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
178	0.05066	0.7607	lmo0216	N/A	-18.27	0.022949	55 -- 114	166 -- 213		_____________54__________________________________________________________________________________115\n_____________\|___________________________________________________________________________________\|\n5'-GCG...UCCAA__AAU______A______A__A___G__________UUUCCUUGUUUUU___CUA______A______U___U____A_____UUUGU...CGG-3'\n______________GC_____UGUU___GUGC_CU_GUG_GUGGCGGGAU_____________GCA___AGAUAU_AAUUAC_CGG_CCAA__AGAU\n______________\|\|_____\|\|\|\|___\|:\|\|_\|\|_:\|\|_:\|::\|\|\|\|\|\|_____________\|\|\|___\|\|\|:\|\|_\|\|:\|\|\|_\|\|\|_\|\|\|\|__\|\|\|\|\n______________CG_____ACAA___CGCG_GA_UAC_UAUUGCCCUA_____________CGU___UCUGUA_UUGAUG_GCC_GGUU__UCUA\n3'-GUU...CGCAA__GUAGU____GCC___________G__________CUC_____________A________C______U________AC____CUUAC...GGA-5'\n_____________\|___________________________________________________________________________________\|\n_____________214_________________________________________________________________________________165\n	62 -- 68	200 -- 206	-50.1796 kcal/mol	16.7648 kcal/mol	22.1647 kcal/mol	54 115@LB@ \| \|@LB@5'-GCG...UCCAA AAU A A A G UUUCCUUGUUUUU CUA A U U A UUUGU...CGG-3'@LB@ GC UGUU GUGC CU GUG GUGGCGGGAU GCA AGAUAU AAUUAC CGG CCAA AGAU@LB@ \|\| \|\|\|\| \|:\|\| \|\| :\|\| :\|::\|\|\|\|\|\| \|\|\| \|\|\|:\|\| \|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|@LB@ CG ACAA CGCG GA UAC UAUUGCCCUA CGU UCUGUA UUGAUG GCC GGUU UCUA@LB@3'-GUU...CGCAA GUAGU GCC G CUC A C U AC CUUAC...GGA-5'@LB@ \| \|@LB@ 214 165@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -50.1796 kcal/mol@LB@Unfolding Energy - mRNA 16.7648 kcal/mol@LB@Unfolding Energy - sRNA 22.1647 kcal/mol@LB@@LB@Position - mRNA 55 -- 114@LB@Position - sRNA 166 -- 213@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 200 -- 206@LB@
19	0.003536	0.4469	lmo0321	N/A	-22.74	0.002408	114 -- 157	167 -- 207		_____________113____________________________________________158\n_____________\|______________________________________________\|\n5'-AUU...UGUUA________UA____G_AC__________GGA_____U_________AUGUU...AGG-3'\n______________AGCGGGAU__GAGG_A__UAGGUA_GAA____ACGG_CUAAUGAGA\n______________\|:\|\|\|\|\|\|__\|\|\|\|_\|__\|\|\|::\|_\|\|\|____\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________UUGCCCUA__CUCC_U__AUCUGU_CUU____UGCC_GGUUACUCU\n3'-GUU...ACGUA______________G_________A___GAUG______________ACUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________208____________________________________________166\n	151 -- 157	167 -- 173	-39.7249 kcal/mol	9.73371 kcal/mol	18.0488 kcal/mol	113 158@LB@ \| \|@LB@5'-AUU...UGUUA UA G AC GGA U AUGUU...AGG-3'@LB@ AGCGGGAU GAGG A UAGGUA GAA ACGG CUAAUGAGA@LB@ \|:\|\|\|\|\|\| \|\|\|\| \| \|\|\|::\| \|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ UUGCCCUA CUCC U AUCUGU CUU UGCC GGUUACUCU@LB@3'-GUU...ACGUA G A GAUG ACUUA...GGA-5'@LB@ \| \|@LB@ 208 166@LB@@LB@@LB@Energy -22.74 kcal/mol@LB@Hybridization Energy -39.7249 kcal/mol@LB@Unfolding Energy - mRNA 9.73371 kcal/mol@LB@Unfolding Energy - sRNA 18.0488 kcal/mol@LB@@LB@Position - mRNA 114 -- 157@LB@Position - sRNA 167 -- 207@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 167 -- 173@LB@
39	0.008114	0.5599	lmo0390	N/A	-15.77	0.070471	151 -- 193	167 -- 211	uracil-DNA glycosylase	_____________150________194\n_____________\|__________\|\n5'-UCG...ACUGA__________AUUAA...AUG-3'\n______________GACGGGA_GA\n______________:\|\|\|\|\|\|_\|\|\n______________UUGCCCU_CU\n3'-GUU...ACGUA_______A__CCGUA...GGA-5'\n_____________\|__________\|\n_____________212________166\n	185 -- 191	201 -- 207	-12.4012 kcal/mol	0.989391 kcal/mol	0.374399 kcal/mol	150 194@LB@ \| \|@LB@5'-UCG...ACUGA AUUAA...AUG-3'@LB@ GACGGGA GA@LB@ :\|\|\|\|\|\| \|\|@LB@ UUGCCCU CU@LB@3'-GUU...ACGUA A CCGUA...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -12.4012 kcal/mol@LB@Unfolding Energy - mRNA 0.989391 kcal/mol@LB@Unfolding Energy - sRNA 0.374399 kcal/mol@LB@@LB@Position - mRNA 151 -- 193@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@LB@
106	0.02722	0.6733	lmo1616	N/A	-15.61	0.075454	67 -- 108	167 -- 211		_____________66______________________109\n_____________\|_______________________\|\n5'-AAG...AUAAC_____U_____GACU________AGGGC...UUU-3'\n______________GAACA_AUGUU____UGACUAGU\n______________:\|\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\|\n______________UUUGU_UACAG____ACUGAUCA\n3'-GUU...ACAGA_____C_________________ACGGU...GGA-5'\n_____________\|_______________________\|\n_____________212_____________________166\n	90 -- 96	117 -- 123	-17.5219 kcal/mol	5.32799 kcal/mol	5.058 kcal/mol	66 109@LB@ \| \|@LB@5'-AAG...AUAAC U GACU AGGGC...UUU-3'@LB@ GAACA AUGUU UGACUAGU@LB@ :\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUUGU UACAG ACUGAUCA@LB@3'-GUU...ACAGA C ACGGU...GGA-5'@LB@ \| \|@LB@ 212 166@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -17.5219 kcal/mol@LB@Unfolding Energy - mRNA 5.32799 kcal/mol@LB@Unfolding Energy - sRNA 5.058 kcal/mol@LB@@LB@Position - mRNA 67 -- 108@LB@Position - sRNA 167 -- 211@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 117 -- 123@LB@
157	0.0414	0.7058	lmo0010	N/A	-15.41	0.081879	188 -- 219	167 -- 203	mevalonate kinase	_____________187_____220\n_____________\|_______\|\n5'-AUC...AUGCG_______UGCAG...UAG-3'\n______________GAGAACA\n______________\|\|:\|\|\|\|\n______________CUUUUGU\n3'-GUU...ACUUA_______UUAUU...GGA-5'\n_____________\|_______\|\n_____________204_____166\n	241 -- 247	155 -- 161	-5.76961 kcal/mol	0.621388 kcal/mol	0.528569 kcal/mol	187 220@LB@ \| \|@LB@5'-AUC...AUGCG UGCAG...UAG-3'@LB@ GAGAACA@LB@ \|\|:\|\|\|\|@LB@ CUUUUGU@LB@3'-GUU...ACUUA UUAUU...GGA-5'@LB@ \| \|@LB@ 204 166@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -5.76961 kcal/mol@LB@Unfolding Energy - mRNA 0.621388 kcal/mol@LB@Unfolding Energy - sRNA 0.528569 kcal/mol@LB@@LB@Position - mRNA 188 -- 219@LB@Position - sRNA 167 -- 203@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 155 -- 161@LB@
29	0.005638	0.5232	lmo0014	qoxB	-19.61	0.012062	164 -- 215	168 -- 211	AA3-600 quinol oxidase subunit I	_____________163____________216\n_____________\|______________\|\n5'-CGG...CGCGA_____A________AAAUG...CUU-3'\n______________AGAUG_AAUGAAGA\n______________\|\|\|\|\|_\|\|\|\|\|\|:\|\n______________UCUAC_UUACUUUU\n3'-GUU...GUUAC______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________212____________167\n	111 -- 117	157 -- 163	-11.9482 kcal/mol	0.56531 kcal/mol	0.884237 kcal/mol	163 216@LB@ \| \|@LB@5'-CGG...CGCGA A AAAUG...CUU-3'@LB@ AGAUG AAUGAAGA@LB@ \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ UCUAC UUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 212 167@LB@@LB@@LB@Energy -19.61 kcal/mol@LB@Hybridization Energy -11.9482 kcal/mol@LB@Unfolding Energy - mRNA 0.56531 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 164 -- 215@LB@Position - sRNA 168 -- 211@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 157 -- 163@LB@
59	0.0137	0.6248	lmo0642	N/A	-14.84	0.103863	179 -- 256	168 -- 213	lmo0642	_____________178________257\n_____________\|__________\|\n5'-UUC...GAUUG__________CAUGA...CAA-3'\n______________GAGAUGAGUG\n______________\|\|\|\|\|\|\|:\|\|\n______________CUCUACUUAC\n3'-GUU...GGUUA__________UUUUG...GGA-5'\n_____________\|__________\|\n_____________214________167\n	193 -- 199	161 -- 167	-14.0942 kcal/mol	3.54513 kcal/mol	0.812237 kcal/mol	178 257@LB@ \| \|@LB@5'-UUC...GAUUG CAUGA...CAA-3'@LB@ GAGAUGAGUG@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUCUACUUAC@LB@3'-GUU...GGUUA UUUUG...GGA-5'@LB@ \| \|@LB@ 214 167@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -14.0942 kcal/mol@LB@Unfolding Energy - mRNA 3.54513 kcal/mol@LB@Unfolding Energy - sRNA 0.812237 kcal/mol@LB@@LB@Position - mRNA 179 -- 256@LB@Position - sRNA 168 -- 213@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
187	0.05427	0.7607	lmo2654	fus	-15.17	0.090605	196 -- 212	168 -- 184	elongation factor G	_____________195____________213\n_____________\|______________\|\n5'-GAG...AUACA__________A___UUCUC...AUA-3'\n______________ACAUGGCUAG_GAG\n______________\|\|\|:\|\|\|:\|:_\|\|\|\n______________UGUGCCGGUU_CUC\n3'-GUU...CUUGA__________A___UACUU...GGA-5'\n_____________\|______________\|\n_____________185____________167\n	202 -- 208	172 -- 178	-17.9516 kcal/mol	0.731619 kcal/mol	6.23346 kcal/mol	195 213@LB@ \| \|@LB@5'-GAG...AUACA A UUCUC...AUA-3'@LB@ ACAUGGCUAG GAG@LB@ \|\|\|:\|\|\|:\|: \|\|\|@LB@ UGUGCCGGUU CUC@LB@3'-GUU...CUUGA A UACUU...GGA-5'@LB@ \| \|@LB@ 185 167@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -17.9516 kcal/mol@LB@Unfolding Energy - mRNA 0.731619 kcal/mol@LB@Unfolding Energy - sRNA 6.23346 kcal/mol@LB@@LB@Position - mRNA 196 -- 212@LB@Position - sRNA 168 -- 184@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 172 -- 178@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@
25	0.004689	0.5029	lmo1584	N/A	-20.33	0.008463	183 -- 211	169 -- 209		_____________182___________212\n_____________\|_____________\|\n5'-GAA...GGCGC_____________AAAUG...CUG-3'\n______________ACAUGGCUAAUGA\n______________\|\|\|:\|\|\|:\|\|\|\|\|\n______________UGUGCCGGUUACU\n3'-GUU...CUUGA_____________CUACU...GGA-5'\n_____________\|_____________\|\n_____________210___________168\n	205 -- 211	169 -- 175	-19.4521 kcal/mol	2.17631 kcal/mol	6.15322 kcal/mol	182 212@LB@ \| \|@LB@5'-GAA...GGCGC AAAUG...CUG-3'@LB@ ACAUGGCUAAUGA@LB@ \|\|\|:\|\|\|:\|\|\|\|\|@LB@ UGUGCCGGUUACU@LB@3'-GUU...CUUGA CUACU...GGA-5'@LB@ \| \|@LB@ 210 168@LB@@LB@@LB@Energy -20.33 kcal/mol@LB@Hybridization Energy -19.4521 kcal/mol@LB@Unfolding Energy - mRNA 2.17631 kcal/mol@LB@Unfolding Energy - sRNA 6.15322 kcal/mol@LB@@LB@Position - mRNA 183 -- 211@LB@Position - sRNA 169 -- 209@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 169 -- 175@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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