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
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@
86	0.02293	0.6733	lmo0853	N/A	-17.72	0.029549	77 -- 124	163 -- 214	SugE protein	_____________76__________________________________________________________125\n_____________\|___________________________________________________________\|\n5'-GAC...CGUUU________CUUCU______AC__________________________AUUUAU______ACGGA...UUU-3'\n______________UUUAUGCA_____UGAUGG__UGA_GUGUGGA________ACACGGC______GAUGAA\n______________::\|\|\|\|\|\|_____\|:\|:\|\|__\|\|\|_\|::\|:\|\|________\|\|\|\|\|\|\|______\|\|\|\|\|\|\n______________GGAUACGU_____AUUGCC__ACU_CGUAUCU________UGUGCCG______CUACUU\n3'-GUU...CCCGC___________________CU___C_______GUACUUGA_______GUUACU______ACUUU...GGA-5'\n_____________\|___________________________________________________________\|\n_____________215_________________________________________________________162\n	106 -- 112	175 -- 181	-38.3816 kcal/mol	10.3843 kcal/mol	19.6349 kcal/mol	76 125@LB@ \| \|@LB@5'-GAC...CGUUU CUUCU AC AUUUAU ACGGA...UUU-3'@LB@ UUUAUGCA UGAUGG UGA GUGUGGA ACACGGC GAUGAA@LB@ ::\|\|\|\|\|\| \|:\|:\|\| \|\|\| \|::\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GGAUACGU AUUGCC ACU CGUAUCU UGUGCCG CUACUU@LB@3'-GUU...CCCGC CU C GUACUUGA GUUACU ACUUU...GGA-5'@LB@ \| \|@LB@ 215 162@LB@@LB@@LB@Energy -17.72 kcal/mol@LB@Hybridization Energy -38.3816 kcal/mol@LB@Unfolding Energy - mRNA 10.3843 kcal/mol@LB@Unfolding Energy - sRNA 19.6349 kcal/mol@LB@@LB@Position - mRNA 77 -- 124@LB@Position - sRNA 163 -- 214@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 175 -- 181@LB@
181	0.05165	0.7607	lmo2287	N/A	-16.24	0.057456	190 -- 241	154 -- 199	tape-measure	_____________189________________________________________________242\n_____________\|__________________________________________________\|\n5'-UGA...CUGAA________AUAA___AAAA______AG__G_GAACAU_____C_______CAGUA...CAA-3'\n______________AAACAGAU____GUU____GAUUAG__GU_A________GAG_GAUGGAU\n______________\|\|\|\|\|\|\|\|____\|\|:____\|\|:\|\|\|__\|:_\|________\|\|:_\|\|\|\|\|\|\|\n______________UUUGUCUA____CAG____CUGAUC__CG_U________CUU_CUACCUA\n3'-GUU...ACAGA_______________A_________AA__G_AAGAUAAC___________UGUGG...GGA-5'\n_____________\|__________________________________________________\|\n_____________200________________________________________________153\n	207 -- 213	94 -- 100	-23.404 kcal/mol	6.71689 kcal/mol	9.49359 kcal/mol	189 242@LB@ \| \|@LB@5'-UGA...CUGAA AUAA AAAA AG G GAACAU C CAGUA...CAA-3'@LB@ AAACAGAU GUU GAUUAG GU A GAG GAUGGAU@LB@ \|\|\|\|\|\|\|\| \|\|: \|\|:\|\|\| \|: \| \|\|: \|\|\|\|\|\|\|@LB@ UUUGUCUA CAG CUGAUC CG U CUU CUACCUA@LB@3'-GUU...ACAGA A AA G AAGAUAAC UGUGG...GGA-5'@LB@ \| \|@LB@ 200 153@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -23.404 kcal/mol@LB@Unfolding Energy - mRNA 6.71689 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 190 -- 241@LB@Position - sRNA 154 -- 199@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 94 -- 100@LB@
61	0.01458	0.6412	lmo2589	N/A	-18.59	0.019740	180 -- 258	153 -- 210	TetR family transcriptional regulator	_____________179__________259\n_____________\|____________\|\n5'-ACU...AACAG____________UGUUU...CUG-3'\n______________AAC_GGGUGGGG\n______________\|\|\|_\|\|:\|\|:\|\|\n______________UUG_CCUACUCC\n3'-GUU...ACGUA___C________GUAUC...GGA-5'\n_____________\|____________\|\n_____________211__________152\n	186 -- 192	197 -- 203	-13.3669 kcal/mol	1.19489 kcal/mol	3.58567 kcal/mol	179 259@LB@ \| \|@LB@5'-ACU...AACAG UGUUU...CUG-3'@LB@ AAC GGGUGGGG@LB@ \|\|\| \|\|:\|\|:\|\|@LB@ UUG CCUACUCC@LB@3'-GUU...ACGUA C GUAUC...GGA-5'@LB@ \| \|@LB@ 211 152@LB@@LB@@LB@Energy -18.59 kcal/mol@LB@Hybridization Energy -13.3669 kcal/mol@LB@Unfolding Energy - mRNA 1.19489 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 180 -- 258@LB@Position - sRNA 153 -- 210@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 197 -- 203@LB@
122	0.03252	0.6968	lmo0926	N/A	-16.71	0.046694	198 -- 274	155 -- 207	TetR family transcriptional regulator	_____________197______________275\n_____________\|________________\|\n5'-GCU...AACCA_____________G__GCGCC...UCG-3'\n______________AGAUGAGUGAAAA_CA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|_\|\|\n______________UCUACUUACUUUU_GU\n3'-GUU...GUUAC________________UUAUU...GGA-5'\n_____________\|________________\|\n_____________208______________154\n	265 -- 271	157 -- 163	-16.1904 kcal/mol	1.95479 kcal/mol	0.920152 kcal/mol	197 275@LB@ \| \|@LB@5'-GCU...AACCA G GCGCC...UCG-3'@LB@ AGAUGAGUGAAAA CA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\| \|\|@LB@ UCUACUUACUUUU GU@LB@3'-GUU...GUUAC UUAUU...GGA-5'@LB@ \| \|@LB@ 208 154@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -16.1904 kcal/mol@LB@Unfolding Energy - mRNA 1.95479 kcal/mol@LB@Unfolding Energy - sRNA 0.920152 kcal/mol@LB@@LB@Position - mRNA 198 -- 274@LB@Position - sRNA 155 -- 207@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 157 -- 163@LB@
45	0.0103	0.599	lmo0066	N/A	-17.00	0.040990	179 -- 207	157 -- 199	toxin	_____________178___________208\n_____________\|_____________\|\n5'-AAA...AGGCC_____________AAGUC...AUU-3'\n______________AGAUGAAUGAAAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCUACUUACUUUU\n3'-GUU...GUUAC_____________GUUUA...GGA-5'\n_____________\|_____________\|\n_____________200___________156\n	201 -- 207	157 -- 163	-14.7839 kcal/mol	1.76886 kcal/mol	0.884237 kcal/mol	178 208@LB@ \| \|@LB@5'-AAA...AGGCC AAGUC...AUU-3'@LB@ AGAUGAAUGAAAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCUACUUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -14.7839 kcal/mol@LB@Unfolding Energy - mRNA 1.76886 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 179 -- 207@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
36	0.007609	0.5562	lmo0649	N/A	-18.52	0.020396	192 -- 219	177 -- 204	transcriptional regulator	_____________191______220\n_____________\|________\|\n5'-UUU...AACGA________CAUGG...GUA-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______176\n	193 -- 199	197 -- 203	-13.9784 kcal/mol	1.5957 kcal/mol	0.386531 kcal/mol	191 220@LB@ \| \|@LB@5'-UUU...AACGA CAUGG...GUA-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 176@LB@@LB@@LB@Energy -18.52 kcal/mol@LB@Hybridization Energy -13.9784 kcal/mol@LB@Unfolding Energy - mRNA 1.5957 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 192 -- 219@LB@Position - sRNA 177 -- 204@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 197 -- 203@LB@
43	0.009411	0.5889	lmo0325	N/A	-15.65	0.074138	261 -- 289	174 -- 199	transcriptional regulator	______________261_________________________290\n______________\|___________________________\|\n___________5'-_______AAUACUUAAAAAA________ACGAU...UCG-3'\n______________UGCUAUU_____________GGAAGAUG\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|\|\|\n______________ACGGUAA_____________CCUUCUAC\n3'-GUU...GAUCA_______GAUAA________________CUAUG...GGA-5'\n_____________\|____________________________\|\n_____________200__________________________173\n	22 -- 28	97 -- 103	-16.3216 kcal/mol	2.64423 kcal/mol	5.20765 kcal/mol	261 290@LB@ \| \|@LB@ 5'- AAUACUUAAAAAA ACGAU...UCG-3'@LB@ UGCUAUU GGAAGAUG@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ ACGGUAA CCUUCUAC@LB@3'-GUU...GAUCA GAUAA CUAUG...GGA-5'@LB@ \| \|@LB@ 200 173@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -16.3216 kcal/mol@LB@Unfolding Energy - mRNA 2.64423 kcal/mol@LB@Unfolding Energy - sRNA 5.20765 kcal/mol@LB@@LB@Position - mRNA 261 -- 289@LB@Position - sRNA 174 -- 199@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 97 -- 103@LB@
85	0.0229	0.6733	lmo1788	N/A	-18.82	0.017630	177 -- 227	165 -- 211	transcriptional regulator	_____________176______________________________________________________228\n_____________\|________________________________________________________\|\n5'-UCU...AAAUG_______C______G____AA__G_____AAAA__A____CUGCUUAU________UUCAG...GGC-3'\n______________GAGGUGU_AGAUAU_GAAC__UG_ACGGU____GA_AUGG________GUGGGGAU\n______________\|\|\|\|::\|_\|\|\|:\|\|_\|\|\|\|__\|:_\|\|\|\|:____\|\|_\|\|\|:________:\|\|:::\|:\n______________CUCCGUA_UCUGUA_CUUG__AU_UGCCG____CU_UACU________UACUUUUG\n3'-GUU...CCCUA_______________________G_____GUUA__C____________________UUUAU...GGA-5'\n_____________\|________________________________________________________\|\n_____________212______________________________________________________164\n	238 -- 244	156 -- 162	-32.2408 kcal/mol	14.3369 kcal/mol	13.9689 kcal/mol	176 228@LB@ \| \|@LB@5'-UCU...AAAUG C G AA G AAAA A CUGCUUAU UUCAG...GGC-3'@LB@ GAGGUGU AGAUAU GAAC UG ACGGU GA AUGG GUGGGGAU@LB@ \|\|\|\|::\| \|\|\|:\|\| \|\|\|\| \|: \|\|\|\|: \|\| \|\|\|: :\|\|:::\|:@LB@ CUCCGUA UCUGUA CUUG AU UGCCG CU UACU UACUUUUG@LB@3'-GUU...CCCUA G GUUA C UUUAU...GGA-5'@LB@ \| \|@LB@ 212 164@LB@@LB@@LB@Energy -18.82 kcal/mol@LB@Hybridization Energy -32.2408 kcal/mol@LB@Unfolding Energy - mRNA 14.3369 kcal/mol@LB@Unfolding Energy - sRNA 13.9689 kcal/mol@LB@@LB@Position - mRNA 177 -- 227@LB@Position - sRNA 165 -- 211@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 156 -- 162@LB@
174	0.04903	0.7583	lmo1615	trmB	-12.39	0.264018	169 -- 243	157 -- 213	tRNA (guanine-N(7)-)-methyltransferase	_____________168________________244\n_____________\|__________________\|\n5'-AAU...AAGAU_________U__A_____AUGCG...AAG-3'\n______________GAUGAGGUG_AA_GAAAG\n______________:\|\|\|\|\|:\|\|_\|\|_\|\|\|\|:\n______________UUACUCUAC_UU_CUUUU\n3'-GUU...GCCGG____________A_____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________214________________156\n	185 -- 191	165 -- 171	-13.3606 kcal/mol	4.29808 kcal/mol	0.930085 kcal/mol	168 244@LB@ \| \|@LB@5'-AAU...AAGAU U A AUGCG...AAG-3'@LB@ GAUGAGGUG AA GAAAG@LB@ :\|\|\|\|\|:\|\| \|\| \|\|\|\|:@LB@ UUACUCUAC UU CUUUU@LB@3'-GUU...GCCGG A GUUUA...GGA-5'@LB@ \| \|@LB@ 214 156@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -13.3606 kcal/mol@LB@Unfolding Energy - mRNA 4.29808 kcal/mol@LB@Unfolding Energy - sRNA 0.930085 kcal/mol@LB@@LB@Position - mRNA 169 -- 243@LB@Position - sRNA 157 -- 213@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 165 -- 171@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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