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	Additional homologs
58	0.0137	0.6248	lmo1724	N/A	-17.96	0.026530	144 -- 212	156 -- 211	ABC transporter ATP-binding protein		_____________143__________213\n_____________\|____________\|\n5'-UUA...CAACC____________CUGAU...UCA-3'\n______________AUGAAUGAAAAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACUUACUUUUG\n3'-GUU...UACUC____________UUUAU...GGA-5'\n_____________\|____________\|\n_____________212__________155\n	206 -- 212	156 -- 162	-13.4321 kcal/mol	1.37849 kcal/mol	0.849227 kcal/mol	143 213@LB@ \| \|@LB@5'-UUA...CAACC CUGAU...UCA-3'@LB@ AUGAAUGAAAAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACUUACUUUUG@LB@3'-GUU...UACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 212 155@LB@@LB@@LB@Energy -17.96 kcal/mol@LB@Hybridization Energy -13.4321 kcal/mol@LB@Unfolding Energy - mRNA 1.37849 kcal/mol@LB@Unfolding Energy - sRNA 0.849227 kcal/mol@LB@@LB@Position - mRNA 144 -- 212@LB@Position - sRNA 156 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 156 -- 162@LB@
47	0.01063	0.599	lmo0138	N/A	-20.04	0.009767	146 -- 210	158 -- 213	lmo0138		_____________145_________________________________________________________________________211\n_____________\|___________________________________________________________________________\|\n5'-AAA...AAUGC____G_____U_____UAA_____A____UUCAUUAUU________________A___GCA___A__________UAAAA...GCA-3'\n______________GUGC__AUGC_AUAAU___GGGAU_AGGU_________AUAGACA_GAG__AUG_GGC____GA_AUGAGUGAAA\n______________\|:\|\|__\|\|\|\|_\|\|\|\|:___\|\|\|\|\|_\|\|\|:_________\|\|\|\|\|\|\|_\|\|:__\|::_\|\|\|____\|\|_\|\|\|\|:\|\|\|\|\|\n______________CGCG__UACG_UAUUG___CCCUA_UCCG_________UAUCUGU_CUU__UGU_CCG____CU_UACUUACUUU\n3'-GUU...AAGCC____GA__________________C____________________A___GA___G___GUUA__C__________UGUUU...GGA-5'\n_____________\|___________________________________________________________________________\|\n_____________214_________________________________________________________________________157\n	204 -- 210	158 -- 164	-47.7003 kcal/mol	15.2802 kcal/mol	21.9717 kcal/mol	145 211@LB@ \| \|@LB@5'-AAA...AAUGC G U UAA A UUCAUUAUU A GCA A UAAAA...GCA-3'@LB@ GUGC AUGC AUAAU GGGAU AGGU AUAGACA GAG AUG GGC GA AUGAGUGAAA@LB@ \|:\|\| \|\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|: \|\|\|\|\|\|\| \|\|: \|:: \|\|\| \|\| \|\|\|\|:\|\|\|\|\|@LB@ CGCG UACG UAUUG CCCUA UCCG UAUCUGU CUU UGU CCG CU UACUUACUUU@LB@3'-GUU...AAGCC GA C A GA G GUUA C UGUUU...GGA-5'@LB@ \| \|@LB@ 214 157@LB@@LB@@LB@Energy -20.04 kcal/mol@LB@Hybridization Energy -47.7003 kcal/mol@LB@Unfolding Energy - mRNA 15.2802 kcal/mol@LB@Unfolding Energy - sRNA 21.9717 kcal/mol@LB@@LB@Position - mRNA 146 -- 210@LB@Position - sRNA 158 -- 213@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 158 -- 164@LB@
49	0.01139	0.599	lmo0181	N/A	-18.25	0.023109	147 -- 168	157 -- 179	sugar ABC transporter substrate-binding protein		_____________146________________169\n_____________\|__________________\|\n5'-AAG...AAUGG_______CG_________AAUAA...UUA-3'\n______________CAAUGAG__GAAUGAAAG\n______________\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\|:\n______________GUUACUC__CUUACUUUU\n3'-GUU...UGCCG_______UA_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________180________________156\n	162 -- 168	157 -- 163	-17.3464 kcal/mol	2.46271 kcal/mol	0.933292 kcal/mol	146 169@LB@ \| \|@LB@5'-AAG...AAUGG CG AAUAA...UUA-3'@LB@ CAAUGAG GAAUGAAAG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:@LB@ GUUACUC CUUACUUUU@LB@3'-GUU...UGCCG UA GUUUA...GGA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -18.25 kcal/mol@LB@Hybridization Energy -17.3464 kcal/mol@LB@Unfolding Energy - mRNA 2.46271 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 147 -- 168@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 157 -- 163@LB@
93	0.02416	0.6733	lmo2042	N/A	-17.13	0.038629	149 -- 196	158 -- 206	cell division protein MraZ		_____________148_____________________________________________197\n_____________\|_______________________________________________\|\n5'-UUU...GCGAA_________________UAAAG_____AUGU____AA__________UCUAA...CCC-3'\n______________GUGGGG___AGAUGUGG______UGGU____AUGA__GUGGGUGAAG\n______________:\|\|:\|\|___\|\|\|::\|\|:______:\|\|:____\|\|\|\|__:\|\|::\|\|\|\|:\n______________UACUCC___UCUGUACU______GCCG____UACU__UACUUACUUU\n3'-GUU...UGCCC______GUA________UGAUGU____GU______C___________UGUUU...GGA-5'\n_____________\|_______________________________________________\|\n_____________207_____________________________________________157\n	190 -- 196	158 -- 164	-27.738 kcal/mol	5.20754 kcal/mol	13.9391 kcal/mol	148 197@LB@ \| \|@LB@5'-UUU...GCGAA UAAAG AUGU AA UCUAA...CCC-3'@LB@ GUGGGG AGAUGUGG UGGU AUGA GUGGGUGAAG@LB@ :\|\|:\|\| \|\|\|::\|\|: :\|\|: \|\|\|\| :\|\|::\|\|\|\|:@LB@ UACUCC UCUGUACU GCCG UACU UACUUACUUU@LB@3'-GUU...UGCCC GUA UGAUGU GU C UGUUU...GGA-5'@LB@ \| \|@LB@ 207 157@LB@@LB@@LB@Energy -17.13 kcal/mol@LB@Hybridization Energy -27.738 kcal/mol@LB@Unfolding Energy - mRNA 5.20754 kcal/mol@LB@Unfolding Energy - sRNA 13.9391 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 158 -- 206@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 158 -- 164@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@
46	0.01036	0.599	lmo2695	N/A	-19.87	0.010617	150 -- 211	156 -- 209	dihydroxyacetone kinase subunit DhaK		_____________149_________________________________________________________________212\n_____________\|___________________________________________________________________\|\n5'-UUA...UUCUA____A____AAU_____________________UAUAAAGGA____UUU__UC______________UCUUA...CUC-3'\n______________GUAA_GGGA___UGAGGUA_AGA___GGACUAU_________GGUU___UG__AGAUGAA_GAAGAU\n______________:\|\|\|_\|\|\|\|___\|\|\|\|\|:\|_\|\|\|___\|:\|\|\|\|:_________\|\|::___\|\|__\|\|\|\|\|\|\|_\|\|\|:\|:\n______________UAUU_CCCU___ACUCCGU_UCU___CUUGAUG_________CCGG___AC__UCUACUU_CUUUUG\n3'-GUU...AUACG____G______________A___GUA_______UG___________UU____________A______UUUAU...GGA-5'\n_____________\|___________________________________________________________________\|\n_____________210_________________________________________________________________155\n	199 -- 205	163 -- 169	-36.4151 kcal/mol	9.16424 kcal/mol	18.7057 kcal/mol	149 212@LB@ \| \|@LB@5'-UUA...UUCUA A AAU UAUAAAGGA UUU UC UCUUA...CUC-3'@LB@ GUAA GGGA UGAGGUA AGA GGACUAU GGUU UG AGAUGAA GAAGAU@LB@ :\|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\| \|:\|\|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|:\|:@LB@ UAUU CCCU ACUCCGU UCU CUUGAUG CCGG AC UCUACUU CUUUUG@LB@3'-GUU...AUACG G A GUA UG UU A UUUAU...GGA-5'@LB@ \| \|@LB@ 210 155@LB@@LB@@LB@Energy -19.87 kcal/mol@LB@Hybridization Energy -36.4151 kcal/mol@LB@Unfolding Energy - mRNA 9.16424 kcal/mol@LB@Unfolding Energy - sRNA 18.7057 kcal/mol@LB@@LB@Position - mRNA 150 -- 211@LB@Position - sRNA 156 -- 209@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
2	0.0002774	0.3688	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
7	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
8	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@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@

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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