Mercurial > repos > drosofff > repenrich

changeset 3:1805b262c12d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ca572343d2a24d645dedd6c5d2cb352115ed8bf3
author drosofff
date Tue, 30 May 2017 10:34:53 -0400
parents aed130b47d36
children d359ec9f0fe1
files edgeR_repenrich.R edger-repenrich.xml repenrich.xml test-data/Normalized_counts_file.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab
diffstat 6 files changed, 365 insertions(+), 369 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_repenrich.R	Mon May 29 17:08:36 2017 -0400
+++ b/edgeR_repenrich.R	Tue May 30 10:34:53 2017 -0400
@@ -147,10 +147,6 @@
     write.table(normalizedAbundance, file=opt$countsfile, sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE)
 }
 
-# test
-print(counts)
-print(cpm)
-
 # Conduct fitting of the GLM
 yfit <- glmFit(y, design)
 
@@ -160,12 +156,12 @@
 
 # Make the comparisons for the GLM
 my.contrasts <- makeContrasts(
-    paste0(opt$levelNameB,"_",opt$levelNameA," = ", opt$levelNameB, " - ", opt$levelNameA),
+    paste0(opt$levelNameA,"_",opt$levelNameB," = ", opt$levelNameA, " - ", opt$levelNameB),
     levels = design
 )
 
 # Define the contrasts used in the comparisons
-allcontrasts =  paste0(opt$levelNameB," vs ",opt$levelNameA)
+allcontrasts =  paste0(opt$levelNameA," vs ",opt$levelNameB)
 
 # Conduct a for loop that will do the fitting of the GLM for each comparison
 # Put the results into the results objects
--- a/edger-repenrich.xml	Mon May 29 17:08:36 2017 -0400
+++ b/edger-repenrich.xml	Tue May 30 10:34:53 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="edger-repenrich" name="edgeR-repenrich" version="1.0.0">
+<tool id="edger-repenrich" name="edgeR-repenrich" version="1.1.0">
     <description>Determines differentially expressed features from RepEnrich counts</description>
     <requirements>
         <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
@@ -98,25 +98,25 @@
             label="Output normalized counts table" />
     </inputs>
     <outputs>
-        <data format="tabular" name="edger_out" label="edgeR result file on ${on_string}">
+        <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}">
             <actions>
                 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" />
             </actions>
         </data>
-        <data format="pdf" name="plots" label="edgeR plots on ${on_string}" />
-        <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
+        <data format="pdf" name="plots" label="edgeR plots" />
+        <data format="tabular" name="counts_out" label="Normalized counts file">
             <filter>normCounts == True</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="factorName" value="genotype"/>
-            <param name="factorLevel_A" value="wildtype"/>
-            <param name="countsFiles_A" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
-            <param name="alignmentFiles_A" value="aligned_353.tab,aligned_354.tab"/>
-            <param name="factorLevel_B" value="mutant"/>
-            <param name="countsFiles_B" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
-            <param name="alignmentFiles_B" value="aligned_355.tab,aligned_356.tab"/>
+            <param name="factorName" value="Genotype"/>
+            <param name="factorLevel_A" value="Mutant"/>
+            <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
+            <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/>
+            <param name="factorLevel_B" value="Wildtype"/>
+            <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
+            <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/>
             <param name="normCounts" value="True"/>
             <output name="counts_out" file="Normalized_counts_file.tab"/>
             <output name="plots" file="edgeR_plots.pdf"/>
--- a/repenrich.xml	Mon May 29 17:08:36 2017 -0400
+++ b/repenrich.xml	Tue May 30 10:34:53 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="repenrich" name="RepEnrich" version="1.0.0">
+<tool id="repenrich" name="RepEnrich" version="1.1.0">
     <description>Repeat Element Profiling</description>
     <requirements>
         <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -36,7 +36,7 @@
     <!-- basic error handling -->
     <inputs>
     <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
-    <param format="fastq,fastqsanger" label="Single-reads equencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
+    <param format="fastq,fastqsanger" label="Single-reads sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
     <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
     </inputs>
 
--- a/test-data/Normalized_counts_file.tab	Mon May 29 17:08:36 2017 -0400
+++ b/test-data/Normalized_counts_file.tab	Tue May 30 10:34:53 2017 -0400
@@ -1,211 +1,211 @@
-Tag	wildtype_1	wildtype_2	mutant_1	mutant_2
-LSU-rRNA_Dme	157455.221275418	149201.031867455	218650.181450173	354466.098949349
-FW3_DM	35.756634311884	44.2453336153694	25.3386538652006	32.2981814492716
-DMTOM1_LTR	43.2005545717588	49.0430203929395	54.9461072223747	39.3419337866127
-R1_DM	315.957840856997	262.031236427494	604.054709763298	517.028601444589
-TAHRE	196.209690086873	189.678242903128	149.055512536249	121.719476366005
-G4_DM	157.828320885669	165.108271224056	87.0600116574048	105.226787966377
-BS	313.935504138996	242.355874491196	203.649150075801	355.194096523239
-Stalker2_I-int	527.184456786045	604.508533973842	429.46472687139	413.519801853174
-Stalker3_LTR	25.5158653994552	21.2745908621546	21.2656708636846	20.1863634057947
-TABOR_I-int	169.833255871247	149.309827895896	215.554792695617	317.054754599099
-G7_DM	6.97060741098101	4.74922529496845	76.3292679803337	35.9059570366902
-BEL_I-int	1022.22666828812	1059.36800967358	1148.97283940843	1304.98396962057
-Gypsy6_I-int	322.239993215042	326.921161631196	445.717495579363	323.23951274896
-ACCORD_I-int	117.166444321613	104.919109832721	160.687012069425	174.461719477315
-DM412B_LTR	132.441540808639	141.022914371002	219.588612399041	257.784155662936
-G2_DM	57.1417693937208	54.8583983051458	48.3666731430026	65.6271559235199
-SSU-rRNA_Hsa	13684.9804569472	8340.22115575582	22075.2937251301	25925.561270609
-TART_B1	1086.38207353363	1042.55187521078	524.083255060455	437.142142008891
-S2_DM	32.9167572185214	35.52226674706	28.0409214335141	17.6093808433528
-LOOPER1_DM	35.3263499037988	28.5438132524124	8.61592558013002	2.66288198118994
-HOBO	216.476085707688	213.42436937797	171.339429150313	182.020868327145
-ARS406_DM	24.2250121751994	34.8438059906359	29.5682900590826	19.7568663120544
-G6_DM	207.698283782749	168.30672907577	112.555318714971	67.5169431359773
-DOC2_DM	190.960220308233	219.9182080466	176.665637690757	176.265607271025
-Baggins1	220.994071992583	188.660551768492	215.398139503251	157.367735146451
-NINJA_LTR	21.1269644369856	19.6753619362979	11.6314995331755	9.79253373727915
-TRANSIB2	137.561925264854	149.067520482887	131.471191693166	127.474737422125
-Gypsy5_LTR	28.0115149663496	21.8561286533752	19.6599756419331	28.0032105118684
-MDG3_LTR	44.6204931184401	41.0953372462576	36.2652140327291	38.9983361116205
-Gypsy12A_LTR	131.624000433277	108.650643993054	95.4017941508943	92.5136739916635
-Gypsy_LTR	56.1951436959333	44.4391795457762	147.684797103047	149.207290365385
-TIRANT_LTR	58.9919923484874	61.9822362475985	126.301636345088	137.095472321908
-I_DM	343.668156737687	339.860377485855	449.55549879233	957.692619622151
-DIVER2_I-int	287.386956160137	272.692762599872	252.44661949781	229.179649219831
-P-1_DY	0.344227526468198	0.0969229652034378	0.509122875189502	0.343597674992251
-Invader2_I-int	293.583051636564	267.022769135471	233.804889606256	271.184464987634
-DOC6_DM	54.1728069779326	60.0922384261314	67.2825461211972	65.9707535985121
-BURDOCK_LTR	12.3491625120466	17.930748562636	21.2656708636846	16.5785878183761
-SSU-rRNA_Dme	306.061299471036	201.260537244939	389.988122395158	328.307578455096
-MAX_LTR	43.7599243022696	36.4914963990943	37.5184395716571	29.4635006305855
-STALKER4_LTR	55.5927455246139	58.6383939480799	79.8931281066602	68.9772332546943
-XDMR_DM	142.725338161877	209.741296700239	158.572193972484	136.322377553175
-BARI_DM	42.5981564004395	43.7122573067505	43.7454039682056	44.8394965864887
-Transib-N1_DM	13.2527597690256	17.9792100452377	14.333767101489	11.1669244372481
-Gypsy5_I-int	105.333623099269	105.936800967358	110.988786791311	88.9917978229929
-XDMR	53.7425225698474	69.7845349464752	69.3582009200467	77.5671751295006
-ACCORD2_LTR	10.1116835900033	9.30460465953003	8.34178249348953	6.52835582485276
-POGON1	14.2424139076217	19.5299774884927	25.1036740766516	21.990251199504
-BS4_DM	1.46296698748984	1.0176911346361	0.313306384732001	1.97568663120544
-ALA_DM	0.215142204042624	0.290768895610313	0.352469682823501	0
-Gypsy1-I_DM	351.112076997562	305.161955943024	1447.55382405803	1954.46947477467
-ACCORD_LTR	12.6933900385148	10.6615261723782	30.9390054922851	29.5494000493336
-BURDOCK_I-int	134.205706881789	161.473660028927	203.257517094886	191.727502645676
-ZAM_I-int	220.692872906923	214.490521995208	270.070103638985	248.421119019397
-Invader5_I-int	17.8998313763463	16.2345966715758	7.48018993547652	10.0502319935233
-G3_DM	34.2936673243942	26.9445843265557	18.7983830839201	21.4748546870157
-ROOA_I-int	214.496777430496	222.389743659288	160.687012069425	221.534600951254
-Gypsy1-LTR_DM	44.8356353224828	38.5268786683665	56.0818428670282	49.4780651988841
-DM1731_I-int	222.887323388158	236.54049657899	737.405739764856	590.386705055435
-ROO_I-int	1368.00321862543	1358.56920325659	1332.45289096711	1970.61856549931
-DM412	1036.38302531413	1142.04329899211	1711.00533031955	2019.32353592946
-PROTOP	212.646554475729	210.952833765282	187.004748386913	176.866903202261
-TART-A	159.076145669116	165.156732706658	199.419513881919	156.766439215214
-ROO_LTR	70.523614485172	89.7022042957817	86.9033584650388	124.811855440935
-DIVER_LTR	20.1803387391981	20.7899760361374	21.4223240560506	28.1750093493646
-Gypsy3_I-int	146.253670308176	133.414461602532	225.81557679559	193.960887533126
-BATUMI_LTR	23.8377562079227	19.5299774884927	13.628827735842	14.5170017684226
-IDEFIX_LTR	94.2753138114777	89.3629739175697	99.3964505562273	86.9302117730394
-G5_DM	111.916974542973	123.625242116985	106.289191020331	111.669244372481
-HETA	990.729849616282	1182.31479103414	879.568511837001	887.083297411243
-Gypsy11_I-int	28.8720837825201	27.1384302569626	19.0725261705606	14.4311023496745
-R1-2_DM	11.4885936958761	8.57768242050425	7.20604684883602	5.84116047486826
-Gypsy11_LTR	5.76581106834231	7.22076090765612	6.22696439654852	4.12317209990701
-HELENA_RT	28.0975718479666	30.3853495912778	36.5785204174611	35.7341581991941
+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
+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
+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
+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
+DM1731_I-int	737.405739764856	590.386705055435	222.887323388158	236.54049657899
+ROO_I-int	1332.45289096711	1970.61856549931	1368.00321862543	1358.56920325659
+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	436.695645765717	501.818652340799	271.832452053102	285.787366174805
-Invader4_I-int	61.9179263234671	59.0745472914953	73.9403067967522	101.361314122714
-PLACW_DM	6.41123768047018	6.1546082904183	10.8482335713455	17.5234814246048
-BLOOD_LTR	32.1852737247765	36.1522660208823	49.6982252781136	46.55748496145
-R2_DM	659.496912272258	407.415684232651	2116.46295546085	1299.48640682069
-Copia1-I_DM	154.386045620987	170.487495792847	160.56952217515	167.16026888373
-Gypsy4_I-int	521.20350351366	487.328669042885	513.587491171932	459.390091464639
-Chouto_LTR	12.8655038017489	13.617676611083	6.34445429082302	13.658007580942
-BATUMI_I-int	275.166878970516	232.082040179632	184.968256886155	158.226729333931
-DNAREP1_DM	2918.23188407496	3099.30565831033	3009.73862162988	3174.24122099716
-DMRT1B	417.634046487541	344.997294641637	352.587172717776	353.476108148278
-DMRT1C	108.861955245568	101.139114189787	74.6844094604907	57.552610561202
-TLD2	2.79684865255411	0.823845204229221	1.2923888370195	0.0858994187480627
-DMRT1A	191.734732242786	171.553648410085	148.703042853426	106.085782153857
-DM1731_LTR	24.8274103465188	21.3230523447563	49.8940417685711	27.5737134181281
-LSU-rRNA_Cel	22382.0179984887	15843.270199567	14243.5740259843	21618.3926157437
-Copia_LTR	60.5840446584028	54.7130138573406	102.294534614998	264.140712650293
-Gypsy6_LTR	18.4161726660486	23.455357579232	55.7293731842047	65.2835582485276
-Gypsy12_I-int	420.732094225755	466.538693006748	195.894817053684	211.827966632723
-BLASTOPIA_LTR	23.6656424446886	23.1645886836216	40.6515034189771	78.9415658294696
-Bica_LTR	6.02398171319346	6.05768532521486	4.81708566525451	5.7552610561202
-Gypsy8_LTR	56.4102858999759	60.1406999087332	57.4525583002307	41.7471175115585
-NINJA_I-int	226.931996824159	218.22205615554	143.964283784354	98.4407338852798
-PROTOP_B	373.91715062608	401.503383355241	366.999266415448	369.367500616669
-PROTOP_A	152.019481376518	163.993657124217	174.864125978548	170.768044471149
-Invader3_LTR	28.2696856112007	29.4645814218451	19.8166288342991	19.4991680558102
-Chimpo_LTR	4.04467343600132	5.81537791220627	4.19047289579051	2.83468081868607
-Invader2_LTR	21.1699928777942	22.8738197880113	16.3310953041555	18.2965761933373
-BLASTOPIA_I-int	443.580196295081	462.322544020398	539.670247700872	1034.65849882041
-FROGGER_LTR	1.76416607314951	2.61692006049282	3.32888033777751	4.89626686863957
-NOMAD_I-int	708.635391675594	561.862429284329	454.842544034682	700.423860471703
-QUASIMODO_LTR	57.3138831569549	56.893780574418	63.6403593986877	45.3548930989771
-TABOR_LTR	16.5229212704735	13.2299847502693	17.3493410545346	7.55914884982952
-Stalker2_LTR	31.238648026989	32.5661163083551	30.9390054922851	30.5801930743103
-MICROPIA_LTR	34.2936673243942	41.8222594852834	18.0151171220901	12.7990133934613
-Gypsy9_I-int	21.6863341674965	22.9707427532148	16.8010548812535	16.1490907246358
-STALKER4_I-int	267.077532098513	278.217371616468	285.382953192761	269.036979518932
-TRANSIB1	89.5852137633485	102.544497185237	48.1316933544536	24.8249320181901
-DOC	769.477606978848	795.446775424614	1138.94703509701	1864.01738683296
-TRANSIB3	50.9456739172933	54.8583983051458	70.5722631608832	63.6514692923144
-Copia_I-int	1188.10130760498	1295.52081439175	1992.94191328026	7492.14730320603
-TRANSIB4	27.3230599134132	27.6715065655815	14.255440505306	13.1426110684536
-Gypsy10_LTR	13.5109304138768	17.8338255974326	14.2162772072145	13.9157058371862
-Invader3_I-int	200.813733253385	180.373638243598	172.749307881607	173.688624708583
-Invader1_I-int	78.8281035612173	81.027598910074	117.21575118786	151.870172346575
-BS3_DM	53.871607892273	42.5007202417075	33.3279666758666	38.9124366928724
-Gypsy2-LTR_DM	41.5654738210349	33.438422995186	45.2336092956826	33.0712762180041
-LSU-rRNA_Hsa	0.215142204042624	0	0.587449471372502	0.944893606228689
-NOMAD_LTR	26.6346048604768	39.8353386986129	29.6466166552656	23.7941389932134
-Helitron1_DM	0.129085322425574	0.290768895610313	0	0
-LINEJ1_DM	302.274796679886	306.712723386279	974.813652795529	1369.15083542537
-Invader4_LTR	61.1003859481051	59.5107006349108	63.6011961005962	58.3257053299346
-MDG3_I-int	232.009352839565	240.902030013145	307.706033104916	323.840808680196
-LmeSINE1c	25.7740360443063	68.5245363988305	24.5553879033706	56.0923204424849
-ROVER-LTR_DM	24.2680406160079	20.1115152797133	16.2527687079725	14.4311023496745
-S_DM	155.418728200391	168.452113523575	194.798244707122	175.320713664796
-Invader6_I-int	298.230123243885	324.740394914118	257.14621526879	283.296283031111
-ROVER-I_DM	280.244234985922	270.851226261007	272.067431841651	263.625316137804
-QUASIMODO_I-int	641.38193869187	630.871580509177	701.414668818767	687.195349984501
-Chouto_I-int	72.7180649664068	63.1937733126415	48.2100199506366	44.4958989114965
-NTS_DM	2837.89778508544	1754.54797759523	2194.82871494194	1868.57005602661
-Gypsy3_LTR	24.354097497625	21.6622827229683	26.6702060003116	18.2106767745893
-SSU-rRNA_Cel	149.007490519921	105.791416519552	150.974514142733	156.07924386523
-MINOS	7.44392025987478	10.9522950679885	10.6915803789795	7.98864594356983
-DOC4_DM	34.9821223773306	40.2230305594267	40.3381970342451	56.5218175362252
-ZAM_LTR	11.1443661694079	10.9038335853868	14.7645633804955	10.1361314122714
-QUASIMODO2-LTR_DM	13.4679019730682	9.69229652034378	11.670662831267	9.01943896854658
-Gypsy2-I_DM	198.188998364065	188.805936216297	288.790160126722	228.320655032351
-TRANSPAC_I-int	416.257136381668	726.049932338953	1115.13574985737	1439.67425821753
-Bica_I-int	79.6886723773878	67.3614608163893	61.1339083208317	53.0858407863027
-BS2	240.744126323696	241.871259665179	204.197436249082	179.186187508459
-BLOOD_I-int	960.825083254357	834.603653366803	1071.58616237963	1140.74428097427
-DMCR1A	876.919623677734	870.222843079066	684.926920322246	693.380108134362
-QUASIMODO2-I_DM	116.908273676762	107.826798788825	155.752436509896	155.563847352742
-HMSBEAGLE_I-int	311.48288301291	286.310439210955	307.941012893465	350.383729073348
-DMLTR5	6.92757897017248	7.75383721627503	7.40186333929352	8.07454536231789
-Gypsy7_LTR	4.81918537055477	4.21614898634954	3.13306384732001	3.35007733117444
-G5A_DM	77.6233072185786	77.2960647497417	61.7996843883872	49.9934617113725
-MDG1_I-int	702.009011791081	665.860770947618	638.596738680001	690.889024990668
-Gypsy2_I-int	137.260726179194	167.337499423735	165.50409773468	133.315897896993
-BARI1	16.9962341193673	15.6045973977535	14.490420293855	10.7374273435078
-Invader5_LTR	2.96896241578821	3.10153488651001	1.84067501030051	1.97568663120544
-DM176_LTR	38.6825682868637	42.2584128286989	21.9314469312401	28.3468081868607
-DOC3_DM	513.802611694594	516.550943051722	433.420219978632	447.106474583666
-Copia1-LTR_DM	33.1749278633726	27.4291991525729	23.4979788549001	33.4148738929964
-TOM_I-int	110.281893792249	111.994486292572	271.362492476004	291.199029555932
-NOF_FB	54.7321767084434	46.5230232976501	8.92923196486203	5.41166338112795
-Chimpo_I-int	55.4206317613798	51.369171557822	53.4970651929892	31.7827849367832
-DIVER_I-int	567.028792974739	757.307588617061	968.978321379896	1009.40406970848
-TIRANT_I-int	469.741488306664	414.781829588112	907.2178002896	1093.32780182534
-Gypsy2_LTR	20.6106231472833	23.5038190618337	34.0329060415136	21.4748546870157
-FB4_DM	307.610323340143	336.274227773327	307.040257037361	287.591253968514
-GTWIN_LTR	25.7310076034978	22.6315123750027	99.2006340657698	80.5736547856828
-Invader6_LTR	27.9254580847325	28.4953517698107	12.218949004548	12.5413151372172
-Gypsy8_I-int	206.923771848195	197.868233462818	163.545932830104	107.116575178834
-G_DM	383.168265399913	389.388012704811	428.759787505743	393.591136703623
-TRANSPAC_LTR	23.1493011549863	26.896122843954	57.0609253193157	84.0955309543534
+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
+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
+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
+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
+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
+NOMAD_I-int	454.842544034682	700.423860471703	708.635391675594	561.862429284329
+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
+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
+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
+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
-Transib5	48.3209390279733	46.7653307106587	38.1058890430296	28.1750093493646
-MuDR-1_DEl	0.258170644851148	0.43615334341547	1.253225538928	0.343597674992251
-Mariner2_DM	86.5301944659432	77.1022188193348	42.9229747082841	79.542861760706
-DOC5_DM	130.67737473549	105.791416519552	70.2197934780597	64.5963628985431
-TC1_DM	79.1723310876855	94.9845058993691	102.529514403547	127.560636840873
-Gypsy9_LTR	2.19445048123476	2.03538226927219	2.42812448167301	0.687195349984501
-DMRP1	11.2734514918335	11.0007565505902	11.5531729369925	12.369516299721
-Gypsy10_I-int	97.1582193456488	93.5306614213175	87.5691345325943	79.6287611794541
-Gypsy4_LTR	11.7897927815358	9.40152762473347	15.273686255685	18.7260732870777
-DM297_LTR	64.0693483638933	71.6260712853405	239.992690704713	216.122937570126
-ACCORD2_I-int	126.245445332212	119.118324235025	89.5272994371693	103.079302497675
-Invader1_LTR	143.973162945324	93.5791229039192	98.8873276810378	163.466593877563
-BEL_LTR	37.6498857074591	41.5799520722748	36.3043773308206	51.9691483425779
-IVK_DM	144.102248267749	141.555990679621	118.468976726788	151.956071765323
-M4DM	74.3101172763222	79.9614462928362	73.6270004120202	78.8556664107215
-FW2_DM	612.466826468541	671.046149586002	694.091132075657	761.412447782827
-Copia2_I-int	181.493963330357	167.434422388939	141.536159302681	162.521700271335
-MDG1_LTR	29.6896241578821	28.2045828742004	25.4561437594751	24.1377366682056
-Gypsy12_LTR	270.734949567238	287.5704377586	296.544493148839	230.210442244808
-Gypsy7_I-int	54.0437216555071	48.8976359451344	45.5077523823231	63.7373687110625
-FROGGER_I-int	69.3188181425333	65.9560778209394	42.1005454483626	46.9010826364422
-Gypsy_I-int	293.540023195756	273.031992978084	943.130544639506	958.723412647127
-5S_DM	271.810660587451	503.611727197063	247.942840217287	356.138990129468
-GTWIN_I-int	234.418945524843	244.924333069087	296.387839956473	251.685296931824
-CIRCE	162.088136525713	161.037506685512	143.964283784354	134.862087434458
-DIVER2_LTR	34.1215535611601	25.9268931919196	25.3778171632921	20.615860499535
-POGO	104.43002584229	120.766014643484	113.926034148174	88.6482001480007
-Gypsy6A_LTR	26.5485479788598	27.7684295307849	31.0564953865596	18.8119727058257
-MAX_I-int	533.337523821664	445.894101418416	349.101639187632	335.437230211185
-ROOA_LTR	17.2113763234099	23.4068960966302	17.0360346698026	23.7082395744653
-DM176_I-int	156.064154812519	136.322150558635	185.08574678043	197.396864283048
-Copia2_LTR_DM	38.3383407603955	23.5522805444354	29.2549836743506	39.5137326241088
-DM297_I-int	509.327653850507	558.760894397819	3226.54663986442	3668.33467763602
-IDEFIX_I-int	266.475133927194	268.815843991735	282.837338816814	282.265490006134
-Jockey2	76.1603402310888	76.9568343715296	71.3946924208047	65.2835582485276
-TC1-2_DM	163.809274158054	191.325933311586	173.806716930078	196.451970676819
-DMRPR	5.50764042349117	9.06229724652144	8.65508887822152	11.6823209497365
+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
Binary file test-data/edgeR_plots.pdf has changed
--- a/test-data/edgeR_result_file.tab	Mon May 29 17:08:36 2017 -0400
+++ b/test-data/edgeR_result_file.tab	Tue May 30 10:34:53 2017 -0400
@@ -1,209 +1,209 @@
 DM297_I-int	2.69047105438237	4.49448726299278e-21	LTR	Gypsy
-DM297_LTR	1.74961921158059	1.33970311551615e-18	LTR	Gypsy
-Gypsy1-I_DM	2.37388633230267	4.48026988289666e-16	LTR	Gypsy
-NOF_FB	-2.79644759297337	4.48026988289666e-16	DNA	MULE-NOF
-G7_DM	3.25987374806405	1.55296802933851e-15	LINE	Jockey
-Gypsy_I-int	1.74702179622354	4.35250852544863e-12	LTR	Gypsy
-LINEJ1_DM	1.94429217926762	5.18070558191679e-12	LINE	Jockey
-TOM_I-int	1.33935222283437	6.69227956217608e-12	LTR	Gypsy
-GTWIN_LTR	1.89490932455113	8.80590960311443e-12	LTR	Gypsy
-Gypsy_LTR	1.56024435809038	2.99852403113839e-11	LTR	Gypsy
+DM297_LTR	1.74961921158059	1.33970311552449e-18	LTR	Gypsy
+Gypsy1-I_DM	2.37388633230267	4.48026988291108e-16	LTR	Gypsy
+NOF_FB	-2.79644759297337	4.48026988291108e-16	DNA	MULE-NOF
+G7_DM	3.25987374806405	1.55296802933692e-15	LINE	Jockey
+Gypsy_I-int	1.74702179622354	4.35250852545265e-12	LTR	Gypsy
+LINEJ1_DM	1.94429217926762	5.18070558194078e-12	LINE	Jockey
+TOM_I-int	1.33935222283437	6.6922795621824e-12	LTR	Gypsy
+GTWIN_LTR	1.89490932455113	8.80590960313784e-12	LTR	Gypsy
+Gypsy_LTR	1.56024435809038	2.99852403114994e-11	LTR	Gypsy
 DM1731_I-int	1.53134429520835	6.4920552091728e-10	LTR	Copia
-Gypsy6_LTR	1.53023046204423	1.07509345482697e-06	LTR	Gypsy
+Gypsy6_LTR	1.53023046204423	1.07509345482848e-06	LTR	Gypsy
 LOOPER1_DM	-2.46983670012103	1.61917280285007e-06	DNA	PiggyBac
-TIRANT_LTR	1.12203469288475	1.7801266502904e-06	LTR	Gypsy
-Gypsy12_I-int	-1.12204057066646	2.19485691074398e-06	LTR	Gypsy
+TIRANT_LTR	1.12203469288475	1.78012665029166e-06	LTR	Gypsy
+Gypsy12_I-int	-1.12204057066646	2.19485691074579e-06	LTR	Gypsy
 R2_DM	1.67889583354494	2.73035057005978e-06	LINE	R2
-TRANSPAC_LTR	1.49364968145495	2.90210475425899e-06	LTR	Gypsy
-Copia_LTR	1.66649088148806	1.186041112787e-05	LTR	Copia
+TRANSPAC_LTR	1.49364968145495	2.9021047542613e-06	LTR	Gypsy
+Copia_LTR	1.66649088148806	1.18604111278586e-05	LTR	Copia
 ACCORD_LTR	1.3724059468295	1.75953804703817e-05	LTR	Gypsy
 TIRANT_I-int	1.17728139313168	2.04686461971632e-05	LTR	Gypsy
-TART_B1	-1.14695345949677	3.0965848472869e-05	LINE	Jockey
-TRANSIB1	-1.3902119423097	6.16503339250287e-05	DNA	CMC-Transib
-DM412B_LTR	0.803090050933452	0.00012443453312394	LTR	Gypsy
+TART_B1	-1.14695345949677	3.09658484730011e-05	LINE	Jockey
+TRANSIB1	-1.3902119423097	6.16503339250305e-05	DNA	CMC-Transib
+DM412B_LTR	0.803090050933452	0.00012443453312414	LTR	Gypsy
 MICROPIA_LTR	-1.29556276189806	0.000129852108160169	LTR	Gypsy
-G6_DM	-1.05894868960943	0.000138305097075555	LINE	Jockey
-NINJA_I-int	-0.874264518473233	0.000155536374045889	LTR	Pao
-R1_DM	0.955905154410719	0.000189845334696753	LINE	R1
+G6_DM	-1.05894868960943	0.000138305097075584	LINE	Jockey
+NINJA_I-int	-0.874264518473233	0.000155536374046075	LTR	Pao
+R1_DM	0.955905154410719	0.000189845334697796	LINE	R1
 Invader6_LTR	-1.18865109431199	0.000212988712815497	LTR	Gypsy
 Copia_I-int	1.9331690527025	0.000223130721644621	LTR	Copia
-BLASTOPIA_LTR	1.34881958569428	0.000364879309201074	LTR	Gypsy
+BLASTOPIA_LTR	1.34881958569428	0.000364879309201161	LTR	Gypsy
 LSU-rRNA_Hsa	2.61189118344978	0.000801598301190925	rRNA	rRNA
-TRANSPAC_I-int	1.16122217809542	0.000845313292127692	LTR	Gypsy
-G4_DM	-0.74970144243323	0.000914365923267139	LINE	Jockey
+TRANSPAC_I-int	1.16122217809542	0.000845313292130344	LTR	Gypsy
+G4_DM	-0.74970144243323	0.000914365923267624	LINE	Jockey
 SSU-rRNA_Hsa	1.12389968473263	0.0010425909765405	rRNA	rRNA
-DOC5_DM	-0.809872869194368	0.00162410751644232	LINE	Jockey
-Invader1_I-int	0.749727833008358	0.00198920329215514	LTR	Gypsy
+DOC5_DM	-0.809872869194368	0.00162410751644423	LINE	Jockey
+Invader1_I-int	0.749727833008358	0.00198920329215702	LTR	Gypsy
 TRANSIB4	-1.00230688125284	0.00206051807311839	DNA	CMC-Transib
 MICROPIA_I-int	-0.751193028928835	0.00292932704926266	LTR	Gypsy
 PLACW_DM	1.16310826488548	0.00305178248567248	DNA	P
-TABOR_I-int	0.737702190628259	0.00354953953974351	LTR	Gypsy
+TABOR_I-int	0.737702190628259	0.00354953953973759	LTR	Gypsy
 I_DM	1.04141382256571	0.00457151681951996	LINE	I
-Gypsy3_I-int	0.586594796021762	0.00533147146680049	LTR	Gypsy
-DOC	0.94015335715084	0.00552118010545893	LINE	Jockey
+Gypsy3_I-int	0.586594796021762	0.00533147146680179	LTR	Gypsy
+DOC	0.94015335715084	0.00552118010544697	LINE	Jockey
 Helitron1_DM	-5.10401049101919	0.00636579556275411	RC	Helitron
 Invader5_I-int	-0.973422642391873	0.00666026639838213	LTR	Gypsy
-ACCORD_I-int	0.593047691019391	0.00701363615971111	LTR	Gypsy
+ACCORD_I-int	0.593047691019391	0.00701363615971209	LTR	Gypsy
 LSU-rRNA_Dme	0.902204791675651	0.0102101724391352	rRNA	rRNA
 DM412	0.775970807845826	0.0108079710929838	LTR	Gypsy
 NINJA_LTR	-0.923408172476265	0.0109563169817133	LTR	Pao
-BATUMI_I-int	-0.562867612987509	0.0148551719821076	LTR	Pao
-DMRT1C	-0.664744166716986	0.0174563775735501	LINE	R1
-TAHRE	-0.509503033739914	0.0198535740576257	LINE	Jockey
-Gypsy8_I-int	-0.578276897527121	0.0248976847994196	LTR	Gypsy
-BLASTOPIA_I-int	0.796987753936179	0.0301824235833281	LTR	Gypsy
+BATUMI_I-int	-0.562867612987509	0.0148551719821132	LTR	Pao
+DMRT1C	-0.664744166716986	0.0174563775735471	LINE	R1
+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
 DMRT1A	-0.509608409844153	0.0432538714324547	LINE	R1
 DM176_LTR	-0.691384671506076	0.0432538714324547	LTR	Gypsy
-QUASIMODO2-I_DM	0.470057940126177	0.044414105251961	LTR	Gypsy
-MuDR-1_DEl	1.35524442785064	0.053231954651916	DNA	MULE-NOF
-DM1731_LTR	0.752238181600754	0.0540130070646255	LTR	Copia
-FROGGER_I-int	-0.60531971025629	0.0540130070646255	LTR	Copia
-MAX_I-int	-0.516456091983578	0.064340206781843	LTR	Pao
-BURDOCK_I-int	0.418223330277469	0.0691214301126655	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
+FROGGER_I-int	-0.60531971025629	0.0540130070646644	LTR	Copia
+MAX_I-int	-0.516456091983578	0.0643402067819527	LTR	Pao
+BURDOCK_I-int	0.418223330277469	0.0691214301126813	LTR	Gypsy
 FROGGER_LTR	0.888326398013863	0.0706362756551064	LTR	Copia
-DIVER_I-int	0.579052226156673	0.0738156276915433	LTR	Pao
-Chouto_I-int	-0.551029990754245	0.0815115938596914	LTR	Gypsy
-DM176_I-int	0.387008766766431	0.0918637211505558	LTR	Gypsy
-Invader4_I-int	0.532747054501905	0.0948962153499253	LTR	Gypsy
+DIVER_I-int	0.579052226156673	0.0738156276916979	LTR	Pao
+Chouto_I-int	-0.551029990754245	0.081511593859774	LTR	Gypsy
+DM176_I-int	0.387008766766431	0.0918637211505497	LTR	Gypsy
+Invader4_I-int	0.532747054501905	0.0948962153500033	LTR	Gypsy
 G3_DM	-0.607648157164968	0.103160664266056	LINE	Jockey
 Gypsy4_LTR	0.67676362702008	0.105307005535582	LTR	Gypsy
 BATUMI_LTR	-0.625598883331715	0.112325719453317	LTR	Pao
-Gypsy2-I_DM	0.418860685191156	0.127538985839663	LTR	Gypsy
+Gypsy2-I_DM	0.418860685191156	0.127538985839499	LTR	Gypsy
 Invader3_LTR	-0.553726127316243	0.130228544874336	LTR	Gypsy
 SSU-rRNA_Dme	0.50182621141568	0.130837858091619	rRNA	rRNA
 MDG3_I-int	0.417195433411295	0.130837858091619	LTR	Gypsy
-G5A_DM	-0.468375220785066	0.142388172856161	LINE	Jockey
-S2_DM	-0.576444154651049	0.154380925206595	DNA	TcMar-Tc1
+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
 Transib5	-0.51646991193603	0.158635278613665	DNA	CMC-Transib
 TLD2	-1.24823548505769	0.158665416598185	LTR	Gypsy
-TC1_DM	0.400572910860442	0.167626897114744	DNA	TcMar-Tc1
-BS2	-0.331386491833491	0.185478101135177	LINE	Jockey
+TC1_DM	0.400572910860442	0.167626897114732	DNA	TcMar-Tc1
+BS2	-0.331386491833491	0.185478101135035	LINE	Jockey
 ROVER-LTR_DM	-0.529681787599071	0.188737381603441	LTR	Gypsy
-ACCORD2_I-int	-0.350572607465432	0.191790844708865	LTR	Gypsy
-Gypsy12A_LTR	-0.354465506898828	0.204428444984683	LTR	Gypsy
-FW3_DM	-0.476342557702003	0.216920256528965	LINE	Jockey
-ROO_LTR	0.400232536676205	0.244465267215694	LTR	Pao
-STALKER4_LTR	0.383349427659289	0.248258091824802	LTR	Gypsy
+ACCORD2_I-int	-0.350572607465432	0.191790844708841	LTR	Gypsy
+Gypsy12A_LTR	-0.354465506898828	0.204428444984748	LTR	Gypsy
+FW3_DM	-0.476342557702003	0.216920256528982	LINE	Jockey
+ROO_LTR	0.400232536676207	0.244465267216066	LTR	Pao
+STALKER4_LTR	0.383349427659289	0.248258091824749	LTR	Gypsy
 POGON1	0.482507112501569	0.255779427421414	DNA	TcMar-Pogo
-HOBO	-0.283220815078204	0.273166685685483	DNA	hAT-hobo
-BS3_DM	-0.418041606433149	0.277910060681488	LINE	Jockey
+HOBO	-0.283220815078204	0.273166685685814	DNA	hAT-hobo
+BS3_DM	-0.418041606433149	0.277910060681416	LINE	Jockey
 P-1_DY	0.969417874734635	0.280951304168472	DNA	P
 Gypsy9_I-int	-0.437336296478435	0.280951304168472	LTR	Gypsy
-Bica_I-int	-0.363151852276852	0.287621291763233	LTR	Gypsy
-DMCR1A	-0.342108879038489	0.320538100201857	LINE	CR1
-Mariner2_DM	-0.422114252836712	0.320538100201857	DNA	TcMar-Tc1
+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
 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	0.384860099197011	LTR	Gypsy
-SSU-rRNA_Cel	0.268693361351043	0.389414554540408	rRNA	rRNA
-DOC4_DM	0.362114244909638	0.389414554540408	LINE	Jockey
-ZAM_I-int	0.25296287202699	0.397202788288859	LTR	Gypsy
-XDMR_DM	-0.256211211677393	0.40891453273183	Unknown	Unknown
+Gypsy1-LTR_DM	0.341547880045558	0.384860099197221	LTR	Gypsy
+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
-DOC2_DM	-0.219218822289782	0.412039231991164	LINE	Jockey
-PROTOP	-0.21894181311432	0.412039231991164	DNA	P
-HETA	-0.298692871636692	0.412039231991164	LINE	Jockey
-HELENA_RT	0.306716860759321	0.412039231991164	LINE	Jockey
-Invader2_LTR	-0.349451178427879	0.412039231991164	LTR	Gypsy
-BLOOD_I-int	0.301193505006723	0.412039231991164	LTR	Gypsy
-5S_DM	-0.36064468671157	0.412039231991164	RNA	RNA
-CIRCE	-0.21220098912431	0.412039231991164	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
+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
 ACCORD2_LTR	-0.373877436518785	0.415323684742582	LTR	Gypsy
 BARI1	-0.361825471165769	0.439062969216072	DNA	TcMar-Tc1
-Copia2_I-int	-0.199651272204726	0.454016393979065	LTR	Copia
+Copia2_I-int	-0.199651272204726	0.454016393978291	LTR	Copia
 Chouto_LTR	-0.42256718750228	0.457631460799645	LTR	Gypsy
-S_DM	0.193275098711318	0.466588891241469	DNA	TcMar-Tc1
-Gypsy6_I-int	0.244887845096584	0.469668398060558	LTR	Gypsy
-NOMAD_LTR	-0.310707505731374	0.469668398060558	LTR	Gypsy
-Chimpo_I-int	-0.3198026895528	0.469668398060558	LTR	Gypsy
-Gypsy2_LTR	0.337405927915915	0.469668398060558	LTR	Gypsy
-DIVER2_I-int	-0.217400353167491	0.48214327316296	LTR	Pao
-DOC3_DM	-0.226748306440889	0.495640056966085	LINE	Jockey
-XDMR	0.249633734746355	0.503551868695272	Unknown	Unknown
-ROO_I-int	0.276608752749181	0.505091620203207	LTR	Pao
+S_DM	0.193275098711318	0.466588891242574	DNA	TcMar-Tc1
+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	0.533794803142518	LTR	Pao
-ROOA_I-int	-0.194233478923581	0.533794803142518	LTR	Pao
-Invader6_I-int	-0.205266937253198	0.533794803142518	LTR	Gypsy
-DOC6_DM	0.222079405295424	0.536617484807693	LINE	Jockey
-DIVER_LTR	0.271030983517942	0.536617484807693	LTR	Pao
-GTWIN_I-int	0.193808394449743	0.536617484807693	LTR	Gypsy
-MAX_LTR	-0.257749452683052	0.540151898310394	LTR	Pao
+BEL_I-int	0.237362494177496	0.533794803142695	LTR	Pao
+ROOA_I-int	-0.194233478923581	0.533794803142695	LTR	Pao
+Invader6_I-int	-0.205266937253198	0.533794803142695	LTR	Gypsy
+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
 Gypsy11_LTR	-0.304519901682671	0.568470618173646	LTR	Gypsy
 Gypsy10_I-int	-0.188834668589015	0.568470618173646	LTR	Gypsy
-Gypsy8_LTR	-0.22930840819102	0.572155988619216	LTR	Gypsy
-MDG1_LTR	-0.222278232633914	0.598330807400729	LTR	Gypsy
-ARS406_DM	-0.253969785738388	0.616310720407917	Unknown	Unknown
-TRANSIB2	-0.146222438911029	0.625405183746989	DNA	CMC-Transib
-Invader3_I-int	-0.138005789457227	0.630870214463397	LTR	Gypsy
-FW2_DM	0.18134923098773	0.631976090646791	LINE	Jockey
+Gypsy8_LTR	-0.22930840819102	0.572155988619062	LTR	Gypsy
+MDG1_LTR	-0.222278232633914	0.598330807400594	LTR	Gypsy
+ARS406_DM	-0.253969785738388	0.616310720408007	Unknown	Unknown
+TRANSIB2	-0.146222438911029	0.625405183746808	DNA	CMC-Transib
+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
-TART-A	0.137000662462686	0.641582941743804	LINE	Jockey
-PROTOP_A	0.129470019526978	0.641582941743804	DNA	P
-MDG3_LTR	-0.188668582948884	0.653366733777971	LTR	Gypsy
-Invader2_I-int	-0.151224307192946	0.653366733777971	LTR	Gypsy
-Jockey2	-0.162959614427421	0.654568430062825	LINE	Jockey
-POGO	-0.150727724968995	0.655487951512125	DNA	TcMar-Pogo
-Baggins1	-0.134826103211095	0.693165877069107	LINE	LOA
-Stalker3_LTR	-0.174018068430168	0.707635948527927	LTR	Gypsy
-Bica_LTR	-0.203027970314789	0.707635948527927	LTR	Gypsy
-HMSBEAGLE_I-int	0.13884460350775	0.707635948527927	LTR	Gypsy
+TART-A	0.137000662462686	0.641582941744779	LINE	Jockey
+PROTOP_A	0.129470019526978	0.641582941744779	DNA	P
+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
 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	0.728328879400811	LINE	Jockey
-QUASIMODO_I-int	0.126271255526405	0.756425760963745	LTR	Gypsy
-FB4_DM	-0.114616335459739	0.756425760963745	DNA	TcMar-Tc1
-Invader1_LTR	0.141219962488351	0.756425760963745	LTR	Gypsy
-BEL_LTR	0.152542861711851	0.756425760963745	LTR	Pao
+G5_DM	-0.112256553949312	0.728328879400999	LINE	Jockey
+QUASIMODO_I-int	0.126271255526405	0.756425760962704	LTR	Gypsy
+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
 DMRT1B	-0.111235216287692	0.760051744799183	LINE	R1
 NOMAD_I-int	-0.137546703453753	0.760051744799183	LTR	Gypsy
-LmeSINE1c	-0.228543531933743	0.76029602974523	SINE	tRNA-Deu-L2
-Gypsy10_LTR	-0.154651074858764	0.762401782894161	LTR	Gypsy
-QUASIMODO2-LTR_DM	-0.155430480903998	0.762401782894161	LTR	Gypsy
-Copia2_LTR_DM	0.147979193864449	0.762401782894161	LTR	Copia
+LmeSINE1c	-0.228543531933743	0.760296029745035	SINE	tRNA-Deu-L2
+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	0.81870908545043	LINE	I
-Gypsy5_I-int	-0.0774807293903186	0.835273508730751	LTR	Gypsy
-Gypsy12_LTR	-0.0832045482918072	0.835273508730751	LTR	Gypsy
-Gypsy6A_LTR	-0.116239966704279	0.835273508730751	LTR	Gypsy
-IDEFIX_I-int	0.0781972363147815	0.835273508730751	LTR	Gypsy
+IVK_DM	-0.0807211765160779	0.818709085450591	LINE	I
+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
 PROTOP_B	-0.0745501769371703	0.846311908195535	DNA	P
 DMRP1	0.100504519100353	0.846311908195535	Unknown	Unknown
-Copia1-LTR_DM	-0.0961752276665428	0.850550157756422	LTR	Copia
-TC1-2_DM	0.0595720035046981	0.853067020850901	DNA	TcMar-Tc1
-LSU-rRNA_Cel	-0.0920825033469626	0.861339242540399	rRNA	rRNA
-Gypsy7_I-int	0.0826410967604942	0.861339242540399	LTR	Gypsy
-Gypsy5_LTR	-0.0710979993807782	0.905487490634908	LTR	Gypsy
-Gypsy4_I-int	-0.0516274039610208	0.905487490634908	LTR	Gypsy
-QUASIMODO_LTR	-0.0643467685962964	0.905487490634908	LTR	Gypsy
-Gypsy2-LTR_DM	0.0652192786223383	0.905487490634908	LTR	Gypsy
-DMLTR5	0.0726894766496021	0.905487490634908	LTR	Gypsy
-Stalker2_LTR	-0.0523210063310555	0.917308330496028	LTR	Gypsy
-ROVER-I_DM	-0.0408110836395496	0.922716163337709	LTR	Gypsy
+Copia1-LTR_DM	-0.0961752276665428	0.850550157756311	LTR	Copia
+TC1-2_DM	0.0595720035046981	0.853067020850826	DNA	TcMar-Tc1
+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
+Gypsy4_I-int	-0.0516274039610208	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
 ALA_DM	-0.11425480149938	0.942917068804402	Unknown	Unknown
 DNAREP1_DM	0.039354033592028	0.942917068804402	RC	Helitron
-BARI_DM	0.0372716083617889	0.94985097135805	DNA	TcMar-Tc1
-Gypsy2_I-int	-0.0261599267227275	0.95196577198178	LTR	Gypsy
-DMTOM1_LTR	0.0349640382618226	0.953829042791583	LTR	Gypsy
-IDEFIX_LTR	0.0219961145617681	0.957715681080671	LTR	Gypsy
-STALKER4_I-int	0.0241275307638275	0.957715681080671	LTR	Gypsy
-Gypsy3_LTR	-0.0298883238815861	0.957715681080671	LTR	Gypsy
-MINOS	0.0330479824589295	0.957715681080671	DNA	TcMar-Tc1
-G2_DM	0.0226097987515835	0.962242582650612	LINE	Jockey
-Copia1-I_DM	0.0124236833262227	0.963045943681216	LTR	Copia
-Invader4_LTR	0.016495431966038	0.963045943681216	LTR	Gypsy
-M4DM	-0.0173659751457427	0.963045943681216	DNA	CMC-Transib
+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
+IDEFIX_LTR	0.0219961145617681	0.957715681080923	LTR	Gypsy
+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
+M4DM	-0.0173659751457427	0.963045943681341	DNA	CMC-Transib
 BS	0.00565217021634194	0.997858051773989	LINE	Jockey
 FTZ_DM	0	1	Unknown	Unknown
 FUSHI_DM	0	1	Unknown	Unknown