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@
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@
64	0.01603	0.6733	lmo0131	N/A	-19.25	0.014339	193 -- 248	149 -- 204		_____________192____________________________________________________249\n_____________\|______________________________________________________\|\n5'-UGU...AAAAG____G_____G______AUCUCGA______AAAU________C___UAG_____AUAGU...UCG-3'\n______________GAGG_AUA_A_AUGGAU_______GCACGG____AUGGGAUG_GAU___GAGAA\n______________\|\|\|\|_\|\|\|_\|_\|\|\|:\|:_______:\|\|\|\|\|____\|\|\|:\|\|\|\|_:\|\|___\|\|:\|\|\n______________CUCC_UAU_U_UACUUG_______UGUGCC____UACUCUAC_UUA___CUUUU\n3'-GUU...CCCUA____G___C_G______A____________GGU_____________________GUUUA...GGA-5'\n_____________\|______________________________________________________\|\n_____________205____________________________________________________148\n	225 -- 231	165 -- 171	-32.0138 kcal/mol	8.31689 kcal/mol	13.9574 kcal/mol	192 249@LB@ \| \|@LB@5'-UGU...AAAAG G G AUCUCGA AAAU C UAG AUAGU...UCG-3'@LB@ GAGG AUA A AUGGAU GCACGG AUGGGAUG GAU GAGAA@LB@ \|\|\|\| \|\|\| \| \|\|\|:\|: :\|\|\|\|\| \|\|\|:\|\|\|\| :\|\| \|\|:\|\|@LB@ CUCC UAU U UACUUG UGUGCC UACUCUAC UUA CUUUU@LB@3'-GUU...CCCUA G C G A GGU GUUUA...GGA-5'@LB@ \| \|@LB@ 205 148@LB@@LB@@LB@Energy -19.25 kcal/mol@LB@Hybridization Energy -32.0138 kcal/mol@LB@Unfolding Energy - mRNA 8.31689 kcal/mol@LB@Unfolding Energy - sRNA 13.9574 kcal/mol@LB@@LB@Position - mRNA 193 -- 248@LB@Position - sRNA 149 -- 204@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 165 -- 171@LB@
145	0.03765	0.6968	lmo0134	N/A	-12.36	0.267504	193 -- 220	147 -- 170		_____________192__________________________221\n_____________\|____________________________\|\n5'-GGG...AGGAG_____UA_______UAUAA_________AAAUA...UUA-3'\n______________GAGAU__AAUGGAA_____AAAUGGUGA\n______________\|\|\|\|\|__\|\|\|\|:\|\|_____\|\|\|\|::\|\|\|\n______________CUCUA__UUACUUU_____UUUAUUACU\n3'-GUU...GGUUA_____C________UG____________AAAAC...GGA-5'\n_____________\|____________________________\|\n_____________171__________________________146\n	200 -- 206	158 -- 164	-15.5721 kcal/mol	1.73331 kcal/mol	5.93585 kcal/mol	192 221@LB@ \| \|@LB@5'-GGG...AGGAG UA UAUAA AAAUA...UUA-3'@LB@ GAGAU AAUGGAA AAAUGGUGA@LB@ \|\|\|\|\| \|\|\|\|:\|\| \|\|\|\|::\|\|\|@LB@ CUCUA UUACUUU UUUAUUACU@LB@3'-GUU...GGUUA C UG AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -15.5721 kcal/mol@LB@Unfolding Energy - mRNA 1.73331 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 193 -- 220@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 158 -- 164@LB@
176	0.04979	0.7607	lmo1340	N/A	-16.63	0.048446	193 -- 216	151 -- 177		_____________192_____________217\n_____________\|_______________\|\n5'-UGC...UUGGA_______________AAAAU...CUG-3'\n______________GGCCA__GAGAUGAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CCGGU__CUCUACUU\n3'-GUU...AUGUG_____UA________ACUUU...GGA-5'\n_____________\|_______________\|\n_____________178_____________150\n	199 -- 205	163 -- 169	-19.0992 kcal/mol	1.80937 kcal/mol	7.44208 kcal/mol	192 217@LB@ \| \|@LB@5'-UGC...UUGGA AAAAU...CUG-3'@LB@ GGCCA GAGAUGAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCGGU CUCUACUU@LB@3'-GUU...AUGUG UA ACUUU...GGA-5'@LB@ \| \|@LB@ 178 150@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -19.0992 kcal/mol@LB@Unfolding Energy - mRNA 1.80937 kcal/mol@LB@Unfolding Energy - sRNA 7.44208 kcal/mol@LB@@LB@Position - mRNA 193 -- 216@LB@Position - sRNA 151 -- 177@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
57	0.01283	0.6057	lmo2379	N/A	-18.13	0.024463	194 -- 217	150 -- 173	monovalent cation/H+ antiporter subunit B	_____________193__________________218\n_____________\|____________________\|\n5'-GUA...AACGA_______AU___________AUGAC...AUA-3'\n______________GGUGAGA__GAUGAAAACGA\n______________::\|\|\|\|\|__:\|\|\|\|\|\|\|\|:\|\n______________UUACUCU__UUACUUUUGUU\n3'-GUU...GCCGG_______AC___________UAUUA...GGA-5'\n_____________\|____________________\|\n_____________174__________________149\n	207 -- 213	154 -- 160	-18.1864 kcal/mol	2.62553 kcal/mol	0.959215 kcal/mol	193 218@LB@ \| \|@LB@5'-GUA...AACGA AU AUGAC...AUA-3'@LB@ GGUGAGA GAUGAAAACGA@LB@ ::\|\|\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UUACUCU UUACUUUUGUU@LB@3'-GUU...GCCGG AC UAUUA...GGA-5'@LB@ \| \|@LB@ 174 149@LB@@LB@@LB@Energy -18.13 kcal/mol@LB@Hybridization Energy -18.1864 kcal/mol@LB@Unfolding Energy - mRNA 2.62553 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 194 -- 217@LB@Position - sRNA 150 -- 173@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 154 -- 160@LB@
108	0.02743	0.6733	lmo2330	N/A	-16.53	0.050546	195 -- 214	191 -- 207		_____________194_________215\n_____________\|___________\|\n5'-ACG...GAGAA___________CAAGU...UUU-3'\n______________AGCGGGAUGAG\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UUGCCCUACUC\n3'-GUU...ACGUA___________CGUAU...GGA-5'\n_____________\|___________\|\n_____________208_________190\n	199 -- 205	197 -- 203	-18.6004 kcal/mol	2.16538 kcal/mol	0.386761 kcal/mol	194 215@LB@ \| \|@LB@5'-ACG...GAGAA CAAGU...UUU-3'@LB@ AGCGGGAUGAG@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UUGCCCUACUC@LB@3'-GUU...ACGUA CGUAU...GGA-5'@LB@ \| \|@LB@ 208 190@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -18.6004 kcal/mol@LB@Unfolding Energy - mRNA 2.16538 kcal/mol@LB@Unfolding Energy - sRNA 0.386761 kcal/mol@LB@@LB@Position - mRNA 195 -- 214@LB@Position - sRNA 191 -- 207@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 197 -- 203@LB@
140	0.0365	0.6968	lmo1717	N/A	-17.46	0.033387	195 -- 217	147 -- 170		_____________194______________________218\n_____________\|________________________\|\n5'-UAG...AGUAG____C___________________AACAC...AAA-3'\n______________GAGA__GAUGAAAAUGGAUAGUGA\n______________\|\|\|\|__:\|\|\|\|\|\|\|:::\|\|\|:\|\|\|\n______________CUCU__UUACUUUUGUUUAUUACU\n3'-GUU...GGUUA____AC__________________AAAAC...GGA-5'\n_____________\|________________________\|\n_____________171______________________146\n	203 -- 209	155 -- 161	-21.6361 kcal/mol	2.67158 kcal/mol	5.93585 kcal/mol	194 218@LB@ \| \|@LB@5'-UAG...AGUAG C AACAC...AAA-3'@LB@ GAGA GAUGAAAAUGGAUAGUGA@LB@ \|\|\|\| :\|\|\|\|\|\|\|:::\|\|\|:\|\|\|@LB@ CUCU UUACUUUUGUUUAUUACU@LB@3'-GUU...GGUUA AC AAAAC...GGA-5'@LB@ \| \|@LB@ 171 146@LB@@LB@@LB@Energy -17.46 kcal/mol@LB@Hybridization Energy -21.6361 kcal/mol@LB@Unfolding Energy - mRNA 2.67158 kcal/mol@LB@Unfolding Energy - sRNA 5.93585 kcal/mol@LB@@LB@Position - mRNA 195 -- 217@LB@Position - sRNA 147 -- 170@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 155 -- 161@LB@
154	0.04021	0.7027	lmo2008	N/A	-17.88	0.027453	195 -- 258	157 -- 220	ABC transporter permease	_____________194___________________259\n_____________\|_____________________\|\n5'-CAG...UGAAG____________AU_______GUCCG...UUG-3'\n______________CAGUGAG_UGAA__AGAACAA\n______________\|\|:\|\|\|\|_\|\|\|\|__\|:\|\|\|\|\|\n______________GUUACUC_ACUU__UUUUGUU\n3'-GUU...UGCCG_______U____AC_______UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________221___________________156\n	233 -- 239	154 -- 160	-15.5955 kcal/mol	3.58965 kcal/mol	0.962339 kcal/mol	194 259@LB@ \| \|@LB@5'-CAG...UGAAG AU GUCCG...UUG-3'@LB@ CAGUGAG UGAA AGAACAA@LB@ \|\|:\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ GUUACUC ACUU UUUUGUU@LB@3'-GUU...UGCCG U AC UAUUA...GGA-5'@LB@ \| \|@LB@ 221 156@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -15.5955 kcal/mol@LB@Unfolding Energy - mRNA 3.58965 kcal/mol@LB@Unfolding Energy - sRNA 0.962339 kcal/mol@LB@@LB@Position - mRNA 195 -- 258@LB@Position - sRNA 157 -- 220@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 154 -- 160@LB@
142	0.03693	0.6968	lmo2586	N/A	-16.96	0.041696	196 -- 266	151 -- 227	formate dehydrogenase subunit alpha	_____________195______267\n_____________\|________\|\n5'-UUU...GUGGC________UGGUG...AUC-3'\n______________GCGGGAUG\n______________:\|\|\|\|\|\|\|\n______________UGCCCUAC\n3'-GUU...CGUAU________UCCGU...GGA-5'\n_____________\|________\|\n_____________228______150\n	240 -- 246	199 -- 205	-13.0644 kcal/mol	3.68871 kcal/mol	0.331032 kcal/mol	195 267@LB@ \| \|@LB@5'-UUU...GUGGC UGGUG...AUC-3'@LB@ GCGGGAUG@LB@ :\|\|\|\|\|\|\|@LB@ UGCCCUAC@LB@3'-GUU...CGUAU UCCGU...GGA-5'@LB@ \| \|@LB@ 228 150@LB@@LB@@LB@Energy -16.96 kcal/mol@LB@Hybridization Energy -13.0644 kcal/mol@LB@Unfolding Energy - mRNA 3.68871 kcal/mol@LB@Unfolding Energy - sRNA 0.331032 kcal/mol@LB@@LB@Position - mRNA 196 -- 266@LB@Position - sRNA 151 -- 227@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 199 -- 205@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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