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
121	0.03234	0.6968	lmo0198	glmU	-15.85	0.067914	228 -- 259	153 -- 184	bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase	_____________227______________________________260\n_____________\|________________________________\|\n5'-UAC...UGCUU_____________GGCACAC________U___AACUU...UGG-3'\n______________GCUGC_UGGCCAA_______GGAUGAAA_CAA\n______________:\|\|:\|_:\|\|\|\|\|\|_______\|:\|\|\|\|\|\|_\|\|\|\n______________UGAUG_GCCGGUU_______CUUACUUU_GUU\n3'-GUU...GUACU_____U_______ACUCUA_________U___UAUUA...GGA-5'\n_____________\|________________________________\|\n_____________185______________________________152\n	248 -- 254	158 -- 164	-25.2592 kcal/mol	7.21839 kcal/mol	9.59579 kcal/mol	227 260@LB@ \| \|@LB@5'-UAC...UGCUU GGCACAC U AACUU...UGG-3'@LB@ GCUGC UGGCCAA GGAUGAAA CAA@LB@ :\|\|:\| :\|\|\|\|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGAUG GCCGGUU CUUACUUU GUU@LB@3'-GUU...GUACU U ACUCUA U UAUUA...GGA-5'@LB@ \| \|@LB@ 185 152@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -25.2592 kcal/mol@LB@Unfolding Energy - mRNA 7.21839 kcal/mol@LB@Unfolding Energy - sRNA 9.59579 kcal/mol@LB@@LB@Position - mRNA 228 -- 259@LB@Position - sRNA 153 -- 184@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 158 -- 164@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@
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@
124	0.03258	0.6968	lmo1611	N/A	-17.32	0.035574	130 -- 182	121 -- 173	aminopeptidase	_____________129_______________________183\n_____________\|_________________________\|\n5'-CAU...AGAGA_______C___C_____________AUUUG...UUG-3'\n______________AGUGAGG_GAG_GGAAACGGAUAAU\n______________\|:\|\|\|\|:_\|\|:_\|:\|\|\|\|::\|\|\|\|\|\n______________UUACUCU_CUU_CUUUUGUUUAUUA\n3'-GUU...GCCGG_______A___A_____________CUAAA...GGA-5'\n_____________\|_________________________\|\n_____________174_______________________120\n	143 -- 149	154 -- 160	-22.8649 kcal/mol	4.94187 kcal/mol	5.58154 kcal/mol	129 183@LB@ \| \|@LB@5'-CAU...AGAGA C C AUUUG...UUG-3'@LB@ AGUGAGG GAG GGAAACGGAUAAU@LB@ \|:\|\|\|\|: \|\|: \|:\|\|\|\|::\|\|\|\|\|@LB@ UUACUCU CUU CUUUUGUUUAUUA@LB@3'-GUU...GCCGG A A CUAAA...GGA-5'@LB@ \| \|@LB@ 174 120@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -22.8649 kcal/mol@LB@Unfolding Energy - mRNA 4.94187 kcal/mol@LB@Unfolding Energy - sRNA 5.58154 kcal/mol@LB@@LB@Position - mRNA 130 -- 182@LB@Position - sRNA 121 -- 173@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 154 -- 160@LB@
125	0.03321	0.6968	lmo2357	N/A	-16.59	0.049158	2 -- 27	152 -- 176		_____________1_____________________28\n_____________\|_____________________\|\n_______5'-AGCU___AU________C_______AUCUU...CAC-3'\n______________GAU__GAUGGAUG_AAAACAA\n______________:\|\|__\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UUA__CUACUUAC_UUUUGUU\n3'-GUU...GCCGG___CU________________UAUUA...GGA-5'\n_____________\|_____________________\|\n_____________177___________________151\n	19 -- 25	154 -- 160	-15.1634 kcal/mol	3.68151 kcal/mol	0.959215 kcal/mol	1 28@LB@ \| \|@LB@ 5'-AGCU AU C AUCUU...CAC-3'@LB@ GAU GAUGGAUG AAAACAA@LB@ :\|\| \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UUA CUACUUAC UUUUGUU@LB@3'-GUU...GCCGG CU UAUUA...GGA-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -15.1634 kcal/mol@LB@Unfolding Energy - mRNA 3.68151 kcal/mol@LB@Unfolding Energy - sRNA 0.959215 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 154 -- 160@LB@
126	0.03359	0.6968	lmo1599	ccpA	-16.59	0.049230	178 -- 221	146 -- 188	catabolite control protein A	_____________177______________222\n_____________\|________________\|\n5'-UUU...GAAUA__________U_____AUUUA...CAA-3'\n______________GAGAUGAAUG__AACA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________CUCUACUUAC__UUGU\n3'-GUU...GGUUA__________UU____UUAUU...GGA-5'\n_____________\|________________\|\n_____________189______________145\n	201 -- 207	161 -- 167	-17.207 kcal/mol	2.33031 kcal/mol	0.929544 kcal/mol	177 222@LB@ \| \|@LB@5'-UUU...GAAUA U AUUUA...CAA-3'@LB@ GAGAUGAAUG AACA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUCUACUUAC UUGU@LB@3'-GUU...GGUUA UU UUAUU...GGA-5'@LB@ \| \|@LB@ 189 145@LB@@LB@@LB@Energy -16.59 kcal/mol@LB@Hybridization Energy -17.207 kcal/mol@LB@Unfolding Energy - mRNA 2.33031 kcal/mol@LB@Unfolding Energy - sRNA 0.929544 kcal/mol@LB@@LB@Position - mRNA 178 -- 221@LB@Position - sRNA 146 -- 188@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@LB@
127	0.03392	0.6968	lmo2096	N/A	-16.75	0.045974	122 -- 137	183 -- 198	PTS galacticol transporter subunit IIC	_____________121___________________138\n_____________\|_____________________\|\n5'-UAG...UUUCU____A__C_____________GAAGA...UGA-3'\n______________UAAC_GG_AUG_GGCAUGGAC\n______________\|\|\|\|_\|\|_\|\|\|_\|\|\|\|\|:\|\|\|\n______________AUUG_CC_UAC_CCGUAUCUG\n3'-GUU...UACGU____C______U_________UACUU...GGA-5'\n_____________\|_____________________\|\n_____________199___________________182\n	129 -- 135	191 -- 197	-23.3255 kcal/mol	4.68556 kcal/mol	9.82628 kcal/mol	121 138@LB@ \| \|@LB@5'-UAG...UUUCU A C GAAGA...UGA-3'@LB@ UAAC GG AUG GGCAUGGAC@LB@ \|\|\|\| \|\| \|\|\| \|\|\|\|\|:\|\|\|@LB@ AUUG CC UAC CCGUAUCUG@LB@3'-GUU...UACGU C U UACUU...GGA-5'@LB@ \| \|@LB@ 199 182@LB@@LB@@LB@Energy -16.75 kcal/mol@LB@Hybridization Energy -23.3255 kcal/mol@LB@Unfolding Energy - mRNA 4.68556 kcal/mol@LB@Unfolding Energy - sRNA 9.82628 kcal/mol@LB@@LB@Position - mRNA 122 -- 137@LB@Position - sRNA 183 -- 198@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 191 -- 197@LB@
128	0.03459	0.6968	lmo1993	pdp	-15.44	0.080912	179 -- 212	139 -- 174	pyrimidine-nucleoside phosphorylase	_____________178_________________213\n_____________\|___________________\|\n5'-AUU...GAAAG____A___GA_________GGUGG...UUC-3'\n______________GGUG_AGA__AAUGAGAAU\n______________::\|\|_\|\|\|__\|\|\|\|\|:\|\|:\n______________UUAC_UCU__UUACUUUUG\n3'-GUU...GCCGG________AC_________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________175_________________138\n	202 -- 208	156 -- 162	-13.005 kcal/mol	2.24337 kcal/mol	0.941471 kcal/mol	178 213@LB@ \| \|@LB@5'-AUU...GAAAG A GA GGUGG...UUC-3'@LB@ GGUG AGA AAUGAGAAU@LB@ ::\|\| \|\|\| \|\|\|\|\|:\|\|:@LB@ UUAC UCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -13.005 kcal/mol@LB@Unfolding Energy - mRNA 2.24337 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@LB@
129	0.03464	0.6968	lmo0756	N/A	-20.18	0.009099	160 -- 214	175 -- 223	ABC transporter ATP-binding protein	_____________159__________215\n_____________\|____________\|\n5'-AGU...AUAGA_______G____AGAAG...UUU-3'\n______________GACGGGA_GGGG\n______________:\|\|\|\|\|\|_\|:\|\|\n______________UUGCCCU_CUCC\n3'-GUU...ACGUA_______A____GUAUC...GGA-5'\n_____________\|____________\|\n_____________224__________174\n	181 -- 187	201 -- 207	-16.8336 kcal/mol	1.76926 kcal/mol	3.58567 kcal/mol	159 215@LB@ \| \|@LB@5'-AGU...AUAGA G AGAAG...UUU-3'@LB@ GACGGGA GGGG@LB@ :\|\|\|\|\|\| \|:\|\|@LB@ UUGCCCU CUCC@LB@3'-GUU...ACGUA A GUAUC...GGA-5'@LB@ \| \|@LB@ 224 174@LB@@LB@@LB@Energy -20.18 kcal/mol@LB@Hybridization Energy -16.8336 kcal/mol@LB@Unfolding Energy - mRNA 1.76926 kcal/mol@LB@Unfolding Energy - sRNA 3.58567 kcal/mol@LB@@LB@Position - mRNA 160 -- 214@LB@Position - sRNA 175 -- 223@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 201 -- 207@LB@
130	0.03486	0.6968	lmo1231	N/A	-15.49	0.079293	19 -- 84	118 -- 185	DNA polymerase beta	_____________18___________________85\n_____________\|____________________\|\n5'-UCU...UUGCC__________CU________CGCCA...GCA-3'\n______________CAGUG_GAUG__UGAAAACA\n______________\|\|:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\n______________GUUAC_CUAC__ACUUUUGU\n3'-GUU...UGCCG_____U____UU________UUAUU...GGA-5'\n_____________\|____________________\|\n_____________186__________________117\n	46 -- 52	155 -- 161	-18.0743 kcal/mol	4.62758 kcal/mol	0.95817 kcal/mol	18 85@LB@ \| \|@LB@5'-UCU...UUGCC CU CGCCA...GCA-3'@LB@ CAGUG GAUG UGAAAACA@LB@ \|\|:\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUAC CUAC ACUUUUGU@LB@3'-GUU...UGCCG U UU UUAUU...GGA-5'@LB@ \| \|@LB@ 186 117@LB@@LB@@LB@Energy -15.49 kcal/mol@LB@Hybridization Energy -18.0743 kcal/mol@LB@Unfolding Energy - mRNA 4.62758 kcal/mol@LB@Unfolding Energy - sRNA 0.95817 kcal/mol@LB@@LB@Position - mRNA 19 -- 84@LB@Position - sRNA 118 -- 185@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 155 -- 161@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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