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
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@
73	0.0193	0.6733	lmo0405	N/A	-18.50	0.020574	154 -- 209	155 -- 199	phosphate transporter		_____________153____________210\n_____________\|______________\|\n5'-GUG...UUAUG________U_____UACGA...CGA-3'\n______________AUGACGGG_AUGAG\n______________\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________UAUUGCCC_UACUC\n3'-GUU...AUACG______________CGUAU...GGA-5'\n_____________\|______________\|\n_____________200____________154\n	50 -- 56	202 -- 208	-16.311 kcal/mol	2.72131 kcal/mol	0.386761 kcal/mol	153 210@LB@ \| \|@LB@5'-GUG...UUAUG U UACGA...CGA-3'@LB@ AUGACGGG AUGAG@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGCCC UACUC@LB@3'-GUU...AUACG CGUAU...GGA-5'@LB@ \| \|@LB@ 200 154@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -16.311 kcal/mol@LB@Unfolding Energy - mRNA 2.72131 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 154 -- 209@LB@Position - sRNA 155 -- 199@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 202 -- 208@LB@
112	0.029	0.6968	lmo0191	N/A	-14.99	0.097641	103 -- 160	154 -- 212	phospho-beta-glucosidase		_____________102__________161\n_____________\|____________\|\n5'-UGU...CCAUG____________GAACG...CGC-3'\n______________GAGUGAAGGCGA\n______________\|\|:\|\|\|\|::\|:\|\n______________CUUACUUUUGUU\n3'-GUU...CUCUA____________UAUUA...GGA-5'\n_____________\|____________\|\n_____________213__________153\n	148 -- 154	154 -- 160	-12.5182 kcal/mol	1.90916 kcal/mol	0.857742 kcal/mol	102 161@LB@ \| \|@LB@5'-UGU...CCAUG GAACG...CGC-3'@LB@ GAGUGAAGGCGA@LB@ \|\|:\|\|\|\|::\|:\|@LB@ CUUACUUUUGUU@LB@3'-GUU...CUCUA UAUUA...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -12.5182 kcal/mol@LB@Unfolding Energy - mRNA 1.90916 kcal/mol@LB@Unfolding Energy - sRNA 0.857742 kcal/mol@LB@@LB@Position - mRNA 103 -- 160@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 154 -- 160@LB@
169	0.04649	0.7403	lmo0268	N/A	-16.22	0.057928	275 -- 284	195 -- 204	phosphoglycerate mutase		_____________274________285\n_____________\|__________\|\n5'-ACC...AUGCA__________GAUUC...UUG-3'\n______________GGGAUGGGGC\n______________\|\|\|\|\|\|:\|\|\|\n______________CCCUACUCCG\n3'-GUU...UAUUG__________UAUCU...GGA-5'\n_____________\|__________\|\n_____________205________194\n	278 -- 284	195 -- 201	-19.94 kcal/mol	1.96731 kcal/mol	6.55531 kcal/mol	274 285@LB@ \| \|@LB@5'-ACC...AUGCA GAUUC...UUG-3'@LB@ GGGAUGGGGC@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CCCUACUCCG@LB@3'-GUU...UAUUG UAUCU...GGA-5'@LB@ \| \|@LB@ 205 194@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -19.94 kcal/mol@LB@Unfolding Energy - mRNA 1.96731 kcal/mol@LB@Unfolding Energy - sRNA 6.55531 kcal/mol@LB@@LB@Position - mRNA 275 -- 284@LB@Position - sRNA 195 -- 204@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 195 -- 201@LB@
56	0.01257	0.6043	lmo2205	N/A	-16.72	0.046467	190 -- 249	147 -- 203	phosphoglyceromutase		_____________189_____________________250\n_____________\|_______________________\|\n5'-AUG...GCGAA____GAA________________AAUUA...UGG-3'\n______________AAUG___GGAUGAG_GAAGAUGA\n______________\|\|\|\|___:\|\|\|\|\|:_\|\|\|:\|::\|\n______________UUAC___UCUACUU_CUUUUGUU\n3'-GUU...GCCGG______________A________UAUUA...GGA-5'\n_____________\|_______________________\|\n_____________204_____________________146\n	197 -- 203	155 -- 161	-13.1674 kcal/mol	1.25432 kcal/mol	0.959215 kcal/mol	189 250@LB@ \| \|@LB@5'-AUG...GCGAA GAA AAUUA...UGG-3'@LB@ AAUG GGAUGAG GAAGAUGA@LB@ \|\|\|\| :\|\|\|\|\|: \|\|\|:\|::\|@LB@ UUAC UCUACUU CUUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 204 146@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -13.1674 kcal/mol@LB@Unfolding Energy - mRNA 1.25432 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 190 -- 249@LB@Position - sRNA 147 -- 203@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
123	0.03258	0.6968	lmo1821	N/A	-14.83	0.104144	189 -- 278	153 -- 220	phosphoprotein phosphatase		_____________188_________279\n_____________\|___________\|\n5'-AGA...AUCAU___________CGGCG...UUG-3'\n______________AAUGAAGACAA\n______________\|\|\|\|\|\|:\|\|\|\|\n______________UUACUUUUGUU\n3'-GUU...UCUAC___________UAUUA...GGA-5'\n_____________\|___________\|\n_____________221_________152\n	250 -- 256	154 -- 160	-9.76744 kcal/mol	1.01794 kcal/mol	0.610258 kcal/mol	188 279@LB@ \| \|@LB@5'-AGA...AUCAU CGGCG...UUG-3'@LB@ AAUGAAGACAA@LB@ \|\|\|\|\|\|:\|\|\|\|@LB@ UUACUUUUGUU@LB@3'-GUU...UCUAC UAUUA...GGA-5'@LB@ \| \|@LB@ 221 152@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -9.76744 kcal/mol@LB@Unfolding Energy - mRNA 1.01794 kcal/mol@LB@Unfolding Energy - sRNA 0.610258 kcal/mol@LB@@LB@Position - mRNA 189 -- 278@LB@Position - sRNA 153 -- 220@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 154 -- 160@LB@
147	0.03815	0.6968	lmo0655	N/A	-15.78	0.070044	227 -- 290	154 -- 212	phosphoprotein phosphatase		_____________226_____________291\n_____________\|_______________\|\n______5'-AACAA______UU_______CCACA...UUG-3'\n______________GAGA_G__UGAAGAC\n______________\|\|\|\|_\|__\|\|\|\|:\|\|\n______________CUCU_C__ACUUUUG\n3'-GUU...GGUUA____A_UU_______UUUAU...GGA-5'\n_____________\|_______________\|\n_____________213_____________153\n	13 -- 19	156 -- 162	-12.8457 kcal/mol	3.32795 kcal/mol	0.916023 kcal/mol	226 291@LB@ \| \|@LB@ 5'-AACAA UU CCACA...UUG-3'@LB@ GAGA G UGAAGAC@LB@ \|\|\|\| \| \|\|\|\|:\|\|@LB@ CUCU C ACUUUUG@LB@3'-GUU...GGUUA A UU UUUAU...GGA-5'@LB@ \| \|@LB@ 213 153@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -12.8457 kcal/mol@LB@Unfolding Energy - mRNA 3.32795 kcal/mol@LB@Unfolding Energy - sRNA 0.916023 kcal/mol@LB@@LB@Position - mRNA 227 -- 290@LB@Position - sRNA 154 -- 212@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 156 -- 162@LB@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase		_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@LB@
42	0.009182	0.5883	lmo1767	purM	-18.99	0.016282	211 -- 267	155 -- 213	phosphoribosylaminoimidazole synthetase		_____________210__________________________________________________________________________268\n_____________\|____________________________________________________________________________\|\n5'-GGA...ACAAA___AAU___A_AAA_______UA_UAAA_C____________A______________UCA__U_________C___UCAAA...UAG-3'\n______________UCG___GGC_G___AUGCAUA__G____G_AGGCGUGGACGU_GAA__GC_UGGCUA___AG___AGUGGAA_GCA\n______________\|\|\|___\|\|\|_\|___\|\|\|\|\|\|\|__\|____\|_\|\|\|\|:\|:\|\|\|:\|_\|\|\|__:\|_:\|\|\|:\|___\|\|___\|:\|\|:\|\|_:\|\|\n______________AGC___CCG_C___UACGUAU__C____C_UCCGUAUCUGUA_CUU__UG_GCCGGU___UC___UUACUUU_UGU\n3'-GUU...GUACA___________GGA_______UG_CCUA__________________GA__U______UAC__UAC___________UUAUU...GGA-5'\n_____________\|____________________________________________________________________________\|\n_____________214__________________________________________________________________________154\n	257 -- 263	158 -- 164	-45.9009 kcal/mol	14.0255 kcal/mol	22.2914 kcal/mol	210 268@LB@ \| \|@LB@5'-GGA...ACAAA AAU A AAA UA UAAA C A UCA U C UCAAA...UAG-3'@LB@ UCG GGC G AUGCAUA G G AGGCGUGGACGU GAA GC UGGCUA AG AGUGGAA GCA@LB@ \|\|\| \|\|\| \| \|\|\|\|\|\|\| \| \| \|\|\|\|:\|:\|\|\|:\| \|\|\| :\| :\|\|\|:\| \|\| \|:\|\|:\|\| :\|\|@LB@ AGC CCG C UACGUAU C C UCCGUAUCUGUA CUU UG GCCGGU UC UUACUUU UGU@LB@3'-GUU...GUACA GGA UG CCUA GA U UAC UAC UUAUU...GGA-5'@LB@ \| \|@LB@ 214 154@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -45.9009 kcal/mol@LB@Unfolding Energy - mRNA 14.0255 kcal/mol@LB@Unfolding Energy - sRNA 22.2914 kcal/mol@LB@@LB@Position - mRNA 211 -- 267@LB@Position - sRNA 155 -- 213@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 158 -- 164@LB@
193	0.05586	0.7607	lmo1772	purC	-15.19	0.089756	256 -- 291	97 -- 135	phosphoribosylaminoimidazole-succinocarboxamide synthase		_____________255_____________________________________292\n_____________\|_______________________________________\|\n5'-UUA...AGAAG____________U__GU______UAUAA______C____CGACA...CGC-3'\n______________AAGCAGGUGUCU_GC__GUUGCU________GGA_GAUG\n______________\|\|:\|\|\|:\|\|\|\|\|_:\|__\|\|\|\|\|:________\|\|\|_\|\|\|\|\n______________UUUGUCUACAGA_UG__CAACGG________CCU_CUAC\n3'-GUU...ACAGA____________C__AU______UAAGAUAA___U____CUAUG...GGA-5'\n_____________\|_______________________________________\|\n_____________136_____________________________________96\n	261 -- 267	124 -- 130	-33.6761 kcal/mol	9.14329 kcal/mol	9.45249 kcal/mol	255 292@LB@ \| \|@LB@5'-UUA...AGAAG U GU UAUAA C CGACA...CGC-3'@LB@ AAGCAGGUGUCU GC GUUGCU GGA GAUG@LB@ \|\|:\|\|\|:\|\|\|\|\| :\| \|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UUUGUCUACAGA UG CAACGG CCU CUAC@LB@3'-GUU...ACAGA C AU UAAGAUAA U CUAUG...GGA-5'@LB@ \| \|@LB@ 136 96@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -33.6761 kcal/mol@LB@Unfolding Energy - mRNA 9.14329 kcal/mol@LB@Unfolding Energy - sRNA 9.45249 kcal/mol@LB@@LB@Position - mRNA 256 -- 291@LB@Position - sRNA 97 -- 135@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 124 -- 130@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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