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
116	0.03152	0.6968	lmo1963	N/A	-17.16	0.038227	218 -- 258	130 -- 166	_____________217___________________________________________259\n_____________\|_____________________________________________\|\n5'-ACA...CACAU_________AAC________A__GUC___U___________U___GGUGA...UCC-3'\n______________UGAAUGGAA___GCGAAUAA_GA___UGG_UGUUUGGGCAG_UGU\n______________\|\|\|\|\|\|:\|\|___:\|:\|\|\|\|\|_\|\|___\|\|\|_\|\|\|:\|:::\|\|\|_\|\|\|\n______________ACUUACUUU___UGUUUAUU_CU___ACC_ACAGAUUUGUC_ACA\n3'-GUU...ACUCU____________________A__AAA_______________U___GACUG...GGA-5'\n_____________\|_____________________________________________\|\n_____________167___________________________________________129\n	220 -- 226	158 -- 164	-34.7415 kcal/mol	9.15867 kcal/mol	13.701 kcal/mol	217 259@LB@ \| \|@LB@5'-ACA...CACAU AAC A GUC U U GGUGA...UCC-3'@LB@ UGAAUGGAA GCGAAUAA GA UGG UGUUUGGGCAG UGU@LB@ \|\|\|\|\|\|:\|\| :\|:\|\|\|\|\| \|\| \|\|\| \|\|\|:\|:::\|\|\| \|\|\|@LB@ ACUUACUUU UGUUUAUU CU ACC ACAGAUUUGUC ACA@LB@3'-GUU...ACUCU A AAA U GACUG...GGA-5'@LB@ \| \|@LB@ 167 129@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -34.7415 kcal/mol@LB@Unfolding Energy - mRNA 9.15867 kcal/mol@LB@Unfolding Energy - sRNA 13.701 kcal/mol@LB@@LB@Position - mRNA 218 -- 258@LB@Position - sRNA 130 -- 166@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 158 -- 164@LB@
120	0.03214	0.6968	lmo0368	N/A	-17.05	0.040150	163 -- 213	95 -- 164	_____________162______________________________________________214\n_____________\|________________________________________________\|\n5'-UGC...AAUGA_____A_____AA_______AGGGA___G______G_______A____AUUUG...UUC-3'\n______________AAGCA___GUC__UGAUUAG_____GCC_AUUUUA_UGGAAGA_UGGG\n______________\|\|:\|\|___\|\|\|__\|\|\|:\|\|\|_____\|\|\|_\|\|\|:\|\|_\|\|\|\|\|\|\|_\|\|\|:\n______________UUUGU___CAG__ACUGAUC_____CGG_UAAGAU_ACCUUCU_ACCU\n3'-GUU...ACAGA_____CUA____________AA_____________A____________AUGUG...GGA-5'\n_____________\|________________________________________________\|\n_____________165______________________________________________94\n	202 -- 208	99 -- 105	-32.1999 kcal/mol	10.9316 kcal/mol	9.49359 kcal/mol	162 214@LB@ \| \|@LB@5'-UGC...AAUGA A AA AGGGA G G A AUUUG...UUC-3'@LB@ AAGCA GUC UGAUUAG GCC AUUUUA UGGAAGA UGGG@LB@ \|\|:\|\| \|\|\| \|\|\|:\|\|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:@LB@ UUUGU CAG ACUGAUC CGG UAAGAU ACCUUCU ACCU@LB@3'-GUU...ACAGA CUA AA A AUGUG...GGA-5'@LB@ \| \|@LB@ 165 94@LB@@LB@@LB@Energy -17.05 kcal/mol@LB@Hybridization Energy -32.1999 kcal/mol@LB@Unfolding Energy - mRNA 10.9316 kcal/mol@LB@Unfolding Energy - sRNA 9.49359 kcal/mol@LB@@LB@Position - mRNA 163 -- 213@LB@Position - sRNA 95 -- 164@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 99 -- 105@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@
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@
141	0.03665	0.6968	lmo1798	N/A	-14.74	0.108024	280 -- 295	194 -- 209	_____________279_______296\n_____________\|_________\|\n5'-GAU...CACUU_________AAUGG...GUU-3'\n______________AUAACGGGA\n______________\|\|\|\|\|\|\|\|\|\n______________UAUUGCCCU\n3'-GUU...AUACG_________ACUCC...GGA-5'\n_____________\|_________\|\n_____________210_______193\n	282 -- 288	201 -- 207	-12.5707 kcal/mol	0.27177 kcal/mol	0.374318 kcal/mol	279 296@LB@ \| \|@LB@5'-GAU...CACUU AAUGG...GUU-3'@LB@ AUAACGGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UAUUGCCCU@LB@3'-GUU...AUACG ACUCC...GGA-5'@LB@ \| \|@LB@ 210 193@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -12.5707 kcal/mol@LB@Unfolding Energy - mRNA 0.27177 kcal/mol@LB@Unfolding Energy - sRNA 0.374318 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 194 -- 209@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 201 -- 207@LB@
143	0.03726	0.6968	lmo2701	N/A	-17.97	0.026314	78 -- 126	156 -- 198	_____________77_________________________________________________127\n_____________\|__________________________________________________\|\n5'-GAA...CCUUC_______AAAGUA___A____AGC________UUCCA_____________UUAGA...UCA-3'\n______________AGGCAUA______ACG_GAAU___GCAUGGCC______GUGGGUGGAGAC\n______________\|\|\|\|\|\|\|______\|\|:_\|\|\|:___:\|\|:\|\|\|\|______:\|\|::\|\|:\|:\|\|\n______________UCCGUAU______UGU_CUUG___UGUGCCGG______UACUUACUUUUG\n3'-GUU...CCUAC_______C________A____A__________UUACUC____________UUUAU...GGA-5'\n_____________\|__________________________________________________\|\n_____________199________________________________________________155\n	120 -- 126	156 -- 162	-37.6493 kcal/mol	12.7788 kcal/mol	13.9626 kcal/mol	77 127@LB@ \| \|@LB@5'-GAA...CCUUC AAAGUA A AGC UUCCA UUAGA...UCA-3'@LB@ AGGCAUA ACG GAAU GCAUGGCC GUGGGUGGAGAC@LB@ \|\|\|\|\|\|\| \|\|: \|\|\|: :\|\|:\|\|\|\| :\|\|::\|\|:\|:\|\|@LB@ UCCGUAU UGU CUUG UGUGCCGG UACUUACUUUUG@LB@3'-GUU...CCUAC C A A UUACUC UUUAU...GGA-5'@LB@ \| \|@LB@ 199 155@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -37.6493 kcal/mol@LB@Unfolding Energy - mRNA 12.7788 kcal/mol@LB@Unfolding Energy - sRNA 13.9626 kcal/mol@LB@@LB@Position - mRNA 78 -- 126@LB@Position - sRNA 156 -- 198@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 156 -- 162@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@
146	0.03799	0.6968	lmo1526	N/A	-15.66	0.073786	160 -- 215	153 -- 207	_____________159____________________216\n_____________\|______________________\|\n5'-AUG...AGGAG____AAACA____A________AGUAC...UAA-3'\n______________GAGA_____UGAA_GAAAAUAA\n______________\|\|\|\|_____\|\|\|\|_\|\|\|\|\|:\|\|\n______________CUCU_____ACUU_CUUUUGUU\n3'-GUU...GGUUA_____________A________UAUUA...GGA-5'\n_____________\|______________________\|\n_____________208____________________152\n	208 -- 214	154 -- 160	-11.4679 kcal/mol	1.00795 kcal/mol	0.933796 kcal/mol	159 216@LB@ \| \|@LB@5'-AUG...AGGAG AAACA A AGUAC...UAA-3'@LB@ GAGA UGAA GAAAAUAA@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|@LB@ CUCU ACUU CUUUUGUU@LB@3'-GUU...GGUUA A UAUUA...GGA-5'@LB@ \| \|@LB@ 208 152@LB@@LB@@LB@Energy -15.66 kcal/mol@LB@Hybridization Energy -11.4679 kcal/mol@LB@Unfolding Energy - mRNA 1.00795 kcal/mol@LB@Unfolding Energy - sRNA 0.933796 kcal/mol@LB@@LB@Position - mRNA 160 -- 215@LB@Position - sRNA 153 -- 207@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 154 -- 160@LB@
151	0.03914	0.6976	lmo1466	N/A	-16.64	0.048271	185 -- 226	158 -- 202	_____________184_______________________________________________227\n_____________\|_________________________________________________\|\n5'-UGA...UUAGA____AGA__A_______A_____________________________G_UUGGU...UUC-3'\n______________GAGG___CA_AGAUGUG_AACUA____GCCAA_GA____AAUGGAGA_A\n______________\|\|\|\|___\|\|_\|\|\|::\|\|_\|\|\|\|\|____\|\|\|\|\|_\|\|____\|\|\|\|:\|:\|_\|\n______________CUCC___GU_UCUGUAC_UUGAU____CGGUU_CU____UUACUUUU_U\n3'-GUU...CCCUA_________A_____________GUGC_____A__CUAC________G_UUAUU...GGA-5'\n_____________\|_________________________________________________\|\n_____________203_______________________________________________157\n	218 -- 224	157 -- 163	-27.6675 kcal/mol	5.9878 kcal/mol	13.9822 kcal/mol	184 227@LB@ \| \|@LB@5'-UGA...UUAGA AGA A A G UUGGU...UUC-3'@LB@ GAGG CA AGAUGUG AACUA GCCAA GA AAUGGAGA A@LB@ \|\|\|\| \|\| \|\|\|::\|\| \|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|:\|:\| \|@LB@ CUCC GU UCUGUAC UUGAU CGGUU CU UUACUUUU U@LB@3'-GUU...CCCUA A GUGC A CUAC G UUAUU...GGA-5'@LB@ \| \|@LB@ 203 157@LB@@LB@@LB@Energy -16.64 kcal/mol@LB@Hybridization Energy -27.6675 kcal/mol@LB@Unfolding Energy - mRNA 5.9878 kcal/mol@LB@Unfolding Energy - sRNA 13.9822 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 158 -- 202@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 157 -- 163@LB@
164	0.04503	0.7389	lmo2361	N/A	-17.31	0.035661	175 -- 215	153 -- 209	_____________174____________216\n_____________\|______________\|\n5'-CCA...AGGUA_________A____GAGGA...ACC-3'\n______________AUAAUGGGA_GAGG\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|\n______________UAUUGCCCU_CUCC\n3'-GUU...AUACG_________A____GUAUC...GGA-5'\n_____________\|______________\|\n_____________210____________152\n	177 -- 183	201 -- 207	-18.1933 kcal/mol	2.24476 kcal/mol	3.5857 kcal/mol	174 216@LB@ \| \|@LB@5'-CCA...AGGUA A GAGGA...ACC-3'@LB@ AUAAUGGGA GAGG@LB@ \|\|\|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGCCCU CUCC@LB@3'-GUU...AUACG A GUAUC...GGA-5'@LB@ \| \|@LB@ 210 152@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -18.1933 kcal/mol@LB@Unfolding Energy - mRNA 2.24476 kcal/mol@LB@Unfolding Energy - sRNA 3.5857 kcal/mol@LB@@LB@Position - mRNA 175 -- 215@LB@Position - sRNA 153 -- 209@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 201 -- 207@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

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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

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