Input and runtime details for job 8257533 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
24	0.004153	0.4656	lmo1386	N/A	-22.14	0.003328	2 -- 37	155 -- 186	DNA translocase	_____________1____________________________________38\n_____________\|____________________________________\|\n__________5'-G___G________G__AAGCU______CAC_______CCGCA...UUA-3'\n______________GAA_UACGCGGC_GA_____GAUGAA___GAAAACA\n______________\|\|\|_\|\|\|:\|\|\|\|_:\|_____\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUU_AUGUGCCG_UU_____CUACUU___CUUUUGU\n3'-GUU...CUGUA___G________G__ACU________A_________UUAUU...GGA-5'\n_____________\|____________________________________\|\n_____________187__________________________________154\n	31 -- 37	155 -- 161	-32.0969 kcal/mol	6.67763 kcal/mol	9.66922 kcal/mol	1 38@LB@ \| \|@LB@ 5'-G G G AAGCU CAC CCGCA...UUA-3'@LB@ GAA UACGCGGC GA GAUGAA GAAAACA@LB@ \|\|\| \|\|\|:\|\|\|\| :\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUU AUGUGCCG UU CUACUU CUUUUGU@LB@3'-GUU...CUGUA G G ACU A UUAUU...GGA-5'@LB@ \| \|@LB@ 187 154@LB@@LB@@LB@Energy -22.14 kcal/mol@LB@Hybridization Energy -32.0969 kcal/mol@LB@Unfolding Energy - mRNA 6.67763 kcal/mol@LB@Unfolding Energy - sRNA 9.66922 kcal/mol@LB@@LB@Position - mRNA 2 -- 37@LB@Position - sRNA 155 -- 186@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 155 -- 161@LB@
77	0.02006	0.6733	lmo1400	N/A	-17.16	0.038248	136 -- 215	157 -- 223	N-acetyltransferase	_____________135_____________216\n_____________\|_______________\|\n5'-AAA...GUUUU_______________AUUUU...AAG-3'\n______________UGAG_UGAGUGGAAA\n______________\|\|\|\|_\|\|\|:\|\|:\|\|\|\n______________ACUC_ACUUACUUUU\n3'-GUU...CGGUU____U__________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________224_____________156\n	209 -- 215	157 -- 163	-14.2437 kcal/mol	2.95971 kcal/mol	0.905109 kcal/mol	135 216@LB@ \| \|@LB@5'-AAA...GUUUU AUUUU...AAG-3'@LB@ UGAG UGAGUGGAAA@LB@ \|\|\|\| \|\|\|:\|\|:\|\|\|@LB@ ACUC ACUUACUUUU@LB@3'-GUU...CGGUU U GUUUA...GGA-5'@LB@ \| \|@LB@ 224 156@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -14.2437 kcal/mol@LB@Unfolding Energy - mRNA 2.95971 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 136 -- 215@LB@Position - sRNA 157 -- 223@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 157 -- 163@LB@
167	0.04638	0.7403	lmo1401	N/A	-16.51	0.050998	149 -- 209	155 -- 204		_____________148________210\n_____________\|__________\|\n5'-AUU...AACAA__________CUAUU...UCA-3'\n______________AAUGAAAAUA\n______________\|\|\|\|\|\|\|\|:\|\n______________UUACUUUUGU\n3'-GUU...UCUAC__________UUAUU...GGA-5'\n_____________\|__________\|\n_____________205________154\n	203 -- 209	155 -- 161	-7.61408 kcal/mol	0.775188 kcal/mol	0.60613 kcal/mol	148 210@LB@ \| \|@LB@5'-AUU...AACAA CUAUU...UCA-3'@LB@ AAUGAAAAUA@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUACUUUUGU@LB@3'-GUU...UCUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 205 154@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -7.61408 kcal/mol@LB@Unfolding Energy - mRNA 0.775188 kcal/mol@LB@Unfolding Energy - sRNA 0.60613 kcal/mol@LB@@LB@Position - mRNA 149 -- 209@LB@Position - sRNA 155 -- 204@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
16	0.003215	0.4469	lmo1403	mutS	-20.74	0.006867	183 -- 222	169 -- 209	DNA mismatch repair protein MutS	_____________182________________223\n_____________\|__________________\|\n5'-ACG...UGCUA__________________AGAAG...UGU-3'\n______________UAAUGAGA_GGAUGAAAA\n______________:\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________GUUACUCU_CUUACUUUU\n3'-GUU...UGCCG________A_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________210________________168\n	172 -- 178	157 -- 163	-16.7756 kcal/mol	1.79354 kcal/mol	0.933292 kcal/mol	182 223@LB@ \| \|@LB@5'-ACG...UGCUA AGAAG...UGU-3'@LB@ UAAUGAGA GGAUGAAAA@LB@ :\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GUUACUCU CUUACUUUU@LB@3'-GUU...UGCCG A GUUUA...GGA-5'@LB@ \| \|@LB@ 210 168@LB@@LB@@LB@Energy -20.74 kcal/mol@LB@Hybridization Energy -16.7756 kcal/mol@LB@Unfolding Energy - mRNA 1.79354 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 183 -- 222@LB@Position - sRNA 169 -- 209@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 157 -- 163@LB@
159	0.04218	0.7139	lmo1454	rpoD	-16.27	0.056776	172 -- 217	153 -- 211	RNA polymerase sigma factor RpoD	_____________171_______________218\n_____________\|_________________\|\n5'-AGA...GUUAA___G________U____UAAUA...UAA-3'\n______________ACA_CGGCCAAU_GGAU\n______________\|\|\|_\|\|\|\|\|\|\|\|_:\|\|\|\n______________UGU_GCCGGUUA_UCUA\n3'-GUU...CUUGA____________C____CUUAC...GGA-5'\n_____________\|_________________\|\n_____________212_______________152\n	92 -- 98	171 -- 177	-19.258 kcal/mol	2.66151 kcal/mol	6.2749 kcal/mol	171 218@LB@ \| \|@LB@5'-AGA...GUUAA G U UAAUA...UAA-3'@LB@ ACA CGGCCAAU GGAU@LB@ \|\|\| \|\|\|\|\|\|\|\| :\|\|\|@LB@ UGU GCCGGUUA UCUA@LB@3'-GUU...CUUGA C CUUAC...GGA-5'@LB@ \| \|@LB@ 212 152@LB@@LB@@LB@Energy -16.27 kcal/mol@LB@Hybridization Energy -19.258 kcal/mol@LB@Unfolding Energy - mRNA 2.66151 kcal/mol@LB@Unfolding Energy - sRNA 6.2749 kcal/mol@LB@@LB@Position - mRNA 172 -- 217@LB@Position - sRNA 153 -- 211@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 171 -- 177@LB@
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202		_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
156	0.04133	0.7058	lmo1481	holA	-16.45	0.052293	189 -- 224	151 -- 199	DNA polymerase III subunit delta	_____________188_________225\n_____________\|___________\|\n5'-CAA...UGCCA___________GAUAC...UUU-3'\n______________GAAUGGAAACA\n______________\|\|\|\|\|:\|\|\|\|\|\n______________CUUACUUUUGU\n3'-GUU...CUCUA___________UUAUU...GGA-5'\n_____________\|___________\|\n_____________200_________150\n	213 -- 219	156 -- 162	-12.8572 kcal/mol	1.78423 kcal/mol	0.853601 kcal/mol	188 225@LB@ \| \|@LB@5'-CAA...UGCCA GAUAC...UUU-3'@LB@ GAAUGGAAACA@LB@ \|\|\|\|\|:\|\|\|\|\|@LB@ CUUACUUUUGU@LB@3'-GUU...CUCUA UUAUU...GGA-5'@LB@ \| \|@LB@ 200 150@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -12.8572 kcal/mol@LB@Unfolding Energy - mRNA 1.78423 kcal/mol@LB@Unfolding Energy - sRNA 0.853601 kcal/mol@LB@@LB@Position - mRNA 189 -- 224@LB@Position - sRNA 151 -- 199@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 156 -- 162@LB@
146	0.03799	0.6968	lmo1526	N/A	-15.66	0.073786	160 -- 215	153 -- 207		_____________159____________________216\n_____________\|______________________\|\n5'-AUG...AGGAG____AAACA____A________AGUAC...UAA-3'\n______________GAGA_____UGAA_GAAAAUAA\n______________\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|\n______________CUCU_____ACUU_CUUUUGUU\n3'-GUU...GGUUA_____________A________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________208____________________152\n	208 -- 214	154 -- 160	-11.4679 kcal/mol	1.00795 kcal/mol	0.933796 kcal/mol	159 216@LB@ \| \|@LB@5'-AUG...AGGAG AAACA A AGUAC...UAA-3'@LB@ GAGA UGAA GAAAAUAA@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|@LB@ CUCU ACUU CUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 208 152@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.4679 kcal/mol@LB@Unfolding Energy - mRNA 1.00795 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 160 -- 215@LB@Position - sRNA 153 -- 207@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 154 -- 160@LB@
136	0.03623	0.6968	lmo1567	citZ	-17.33	0.035419	8 -- 31	169 -- 198	citrate synthase	_____________7______________________________32\n_____________\|______________________________\|\n____5'-CGAAAAA__________________________U___UCCAC...ACG-3'\n______________AGGUGUAG______GCUAUAUGGCCG_UGA\n______________\|\|\|::\|\|\|______:\|\|\|:\|:\|\|\|\|:_\|\|\|\n______________UCCGUAUC______UGAUGUGCCGGU_ACU\n3'-GUU...CCUAC________UGUACU____________U___CUACU...GGA-5'\n_____________\|______________________________\|\n_____________199____________________________168\n	21 -- 27	173 -- 179	-29.4881 kcal/mol	5.57901 kcal/mol	13.3393 kcal/mol	7 32@LB@ \| \|@LB@ 5'-CGAAAAA U UCCAC...ACG-3'@LB@ AGGUGUAG GCUAUAUGGCCG UGA@LB@ \|\|\|::\|\|\| :\|\|\|:\|:\|\|\|\|: \|\|\|@LB@ UCCGUAUC UGAUGUGCCGGU ACU@LB@3'-GUU...CCUAC UGUACU U CUACU...GGA-5'@LB@ \| \|@LB@ 199 168@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -29.4881 kcal/mol@LB@Unfolding Energy - mRNA 5.57901 kcal/mol@LB@Unfolding Energy - sRNA 13.3393 kcal/mol@LB@@LB@Position - mRNA 8 -- 31@LB@Position - sRNA 169 -- 198@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 173 -- 179@LB@
23	0.00382	0.4469	lmo1572	accA	-20.61	0.007329	192 -- 226	157 -- 188	acetyl-CoA carboxylase carboxyltransferase subunit alpha	_____________191______________________________________________________________________________227\n_____________\|________________________________________________________________________________\|\n5'-AGG...UUUAA__AU______GAAA__A____GA_____________A__UG__________________G___________AUU______ACCGA...CCA-3'\n______________GC__UCAUGU____GC_CCUG___GUAG_GGGGUGA_GU_______________AUGGC_AAUGAGAUGGA___UGAGAA\n______________\|\|__\|\|\|\|\|\|____\|\|_\|\|\|:___:\|\|:_\|\|\|:\|\|\|_\|:_______________\|:\|\|\|_\|\|\|\|\|\|\|\|\|:\|___\|\|\|:\|\|\n______________CG__AGUACA____CG_GGAU___UAUU_CCCUACU_CG_______________UGCCG_UUACUCUACUU___ACUUUU\n3'-GUU...CGCAA__GU______AGCC__C____ACG____G_______C__UAUCUGUACUUGAUG_____G____________________GUUUA...GGA-5'\n_____________\|________________________________________________________________________________\|\n_____________189______________________________________________________________________________156\n	211 -- 217	163 -- 169	-59.1532 kcal/mol	18.9584 kcal/mol	22.6787 kcal/mol	191 227@LB@ \| \|@LB@5'-AGG...UUUAA AU GAAA A GA A UG G AUU ACCGA...CCA-3'@LB@ GC UCAUGU GC CCUG GUAG GGGGUGA GU AUGGC AAUGAGAUGGA UGAGAA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|\|: :\|\|: \|\|\|:\|\|\| \|: \|:\|\|\| \|\|\|\|\|\|\|\|\|:\| \|\|\|:\|\|@LB@ CG AGUACA CG GGAU UAUU CCCUACU CG UGCCG UUACUCUACUU ACUUUU@LB@3'-GUU...CGCAA GU AGCC C ACG G C UAUCUGUACUUGAUG G GUUUA...GGA-5'@LB@ \| \|@LB@ 189 156@LB@@LB@@LB@Energy -20.61 kcal/mol@LB@Hybridization Energy -59.1532 kcal/mol@LB@Unfolding Energy - mRNA 18.9584 kcal/mol@LB@Unfolding Energy - sRNA 22.6787 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 157 -- 188@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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