTR	LTR	Gypsy	1625
-TABOR_LTR	LTR	Gypsy	443
-Stalker2_LTR	LTR	Gypsy	790
-MICROPIA_LTR	LTR	Gypsy	460
-Gypsy9_I-int	LTR	Gypsy	429
-STALKER4_I-int	LTR	Gypsy	7287
-TRANSIB1	DNA	CMC-Transib	1229
-DOC	LINE	Jockey	29082
-TRANSIB3	DNA	CMC-Transib	1802
-Copia_I-int	LTR	Copia	50888
-TRANSIB4	DNA	CMC-Transib	364
-Gypsy10_LTR	LTR	Gypsy	363
-Invader3_I-int	LTR	Gypsy	4411
-Invader1_I-int	LTR	Gypsy	2993
-BS3_DM	LINE	Jockey	851
-Gypsy2-LTR_DM	LTR	Gypsy	1155
-LSU-rRNA_Hsa	rRNA	rRNA	15
-NOMAD_LTR	LTR	Gypsy	757
-Helitron1_DM	RC	Helitron	0
-LINEJ1_DM	LINE	Jockey	24891
-Invader4_LTR	LTR	Gypsy	1624
-MDG3_I-int	LTR	Gypsy	7857
-LmeSINE1c	SINE	tRNA-Deu-L2	627
+QUASIMODO2-I_DM	LTR	Gypsy	3977
+QUASIMODO2-LTR_DM	LTR	Gypsy	298
+R1_DM	LINE	R1	15424
+R1-2_DM	LINE	R1	184
+R2_DM	LINE	R2	54042
+ROO_I-int	LTR	Pao	34023
+ROO_LTR	LTR	Pao	2219
+ROOA_I-int	LTR	Pao	4103
+ROOA_LTR	LTR	Pao	435
+ROVER-I_DM	LTR	Gypsy	6947
 ROVER-LTR_DM	LTR	Gypsy	415
 S_DM	DNA	TcMar-Tc1	4974
-Invader6_I-int	LTR	Gypsy	6566
-ROVER-I_DM	LTR	Gypsy	6947
-QUASIMODO_I-int	LTR	Gypsy	17910
-Chouto_I-int	LTR	Gypsy	1231
-NTS_DM	Other	Other	56043
-Gypsy3_LTR	LTR	Gypsy	681
+S2_DM	DNA	TcMar-Tc1	716
 SSU-rRNA_Cel	rRNA	rRNA	3855
-MINOS	DNA	TcMar-Tc1	273
-DOC4_DM	LINE	Jockey	1030
-ZAM_LTR	LTR	Gypsy	377
-QUASIMODO2-LTR_DM	LTR	Gypsy	298
-Gypsy2-I_DM	LTR	Gypsy	7374
-TRANSPAC_I-int	LTR	Gypsy	28474
-Bica_I-int	LTR	Gypsy	1561
-BS2	LINE	Jockey	5214
-BLOOD_I-int	LTR	Gypsy	27362
-DMCR1A	LINE	CR1	17489
-QUASIMODO2-I_DM	LTR	Gypsy	3977
-HMSBEAGLE_I-int	LTR	Gypsy	7863
-DMLTR5	LTR	Gypsy	189
-Gypsy7_LTR	LTR	Gypsy	80
-G5A_DM	LINE	Jockey	1578
-MDG1_I-int	LTR	Gypsy	16306
-Gypsy2_I-int	LTR	Gypsy	4226
-BARI1	DNA	TcMar-Tc1	370
-Invader5_LTR	LTR	Gypsy	47
-DM176_LTR	LTR	Gypsy	560
-DOC3_DM	LINE	Jockey	11067
-Copia1-LTR_DM	LTR	Copia	600
-TOM_I-int	LTR	Gypsy	6929
-NOF_FB	DNA	MULE-NOF	228
-Chimpo_I-int	LTR	Gypsy	1366
-DIVER_I-int	LTR	Pao	24742
+SSU-rRNA_Dme	rRNA	rRNA	9958
+SSU-rRNA_Hsa	rRNA	rRNA	563673
+Stalker2_I-int	LTR	Gypsy	10966
+Stalker2_LTR	LTR	Gypsy	790
+Stalker3_LTR	LTR	Gypsy	543
+STALKER4_I-int	LTR	Gypsy	7287
+STALKER4_LTR	LTR	Gypsy	2040
+TABOR_I-int	LTR	Gypsy	5504
+TABOR_LTR	LTR	Gypsy	443
+TAHRE	LINE	Jockey	3806
+TART_B1	LINE	Jockey	13382
+TART-A	LINE	Jockey	5092
+TC1_DM	DNA	TcMar-Tc1	2618
+TC1-2_DM	DNA	TcMar-Tc1	4438
 TIRANT_I-int	LTR	Gypsy	23165
-Gypsy2_LTR	LTR	Gypsy	869
-FB4_DM	DNA	TcMar-Tc1	7840
-GTWIN_LTR	LTR	Gypsy	2533
-Invader6_LTR	LTR	Gypsy	312
-Gypsy8_I-int	LTR	Gypsy	4176
-G_DM	LINE	Jockey	10948
-TRANSPAC_LTR	LTR	Gypsy	1457
-FUSHI_DM	Unknown	Unknown	0
+TIRANT_LTR	LTR	Gypsy	3225
+TLD2	LTR	Gypsy	33
+TOM_I-int	LTR	Gypsy	6929
+Transib-N1_DM	DNA	CMC-Transib	366
+TRANSIB1	DNA	CMC-Transib	1229
+TRANSIB2	DNA	CMC-Transib	3357
+TRANSIB3	DNA	CMC-Transib	1802
+TRANSIB4	DNA	CMC-Transib	364
 Transib5	DNA	CMC-Transib	973
-MuDR-1_DEl	DNA	MULE-NOF	32
-Mariner2_DM	DNA	TcMar-Tc1	1096
-DOC5_DM	LINE	Jockey	1793
-TC1_DM	DNA	TcMar-Tc1	2618
-Gypsy9_LTR	LTR	Gypsy	62
-DMRP1	Unknown	Unknown	295
-Gypsy10_I-int	LTR	Gypsy	2236
-Gypsy4_LTR	LTR	Gypsy	390
-DM297_LTR	LTR	Gypsy	6128
-ACCORD2_I-int	LTR	Gypsy	2286
-Invader1_LTR	LTR	Gypsy	2525
-BEL_LTR	LTR	Pao	927
-IVK_DM	LINE	I	3025
-M4DM	DNA	CMC-Transib	1880
-FW2_DM	LINE	Jockey	17723
-Copia2_I-int	LTR	Copia	3614
-MDG1_LTR	LTR	Gypsy	650
-Gypsy12_LTR	LTR	Gypsy	7572
-Gypsy7_I-int	LTR	Gypsy	1162
-FROGGER_I-int	LTR	Copia	1075
-Gypsy_I-int	LTR	Gypsy	24082
-5S_DM	RNA	RNA	6331
-GTWIN_I-int	LTR	Gypsy	7568
-CIRCE	LTR	Gypsy	3676
-DIVER2_LTR	LTR	Pao	648
-POGO	DNA	TcMar-Pogo	2909
-Gypsy6A_LTR	LTR	Gypsy	793
-MAX_I-int	LTR	Pao	8914
-ROOA_LTR	LTR	Pao	435
-DM176_I-int	LTR	Gypsy	4726
-Copia2_LTR_DM	LTR	Copia	747
-DM297_I-int	LTR	Gypsy	82387
-IDEFIX_I-int	LTR	Gypsy	7222
-Jockey2	LINE	Jockey	1823
-TC1-2_DM	DNA	TcMar-Tc1	4438
-DMRPR	Unknown	Unknown	221
+TRANSPAC_I-int	LTR	Gypsy	28474
+TRANSPAC_LTR	LTR	Gypsy	1457
+XDMR	Unknown	Unknown	1771
+XDMR_DM	Unknown	Unknown	4049
+ZAM_I-int	LTR	Gypsy	6896
+ZAM_LTR	LTR	Gypsy	377
diff -r 51b4590a972d -r 15e3e29f310e test-data/Normalized_counts_file.tab
--- a/test-data/Normalized_counts_file.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/Normalized_counts_file.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,211 +1,211 @@
 Tag	Mutant_1	Mutant_2	Wildtype_1	Wildtype_2
-LSU-rRNA_Dme	218650.181450173	354466.098949349	157455.221275418	149201.031867455
-FW3_DM	25.3386538652006	32.2981814492716	35.756634311884	44.2453336153694
-DMTOM1_LTR	54.9461072223747	39.3419337866127	43.2005545717588	49.0430203929395
-R1_DM	604.054709763298	517.028601444589	315.957840856997	262.031236427494
-TAHRE	149.055512536249	121.719476366005	196.209690086873	189.678242903128
-G4_DM	87.0600116574048	105.226787966377	157.828320885669	165.108271224056
-BS	203.649150075801	355.194096523239	313.935504138996	242.355874491196
-Stalker2_I-int	429.46472687139	413.519801853174	527.184456786045	604.508533973842
-Stalker3_LTR	21.2656708636846	20.1863634057947	25.5158653994552	21.2745908621546
-TABOR_I-int	215.554792695617	317.054754599099	169.833255871247	149.309827895896
-G7_DM	76.3292679803337	35.9059570366902	6.97060741098101	4.74922529496845
-BEL_I-int	1148.97283940843	1304.98396962057	1022.22666828812	1059.36800967358
-Gypsy6_I-int	445.717495579363	323.23951274896	322.239993215042	326.921161631196
+5S_DM	247.942840217287	356.138990129468	271.810660587451	503.611727197063
 ACCORD_I-int	160.687012069425	174.461719477315	117.166444321613	104.919109832721
-DM412B_LTR	219.588612399041	257.784155662936	132.441540808639	141.022914371002
-G2_DM	48.3666731430026	65.6271559235199	57.1417693937208	54.8583983051458
-SSU-rRNA_Hsa	22075.2937251301	25925.561270609	13684.9804569472	8340.22115575582
-TART_B1	524.083255060455	437.142142008891	1086.38207353363	1042.55187521078
-S2_DM	28.0409214335141	17.6093808433528	32.9167572185214	35.52226674706
-LOOPER1_DM	8.61592558013002	2.66288198118994	35.3263499037988	28.5438132524124
-HOBO	171.339429150313	182.020868327145	216.476085707688	213.42436937797
+ACCORD_LTR	30.9390054922851	29.5494000493336	12.6933900385148	10.6615261723782
+ACCORD2_I-int	89.5272994371693	103.079302497675	126.245445332212	119.118324235025
+ACCORD2_LTR	8.34178249348953	6.52835582485276	10.1116835900033	9.30460465953003
+ALA_DM	0.352469682823501	0	0.215142204042624	0.290768895610313
 ARS406_DM	29.5682900590826	19.7568663120544	24.2250121751994	34.8438059906359
-G6_DM	112.555318714971	67.5169431359773	207.698283782749	168.30672907577
-DOC2_DM	176.665637690757	176.265607271025	190.960220308233	219.9182080466
 Baggins1	215.398139503251	157.367735146451	220.994071992583	188.660551768492
-NINJA_LTR	11.6314995331755	9.79253373727915	21.1269644369856	19.6753619362979
-TRANSIB2	131.471191693166	127.474737422125	137.561925264854	149.067520482887
-Gypsy5_LTR	19.6599756419331	28.0032105118684	28.0115149663496	21.8561286533752
-MDG3_LTR	36.2652140327291	38.9983361116205	44.6204931184401	41.0953372462576
-Gypsy12A_LTR	95.4017941508943	92.5136739916635	131.624000433277	108.650643993054
-Gypsy_LTR	147.684797103047	149.207290365385	56.1951436959333	44.4391795457762
-TIRANT_LTR	126.301636345088	137.095472321908	58.9919923484874	61.9822362475985
-I_DM	449.55549879233	957.692619622151	343.668156737687	339.860377485855
-DIVER2_I-int	252.44661949781	229.179649219831	287.386956160137	272.692762599872
-P-1_DY	0.509122875189502	0.343597674992251	0.344227526468198	0.0969229652034378
-Invader2_I-int	233.804889606256	271.184464987634	293.583051636564	267.022769135471
-DOC6_DM	67.2825461211972	65.9707535985121	54.1728069779326	60.0922384261314
+BARI_DM	43.7454039682056	44.8394965864887	42.5981564004395	43.7122573067505
+BARI1	14.490420293855	10.7374273435078	16.9962341193673	15.6045973977535
+BATUMI_I-int	184.968256886155	158.226729333931	275.166878970516	232.082040179632
+BATUMI_LTR	13.628827735842	14.5170017684226	23.8377562079227	19.5299774884927
+BEL_I-int	1148.97283940843	1304.98396962057	1022.22666828812	1059.36800967358
+BEL_LTR	36.3043773308206	51.9691483425779	37.6498857074591	41.5799520722748
+Bica_I-int	61.1339083208317	53.0858407863027	79.6886723773878	67.3614608163893
+Bica_LTR	4.81708566525451	5.7552610561202	6.02398171319346	6.05768532521486
+BLASTOPIA_I-int	539.670247700872	1034.65849882041	443.580196295081	462.322544020398
+BLASTOPIA_LTR	40.6515034189771	78.9415658294696	23.6656424446886	23.1645886836216
+BLOOD_I-int	1071.58616237963	1140.74428097427	960.825083254357	834.603653366803
+BLOOD_LTR	49.6982252781136	46.55748496145	32.1852737247765	36.1522660208823
+BS	203.649150075801	355.194096523239	313.935504138996	242.355874491196
+BS2	204.197436249082	179.186187508459	240.744126323696	241.871259665179
+BS3_DM	33.3279666758666	38.9124366928724	53.871607892273	42.5007202417075
+BS4_DM	0.313306384732001	1.97568663120544	1.46296698748984	1.0176911346361
+BURDOCK_I-int	203.257517094886	191.727502645676	134.205706881789	161.473660028927
 BURDOCK_LTR	21.2656708636846	16.5785878183761	12.3491625120466	17.930748562636
-SSU-rRNA_Dme	389.988122395158	328.307578455096	306.061299471036	201.260537244939
-MAX_LTR	37.5184395716571	29.4635006305855	43.7599243022696	36.4914963990943
-STALKER4_LTR	79.8931281066602	68.9772332546943	55.5927455246139	58.6383939480799
-XDMR_DM	158.572193972484	136.322377553175	142.725338161877	209.741296700239
-BARI_DM	43.7454039682056	44.8394965864887	42.5981564004395	43.7122573067505
-Transib-N1_DM	14.333767101489	11.1669244372481	13.2527597690256	17.9792100452377
-Gypsy5_I-int	110.988786791311	88.9917978229929	105.333623099269	105.936800967358
-XDMR	69.3582009200467	77.5671751295006	53.7425225698474	69.7845349464752
-ACCORD2_LTR	8.34178249348953	6.52835582485276	10.1116835900033	9.30460465953003
-POGON1	25.1036740766516	21.990251199504	14.2424139076217	19.5299774884927
-BS4_DM	0.313306384732001	1.97568663120544	1.46296698748984	1.0176911346361
-ALA_DM	0.352469682823501	0	0.215142204042624	0.290768895610313
-Gypsy1-I_DM	1447.55382405803	1954.46947477467	351.112076997562	305.161955943024
-ACCORD_LTR	30.9390054922851	29.5494000493336	12.6933900385148	10.6615261723782
-BURDOCK_I-int	203.257517094886	191.727502645676	134.205706881789	161.473660028927
-ZAM_I-int	270.070103638985	248.421119019397	220.692872906923	214.490521995208
-Invader5_I-int	7.48018993547652	10.0502319935233	17.8998313763463	16.2345966715758
-G3_DM	18.7983830839201	21.4748546870157	34.2936673243942	26.9445843265557
-ROOA_I-int	160.687012069425	221.534600951254	214.496777430496	222.389743659288
-Gypsy1-LTR_DM	56.0818428670282	49.4780651988841	44.8356353224828	38.5268786683665
+Chimpo_I-int	53.4970651929892	31.7827849367832	55.4206317613798	51.369171557822
+Chimpo_LTR	4.19047289579051	2.83468081868607	4.04467343600132	5.81537791220627
+Chouto_I-int	48.2100199506366	44.4958989114965	72.7180649664068	63.1937733126415
+Chouto_LTR	6.34445429082302	13.658007580942	12.8655038017489	13.617676611083
+CIRCE	143.964283784354	134.862087434458	162.088136525713	161.037506685512
+Copia_I-int	1992.94191328026	7492.14730320603	1188.10130760498	1295.52081439175
+Copia_LTR	102.294534614998	264.140712650293	60.5840446584028	54.7130138573406
+Copia1-I_DM	160.56952217515	167.16026888373	154.386045620987	170.487495792847
+Copia1-LTR_DM	23.4979788549001	33.4148738929964	33.1749278633726	27.4291991525729
+Copia2_I-int	141.536159302681	162.521700271335	181.493963330357	167.434422388939
+Copia2_LTR_DM	29.2549836743506	39.5137326241088	38.3383407603955	23.5522805444354
+DIVER_I-int	968.978321379896	1009.40406970848	567.028792974739	757.307588617061
+DIVER_LTR	21.4223240560506	28.1750093493646	20.1803387391981	20.7899760361374
+DIVER2_I-int	252.44661949781	229.179649219831	287.386956160137	272.692762599872
+DIVER2_LTR	25.3778171632921	20.615860499535	34.1215535611601	25.9268931919196
 DM1731_I-int	737.405739764856	590.386705055435	222.887323388158	236.54049657899
-ROO_I-int	1332.45289096711	1970.61856549931	1368.00321862543	1358.56920325659
+DM1731_LTR	49.8940417685711	27.5737134181281	24.8274103465188	21.3230523447563
+DM176_I-int	185.08574678043	197.396864283048	156.064154812519	136.322150558635
+DM176_LTR	21.9314469312401	28.3468081868607	38.6825682868637	42.2584128286989
+DM297_I-int	3226.54663986442	3668.33467763602	509.327653850507	558.760894397819
+DM297_LTR	239.992690704713	216.122937570126	64.0693483638933	71.6260712853405
 DM412	1711.00533031955	2019.32353592946	1036.38302531413	1142.04329899211
-PROTOP	187.004748386913	176.866903202261	212.646554475729	210.952833765282
-TART-A	199.419513881919	156.766439215214	159.076145669116	165.156732706658
-ROO_LTR	86.9033584650388	124.811855440935	70.523614485172	89.7022042957817
-DIVER_LTR	21.4223240560506	28.1750093493646	20.1803387391981	20.7899760361374
-Gypsy3_I-int	225.81557679559	193.960887533126	146.253670308176	133.414461602532
-BATUMI_LTR	13.628827735842	14.5170017684226	23.8377562079227	19.5299774884927
-IDEFIX_LTR	99.3964505562273	86.9302117730394	94.2753138114777	89.3629739175697
-G5_DM	106.289191020331	111.669244372481	111.916974542973	123.625242116985
-HETA	879.568511837001	887.083297411243	990.729849616282	1182.31479103414
-Gypsy11_I-int	19.0725261705606	14.4311023496745	28.8720837825201	27.1384302569626
-R1-2_DM	7.20604684883602	5.84116047486826	11.4885936958761	8.57768242050425
-Gypsy11_LTR	6.22696439654852	4.12317209990701	5.76581106834231	7.22076090765612
-HELENA_RT	36.5785204174611	35.7341581991941	28.0975718479666	30.3853495912778
-FTZ_DM	0	0	0	0
-MICROPIA_I-int	271.832452053102	285.787366174805	436.695645765717	501.818652340799
-Invader4_I-int	73.9403067967522	101.361314122714	61.9179263234671	59.0745472914953
-PLACW_DM	10.8482335713455	17.5234814246048	6.41123768047018	6.1546082904183
-BLOOD_LTR	49.6982252781136	46.55748496145	32.1852737247765	36.1522660208823
-R2_DM	2116.46295546085	1299.48640682069	659.496912272258	407.415684232651
-Copia1-I_DM	160.56952217515	167.16026888373	154.386045620987	170.487495792847
-Gypsy4_I-int	513.587491171932	459.390091464639	521.20350351366	487.328669042885
-Chouto_LTR	6.34445429082302	13.658007580942	12.8655038017489	13.617676611083
-BATUMI_I-int	184.968256886155	158.226729333931	275.166878970516	232.082040179632
-DNAREP1_DM	3009.73862162988	3174.24122099716	2918.23188407496	3099.30565831033
+DM412B_LTR	219.588612399041	257.784155662936	132.441540808639	141.022914371002
+DMCR1A	684.926920322246	693.380108134362	876.919623677734	870.222843079066
+DMLTR5	7.40186333929352	8.07454536231789	6.92757897017248	7.75383721627503
+DMRP1	11.5531729369925	12.369516299721	11.2734514918335	11.0007565505902
+DMRPR	8.65508887822152	11.6823209497365	5.50764042349117	9.06229724652144
+DMRT1A	148.703042853426	106.085782153857	191.734732242786	171.553648410085
 DMRT1B	352.587172717776	353.476108148278	417.634046487541	344.997294641637
 DMRT1C	74.6844094604907	57.552610561202	108.861955245568	101.139114189787
-TLD2	1.2923888370195	0.0858994187480627	2.79684865255411	0.823845204229221
-DMRT1A	148.703042853426	106.085782153857	191.734732242786	171.553648410085
-DM1731_LTR	49.8940417685711	27.5737134181281	24.8274103465188	21.3230523447563
-LSU-rRNA_Cel	14243.5740259843	21618.3926157437	22382.0179984887	15843.270199567
-Copia_LTR	102.294534614998	264.140712650293	60.5840446584028	54.7130138573406
+DMTOM1_LTR	54.9461072223747	39.3419337866127	43.2005545717588	49.0430203929395
+DNAREP1_DM	3009.73862162988	3174.24122099716	2918.23188407496	3099.30565831033
+DOC	1138.94703509701	1864.01738683296	769.477606978848	795.446775424614
+DOC2_DM	176.665637690757	176.265607271025	190.960220308233	219.9182080466
+DOC3_DM	433.420219978632	447.106474583666	513.802611694594	516.550943051722
+DOC4_DM	40.3381970342451	56.5218175362252	34.9821223773306	40.2230305594267
+DOC5_DM	70.2197934780597	64.5963628985431	130.67737473549	105.791416519552
+DOC6_DM	67.2825461211972	65.9707535985121	54.1728069779326	60.0922384261314
+FB4_DM	307.040257037361	287.591253968514	307.610323340143	336.274227773327
+FROGGER_I-int	42.1005454483626	46.9010826364422	69.3188181425333	65.9560778209394
+FROGGER_LTR	3.32888033777751	4.89626686863957	1.76416607314951	2.61692006049282
+FTZ_DM	0	0	0	0
+FUSHI_DM	0	0	0	0
+FW2_DM	694.091132075657	761.412447782827	612.466826468541	671.046149586002
+FW3_DM	25.3386538652006	32.2981814492716	35.756634311884	44.2453336153694
+G_DM	428.759787505743	393.591136703623	383.168265399913	389.388012704811
+G2_DM	48.3666731430026	65.6271559235199	57.1417693937208	54.8583983051458
+G3_DM	18.7983830839201	21.4748546870157	34.2936673243942	26.9445843265557
+G4_DM	87.0600116574048	105.226787966377	157.828320885669	165.108271224056
+G5_DM	106.289191020331	111.669244372481	111.916974542973	123.625242116985
+G5A_DM	61.7996843883872	49.9934617113725	77.6233072185786	77.2960647497417
+G6_DM	112.555318714971	67.5169431359773	207.698283782749	168.30672907577
+G7_DM	76.3292679803337	35.9059570366902	6.97060741098101	4.74922529496845
+GTWIN_I-int	296.387839956473	251.685296931824	234.418945524843	244.924333069087
+GTWIN_LTR	99.2006340657698	80.5736547856828	25.7310076034978	22.6315123750027
+Gypsy_I-int	943.130544639506	958.723412647127	293.540023195756	273.031992978084
+Gypsy_LTR	147.684797103047	149.207290365385	56.1951436959333	44.4391795457762
+Gypsy1-I_DM	1447.55382405803	1954.46947477467	351.112076997562	305.161955943024
+Gypsy1-LTR_DM	56.0818428670282	49.4780651988841	44.8356353224828	38.5268786683665
+Gypsy10_I-int	87.5691345325943	79.6287611794541	97.1582193456488	93.5306614213175
+Gypsy10_LTR	14.2162772072145	13.9157058371862	13.5109304138768	17.8338255974326
+Gypsy11_I-int	19.0725261705606	14.4311023496745	28.8720837825201	27.1384302569626
+Gypsy11_LTR	6.22696439654852	4.12317209990701	5.76581106834231	7.22076090765612
+Gypsy12_I-int	195.894817053684	211.827966632723	420.732094225755	466.538693006748
+Gypsy12_LTR	296.544493148839	230.210442244808	270.734949567238	287.5704377586
+Gypsy12A_LTR	95.4017941508943	92.5136739916635	131.624000433277	108.650643993054
+Gypsy2_I-int	165.50409773468	133.315897896993	137.260726179194	167.337499423735
+Gypsy2_LTR	34.0329060415136	21.4748546870157	20.6106231472833	23.5038190618337
+Gypsy2-I_DM	288.790160126722	228.320655032351	198.188998364065	188.805936216297
+Gypsy2-LTR_DM	45.2336092956826	33.0712762180041	41.5654738210349	33.438422995186
+Gypsy3_I-int	225.81557679559	193.960887533126	146.253670308176	133.414461602532
+Gypsy3_LTR	26.6702060003116	18.2106767745893	24.354097497625	21.6622827229683
+Gypsy4_I-int	513.587491171932	459.390091464639	521.20350351366	487.328669042885
+Gypsy4_LTR	15.273686255685	18.7260732870777	11.7897927815358	9.40152762473347
+Gypsy5_I-int	110.988786791311	88.9917978229929	105.333623099269	105.936800967358
+Gypsy5_LTR	19.6599756419331	28.0032105118684	28.0115149663496	21.8561286533752
+Gypsy6_I-int	445.717495579363	323.23951274896	322.239993215042	326.921161631196
 Gypsy6_LTR	55.7293731842047	65.2835582485276	18.4161726660486	23.455357579232
-Gypsy12_I-int	195.894817053684	211.827966632723	420.732094225755	466.538693006748
-BLASTOPIA_LTR	40.6515034189771	78.9415658294696	23.6656424446886	23.1645886836216
-Bica_LTR	4.81708566525451	5.7552610561202	6.02398171319346	6.05768532521486
+Gypsy6A_LTR	31.0564953865596	18.8119727058257	26.5485479788598	27.7684295307849
+Gypsy7_I-int	45.5077523823231	63.7373687110625	54.0437216555071	48.8976359451344
+Gypsy7_LTR	3.13306384732001	3.35007733117444	4.81918537055477	4.21614898634954
+Gypsy8_I-int	163.545932830104	107.116575178834	206.923771848195	197.868233462818
 Gypsy8_LTR	57.4525583002307	41.7471175115585	56.4102858999759	60.1406999087332
-NINJA_I-int	143.964283784354	98.4407338852798	226.931996824159	218.22205615554
-PROTOP_B	366.999266415448	369.367500616669	373.91715062608	401.503383355241
-PROTOP_A	174.864125978548	170.768044471149	152.019481376518	163.993657124217
+Gypsy9_I-int	16.8010548812535	16.1490907246358	21.6863341674965	22.9707427532148
+Gypsy9_LTR	2.42812448167301	0.687195349984501	2.19445048123476	2.03538226927219
+HELENA_RT	36.5785204174611	35.7341581991941	28.0975718479666	30.3853495912778
+Helitron1_DM	0	0	0.129085322425574	0.290768895610313
+HETA	879.568511837001	887.083297411243	990.729849616282	1182.31479103414
+HMSBEAGLE_I-int	307.941012893465	350.383729073348	311.48288301291	286.310439210955
+HOBO	171.339429150313	182.020868327145	216.476085707688	213.42436937797
+I_DM	449.55549879233	957.692619622151	343.668156737687	339.860377485855
+IDEFIX_I-int	282.837338816814	282.265490006134	266.475133927194	268.815843991735
+IDEFIX_LTR	99.3964505562273	86.9302117730394	94.2753138114777	89.3629739175697
+Invader1_I-int	117.21575118786	151.870172346575	78.8281035612173	81.027598910074
+Invader1_LTR	98.8873276810378	163.466593877563	143.973162945324	93.5791229039192
+Invader2_I-int	233.804889606256	271.184464987634	293.583051636564	267.022769135471
+Invader2_LTR	16.3310953041555	18.2965761933373	21.1699928777942	22.8738197880113
+Invader3_I-int	172.749307881607	173.688624708583	200.813733253385	180.373638243598
 Invader3_LTR	19.8166288342991	19.4991680558102	28.2696856112007	29.4645814218451
-Chimpo_LTR	4.19047289579051	2.83468081868607	4.04467343600132	5.81537791220627
-Invader2_LTR	16.3310953041555	18.2965761933373	21.1699928777942	22.8738197880113
-BLASTOPIA_I-int	539.670247700872	1034.65849882041	443.580196295081	462.322544020398
-FROGGER_LTR	3.32888033777751	4.89626686863957	1.76416607314951	2.61692006049282
+Invader4_I-int	73.9403067967522	101.361314122714	61.9179263234671	59.0745472914953
+Invader4_LTR	63.6011961005962	58.3257053299346	61.1003859481051	59.5107006349108
+Invader5_I-int	7.48018993547652	10.0502319935233	17.8998313763463	16.2345966715758
+Invader5_LTR	1.84067501030051	1.97568663120544	2.96896241578821	3.10153488651001
+Invader6_I-int	257.14621526879	283.296283031111	298.230123243885	324.740394914118
+Invader6_LTR	12.218949004548	12.5413151372172	27.9254580847325	28.4953517698107
+IVK_DM	118.468976726788	151.956071765323	144.102248267749	141.555990679621
+Jockey2	71.3946924208047	65.2835582485276	76.1603402310888	76.9568343715296
+LINEJ1_DM	974.813652795529	1369.15083542537	302.274796679886	306.712723386279
+LmeSINE1c	24.5553879033706	56.0923204424849	25.7740360443063	68.5245363988305
+LOOPER1_DM	8.61592558013002	2.66288198118994	35.3263499037988	28.5438132524124
+LSU-rRNA_Cel	14243.5740259843	21618.3926157437	22382.0179984887	15843.270199567
+LSU-rRNA_Dme	218650.181450173	354466.098949349	157455.221275418	149201.031867455
+LSU-rRNA_Hsa	0.587449471372502	0.944893606228689	0.215142204042624	0
+M4DM	73.6270004120202	78.8556664107215	74.3101172763222	79.9614462928362
+Mariner2_DM	42.9229747082841	79.542861760706	86.5301944659432	77.1022188193348
+MAX_I-int	349.101639187632	335.437230211185	533.337523821664	445.894101418416
+MAX_LTR	37.5184395716571	29.4635006305855	43.7599243022696	36.4914963990943
+MDG1_I-int	638.596738680001	690.889024990668	702.009011791081	665.860770947618
+MDG1_LTR	25.4561437594751	24.1377366682056	29.6896241578821	28.2045828742004
+MDG3_I-int	307.706033104916	323.840808680196	232.009352839565	240.902030013145
+MDG3_LTR	36.2652140327291	38.9983361116205	44.6204931184401	41.0953372462576
+MICROPIA_I-int	271.832452053102	285.787366174805	436.695645765717	501.818652340799
+MICROPIA_LTR	18.0151171220901	12.7990133934613	34.2936673243942	41.8222594852834
+MINOS	10.6915803789795	7.98864594356983	7.44392025987478	10.9522950679885
+MuDR-1_DEl	1.253225538928	0.343597674992251	0.258170644851148	0.43615334341547
+NINJA_I-int	143.964283784354	98.4407338852798	226.931996824159	218.22205615554
+NINJA_LTR	11.6314995331755	9.79253373727915	21.1269644369856	19.6753619362979
+NOF_FB	8.92923196486203	5.41166338112795	54.7321767084434	46.5230232976501
 NOMAD_I-int	454.842544034682	700.423860471703	708.635391675594	561.862429284329
+NOMAD_LTR	29.6466166552656	23.7941389932134	26.6346048604768	39.8353386986129
+NTS_DM	2194.82871494194	1868.57005602661	2837.89778508544	1754.54797759523
+P-1_DY	0.509122875189502	0.343597674992251	0.344227526468198	0.0969229652034378
+PLACW_DM	10.8482335713455	17.5234814246048	6.41123768047018	6.1546082904183
+POGO	113.926034148174	88.6482001480007	104.43002584229	120.766014643484
+POGON1	25.1036740766516	21.990251199504	14.2424139076217	19.5299774884927
+PROTOP	187.004748386913	176.866903202261	212.646554475729	210.952833765282
+PROTOP_A	174.864125978548	170.768044471149	152.019481376518	163.993657124217
+PROTOP_B	366.999266415448	369.367500616669	373.91715062608	401.503383355241
+QUASIMODO_I-int	701.414668818767	687.195349984501	641.38193869187	630.871580509177
 QUASIMODO_LTR	63.6403593986877	45.3548930989771	57.3138831569549	56.893780574418
-TABOR_LTR	17.3493410545346	7.55914884982952	16.5229212704735	13.2299847502693
-Stalker2_LTR	30.9390054922851	30.5801930743103	31.238648026989	32.5661163083551
-MICROPIA_LTR	18.0151171220901	12.7990133934613	34.2936673243942	41.8222594852834
-Gypsy9_I-int	16.8010548812535	16.1490907246358	21.6863341674965	22.9707427532148
-STALKER4_I-int	285.382953192761	269.036979518932	267.077532098513	278.217371616468
-TRANSIB1	48.1316933544536	24.8249320181901	89.5852137633485	102.544497185237
-DOC	1138.94703509701	1864.01738683296	769.477606978848	795.446775424614
-TRANSIB3	70.5722631608832	63.6514692923144	50.9456739172933	54.8583983051458
-Copia_I-int	1992.94191328026	7492.14730320603	1188.10130760498	1295.52081439175
-TRANSIB4	14.255440505306	13.1426110684536	27.3230599134132	27.6715065655815
-Gypsy10_LTR	14.2162772072145	13.9157058371862	13.5109304138768	17.8338255974326
-Invader3_I-int	172.749307881607	173.688624708583	200.813733253385	180.373638243598
-Invader1_I-int	117.21575118786	151.870172346575	78.8281035612173	81.027598910074
-BS3_DM	33.3279666758666	38.9124366928724	53.871607892273	42.5007202417075
-Gypsy2-LTR_DM	45.2336092956826	33.0712762180041	41.5654738210349	33.438422995186
-LSU-rRNA_Hsa	0.587449471372502	0.944893606228689	0.215142204042624	0
-NOMAD_LTR	29.6466166552656	23.7941389932134	26.6346048604768	39.8353386986129
-Helitron1_DM	0	0	0.129085322425574	0.290768895610313
-LINEJ1_DM	974.813652795529	1369.15083542537	302.274796679886	306.712723386279
-Invader4_LTR	63.6011961005962	58.3257053299346	61.1003859481051	59.5107006349108
-MDG3_I-int	307.706033104916	323.840808680196	232.009352839565	240.902030013145
-LmeSINE1c	24.5553879033706	56.0923204424849	25.7740360443063	68.5245363988305
+QUASIMODO2-I_DM	155.752436509896	155.563847352742	116.908273676762	107.826798788825
+QUASIMODO2-LTR_DM	11.670662831267	9.01943896854658	13.4679019730682	9.69229652034378
+R1_DM	604.054709763298	517.028601444589	315.957840856997	262.031236427494
+R1-2_DM	7.20604684883602	5.84116047486826	11.4885936958761	8.57768242050425
+R2_DM	2116.46295546085	1299.48640682069	659.496912272258	407.415684232651
+ROO_I-int	1332.45289096711	1970.61856549931	1368.00321862543	1358.56920325659
+ROO_LTR	86.9033584650388	124.811855440935	70.523614485172	89.7022042957817
+ROOA_I-int	160.687012069425	221.534600951254	214.496777430496	222.389743659288
+ROOA_LTR	17.0360346698026	23.7082395744653	17.2113763234099	23.4068960966302
+ROVER-I_DM	272.067431841651	263.625316137804	280.244234985922	270.851226261007
 ROVER-LTR_DM	16.2527687079725	14.4311023496745	24.2680406160079	20.1115152797133
 S_DM	194.798244707122	175.320713664796	155.418728200391	168.452113523575
-Invader6_I-int	257.14621526879	283.296283031111	298.230123243885	324.740394914118
-ROVER-I_DM	272.067431841651	263.625316137804	280.244234985922	270.851226261007
-QUASIMODO_I-int	701.414668818767	687.195349984501	641.38193869187	630.871580509177
-Chouto_I-int	48.2100199506366	44.4958989114965	72.7180649664068	63.1937733126415
-NTS_DM	2194.82871494194	1868.57005602661	2837.89778508544	1754.54797759523
-Gypsy3_LTR	26.6702060003116	18.2106767745893	24.354097497625	21.6622827229683
+S2_DM	28.0409214335141	17.6093808433528	32.9167572185214	35.52226674706
 SSU-rRNA_Cel	150.974514142733	156.07924386523	149.007490519921	105.791416519552
-MINOS	10.6915803789795	7.98864594356983	7.44392025987478	10.9522950679885
-DOC4_DM	40.3381970342451	56.5218175362252	34.9821223773306	40.2230305594267
-ZAM_LTR	14.7645633804955	10.1361314122714	11.1443661694079	10.9038335853868
-QUASIMODO2-LTR_DM	11.670662831267	9.01943896854658	13.4679019730682	9.69229652034378
-Gypsy2-I_DM	288.790160126722	228.320655032351	198.188998364065	188.805936216297
-TRANSPAC_I-int	1115.13574985737	1439.67425821753	416.257136381668	726.049932338953
-Bica_I-int	61.1339083208317	53.0858407863027	79.6886723773878	67.3614608163893
-BS2	204.197436249082	179.186187508459	240.744126323696	241.871259665179
-BLOOD_I-int	1071.58616237963	1140.74428097427	960.825083254357	834.603653366803
-DMCR1A	684.926920322246	693.380108134362	876.919623677734	870.222843079066
-QUASIMODO2-I_DM	155.752436509896	155.563847352742	116.908273676762	107.826798788825
-HMSBEAGLE_I-int	307.941012893465	350.383729073348	311.48288301291	286.310439210955
-DMLTR5	7.40186333929352	8.07454536231789	6.92757897017248	7.75383721627503
-Gypsy7_LTR	3.13306384732001	3.35007733117444	4.81918537055477	4.21614898634954
-G5A_DM	61.7996843883872	49.9934617113725	77.6233072185786	77.2960647497417
-MDG1_I-int	638.596738680001	690.889024990668	702.009011791081	665.860770947618
-Gypsy2_I-int	165.50409773468	133.315897896993	137.260726179194	167.337499423735
-BARI1	14.490420293855	10.7374273435078	16.9962341193673	15.6045973977535
-Invader5_LTR	1.84067501030051	1.97568663120544	2.96896241578821	3.10153488651001
-DM176_LTR	21.9314469312401	28.3468081868607	38.6825682868637	42.2584128286989
-DOC3_DM	433.420219978632	447.106474583666	513.802611694594	516.550943051722
-Copia1-LTR_DM	23.4979788549001	33.4148738929964	33.1749278633726	27.4291991525729
-TOM_I-int	271.362492476004	291.199029555932	110.281893792249	111.994486292572
-NOF_FB	8.92923196486203	5.41166338112795	54.7321767084434	46.5230232976501
-Chimpo_I-int	53.4970651929892	31.7827849367832	55.4206317613798	51.369171557822
-DIVER_I-int	968.978321379896	1009.40406970848	567.028792974739	757.307588617061
+SSU-rRNA_Dme	389.988122395158	328.307578455096	306.061299471036	201.260537244939
+SSU-rRNA_Hsa	22075.2937251301	25925.561270609	13684.9804569472	8340.22115575582
+Stalker2_I-int	429.46472687139	413.519801853174	527.184456786045	604.508533973842
+Stalker2_LTR	30.9390054922851	30.5801930743103	31.238648026989	32.5661163083551
+Stalker3_LTR	21.2656708636846	20.1863634057947	25.5158653994552	21.2745908621546
+STALKER4_I-int	285.382953192761	269.036979518932	267.077532098513	278.217371616468
+STALKER4_LTR	79.8931281066602	68.9772332546943	55.5927455246139	58.6383939480799
+TABOR_I-int	215.554792695617	317.054754599099	169.833255871247	149.309827895896
+TABOR_LTR	17.3493410545346	7.55914884982952	16.5229212704735	13.2299847502693
+TAHRE	149.055512536249	121.719476366005	196.209690086873	189.678242903128
+TART_B1	524.083255060455	437.142142008891	1086.38207353363	1042.55187521078
+TART-A	199.419513881919	156.766439215214	159.076145669116	165.156732706658
+TC1_DM	102.529514403547	127.560636840873	79.1723310876855	94.9845058993691
+TC1-2_DM	173.806716930078	196.451970676819	163.809274158054	191.325933311586
 TIRANT_I-int	907.2178002896	1093.32780182534	469.741488306664	414.781829588112
-Gypsy2_LTR	34.0329060415136	21.4748546870157	20.6106231472833	23.5038190618337
-FB4_DM	307.040257037361	287.591253968514	307.610323340143	336.274227773327
-GTWIN_LTR	99.2006340657698	80.5736547856828	25.7310076034978	22.6315123750027
-Invader6_LTR	12.218949004548	12.5413151372172	27.9254580847325	28.4953517698107
-Gypsy8_I-int	163.545932830104	107.116575178834	206.923771848195	197.868233462818
-G_DM	428.759787505743	393.591136703623	383.168265399913	389.388012704811
-TRANSPAC_LTR	57.0609253193157	84.0955309543534	23.1493011549863	26.896122843954
-FUSHI_DM	0	0	0	0
+TIRANT_LTR	126.301636345088	137.095472321908	58.9919923484874	61.9822362475985
+TLD2	1.2923888370195	0.0858994187480627	2.79684865255411	0.823845204229221
+TOM_I-int	271.362492476004	291.199029555932	110.281893792249	111.994486292572
+Transib-N1_DM	14.333767101489	11.1669244372481	13.2527597690256	17.9792100452377
+TRANSIB1	48.1316933544536	24.8249320181901	89.5852137633485	102.544497185237
+TRANSIB2	131.471191693166	127.474737422125	137.561925264854	149.067520482887
+TRANSIB3	70.5722631608832	63.6514692923144	50.9456739172933	54.8583983051458
+TRANSIB4	14.255440505306	13.1426110684536	27.3230599134132	27.6715065655815
 Transib5	38.1058890430296	28.1750093493646	48.3209390279733	46.7653307106587
-MuDR-1_DEl	1.253225538928	0.343597674992251	0.258170644851148	0.43615334341547
-Mariner2_DM	42.9229747082841	79.542861760706	86.5301944659432	77.1022188193348
-DOC5_DM	70.2197934780597	64.5963628985431	130.67737473549	105.791416519552
-TC1_DM	102.529514403547	127.560636840873	79.1723310876855	94.9845058993691
-Gypsy9_LTR	2.42812448167301	0.687195349984501	2.19445048123476	2.03538226927219
-DMRP1	11.5531729369925	12.369516299721	11.2734514918335	11.0007565505902
-Gypsy10_I-int	87.5691345325943	79.6287611794541	97.1582193456488	93.5306614213175
-Gypsy4_LTR	15.273686255685	18.7260732870777	11.7897927815358	9.40152762473347
-DM297_LTR	239.992690704713	216.122937570126	64.0693483638933	71.6260712853405
-ACCORD2_I-int	89.5272994371693	103.079302497675	126.245445332212	119.118324235025
-Invader1_LTR	98.8873276810378	163.466593877563	143.973162945324	93.5791229039192
-BEL_LTR	36.3043773308206	51.9691483425779	37.6498857074591	41.5799520722748
-IVK_DM	118.468976726788	151.956071765323	144.102248267749	141.555990679621
-M4DM	73.6270004120202	78.8556664107215	74.3101172763222	79.9614462928362
-FW2_DM	694.091132075657	761.412447782827	612.466826468541	671.046149586002
-Copia2_I-int	141.536159302681	162.521700271335	181.493963330357	167.434422388939
-MDG1_LTR	25.4561437594751	24.1377366682056	29.6896241578821	28.2045828742004
-Gypsy12_LTR	296.544493148839	230.210442244808	270.734949567238	287.5704377586
-Gypsy7_I-int	45.5077523823231	63.7373687110625	54.0437216555071	48.8976359451344
-FROGGER_I-int	42.1005454483626	46.9010826364422	69.3188181425333	65.9560778209394
-Gypsy_I-int	943.130544639506	958.723412647127	293.540023195756	273.031992978084
-5S_DM	247.942840217287	356.138990129468	271.810660587451	503.611727197063
-GTWIN_I-int	296.387839956473	251.685296931824	234.418945524843	244.924333069087
-CIRCE	143.964283784354	134.862087434458	162.088136525713	161.037506685512
-DIVER2_LTR	25.3778171632921	20.615860499535	34.1215535611601	25.9268931919196
-POGO	113.926034148174	88.6482001480007	104.43002584229	120.766014643484
-Gypsy6A_LTR	31.0564953865596	18.8119727058257	26.5485479788598	27.7684295307849
-MAX_I-int	349.101639187632	335.437230211185	533.337523821664	445.894101418416
-ROOA_LTR	17.0360346698026	23.7082395744653	17.2113763234099	23.4068960966302
-DM176_I-int	185.08574678043	197.396864283048	156.064154812519	136.322150558635
-Copia2_LTR_DM	29.2549836743506	39.5137326241088	38.3383407603955	23.5522805444354
-DM297_I-int	3226.54663986442	3668.33467763602	509.327653850507	558.760894397819
-IDEFIX_I-int	282.837338816814	282.265490006134	266.475133927194	268.815843991735
-Jockey2	71.3946924208047	65.2835582485276	76.1603402310888	76.9568343715296
-TC1-2_DM	173.806716930078	196.451970676819	163.809274158054	191.325933311586
-DMRPR	8.65508887822152	11.6823209497365	5.50764042349117	9.06229724652144
+TRANSPAC_I-int	1115.13574985737	1439.67425821753	416.257136381668	726.049932338953
+TRANSPAC_LTR	57.0609253193157	84.0955309543534	23.1493011549863	26.896122843954
+XDMR	69.3582009200467	77.5671751295006	53.7425225698474	69.7845349464752
+XDMR_DM	158.572193972484	136.322377553175	142.725338161877	209.741296700239
+ZAM_I-int	270.070103638985	248.421119019397	220.692872906923	214.490521995208
+ZAM_LTR	14.7645633804955	10.1361314122714	11.1443661694079	10.9038335853868
diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp-paired_class_fraction_counts.tab
--- a/test-data/Samp-paired_class_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/Samp-paired_class_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,3 +1,3 @@
 Low_complexity	2.0
+Simple_repeat	121.0
 rRNA	111.0
-Simple_repeat	121.0
diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp-paired_family_fraction_counts.tab
--- a/test-data/Samp-paired_family_fraction_counts.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/Samp-paired_family_fraction_counts.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,3 +1,3 @@
 Low_complexity	2.0
+Simple_repeat	121.0
 rRNA	111.0
-Simple_repeat	121.0
diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp_class_fraction_counts.tabular
--- a/test-data/Samp_class_fraction_counts.tabular	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/Samp_class_fraction_counts.tabular	Tue Sep 19 17:23:15 2017 -0400
@@ -1,3 +1,3 @@
 Low_complexity	0.0
+Simple_repeat	98.0
 rRNA	772.0
-Simple_repeat	98.0
diff -r 51b4590a972d -r 15e3e29f310e test-data/Samp_family_fraction_counts.tabular
--- a/test-data/Samp_family_fraction_counts.tabular	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/Samp_family_fraction_counts.tabular	Tue Sep 19 17:23:15 2017 -0400
@@ -1,3 +1,3 @@
 Low_complexity	0.0
+Simple_repeat	98.0
 rRNA	772.0
-Simple_repeat	98.0
diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_353.tab
--- a/test-data/aligned_353.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/aligned_353.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,2 @@
+# Total reads aligned to repeated sequences
 15862067
diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_354.tab
--- a/test-data/aligned_354.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/aligned_354.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,2 @@
+# Total reads aligned to repeated sequences
 28421096
diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_355.tab
--- a/test-data/aligned_355.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/aligned_355.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,2 @@
+# Total reads aligned to repeated sequences
 10808170
diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_356.tab
--- a/test-data/aligned_356.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/aligned_356.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,2 @@
+# Total reads aligned to repeated sequences
 29256707
diff -r 51b4590a972d -r 15e3e29f310e test-data/aligned_reads.tab
--- a/test-data/aligned_reads.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/aligned_reads.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,3 @@
+# Total reads aligned to repeated sequences
+
 2510
diff -r 51b4590a972d -r 15e3e29f310e test-data/edgeR_plots.pdf
Binary file test-data/edgeR_plots.pdf has changed
diff -r 51b4590a972d -r 15e3e29f310e test-data/edgeR_result_file.tab
--- a/test-data/edgeR_result_file.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/edgeR_result_file.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -52,9 +52,9 @@
 TAHRE	-0.509503033739914	0.0198535740576507	LINE	Jockey
 Gypsy8_I-int	-0.578276897527121	0.0248976847994314	LTR	Gypsy
 BLASTOPIA_I-int	0.796987753936179	0.0301824235833205	LTR	Gypsy
-Gypsy11_I-int	-0.734634622561586	0.0432538714324547	LTR	Gypsy
+DM176_LTR	-0.691384671506076	0.0432538714324547	LTR	Gypsy
 DMRT1A	-0.509608409844153	0.0432538714324547	LINE	R1
-DM176_LTR	-0.691384671506076	0.0432538714324547	LTR	Gypsy
+Gypsy11_I-int	-0.734634622561586	0.0432538714324547	LTR	Gypsy
 QUASIMODO2-I_DM	0.470057940126177	0.044414105251971	LTR	Gypsy
 MuDR-1_DEl	1.35524442785064	0.0532319546519159	DNA	MULE-NOF
 DM1731_LTR	0.752238181600754	0.0540130070646644	LTR	Copia
@@ -71,14 +71,14 @@
 BATUMI_LTR	-0.625598883331715	0.112325719453317	LTR	Pao
 Gypsy2-I_DM	0.418860685191156	0.127538985839499	LTR	Gypsy
 Invader3_LTR	-0.553726127316243	0.130228544874336	LTR	Gypsy
+MDG3_I-int	0.417195433411295	0.130837858091619	LTR	Gypsy
 SSU-rRNA_Dme	0.50182621141568	0.130837858091619	rRNA	rRNA
-MDG3_I-int	0.417195433411295	0.130837858091619	LTR	Gypsy
 G5A_DM	-0.468375220785066	0.142388172856184	LINE	Jockey
 S2_DM	-0.576444154651051	0.154380925206633	DNA	TcMar-Tc1
 Stalker2_I-int	-0.424817076156048	0.157921464286182	LTR	Gypsy
-R1-2_DM	-0.611853226580459	0.158635278613665	LINE	R1
 BLOOD_LTR	0.494999752604753	0.158635278613665	LTR	Gypsy
 Invader5_LTR	-0.675984091871337	0.158635278613665	LTR	Gypsy
+R1-2_DM	-0.611853226580459	0.158635278613665	LINE	R1
 Transib5	-0.51646991193603	0.158635278613665	DNA	CMC-Transib
 TLD2	-1.24823548505769	0.158665416598185	LTR	Gypsy
 TC1_DM	0.400572910860442	0.167626897114732	DNA	TcMar-Tc1
@@ -92,53 +92,53 @@
 POGON1	0.482507112501569	0.255779427421414	DNA	TcMar-Pogo
 HOBO	-0.283220815078204	0.273166685685814	DNA	hAT-hobo
 BS3_DM	-0.418041606433149	0.277910060681416	LINE	Jockey
+Gypsy9_I-int	-0.437336296478435	0.280951304168472	LTR	Gypsy
 P-1_DY	0.969417874734635	0.280951304168472	DNA	P
-Gypsy9_I-int	-0.437336296478435	0.280951304168472	LTR	Gypsy
 Bica_I-int	-0.363151852276854	0.287621291763315	LTR	Gypsy
 DMCR1A	-0.342108879038489	0.320538100201906	LINE	CR1
 Mariner2_DM	-0.422114252836712	0.320538100201906	DNA	TcMar-Tc1
+Gypsy7_LTR	-0.484940393339899	0.322658401361327	LTR	Gypsy
 TRANSIB3	0.344232145502121	0.322658401361327	DNA	CMC-Transib
-Gypsy7_LTR	-0.484940393339899	0.322658401361327	LTR	Gypsy
 DMRPR	0.474671090698546	0.369600785239272	Unknown	Unknown
 DIVER2_LTR	-0.381362071713278	0.384462351162869	LTR	Pao
 Gypsy1-LTR_DM	0.341547880045558	0.384860099197221	LTR	Gypsy
+DOC4_DM	0.362114244909638	0.389414554540185	LINE	Jockey
 SSU-rRNA_Cel	0.268693361351043	0.389414554540185	rRNA	rRNA
-DOC4_DM	0.362114244909638	0.389414554540185	LINE	Jockey
 ZAM_I-int	0.25296287202699	0.397202788288282	LTR	Gypsy
 XDMR_DM	-0.256211211677393	0.408914532732159	Unknown	Unknown
 Chimpo_LTR	-0.460515218470088	0.409319591327129	LTR	Gypsy
+5S_DM	-0.36064468671157	0.412039231991319	RNA	RNA
+BLOOD_I-int	0.301193505006723	0.412039231991319	LTR	Gypsy
+CIRCE	-0.21220098912431	0.412039231991319	LTR	Gypsy
 DOC2_DM	-0.219218822289782	0.412039231991319	LINE	Jockey
-PROTOP	-0.21894181311432	0.412039231991319	DNA	P
-HETA	-0.298692871636692	0.412039231991319	LINE	Jockey
 HELENA_RT	0.306716860759321	0.412039231991319	LINE	Jockey
+HETA	-0.298692871636692	0.412039231991319	LINE	Jockey
 Invader2_LTR	-0.349451178427879	0.412039231991319	LTR	Gypsy
-BLOOD_I-int	0.301193505006723	0.412039231991319	LTR	Gypsy
-5S_DM	-0.36064468671157	0.412039231991319	RNA	RNA
-CIRCE	-0.21220098912431	0.412039231991319	LTR	Gypsy
+PROTOP	-0.21894181311432	0.412039231991319	DNA	P
 ACCORD2_LTR	-0.373877436518785	0.415323684742582	LTR	Gypsy
 BARI1	-0.361825471165769	0.439062969216072	DNA	TcMar-Tc1
 Copia2_I-int	-0.199651272204726	0.454016393978291	LTR	Copia
 Chouto_LTR	-0.42256718750228	0.457631460799645	LTR	Gypsy
 S_DM	0.193275098711318	0.466588891242574	DNA	TcMar-Tc1
+Chimpo_I-int	-0.3198026895528	0.469668398060595	LTR	Gypsy
+Gypsy2_LTR	0.337405927915915	0.469668398060595	LTR	Gypsy
 Gypsy6_I-int	0.244887845096584	0.469668398060595	LTR	Gypsy
 NOMAD_LTR	-0.310707505731374	0.469668398060595	LTR	Gypsy
-Chimpo_I-int	-0.3198026895528	0.469668398060595	LTR	Gypsy
-Gypsy2_LTR	0.337405927915915	0.469668398060595	LTR	Gypsy
 DIVER2_I-int	-0.217400353167491	0.482143273163041	LTR	Pao
 DOC3_DM	-0.226748306440889	0.495640056965812	LINE	Jockey
 XDMR	0.249633734746355	0.503551868695532	Unknown	Unknown
 ROO_I-int	0.276608752749181	0.50509162020251	LTR	Pao
 BURDOCK_LTR	0.32676718204459	0.510777537217992	LTR	Gypsy
 BEL_I-int	0.237362494177496	0.533794803142695	LTR	Pao
+Invader6_I-int	-0.205266937253198	0.533794803142695	LTR	Gypsy
 ROOA_I-int	-0.194233478923581	0.533794803142695	LTR	Pao
-Invader6_I-int	-0.205266937253198	0.533794803142695	LTR	Gypsy
+DIVER_LTR	0.271030983517942	0.536617484807809	LTR	Pao
 DOC6_DM	0.222079405295424	0.536617484807809	LINE	Jockey
-DIVER_LTR	0.271030983517942	0.536617484807809	LTR	Pao
 GTWIN_I-int	0.193808394449743	0.536617484807809	LTR	Gypsy
 MAX_LTR	-0.257749452683052	0.540151898310569	LTR	Pao
-Transib-N1_DM	-0.285359544492984	0.568470618173646	DNA	CMC-Transib
+Gypsy10_I-int	-0.188834668589015	0.568470618173646	LTR	Gypsy
 Gypsy11_LTR	-0.304519901682671	0.568470618173646	LTR	Gypsy
-Gypsy10_I-int	-0.188834668589015	0.568470618173646	LTR	Gypsy
+Transib-N1_DM	-0.285359544492984	0.568470618173646	DNA	CMC-Transib
 Gypsy8_LTR	-0.22930840819102	0.572155988619062	LTR	Gypsy
 MDG1_LTR	-0.222278232633914	0.598330807400594	LTR	Gypsy
 ARS406_DM	-0.253969785738388	0.616310720408007	Unknown	Unknown
@@ -146,48 +146,48 @@
 Invader3_I-int	-0.138005789457227	0.63087021446348	LTR	Gypsy
 FW2_DM	0.18134923098773	0.631976090641453	LINE	Jockey
 Gypsy9_LTR	-0.341386719736692	0.637388403082853	LTR	Gypsy
+PROTOP_A	0.129470019526978	0.641582941744779	DNA	P
 TART-A	0.137000662462686	0.641582941744779	LINE	Jockey
-PROTOP_A	0.129470019526978	0.641582941744779	DNA	P
+Invader2_I-int	-0.151224307192946	0.653366733778121	LTR	Gypsy
 MDG3_LTR	-0.188668582948884	0.653366733778121	LTR	Gypsy
-Invader2_I-int	-0.151224307192946	0.653366733778121	LTR	Gypsy
 Jockey2	-0.162959614427421	0.6545684300628	LINE	Jockey
 POGO	-0.150727724968995	0.655487951511946	DNA	TcMar-Pogo
 Baggins1	-0.134826103211095	0.693165877070164	LINE	LOA
-Stalker3_LTR	-0.174018068430168	0.707635948527852	LTR	Gypsy
 Bica_LTR	-0.203027970314789	0.707635948527852	LTR	Gypsy
 HMSBEAGLE_I-int	0.13884460350775	0.707635948527852	LTR	Gypsy
+Stalker3_LTR	-0.174018068430168	0.707635948527852	LTR	Gypsy
+NTS_DM	-0.176552072990723	0.7126900116144	Other	Other
 TABOR_LTR	-0.243243320673685	0.7126900116144	LTR	Gypsy
-NTS_DM	-0.176552072990723	0.7126900116144	Other	Other
 ZAM_LTR	0.185889162361338	0.717882303973929	LTR	Gypsy
 G5_DM	-0.112256553949312	0.728328879400999	LINE	Jockey
-QUASIMODO_I-int	0.126271255526405	0.756425760962704	LTR	Gypsy
+BEL_LTR	0.152542861711851	0.756425760962704	LTR	Pao
 FB4_DM	-0.114616335459739	0.756425760962704	DNA	TcMar-Tc1
 Invader1_LTR	0.141219962488351	0.756425760962704	LTR	Gypsy
-BEL_LTR	0.152542861711851	0.756425760962704	LTR	Pao
+QUASIMODO_I-int	0.126271255526405	0.756425760962704	LTR	Gypsy
 DMRT1B	-0.111235216287692	0.760051744799183	LINE	R1
 NOMAD_I-int	-0.137546703453753	0.760051744799183	LTR	Gypsy
 LmeSINE1c	-0.228543531933743	0.760296029745035	SINE	tRNA-Deu-L2
+Copia2_LTR_DM	0.147979193864449	0.76240178289376	LTR	Copia
 Gypsy10_LTR	-0.154651074858764	0.76240178289376	LTR	Gypsy
 QUASIMODO2-LTR_DM	-0.155430480903998	0.76240178289376	LTR	Gypsy
-Copia2_LTR_DM	0.147979193864449	0.76240178289376	LTR	Copia
 BS4_DM	-0.253251631796478	0.81092436860891	LINE	Jockey
 G_DM	0.0902785903431559	0.81092436860891	LINE	Jockey
 IVK_DM	-0.0807211765160779	0.818709085450591	LINE	I
+Gypsy12_LTR	-0.0832045482918072	0.835273508731359	LTR	Gypsy
 Gypsy5_I-int	-0.0774807293903186	0.835273508731359	LTR	Gypsy
-Gypsy12_LTR	-0.0832045482918072	0.835273508731359	LTR	Gypsy
 Gypsy6A_LTR	-0.116239966704279	0.835273508731359	LTR	Gypsy
 IDEFIX_I-int	0.0781972363147815	0.835273508731359	LTR	Gypsy
+DMRP1	0.100504519100353	0.846311908195535	Unknown	Unknown
 PROTOP_B	-0.0745501769371703	0.846311908195535	DNA	P
-DMRP1	0.100504519100353	0.846311908195535	Unknown	Unknown
 Copia1-LTR_DM	-0.0961752276665428	0.850550157756311	LTR	Copia
 TC1-2_DM	0.0595720035046981	0.853067020850826	DNA	TcMar-Tc1
+Gypsy7_I-int	0.0826410967604942	0.861339242519926	LTR	Gypsy
 LSU-rRNA_Cel	-0.0920825033469626	0.861339242519926	rRNA	rRNA
-Gypsy7_I-int	0.0826410967604942	0.861339242519926	LTR	Gypsy
-Gypsy5_LTR	-0.0710979993807782	0.905487490633946	LTR	Gypsy
+DMLTR5	0.0726894766496021	0.905487490633946	LTR	Gypsy
+Gypsy2-LTR_DM	0.0652192786223383	0.905487490633946	LTR	Gypsy
 Gypsy4_I-int	-0.0516274039610208	0.905487490633946	LTR	Gypsy
+Gypsy5_LTR	-0.0710979993807782	0.905487490633946	LTR	Gypsy
 QUASIMODO_LTR	-0.0643467685962964	0.905487490633946	LTR	Gypsy
-Gypsy2-LTR_DM	0.0652192786223383	0.905487490633946	LTR	Gypsy
-DMLTR5	0.0726894766496021	0.905487490633946	LTR	Gypsy
 Stalker2_LTR	-0.0523210063310555	0.917308330496379	LTR	Gypsy
 ROVER-I_DM	-0.0408110836395496	0.922716163337686	LTR	Gypsy
 MDG1_I-int	-0.0411424164719924	0.937452811422426	LTR	Gypsy
@@ -196,10 +196,10 @@
 BARI_DM	0.0372716083617889	0.949850971355763	DNA	TcMar-Tc1
 Gypsy2_I-int	-0.0261599267227275	0.951965771983562	LTR	Gypsy
 DMTOM1_LTR	0.0349640382618226	0.953829042793374	LTR	Gypsy
+Gypsy3_LTR	-0.0298883238815861	0.957715681080923	LTR	Gypsy
 IDEFIX_LTR	0.0219961145617681	0.957715681080923	LTR	Gypsy
+MINOS	0.0330479824589295	0.957715681080923	DNA	TcMar-Tc1
 STALKER4_I-int	0.0241275307638275	0.957715681080923	LTR	Gypsy
-Gypsy3_LTR	-0.0298883238815861	0.957715681080923	LTR	Gypsy
-MINOS	0.0330479824589295	0.957715681080923	DNA	TcMar-Tc1
 G2_DM	0.0226097987515835	0.962242582647045	LINE	Jockey
 Copia1-I_DM	0.0124236833262227	0.963045943681341	LTR	Copia
 Invader4_LTR	0.016495431966038	0.963045943681341	LTR	Gypsy
diff -r 51b4590a972d -r 15e3e29f310e test-data/paired-aligned_reads.tab
--- a/test-data/paired-aligned_reads.tab	Mon Sep 18 17:22:07 2017 -0400
+++ b/test-data/paired-aligned_reads.tab	Tue Sep 19 17:23:15 2017 -0400
@@ -1,1 +1,3 @@
+# Total reads aligned to repeated sequences
+
 2082