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
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@
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@
21	0.003699	0.4469	lmo2681	kdpB	-18.50	0.020601	185 -- 204	154 -- 173	potassium-transporting ATPase subunit B	_____________184__________________205\n_____________\|____________________\|\n5'-GCA...UUUCA____________________UGGAA...AUG-3'\n______________AAUGAGGUGAAUGGAAAUGA\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|\n______________UUACUCUACUUACUUUUGUU\n3'-GUU...GCCGG____________________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________153\n	197 -- 203	155 -- 161	-22.9313 kcal/mol	3.41 kcal/mol	0.959215 kcal/mol	184 205@LB@ \| \|@LB@5'-GCA...UUUCA UGGAA...AUG-3'@LB@ AAUGAGGUGAAUGGAAAUGA@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|\|\|::\|@LB@ UUACUCUACUUACUUUUGUU@LB@3'-GUU...GCCGG UAUUA...GGA-5'@LB@ \| \|@LB@ 174 153@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -22.9313 kcal/mol@LB@Unfolding Energy - mRNA 3.41 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 154 -- 173@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 155 -- 161@LB@
95	0.02474	0.6733	lmo2446	N/A	-18.44	0.021161	178 -- 278	95 -- 188	glycosidase	_____________177____________________279\n_____________\|______________________\|\n5'-UGA...AGGAA___________GC_A_______GAAAA...ACG-3'\n______________AGUGAGAUGAA__G_AGAACGA\n______________\|:\|\|\|\|\|\|\|\|\|__\|_\|:\|\|\|:\|\n______________UUACUCUACUU__C_UUUUGUU\n3'-GUU...GCCGG___________A__________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________189____________________94\n	210 -- 216	154 -- 160	-17.9823 kcal/mol	4.45349 kcal/mol	0.959215 kcal/mol	177 279@LB@ \| \|@LB@5'-UGA...AGGAA GC A GAAAA...ACG-3'@LB@ AGUGAGAUGAA G AGAACGA@LB@ \|:\|\|\|\|\|\|\|\|\| \| \|:\|\|\|:\|@LB@ UUACUCUACUU C UUUUGUU@LB@3'-GUU...GCCGG A UAUUA...GGA-5'@LB@ \| \|@LB@ 189 94@LB@@LB@@LB@Energy -18.44 kcal/mol@LB@Hybridization Energy -17.9823 kcal/mol@LB@Unfolding Energy - mRNA 4.45349 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 178 -- 278@LB@Position - sRNA 95 -- 188@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 154 -- 160@LB@
168	0.04649	0.7403	lmo1875	N/A	-18.37	0.021889	174 -- 204	150 -- 181	ABC transporter ATP-binding protein	_____________173_______________205\n_____________\|_________________\|\n5'-ACA...AACAG__A______________AUGAA...GUU-3'\n______________GA_AUGGAUGGGAAUAA\n______________\|\|_\|\|\|:\|\|\|::\|\|:\|\|\n______________CU_UACUUACUUUUGUU\n3'-GUU...GGUUA__C______________UAUUA...GGA-5'\n_____________\|_________________\|\n_____________182_______________149\n	193 -- 199	155 -- 161	-14.111 kcal/mol	2.1341 kcal/mol	0.933796 kcal/mol	173 205@LB@ \| \|@LB@5'-ACA...AACAG A AUGAA...GUU-3'@LB@ GA AUGGAUGGGAAUAA@LB@ \|\| \|\|\|:\|\|\|::\|\|:\|\|@LB@ CU UACUUACUUUUGUU@LB@3'-GUU...GGUUA C UAUUA...GGA-5'@LB@ \| \|@LB@ 182 149@LB@@LB@@LB@Energy -18.37 kcal/mol@LB@Hybridization Energy -14.111 kcal/mol@LB@Unfolding Energy - mRNA 2.1341 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 174 -- 204@LB@Position - sRNA 150 -- 181@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 155 -- 161@LB@
99	0.02562	0.6733	lmo2201	N/A	-18.35	0.022079	190 -- 255	101 -- 170	3-oxoacyl-ACP synthase	_____________189_____________________________________________________________________256\n_____________\|_______________________________________________________________________\|\n5'-AAC...AUAAG________________________GAAGA__A___GUU__U______G__GCU___A___C__________ACGAU...AUG-3'\n______________GAGAUGAGU__AAAUGGAUAA_GA_____GU_GUU___AC_GGUGUU_GA___GUU__CA__CUAUUGGAA\n______________\|\|\|\|\|\|\|:\|__\|\|\|:::\|\|\|\|_\|\|_____\|\|_\|\|:___\|\|_\|:\|\|\|:_\|\|___\|\|\|__\|\|__\|\|\|\|\|\|\|\|\|\n______________CUCUACUUA__UUUGUUUAUU_CU_____CA_CAG___UG_CUACAG_CU___CAA__GU__GAUAACCUU\n3'-GUU...GGUUA_________CU__________A__AAAAC______AUU__U______A__GAU___CG__AA_________CUACC...GGA-5'\n_____________\|_______________________________________________________________________\|\n_____________171_____________________________________________________________________100\n	249 -- 255	101 -- 107	-41.8612 kcal/mol	11.5076 kcal/mol	19.339 kcal/mol	189 256@LB@ \| \|@LB@5'-AAC...AUAAG GAAGA A GUU U G GCU A C ACGAU...AUG-3'@LB@ GAGAUGAGU AAAUGGAUAA GA GU GUU AC GGUGUU GA GUU CA CUAUUGGAA@LB@ \|\|\|\|\|\|\|:\| \|\|\|:::\|\|\|\| \|\| \|\| \|\|: \|\| \|:\|\|\|: \|\| \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CUCUACUUA UUUGUUUAUU CU CA CAG UG CUACAG CU CAA GU GAUAACCUU@LB@3'-GUU...GGUUA CU A AAAAC AUU U A GAU CG AA CUACC...GGA-5'@LB@ \| \|@LB@ 171 100@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -41.8612 kcal/mol@LB@Unfolding Energy - mRNA 11.5076 kcal/mol@LB@Unfolding Energy - sRNA 19.339 kcal/mol@LB@@LB@Position - mRNA 190 -- 255@LB@Position - sRNA 101 -- 170@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 101 -- 107@LB@
38	0.007855	0.5562	lmo1229	N/A	-18.27	0.022927	193 -- 228	147 -- 186		_____________192_______________________________________229\n_____________\|_________________________________________\|\n5'-AUU...AGGAG___U_________A________________UA_________CAACA...GCG-3'\n______________GAA_UUACGUGGC_AAUGAGA_____GAAA__AAGUAGUGA\n______________\|\|\|_:\|\|\|::\|\|\|_\|\|\|\|\|\|\|_____\|\|\|\|__\|\|:\|\|:\|\|\|\n______________CUU_GAUGUGCCG_UUACUCU_____CUUU__UUUAUUACU\n3'-GUU...CUGUA_____________G_______ACUUA____UG_________AAAAC...GGA-5'\n_____________\|_________________________________________\|\n_____________187_______________________________________146\n	207 -- 213	167 -- 173	-29.0601 kcal/mol	3.84241 kcal/mol	14.4129 kcal/mol	192 229@LB@ \| \|@LB@5'-AUU...AGGAG U A UA CAACA...GCG-3'@LB@ GAA UUACGUGGC AAUGAGA GAAA AAGUAGUGA@LB@ \|\|\| :\|\|\|::\|\|\| \|\|\|\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\|@LB@ CUU GAUGUGCCG UUACUCU CUUU UUUAUUACU@LB@3'-GUU...CUGUA G ACUUA UG AAAAC...GGA-5'@LB@ \| \|@LB@ 187 146@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -29.0601 kcal/mol@LB@Unfolding Energy - mRNA 3.84241 kcal/mol@LB@Unfolding Energy - sRNA 14.4129 kcal/mol@LB@@LB@Position - mRNA 193 -- 228@LB@Position - sRNA 147 -- 186@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 167 -- 173@LB@
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@
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@
66	0.01668	0.6733	lmo0959	N/A	-18.16	0.024105	185 -- 212	177 -- 206	undacaprenyl-phosphate N-acetylglucosaminyltransferase	_____________184________________213\n_____________\|__________________\|\n5'-GAA...AAGUA_____________A____AUUUG...CAG-3'\n______________UAAUGAGAUGAGU_AAAA\n______________:\|\|\|\|\|\|\|\|\|\|:\|_\|\|\|\|\n______________GUUACUCUACUUA_UUUU\n3'-GUU...UGCCG_____________C____GUUUA...GGA-5'\n_____________\|__________________\|\n_____________207________________176\n	169 -- 175	162 -- 168	-15.497 kcal/mol	1.5517 kcal/mol	0.933292 kcal/mol	184 213@LB@ \| \|@LB@5'-GAA...AAGUA A AUUUG...CAG-3'@LB@ UAAUGAGAUGAGU AAAA@LB@ :\|\|\|\|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GUUACUCUACUUA UUUU@LB@3'-GUU...UGCCG C GUUUA...GGA-5'@LB@ \| \|@LB@ 207 176@LB@@LB@@LB@Energy -18.16 kcal/mol@LB@Hybridization Energy -15.497 kcal/mol@LB@Unfolding Energy - mRNA 1.5517 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 185 -- 212@LB@Position - sRNA 177 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 162 -- 168@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching