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
58	0.004088	0.237	b0998	torD	-12.26	0.038501	93 -- 144	1 -- 57	TorA-maturation chaperone	_____________92__________________________________________________________145\n_____________\|___________________________________________________________\|\n5'-GGU...ACGCU_____AAAU__AGAA___A________C_______CAG________________U____GGCCC...CCA-3'\n______________GGUGG____UG_____GU_CAACGGAA_AGUGGAG___GUGAC______GGCGU_UAAC\n______________:\|\|\|\|____\|\|_____\|:_\|\|\|\|:\|\|\|_\|:\|::\|:___\|\|\|\|\|______\|\|\|:\|_\|\|\|\|\n______________UCACC____AC_____CG_GUUGUCUU_UUAUUUU___CACUG______CCGUA_AUUG\n3'-UUU...UUUAG_____GUU___GUUAC__G________________AGA_____UUAUUU_____U____-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________1\n	111 -- 117	33 -- 39	-35.8821 kcal/mol	11.4978 kcal/mol	12.1233 kcal/mol	92 145@LB@ \| \|@LB@5'-GGU...ACGCU AAAU AGAA A C CAG U GGCCC...CCA-3'@LB@ GGUGG UG GU CAACGGAA AGUGGAG GUGAC GGCGU UAAC@LB@ :\|\|\|\| \|\| \|: \|\|\|\|:\|\|\| \|:\|::\|: \|\|\|\|\| \|\|\|:\| \|\|\|\|@LB@ UCACC AC CG GUUGUCUU UUAUUUU CACUG CCGUA AUUG@LB@3'-UUU...UUUAG GUU GUUAC G AGA UUAUUU U -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -35.8821 kcal/mol@LB@Unfolding Energy - mRNA 11.4978 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 93 -- 144@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 33 -- 39@LB@
59	0.004284	0.2442	b0094	ftsA	-10.23	0.109208	176 -- 218	1 -- 63	ATP-binding cell division FtsK recruitment protein	_____________175________________________________________________________________219\n_____________\|__________________________________________________________________\|\n5'-AAU...GCAAC__________________CA___AG___________________________UCA_____ACG___AGAAA...UCA-3'\n______________AAAAUCAG_______GCA__GGC__AACA________________ACAAUGA___AGGCG___GAC\n______________\|\|\|\|\|\|\|\|_______\|\|\|__\|\|\|__\|\|\|\|________________\|\|\|\|\|:\|___\|\|\|\|:___:\|\|\n______________UUUUAGUC_______CGU__CCG__UUGU________________UGUUAUU___UCCGU___UUG\n3'-UUU...CAACC________ACCGUUA___UA___GG____CUUUUAUUUUAGACAC_______________AUA___-5'\n_____________\|_________________________________________________________________\|\n_____________64________________________________________________________________1\n	198 -- 204	12 -- 18	-27.1283 kcal/mol	4.74085 kcal/mol	12.1605 kcal/mol	175 219@LB@ \| \|@LB@5'-AAU...GCAAC CA AG UCA ACG AGAAA...UCA-3'@LB@ AAAAUCAG GCA GGC AACA ACAAUGA AGGCG GAC@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\|\|: :\|\|@LB@ UUUUAGUC CGU CCG UUGU UGUUAUU UCCGU UUG@LB@3'-UUU...CAACC ACCGUUA UA GG CUUUUAUUUUAGACAC AUA -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.1283 kcal/mol@LB@Unfolding Energy - mRNA 4.74085 kcal/mol@LB@Unfolding Energy - sRNA 12.1605 kcal/mol@LB@@LB@Position - mRNA 176 -- 218@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
60	0.004583	0.2539	b0674	asnB	-9.07	0.186262	281 -- 298	39 -- 51	asparagine synthetase B	_____________280________________299\n_____________\|__________________\|\n5'-ACA...CGCCU______UCAUC_______GG-3'\n______________GAUGCG_____GUGGCCC\n______________:\|\|\|\|:_____:\|\|\|\|\|\|\n______________UUACGU_____UACCGGG\n3'-UUU...CACCG__________________UUGUC...UUG-5'\n_____________\|__________________\|\n_____________52_________________38\n	292 -- 298	39 -- 45	-18.7239 kcal/mol	4.90882 kcal/mol	4.74571 kcal/mol	280 299@LB@ \| \|@LB@5'-ACA...CGCCU UCAUC GG-3'@LB@ GAUGCG GUGGCCC@LB@ :\|\|\|\|: :\|\|\|\|\|\|@LB@ UUACGU UACCGGG@LB@3'-UUU...CACCG UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -18.7239 kcal/mol@LB@Unfolding Energy - mRNA 4.90882 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 281 -- 298@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
61	0.004706	0.2539	b3713	chrR	-11.93	0.045896	122 -- 163	8 -- 58	chromate reductase Class I flavoprotein	_____________121____________________________________________________164\n_____________\|______________________________________________________\|\n5'-ACG...CCUAC___CC__A_______UUUU_____________________CU___C________UUUUU...CGA-3'\n______________CAG__GG_UGAUGCG____GCCCAAC___________UCU___AC_GUGAAGGC\n______________\|\|\|__\|\|_::\|\|\|\|:____\|\|\|\|\|\|\|___________\|\|\|___\|\|_:\|:\|\|\|\|\|\n______________GUC__CC_GUUACGU____CGGGUUG___________AGA___UG_UAUUUCCG\n3'-UUU...UUUUA___A___________UAC________UCUUUUAUUUU___CAC__U________UAUAUUG-5'\n_____________\|______________________________________________________\|\n_____________59_____________________________________________________7\n	157 -- 163	8 -- 14	-33.8478 kcal/mol	9.79541 kcal/mol	12.1181 kcal/mol	121 164@LB@ \| \|@LB@5'-ACG...CCUAC CC A UUUU CU C UUUUU...CGA-3'@LB@ CAG GG UGAUGCG GCCCAAC UCU AC GUGAAGGC@LB@ \|\|\| \|\| ::\|\|\|\|: \|\|\|\|\|\|\| \|\|\| \|\| :\|:\|\|\|\|\|@LB@ GUC CC GUUACGU CGGGUUG AGA UG UAUUUCCG@LB@3'-UUU...UUUUA A UAC UCUUUUAUUUU CAC U UAUAUUG-5'@LB@ \| \|@LB@ 59 7@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -33.8478 kcal/mol@LB@Unfolding Energy - mRNA 9.79541 kcal/mol@LB@Unfolding Energy - sRNA 12.1181 kcal/mol@LB@@LB@Position - mRNA 122 -- 163@LB@Position - sRNA 8 -- 58@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 8 -- 14@LB@
62	0.004714	0.2539	b0973	hyaB	-9.08	0.185506	169 -- 187	48 -- 64	hydrogenase 1 large subunit	_____________168_________________188\n_____________\|___________________\|\n5'-GGU...AAACC___C_____CCA_______AGGAU...GCG-3'\n______________GAA_AUCAG___GGCAAUG\n______________\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUU_UAGUC___CCGUUAC\n3'-UUU...ACAAC___U_____A_________GUUAC...UUG-5'\n_____________\|___________________\|\n_____________65__________________47\n	181 -- 187	48 -- 54	-17.0784 kcal/mol	4.02672 kcal/mol	3.97302 kcal/mol	168 188@LB@ \| \|@LB@5'-GGU...AAACC C CCA AGGAU...GCG-3'@LB@ GAA AUCAG GGCAAUG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUU UAGUC CCGUUAC@LB@3'-UUU...ACAAC U A GUUAC...UUG-5'@LB@ \| \|@LB@ 65 47@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -17.0784 kcal/mol@LB@Unfolding Energy - mRNA 4.02672 kcal/mol@LB@Unfolding Energy - sRNA 3.97302 kcal/mol@LB@@LB@Position - mRNA 169 -- 187@LB@Position - sRNA 48 -- 64@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 48 -- 54@LB@
63	0.004757	0.2539	b1342	ydaN	-13.10	0.024145	140 -- 198	7 -- 70	putative Zn(II) transporter	_____________139_______________________________________________________________199\n_____________\|_________________________________________________________________\|\n5'-CGU...AUGAG______CGU__________CA_____A____A___UAC_______UGCGU_______________CUGUG...AUG-3'\n______________AUGUUG___AA_CAG_GGC_____GA_GGCU_GAC___AAAAUAA______UGAUGAUGGAGGCA\n______________\|\|\|\|\|\|___\|\|_\|\|\|_\|\|\|_____:\|_\|\|\|:_:\|\|___\|\|\|\|\|\|\|______\|\|\|::\|\|::\|\|\|\|\|\n______________UACAAC___UU_GUC_CCG_____UU_CCGG_UUG___UUUUAUU______ACUGUUAUUUCCGU\n3'-UUU...AAAUA______CUU__A___A___UUACG__A____G___UC________UUAGAC______________AUAUUG-5'\n_____________\|_________________________________________________________________\|\n_____________71________________________________________________________________6\n	192 -- 198	7 -- 13	-39.9747 kcal/mol	14.7113 kcal/mol	12.1606 kcal/mol	139 199@LB@ \| \|@LB@5'-CGU...AUGAG CGU CA A A UAC UGCGU CUGUG...AUG-3'@LB@ AUGUUG AA CAG GGC GA GGCU GAC AAAAUAA UGAUGAUGGAGGCA@LB@ \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|::\|\|::\|\|\|\|\|@LB@ UACAAC UU GUC CCG UU CCGG UUG UUUUAUU ACUGUUAUUUCCGU@LB@3'-UUU...AAAUA CUU A A UUACG A G UC UUAGAC AUAUUG-5'@LB@ \| \|@LB@ 71 6@LB@@LB@@LB@Energy -13.10 kcal/mol@LB@Hybridization Energy -39.9747 kcal/mol@LB@Unfolding Energy - mRNA 14.7113 kcal/mol@LB@Unfolding Energy - sRNA 12.1606 kcal/mol@LB@@LB@Position - mRNA 140 -- 198@LB@Position - sRNA 7 -- 70@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
64	0.005005	0.2614	b3795	yifK	-6.27	0.531551	193 -- 206	51 -- 64	putative APC family amino acid transporter	_____________192____________207\n_____________\|______________\|\n5'-CAA...AACAC_______UA_____GAUAA...GGG-3'\n______________GAGGAUU__UGGCA\n______________\|\|::\|\|:__\|\|\|\|\|\n______________CUUUUAG__ACCGU\n3'-UUU...ACAAC_______UC_____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	193 -- 199	58 -- 64	-12.618 kcal/mol	3.46106 kcal/mol	2.8882 kcal/mol	192 207@LB@ \| \|@LB@5'-CAA...AACAC UA GAUAA...GGG-3'@LB@ GAGGAUU UGGCA@LB@ \|\|::\|\|: \|\|\|\|\|@LB@ CUUUUAG ACCGU@LB@3'-UUU...ACAAC UC UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -12.618 kcal/mol@LB@Unfolding Energy - mRNA 3.46106 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 193 -- 206@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 58 -- 64@LB@
65	0.005052	0.2614	b0451	amtB	-9.90	0.127883	170 -- 220	11 -- 61	ammonium transporter	_____________169____________________________________________________221\n_____________\|______________________________________________________\|\n5'-CCA...GCUGU____UC_____CACA____CA__AA_______________AUA_C_________AACUG...CGU-3'\n______________AAUC__UGGCA____GCAA__GG__CGA___AAAAUGAAG___G_GACGAUAAA\n______________\|\|\|\|__\|\|\|\|\|____\|\|\|\|__\|\|__\|:\|___\|\|\|\|\|:\|\|:___\|_\|\|\|:\|\|\|\|\|\n______________UUAG__ACCGU____CGUU__CC__GUU___UUUUAUUUU___C_CUGUUAUUU\n3'-UUU...ACCUU____UC_____UA______A___GG___GUC_________AGA_A_________CCGUA...UUG-5'\n_____________\|______________________________________________________\|\n_____________62_____________________________________________________10\n	214 -- 220	11 -- 17	-30.4323 kcal/mol	9.41224 kcal/mol	11.1248 kcal/mol	169 221@LB@ \| \|@LB@5'-CCA...GCUGU UC CACA CA AA AUA C AACUG...CGU-3'@LB@ AAUC UGGCA GCAA GG CGA AAAAUGAAG G GACGAUAAA@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\| \|\| \|:\| \|\|\|\|\|:\|\|: \| \|\|\|:\|\|\|\|\|@LB@ UUAG ACCGU CGUU CC GUU UUUUAUUUU C CUGUUAUUU@LB@3'-UUU...ACCUU UC UA A GG GUC AGA A CCGUA...UUG-5'@LB@ \| \|@LB@ 62 10@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -30.4323 kcal/mol@LB@Unfolding Energy - mRNA 9.41224 kcal/mol@LB@Unfolding Energy - sRNA 11.1248 kcal/mol@LB@@LB@Position - mRNA 170 -- 220@LB@Position - sRNA 11 -- 61@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@LB@
66	0.005339	0.2645	b1476	fdnI	-10.79	0.082799	156 -- 194	9 -- 48	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________155________________________________________195\n_____________\|__________________________________________\|\n5'-CGU...CAUCG___U________AUA_____________GA______G_____AUCAU...UUU-3'\n______________GUA_UGGCCCGA___AGGAAGUGGA__C__UGACGA__GAGG\n______________\|:\|_\|\|\|\|\|\|:\|___\|\|:\|\|:\|::\|__\|__\|\|\|\|:\|__:\|\|\|\n______________CGU_ACCGGGUU___UCUUUUAUUU__G__ACUGUU__UUCC\n3'-UUU...CGUUA___U________G____________UA_AC______AU____GUAUAUUG-5'\n_____________\|__________________________________________\|\n_____________49_________________________________________8\n	161 -- 167	37 -- 43	-34.1322 kcal/mol	12.2398 kcal/mol	11.1008 kcal/mol	155 195@LB@ \| \|@LB@5'-CGU...CAUCG U AUA GA G AUCAU...UUU-3'@LB@ GUA UGGCCCGA AGGAAGUGGA C UGACGA GAGG@LB@ \|:\| \|\|\|\|\|\|:\| \|\|:\|\|:\|::\| \| \|\|\|\|:\| :\|\|\|@LB@ CGU ACCGGGUU UCUUUUAUUU G ACUGUU UUCC@LB@3'-UUU...CGUUA U G UA AC AU GUAUAUUG-5'@LB@ \| \|@LB@ 49 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -34.1322 kcal/mol@LB@Unfolding Energy - mRNA 12.2398 kcal/mol@LB@Unfolding Energy - sRNA 11.1008 kcal/mol@LB@@LB@Position - mRNA 156 -- 194@LB@Position - sRNA 9 -- 48@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 37 -- 43@LB@
67	0.005347	0.2645	b4278	insG	-9.22	0.173962	151 -- 164	45 -- 58	IS4 transposase	_____________150____________165\n_____________\|______________\|\n5'-GUU...CGAUC_______U______GAAUC...CUC-3'\n______________CAGUGGC_GUGUAA\n______________\|\|\|\|\|\|\|_:\|\|:\|\|\n______________GUCACCG_UACGUU\n3'-UUU...UUUUA_______U______ACCGG...UUG-5'\n_____________\|______________\|\n_____________59_____________44\n	151 -- 157	52 -- 58	-18.8848 kcal/mol	6.17717 kcal/mol	3.48403 kcal/mol	150 165@LB@ \| \|@LB@5'-GUU...CGAUC U GAAUC...CUC-3'@LB@ CAGUGGC GUGUAA@LB@ \|\|\|\|\|\|\| :\|\|:\|\|@LB@ GUCACCG UACGUU@LB@3'-UUU...UUUUA U ACCGG...UUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -18.8848 kcal/mol@LB@Unfolding Energy - mRNA 6.17717 kcal/mol@LB@Unfolding Energy - sRNA 3.48403 kcal/mol@LB@@LB@Position - mRNA 151 -- 164@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 52 -- 58@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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