Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
135	0.02191	0.526	b1342	ydaN	-17.19	0.001818	129 -- 197	1 -- 58	putative Zn(II) transporter	_____________128______________________________________________________________________198\n_____________\|________________________________________________________________________\|\n5'-CGU...GUAAU_______UG_______GCGUAACAGGGC______GCUA____UACA________UGC___________A___ACUGU...AUG-3'\n______________GGGGUGA__AGAUGUU____________CAGAAG_____GAC______AAAUAA___GUUGAUGAUGG_GGC\n______________\|\|\|\|\|:\|__\|\|\|::\|\|____________\|\|\|\|\|:_____\|\|\|______\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|:_:\|\|\n______________CCCCAUU__UCUGUAA____________GUCUUU_____CUG______UUUAUU___CAAUUACUACU_UCG\n3'-UUU...UUUAU_______UG_________________________ACUUA___CCAUUA______U_____________A___-5'\n_____________\|_______________________________________________________________________\|\n_____________59______________________________________________________________________1\n	187 -- 193	5 -- 11	-40.4273 kcal/mol	16.9018 kcal/mol	6.33758 kcal/mol	128 198@LB@ \| \|@LB@5'-CGU...GUAAU UG GCGUAACAGGGC GCUA UACA UGC A ACUGU...AUG-3'@LB@ GGGGUGA AGAUGUU CAGAAG GAC AAAUAA GUUGAUGAUGG GGC@LB@ \|\|\|\|\|:\| \|\|\|::\|\| \|\|\|\|\|: \|\|\| \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|: :\|\|@LB@ CCCCAUU UCUGUAA GUCUUU CUG UUUAUU CAAUUACUACU UCG@LB@3'-UUU...UUUAU UG ACUUA CCAUUA U A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -17.19 kcal/mol@LB@Hybridization Energy -40.4273 kcal/mol@LB@Unfolding Energy - mRNA 16.9018 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 129 -- 197@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 5 -- 11@LB@
166	0.02659	0.526	b1580	rspB	-9.76	0.108040	184 -- 209	1 -- 29	putative Zn-dependent NAD(P)-binding oxidoreductase	_____________183___________________________210\n_____________\|_____________________________\|\n5'-AUG...GGAAC______G_______A_______AA_____AUAUU...UUG-3'\n______________UGGUAA_GAGUAAG__UAAUGA____AGC\n______________:\|\|\|\|\|_:\|:\|\|\|:__\|\|\|\|\|\|____\|\|\|\n______________GCCAUU_UUUAUUU__AUUACU____UCG\n3'-UUU...UUACU______A_______CA______ACUA___-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	191 -- 197	16 -- 22	-16.0836 kcal/mol	4.192 kcal/mol	2.12711 kcal/mol	183 210@LB@ \| \|@LB@5'-AUG...GGAAC G A AA AUAUU...UUG-3'@LB@ UGGUAA GAGUAAG UAAUGA AGC@LB@ :\|\|\|\|\| :\|:\|\|\|: \|\|\|\|\|\| \|\|\|@LB@ GCCAUU UUUAUUU AUUACU UCG@LB@3'-UUU...UUACU A CA ACUA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -16.0836 kcal/mol@LB@Unfolding Energy - mRNA 4.192 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 184 -- 209@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 16 -- 22@LB@
154	0.02518	0.526	b1602	pntB	-9.01	0.150855	190 -- 197	52 -- 59	pyridine nucleotide transhydrogenase beta subunit	_____________189______198\n_____________\|________\|\n5'-GCU...AAUUA________CAUAU...GUA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	191 -- 197	52 -- 58	-12.5664 kcal/mol	3.49825 kcal/mol	0.0599826 kcal/mol	189 198@LB@ \| \|@LB@5'-GCU...AAUUA CAUAU...GUA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -12.5664 kcal/mol@LB@Unfolding Energy - mRNA 3.49825 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 190 -- 197@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
65	0.009342	0.4523	b0871	poxB	-9.00	0.151653	248 -- 256	51 -- 59	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________247_______257\n_____________\|_________\|\n5'-CCG...UCGGC_________ACGCA...GUG-3'\n______________AGGGGUGAA\n______________\|\|\|\|\|\|:\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	250 -- 256	51 -- 57	-12.9194 kcal/mol	3.39064 kcal/mol	0.532875 kcal/mol	247 257@LB@ \| \|@LB@5'-CCG...UCGGC ACGCA...GUG-3'@LB@ AGGGGUGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -12.9194 kcal/mol@LB@Unfolding Energy - mRNA 3.39064 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 248 -- 256@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 51 -- 57@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase	_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
42	0.004307	0.3367	b4051	qorA	-12.29	0.031673	118 -- 140	3 -- 26	quinone oxidoreductase NADPH-dependent	_____________117______________________141\n_____________\|________________________\|\n5'-CGC...UGCCA_______________CC_______AAGAA...UCG-3'\n______________UAGUGAAUGGAGUUA__GA_GAUA\n______________\|\|:\|:\|\|\|::\|\|\|\|\|__\|\|_\|\|\|\|\n______________AUUAUUUAUUUCAAU__CU_CUAU\n3'-UUU...CUGCC_______________UA__A____CG-5'\n_____________\|________________________\|\n_____________27_______________________2\n	126 -- 132	12 -- 18	-16.4059 kcal/mol	3.53962 kcal/mol	0.580109 kcal/mol	117 141@LB@ \| \|@LB@5'-CGC...UGCCA CC AAGAA...UCG-3'@LB@ UAGUGAAUGGAGUUA GA GAUA@LB@ \|\|:\|:\|\|\|::\|\|\|\|\| \|\| \|\|\|\|@LB@ AUUAUUUAUUUCAAU CU CUAU@LB@3'-UUU...CUGCC UA A CG-5'@LB@ \| \|@LB@ 27 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -16.4059 kcal/mol@LB@Unfolding Energy - mRNA 3.53962 kcal/mol@LB@Unfolding Energy - sRNA 0.580109 kcal/mol@LB@@LB@Position - mRNA 118 -- 140@LB@Position - sRNA 3 -- 26@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 12 -- 18@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding	_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
9	0.000223	0.08136	b1826	mgrB	-16.34	0.003128	178 -- 244	1 -- 63	regulatory peptide for PhoPQ feedback inhibition	_____________177______________________________________________________________________245\n_____________\|________________________________________________________________________\|\n5'-UAC...ACAUA_______U_________G_____________AAAGUUUC_____GUCGUUCU_______UC______U____UUGCU...AAU-3'\n______________AGGUAGG_G_AAACGGA_AUU__GGAGUGAA________GAUGG__________GGUUG__GUGGUG_UGGC\n______________\|::\|\|\|\|_\|_\|\|\|\|:\|\|_\|\|\|__\|:\|:\|\|\|\|________\|\|:\|\|__________:\|\|\|:__:\|\|:\|\|_\|:\|\|\n______________UUUAUCC_C_UUUGUCU_UAA__CUUUACUU________CUGCC__________UCAAU__UACUAC_AUCG\n3'-UUU...CCAAC_______C_A_______G___GU________A____________AUUAUUUAUU_____________U____-5'\n_____________\|_______________________________________________________________________\|\n_____________64______________________________________________________________________1\n	187 -- 193	47 -- 53	-38.9165 kcal/mol	16.2325 kcal/mol	6.344 kcal/mol	177 245@LB@ \| \|@LB@5'-UAC...ACAUA U G AAAGUUUC GUCGUUCU UC U UUGCU...AAU-3'@LB@ AGGUAGG G AAACGGA AUU GGAGUGAA GAUGG GGUUG GUGGUG UGGC@LB@ \|::\|\|\|\| \| \|\|\|\|:\|\| \|\|\| \|:\|:\|\|\|\| \|\|:\|\| :\|\|\|: :\|\|:\|\| \|:\|\|@LB@ UUUAUCC C UUUGUCU UAA CUUUACUU CUGCC UCAAU UACUAC AUCG@LB@3'-UUU...CCAAC C A G GU A AUUAUUUAUU U -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -38.9165 kcal/mol@LB@Unfolding Energy - mRNA 16.2325 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 178 -- 244@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
60	0.008489	0.4523	b3912	cpxR	-10.34	0.082729	218 -- 229	5 -- 16	response regulator in two-component regulatory system with CpxA	_____________217__________230\n_____________\|____________\|\n5'-UGA...CUGUU____________CCGAG...AUG-3'\n______________AGUUGAUGAUGA\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________UCAAUUACUACU\n3'-UUU...UUAUU____________AUCG-5'\n_____________\|____________\|\n_____________17___________4\n	223 -- 229	5 -- 11	-14.1725 kcal/mol	3.78244 kcal/mol	0.0462955 kcal/mol	217 230@LB@ \| \|@LB@5'-UGA...CUGUU CCGAG...AUG-3'@LB@ AGUUGAUGAUGA@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ UCAAUUACUACU@LB@3'-UUU...UUAUU AUCG-5'@LB@ \| \|@LB@ 17 4@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -14.1725 kcal/mol@LB@Unfolding Energy - mRNA 3.78244 kcal/mol@LB@Unfolding Energy - sRNA 0.0462955 kcal/mol@LB@@LB@Position - mRNA 218 -- 229@LB@Position - sRNA 5 -- 16@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 5 -- 11@LB@
188	0.03165	0.5492	b3247	rng	-10.28	0.085420	187 -- 220	10 -- 64	ribonuclease G	_____________186_____________________________________________________221\n_____________\|_______________________________________________________\|\n5'-GUU...CGUGA_________A____________________________C_______U________AAACG...CGC-3'\n______________GAAA_AGGG_UAAAC________________AUGACGG___UGAAU___GUUAGU\n______________\|\|\|\|_\|\|\|\|_\|\|\|\|\|________________\|\|\|\|\|\|\|___\|:\|\|\|___\|\|\|\|:\|\n______________CUUU_UCCC_AUUUG________________UACUGCC___AUUUA___CAAUUA\n3'-UUU...GCCAA____A____C_____UCUGUAAGUCUUUACU_______AUU_____UUU______CUACU...UCG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________9\n	201 -- 207	27 -- 33	-22.7807 kcal/mol	6.16544 kcal/mol	6.33995 kcal/mol	186 221@LB@ \| \|@LB@5'-GUU...CGUGA A C U AAACG...CGC-3'@LB@ GAAA AGGG UAAAC AUGACGG UGAAU GUUAGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|:\|@LB@ CUUU UCCC AUUUG UACUGCC AUUUA CAAUUA@LB@3'-UUU...GCCAA A C UCUGUAAGUCUUUACU AUU UUU CUACU...UCG-5'@LB@ \| \|@LB@ 65 9@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -22.7807 kcal/mol@LB@Unfolding Energy - mRNA 6.16544 kcal/mol@LB@Unfolding Energy - sRNA 6.33995 kcal/mol@LB@@LB@Position - mRNA 187 -- 220@LB@Position - sRNA 10 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 27 -- 33@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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