Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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_000913 Escherichia coli str. K-12 substr. MG1655

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
149	0.01777	0.3828	b3024	ygiW	-12.90	0.027028	214 -- 237	39 -- 58	hydrogen peroxide and cadmium resistance periplasmic protein; stress-induced OB-fold protein	_____________213______________________238\n_____________\|________________________\|\n5'-UGA...AUUCG___CA_____CGCA__________UGUGC...AAA-3'\n______________CAG__GUAAU____GUAAUGGCCC\n______________\|\|\|__\|:\|\|\|____\|:\|\|\|\|\|\|\|\|\n______________GUC__CGUUA____CGUUACCGGG\n3'-UUU...UUUUA___AC___________________UUGUC...UUG-5'\n_____________\|________________________\|\n_____________59_______________________38\n	231 -- 237	39 -- 45	-23.1488 kcal/mol	3.67833 kcal/mol	6.56779 kcal/mol	213 238@LB@ \| \|@LB@5'-UGA...AUUCG CA CGCA UGUGC...AAA-3'@LB@ CAG GUAAU GUAAUGGCCC@LB@ \|\|\| \|:\|\|\| \|:\|\|\|\|\|\|\|\|@LB@ GUC CGUUA CGUUACCGGG@LB@3'-UUU...UUUUA AC UUGUC...UUG-5'@LB@ \| \|@LB@ 59 38@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -23.1488 kcal/mol@LB@Unfolding Energy - mRNA 3.67833 kcal/mol@LB@Unfolding Energy - sRNA 6.56779 kcal/mol@LB@@LB@Position - mRNA 214 -- 237@LB@Position - sRNA 39 -- 58@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 39 -- 45@LB@
165	0.01953	0.3981	b0603	ybdO	-12.89	0.027143	166 -- 206	40 -- 73	putative DNA-binding transcriptional regulator	_____________165_________________________________________207\n_____________\|___________________________________________\|\n5'-UCA...GUGAA_____CA_______AAAAUAUAAC___A_______________AAUCU...CAC-3'\n______________UAUAU__UGGAAGA__________CGG__GUAGUGUA_UGGCC\n______________\|\|\|\|\|__\|\|\|\|\|:\|__________\|:\|__\|:\|:\|\|:\|_\|\|\|\|\|\n______________AUAUA__ACCUUUU__________GUC__CGUUACGU_ACCGG\n3'-UUU...GAAAA_____CA_______A____________AC________U_____GUUGU...UUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________39\n	195 -- 201	46 -- 52	-24.6879 kcal/mol	4.92423 kcal/mol	6.86861 kcal/mol	165 207@LB@ \| \|@LB@5'-UCA...GUGAA CA AAAAUAUAAC A AAUCU...CAC-3'@LB@ UAUAU UGGAAGA CGG GUAGUGUA UGGCC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\| \|:\|:\|\|:\| \|\|\|\|\|@LB@ AUAUA ACCUUUU GUC CGUUACGU ACCGG@LB@3'-UUU...GAAAA CA A AC U GUUGU...UUG-5'@LB@ \| \|@LB@ 74 39@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -24.6879 kcal/mol@LB@Unfolding Energy - mRNA 4.92423 kcal/mol@LB@Unfolding Energy - sRNA 6.86861 kcal/mol@LB@@LB@Position - mRNA 166 -- 206@LB@Position - sRNA 40 -- 73@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
42	0.002679	0.2088	b1427	rimL	-12.89	0.027177	178 -- 217	11 -- 49	ribosomal-protein-L7/L12-serine acetyltransferase	_____________177_______________________________________218\n_____________\|_________________________________________\|\n5'-GAU...ACAAC________AU____U___________GA___AA________AGUAA...CCU-3'\n______________UGC_AUGG__UGAC_GGAGAUAAGAU__CUG__ACGAUAAA\n______________\|\|\|_\|\|\|\|__::\|\|_\|:\|:\|\|\|\|:\|\|__\|\|\|__\|\|:\|\|\|\|\|\n______________ACG_UACC__GUUG_CUUUUAUUUUA__GAC__UGUUAUUU\n3'-UUU...CCGUU___U____GG____U________________AC________CCGUA...UUG-5'\n_____________\|_________________________________________\|\n_____________50________________________________________10\n	211 -- 217	11 -- 17	-27.9575 kcal/mol	3.9779 kcal/mol	11.0867 kcal/mol	177 218@LB@ \| \|@LB@5'-GAU...ACAAC AU U GA AA AGUAA...CCU-3'@LB@ UGC AUGG UGAC GGAGAUAAGAU CUG ACGAUAAA@LB@ \|\|\| \|\|\|\| ::\|\| \|:\|:\|\|\|\|:\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ ACG UACC GUUG CUUUUAUUUUA GAC UGUUAUUU@LB@3'-UUU...CCGUU U GG U AC CCGUA...UUG-5'@LB@ \| \|@LB@ 50 10@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -27.9575 kcal/mol@LB@Unfolding Energy - mRNA 3.9779 kcal/mol@LB@Unfolding Energy - sRNA 11.0867 kcal/mol@LB@@LB@Position - mRNA 178 -- 217@LB@Position - sRNA 11 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
177	0.02174	0.4127	b1725	yniA	-12.81	0.028485	66 -- 113	12 -- 55	fructosamine kinase family protein	_____________65__________________________________________________114\n_____________\|___________________________________________________\|\n5'-GAG...CGACC___G____G_____AAUAG______________UGGUU_____________UCAGU...GGC-3'\n______________UGG_A__G_AAUGG_____CAACAGAAAAUAAA_____UUUG_GGCAAUAA\n______________\|\|\|_\|__\|_\|\|\|\|\|_____\|\|\|\|\|\|\|\|\|\|\|\|\|\|_____\|:\|\|_\|:\|\|\|\|\|\|\n______________ACC_U__C_UUACC_____GUUGUCUUUUAUUU_____AGAC_CUGUUAUU\n3'-UUU...UAGUC___G_UA_G_____GG_________________U________A________UCCGU...UUG-5'\n_____________\|___________________________________________________\|\n_____________56__________________________________________________11\n	107 -- 113	12 -- 18	-33.1768 kcal/mol	9.27067 kcal/mol	11.0975 kcal/mol	65 114@LB@ \| \|@LB@5'-GAG...CGACC G G AAUAG UGGUU UCAGU...GGC-3'@LB@ UGG A G AAUGG CAACAGAAAAUAAA UUUG GGCAAUAA@LB@ \|\|\| \| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\| \|:\|\| \|:\|\|\|\|\|\|@LB@ ACC U C UUACC GUUGUCUUUUAUUU AGAC CUGUUAUU@LB@3'-UUU...UAGUC G UA G GG U A UCCGU...UUG-5'@LB@ \| \|@LB@ 56 11@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -33.1768 kcal/mol@LB@Unfolding Energy - mRNA 9.27067 kcal/mol@LB@Unfolding Energy - sRNA 11.0975 kcal/mol@LB@@LB@Position - mRNA 66 -- 113@LB@Position - sRNA 12 -- 55@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 12 -- 18@LB@
130	0.01417	0.3654	b3188	sfsB	-12.77	0.029182	125 -- 158	30 -- 65	malPQ operon transcriptional activator	_____________124__________________________________159\n_____________\|____________________________________\|\n5'-CGG...CAAUA__CC______GA___UA___________________AGUGU...UGA-3'\n______________GG___AUCAG__GUA__GUGAU_GCUCGACAGAAGA\n______________\|\|___\|\|\|\|\|__\|:\|__\|::\|\|_\|\|:\|:\|\|\|\|\|\|:\|\n______________CC___UAGUC__CGU__CGUUA_CGGGUUGUCUUUU\n3'-UUU...UACAA__UUU_____AC___UA_____C_____________AUUUU...UUG-5'\n_____________\|____________________________________\|\n_____________66___________________________________29\n	152 -- 158	30 -- 36	-32.1455 kcal/mol	8.39464 kcal/mol	10.9856 kcal/mol	124 159@LB@ \| \|@LB@5'-CGG...CAAUA CC GA UA AGUGU...UGA-3'@LB@ GG AUCAG GUA GUGAU GCUCGACAGAAGA@LB@ \|\| \|\|\|\|\| \|:\| \|::\|\| \|\|:\|:\|\|\|\|\|\|:\|@LB@ CC UAGUC CGU CGUUA CGGGUUGUCUUUU@LB@3'-UUU...UACAA UUU AC UA C AUUUU...UUG-5'@LB@ \| \|@LB@ 66 29@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -32.1455 kcal/mol@LB@Unfolding Energy - mRNA 8.39464 kcal/mol@LB@Unfolding Energy - sRNA 10.9856 kcal/mol@LB@@LB@Position - mRNA 125 -- 158@LB@Position - sRNA 30 -- 65@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 30 -- 36@LB@
183	0.02285	0.4143	b3262	yhdJ	-12.72	0.029953	3 -- 23	44 -- 69	DNA adenine methyltransferase SAM-dependent	_____________2__________________________24\n_____________\|__________________________\|\n_________5'-CC__________________________ACACC...GUG-3'\n______________UGUUGGA____CA_UGGUGAUGCAAU\n______________\|\|\|\|\|\|\|____\|\|_\|\|\|::\|\|\|\|\|\|\|\n______________ACAACCU____GU_ACCGUUACGUUA\n3'-UUU...AAUAU_______UUUA__C____________CCGGG...UUG-5'\n_____________\|__________________________\|\n_____________70_________________________43\n	17 -- 23	44 -- 50	-23.8856 kcal/mol	6.69358 kcal/mol	4.47358 kcal/mol	2 24@LB@ \| \|@LB@ 5'-CC ACACC...GUG-3'@LB@ UGUUGGA CA UGGUGAUGCAAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|::\|\|\|\|\|\|\|@LB@ ACAACCU GU ACCGUUACGUUA@LB@3'-UUU...AAUAU UUUA C CCGGG...UUG-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -23.8856 kcal/mol@LB@Unfolding Energy - mRNA 6.69358 kcal/mol@LB@Unfolding Energy - sRNA 4.47358 kcal/mol@LB@@LB@Position - mRNA 3 -- 23@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 44 -- 50@LB@
185	0.02287	0.4143	b3460	livJ	-12.49	0.033972	245 -- 276	28 -- 54	branched-chain amino acid ABC transporter periplasmic binding protein	_____________244______________________________277\n_____________\|________________________________\|\n5'-AAU...GCGCU____UUCA___AU_______U___________UUAAA...CAA-3'\n______________GGCA____GCA__AUGGCUC_GGCAGAAGAUA\n______________\|\|\|\|____\|\|\|__\|\|\|\|\|:\|_::\|\|\|\|\|:\|\|\|\n______________CCGU____CGU__UACCGGG_UUGUCUUUUAU\n3'-UUU...AGUCA____UA__________________________UUUAG...UUG-5'\n_____________\|________________________________\|\n_____________55_______________________________27\n	258 -- 264	39 -- 45	-29.3573 kcal/mol	7.88401 kcal/mol	8.98285 kcal/mol	244 277@LB@ \| \|@LB@5'-AAU...GCGCU UUCA AU U UUAAA...CAA-3'@LB@ GGCA GCA AUGGCUC GGCAGAAGAUA@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\| ::\|\|\|\|\|:\|\|\|@LB@ CCGU CGU UACCGGG UUGUCUUUUAU@LB@3'-UUU...AGUCA UA UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -29.3573 kcal/mol@LB@Unfolding Energy - mRNA 7.88401 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 245 -- 276@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 39 -- 45@LB@
110	0.01026	0.313	b0063	araB	-12.48	0.034183	202 -- 260	1 -- 55	L-ribulokinase	_____________201___________________________________________________________261\n_____________\|_____________________________________________________________\|\n5'-CGG...AACGA_______U____U_____U____UUU__C_____U___________GCUUU____GUG___UGCGC...GGU-3'\n______________UGGCGAU_GCAA_UGGCC_CGAU___GG_AGUGA__UCUGUG_CGA_____GGCG___GAC\n______________\|\|\|\|:\|\|_\|\|\|\|_\|\|\|\|\|_\|:\|:___\|:_\|:\|:\|__\|\|\|\|\|\|_\|:\|_____\|\|\|:___:\|\|\n______________ACCGUUA_CGUU_ACCGG_GUUG___CU_UUAUU__AGACAC_GUU_____CCGU___UUG\n3'-UUU...UAGUC_______________________U____U_____UU______U___AUUU_____AUA___-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	202 -- 208	49 -- 55	-46.0779 kcal/mol	21.5533 kcal/mol	12.0455 kcal/mol	201 261@LB@ \| \|@LB@5'-CGG...AACGA U U U UUU C U GCUUU GUG UGCGC...GGU-3'@LB@ UGGCGAU GCAA UGGCC CGAU GG AGUGA UCUGUG CGA GGCG GAC@LB@ \|\|\|\|:\|\| \|\|\|\| \|\|\|\|\| \|:\|: \|: \|:\|:\| \|\|\|\|\|\| \|:\| \|\|\|: :\|\|@LB@ ACCGUUA CGUU ACCGG GUUG CU UUAUU AGACAC GUU CCGU UUG@LB@3'-UUU...UAGUC U U UU U AUUU AUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -46.0779 kcal/mol@LB@Unfolding Energy - mRNA 21.5533 kcal/mol@LB@Unfolding Energy - sRNA 12.0455 kcal/mol@LB@@LB@Position - mRNA 202 -- 260@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
32	0.002002	0.2088	b0423	thiI	-12.47	0.034301	40 -- 74	41 -- 65	tRNA s(4)U8 sulfurtransferase	_____________39_____________________________________75\n_____________\|______________________________________\|\n5'-AUG...GUAAC___C____________AUAGCAAAUAACGC________AAGGU...UUU-3'\n______________GGA___UCAG_GGCAA______________GCAAUGGU\n______________\|\|\|___\|\|\|\|_\|\|\|\|\|______________\|\|\|\|\|\|\|:\n______________CCU___AGUC_CCGUU______________CGUUACCG\n3'-UUU...UACAA___UUU____A_____A_____________________GGUUG...UUG-5'\n_____________\|______________________________________\|\n_____________66_____________________________________40\n	68 -- 74	41 -- 47	-23.8518 kcal/mol	5.56921 kcal/mol	5.80973 kcal/mol	39 75@LB@ \| \|@LB@5'-AUG...GUAAC C AUAGCAAAUAACGC AAGGU...UUU-3'@LB@ GGA UCAG GGCAA GCAAUGGU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CCU AGUC CCGUU CGUUACCG@LB@3'-UUU...UACAA UUU A A GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -23.8518 kcal/mol@LB@Unfolding Energy - mRNA 5.56921 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 40 -- 74@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 41 -- 47@LB@
113	0.01136	0.3326	b3417	malP	-12.46	0.034450	250 -- 272	38 -- 60	maltodextrin phosphorylase	_____________249_____________________273\n_____________\|_______________________\|\n5'-ACA...UUCAC___________C__U________AAUUC...GCC-3'\n______________GUCAGUGGCAG_GU_AUGGCUUA\n______________:\|\|\|\|\|\|\|\|\|:_\|:_\|\|\|\|\|::\|\n______________UAGUCACCGUU_CG_UACCGGGU\n3'-UUU...CCUUU___________A__U________UGUCU...UUG-5'\n_____________\|_______________________\|\n_____________61______________________37\n	266 -- 272	38 -- 44	-30.8718 kcal/mol	11.793 kcal/mol	6.61394 kcal/mol	249 273@LB@ \| \|@LB@5'-ACA...UUCAC C U AAUUC...GCC-3'@LB@ GUCAGUGGCAG GU AUGGCUUA@LB@ :\|\|\|\|\|\|\|\|\|: \|: \|\|\|\|\|::\|@LB@ UAGUCACCGUU CG UACCGGGU@LB@3'-UUU...CCUUU A U UGUCU...UUG-5'@LB@ \| \|@LB@ 61 37@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -30.8718 kcal/mol@LB@Unfolding Energy - mRNA 11.793 kcal/mol@LB@Unfolding Energy - sRNA 6.61394 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 38 -- 60@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 38 -- 44@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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