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
112	0.01793	0.5155	b1418	cybB	-10.08	0.093429	125 -- 145	33 -- 57	cytochrome b561	_____________124_______________________146\n_____________\|_________________________\|\n5'-AAC...AAAAC_________________________AUUUU...UCC-3'\n______________GGGUGAACA_AUAUUU___AAUGAA\n______________\|\|\|\|:\|\|\|\|_\|:\|\|\|:___\|\|\|\|\|\|\n______________CCCAUUUGU_UGUAAG___UUACUU\n3'-UUU...UUAUC_________C______UCU______ACUGC...UCG-5'\n_____________\|_________________________\|\n_____________58________________________32\n	127 -- 133	49 -- 55	-19.5073 kcal/mol	3.1607 kcal/mol	6.2643 kcal/mol	124 146@LB@ \| \|@LB@5'-AAC...AAAAC AUUUU...UCC-3'@LB@ GGGUGAACA AUAUUU AAUGAA@LB@ \|\|\|\|:\|\|\|\| \|:\|\|\|: \|\|\|\|\|\|@LB@ CCCAUUUGU UGUAAG UUACUU@LB@3'-UUU...UUAUC C UCU ACUGC...UCG-5'@LB@ \| \|@LB@ 58 32@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -19.5073 kcal/mol@LB@Unfolding Energy - mRNA 3.1607 kcal/mol@LB@Unfolding Energy - sRNA 6.2643 kcal/mol@LB@@LB@Position - mRNA 125 -- 145@LB@Position - sRNA 33 -- 57@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 49 -- 55@LB@
22	0.001016	0.1516	b0734	cydB	-13.57	0.015928	285 -- 300	49 -- 64	cytochrome d terminal oxidase subunit II	_____________284_____________300\n_____________\|_______________\|\n5'-CGA...GUUUC__C_____________-3'\n______________GA_AUGGGGGUGGGCA\n______________\|\|_\|\|:\|\|\|\|\|:::\|\|\n______________CU_UAUCCCCAUUUGU\n3'-UUU...GCCAA__U_____________CUGUA...UCG-5'\n_____________\|________________\|\n_____________65_______________48\n	294 -- 300	49 -- 55	-19.142 kcal/mol	4.83222 kcal/mol	0.738518 kcal/mol	284 300@LB@ \| \|@LB@5'-CGA...GUUUC C -3'@LB@ GA AUGGGGGUGGGCA@LB@ \|\| \|\|:\|\|\|\|\|:::\|\|@LB@ CU UAUCCCCAUUUGU@LB@3'-UUU...GCCAA U CUGUA...UCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.142 kcal/mol@LB@Unfolding Energy - mRNA 4.83222 kcal/mol@LB@Unfolding Energy - sRNA 0.738518 kcal/mol@LB@@LB@Position - mRNA 285 -- 300@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 49 -- 55@LB@
155	0.02521	0.526	b4208	cycA	-8.71	0.171102	175 -- 207	24 -- 51	D-alanine/D-serine/glycine transporter	_____________174________________________________208\n_____________\|__________________________________\|\n5'-AUU...ACAAC_______GGUA__________AAAAAC_______AUCAG...UUG-3'\n______________ACAGACA____CAGGAA_GAA______AUGGUAG\n______________\|\|\|\|\|\|\|____\|\|\|:\|\|_\|\|\|______\|:\|\|\|\|:\n______________UGUCUGU____GUCUUU_CUU______UGCCAUU\n3'-UUU...CCAUU_______AA________A___AC___________AUUUA...UCG-5'\n_____________\|__________________________________\|\n_____________52_________________________________23\n	201 -- 207	24 -- 30	-19.5671 kcal/mol	4.55835 kcal/mol	6.29692 kcal/mol	174 208@LB@ \| \|@LB@5'-AUU...ACAAC GGUA AAAAAC AUCAG...UUG-3'@LB@ ACAGACA CAGGAA GAA AUGGUAG@LB@ \|\|\|\|\|\|\| \|\|\|:\|\| \|\|\| \|:\|\|\|\|:@LB@ UGUCUGU GUCUUU CUU UGCCAUU@LB@3'-UUU...CCAUU AA A AC AUUUA...UCG-5'@LB@ \| \|@LB@ 52 23@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -19.5671 kcal/mol@LB@Unfolding Energy - mRNA 4.55835 kcal/mol@LB@Unfolding Energy - sRNA 6.29692 kcal/mol@LB@@LB@Position - mRNA 175 -- 207@LB@Position - sRNA 24 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 24 -- 30@LB@
37	0.00362	0.3212	b4479	dgoR	-15.45	0.005416	239 -- 256	41 -- 57	D-galactonate catabolism operon transcriptional repressor	_____________238________________257\n_____________\|__________________\|\n5'-UUU...ACGCU___________U______CGGCA...AAC-3'\n______________GGGUAAACAGA_CGUUCA\n______________\|\|\|\|\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________CCCAUUUGUCU_GUAAGU\n3'-UUU...UUAUC__________________CUUUA...UCG-5'\n_____________\|__________________\|\n_____________58_________________40\n	243 -- 249	47 -- 53	-24.0794 kcal/mol	2.38777 kcal/mol	6.24592 kcal/mol	238 257@LB@ \| \|@LB@5'-UUU...ACGCU U CGGCA...AAC-3'@LB@ GGGUAAACAGA CGUUCA@LB@ \|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ CCCAUUUGUCU GUAAGU@LB@3'-UUU...UUAUC CUUUA...UCG-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -15.45 kcal/mol@LB@Hybridization Energy -24.0794 kcal/mol@LB@Unfolding Energy - mRNA 2.38777 kcal/mol@LB@Unfolding Energy - sRNA 6.24592 kcal/mol@LB@@LB@Position - mRNA 239 -- 256@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
110	0.01732	0.5155	b1800	dmlA	-11.31	0.051964	127 -- 183	1 -- 58	D-malate oxidase NAD-dependent; putative tartrate dehydrogenase	_____________126___________________________________________________________184\n_____________\|_____________________________________________________________\|\n5'-GGU...GUUAC____AUU___UCCUU_____UCAAUUAUAG__________UU______C___UU_______CAGGA...GCU-3'\n______________GGGG___AAU_____UUCAG__________GAUGGUGAUG______GU_AAU__UGAUGGU\n______________\|\|\|\|___\|\|:_____\|\|\|\|\|__________\|\|:\|\|\|:\|\|:______\|\|_\|\|\|__\|\|\|\|:\|:\n______________CCCC___UUG_____AAGUC__________CUGCCAUUAU______CA_UUA__ACUAUCG\n3'-UUU...UUUAU____AU____UCUGU_____UUUACUUA____________UUAUUU__A___CU_______-5'\n_____________\|____________________________________________________________\|\n_____________59___________________________________________________________1\n	177 -- 183	1 -- 7	-30.6237 kcal/mol	12.9772 kcal/mol	6.33758 kcal/mol	126 184@LB@ \| \|@LB@5'-GGU...GUUAC AUU UCCUU UCAAUUAUAG UU C UU CAGGA...GCU-3'@LB@ GGGG AAU UUCAG GAUGGUGAUG GU AAU UGAUGGU@LB@ \|\|\|\| \|\|: \|\|\|\|\| \|\|:\|\|\|:\|\|: \|\| \|\|\| \|\|\|\|:\|:@LB@ CCCC UUG AAGUC CUGCCAUUAU CA UUA ACUAUCG@LB@3'-UUU...UUUAU AU UCUGU UUUACUUA UUAUUU A CU -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -30.6237 kcal/mol@LB@Unfolding Energy - mRNA 12.9772 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 127 -- 183@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 1 -- 7@LB@
24	0.001422	0.1946	b0065	yabI	-15.22	0.006192	70 -- 99	1 -- 29	DedA family inner membrane protein	_____________69______________________________100\n_____________\|_______________________________\|\n5'-UGA...CGUGC____U_____GAA_____G____________CGUCA...GUU-3'\n______________CGGU_GUGAA___AAAGU_AAUGAUG_UAGC\n______________\|\|\|\|_:\|:\|\|___\|\|\|\|\|_\|\|\|\|\|\|\|_\|\|\|\|\n______________GCCA_UAUUU___UUUCA_UUACUAC_AUCG\n3'-UUU...UUACU____U_____A_______A_______U____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	89 -- 95	6 -- 12	-22.6746 kcal/mol	5.32597 kcal/mol	2.12711 kcal/mol	69 100@LB@ \| \|@LB@5'-UGA...CGUGC U GAA G CGUCA...GUU-3'@LB@ CGGU GUGAA AAAGU AAUGAUG UAGC@LB@ \|\|\|\| :\|:\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ GCCA UAUUU UUUCA UUACUAC AUCG@LB@3'-UUU...UUACU U A A U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.22 kcal/mol@LB@Hybridization Energy -22.6746 kcal/mol@LB@Unfolding Energy - mRNA 5.32597 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 70 -- 99@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 6 -- 12@LB@
88	0.01388	0.5059	b3809	dapF	-7.53	0.274407	192 -- 207	1 -- 17	diaminopimelate epimerase	_____________191_______________208\n_____________\|_________________\|\n5'-UCU...GAUUG____A_______C____UCUCG...UGG-3'\n______________GAGU_AAUGAUG__AGU\n______________:\|\|\|_\|\|\|\|\|\|\|__\|\|:\n______________UUCA_UUACUAC__UCG\n3'-UUU...UUUAU____A_______UA___-5'\n_____________\|________________\|\n_____________18_______________1\n	197 -- 203	6 -- 12	-9.99588 kcal/mol	2.41483 kcal/mol	0.0529402 kcal/mol	191 208@LB@ \| \|@LB@5'-UCU...GAUUG A C UCUCG...UGG-3'@LB@ GAGU AAUGAUG AGU@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|:@LB@ UUCA UUACUAC UCG@LB@3'-UUU...UUUAU A UA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -9.99588 kcal/mol@LB@Unfolding Energy - mRNA 2.41483 kcal/mol@LB@Unfolding Energy - sRNA 0.0529402 kcal/mol@LB@@LB@Position - mRNA 192 -- 207@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
97	0.01584	0.5059	b0116	lpd	-10.63	0.072174	157 -- 204	5 -- 49	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase	_____________156_______________________________________________205\n_____________\|_________________________________________________\|\n5'-CCG...CUGAA_____A_____U____CC_C___A________UAUA___GUC_______GUACU...UAA-3'\n______________AGACG__CGGG_AUGA__G_CGG_GAUAAAUA____GAG___AUGAUGA\n______________\|\|\|\|:__\|:\|:_\|\|\|\|__\|_\|\|\|_:\|\|\|\|\|\|\|____:\|\|___\|\|\|\|\|\|\|\n______________UCUGU__GUCU_UACU__C_GCC_UUAUUUAU____UUC___UACUACU\n3'-UUU...AUUUG_____AA____U____UA_U___A_______________AAU_______AUCG-5'\n_____________\|_________________________________________________\|\n_____________50________________________________________________4\n	198 -- 204	5 -- 11	-27.6335 kcal/mol	10.6788 kcal/mol	6.32229 kcal/mol	156 205@LB@ \| \|@LB@5'-CCG...CUGAA A U CC C A UAUA GUC GUACU...UAA-3'@LB@ AGACG CGGG AUGA G CGG GAUAAAUA GAG AUGAUGA@LB@ \|\|\|\|: \|:\|: \|\|\|\| \| \|\|\| :\|\|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|@LB@ UCUGU GUCU UACU C GCC UUAUUUAU UUC UACUACU@LB@3'-UUU...AUUUG AA U UA U A AAU AUCG-5'@LB@ \| \|@LB@ 50 4@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -27.6335 kcal/mol@LB@Unfolding Energy - mRNA 10.6788 kcal/mol@LB@Unfolding Energy - sRNA 6.32229 kcal/mol@LB@@LB@Position - mRNA 157 -- 204@LB@Position - sRNA 5 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
41	0.004182	0.3349	b3771	ilvD	-12.17	0.033695	175 -- 200	14 -- 53	dihydroxyacid dehydratase	_____________174______________________________________201\n_____________\|________________________________________\|\n5'-GCG...UUACG_________C_________________GA___________AUGCC...GUA-3'\n______________AGACAGACA_______________UGG__GUAAAUAAAGU\n______________\|:\|\|\|\|\|\|\|_______________:\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________UUUGUCUGU_______________GCC__UAUUUAUUUCA\n3'-UUU...CCCCA_________AAGUCUUUACUUACU___AU___________AUUAC...UCG-5'\n_____________\|________________________________________\|\n_____________54_______________________________________13\n	194 -- 200	14 -- 20	-22.054 kcal/mol	3.56189 kcal/mol	6.32552 kcal/mol	174 201@LB@ \| \|@LB@5'-GCG...UUACG C GA AUGCC...GUA-3'@LB@ AGACAGACA UGG GUAAAUAAAGU@LB@ \|:\|\|\|\|\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ UUUGUCUGU GCC UAUUUAUUUCA@LB@3'-UUU...CCCCA AAGUCUUUACUUACU AU AUUAC...UCG-5'@LB@ \| \|@LB@ 54 13@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -22.054 kcal/mol@LB@Unfolding Energy - mRNA 3.56189 kcal/mol@LB@Unfolding Energy - sRNA 6.32552 kcal/mol@LB@@LB@Position - mRNA 175 -- 200@LB@Position - sRNA 14 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 14 -- 20@LB@
148	0.02477	0.526	b2262	menB	-9.56	0.118602	261 -- 300	25 -- 56	dihydroxynaphthoic acid synthetase	_____________260______________________________________300\n_____________\|________________________________________\|\n5'-CGU...CCGAA___UUCGA__________UU_____AAAUCCACC_______-3'\n______________GGU_____GGACAUUC_G__AUGAA_________GACGGUA\n______________\|\|\|_____:\|\|\|\|\|\|\|_\|__\|\|\|\|\|_________\|\|\|\|\|\|\|\n______________CCA_____UCUGUAAG_C__UACUU_________CUGCCAU\n3'-UUU...UAUCC___UUUG_________U_UU_____A_______________UAUUU...UCG-5'\n_____________\|_________________________________________\|\n_____________57________________________________________24\n	294 -- 300	25 -- 31	-24.8577 kcal/mol	9.0019 kcal/mol	6.29869 kcal/mol	260 300@LB@ \| \|@LB@5'-CGU...CCGAA UUCGA UU AAAUCCACC -3'@LB@ GGU GGACAUUC G AUGAA GACGGUA@LB@ \|\|\| :\|\|\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCA UCUGUAAG C UACUU CUGCCAU@LB@3'-UUU...UAUCC UUUG U UU A UAUUU...UCG-5'@LB@ \| \|@LB@ 57 24@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -24.8577 kcal/mol@LB@Unfolding Energy - mRNA 9.0019 kcal/mol@LB@Unfolding Energy - sRNA 6.29869 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 25 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 25 -- 31@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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