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
11	0.000438	0.1262	b0467	priC	-14.72	0.009297	1 -- 37	32 -- 65	primosomal replication protein N''	______________1____________________________________38\n______________\|____________________________________\|\n___________5'-______GAACG_____A___CCA___CG_________UAAAC...GUU-3'\n______________GGGGAA_____GGCAA_GCA___GGC__CCAGCAGGA\n______________\|\|::\|\|_____\|\|\|\|\|_\|\|\|___\|\|\|__\|\|\|:\|\|\|:\|\n______________CCUUUU_____CCGUU_CGU___CCG__GGUUGUCUU\n3'-UUU...UACAA______AGUCA_____A___UA_______________UUAUU...UUG-5'\n_____________\|_____________________________________\|\n_____________66____________________________________31\n	30 -- 36	33 -- 39	-34.0772 kcal/mol	8.3902 kcal/mol	10.9649 kcal/mol	1 38@LB@ \| \|@LB@ 5'- GAACG A CCA CG UAAAC...GUU-3'@LB@ GGGGAA GGCAA GCA GGC CCAGCAGGA@LB@ \|\|::\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|\|\|:\|@LB@ CCUUUU CCGUU CGU CCG GGUUGUCUU@LB@3'-UUU...UACAA AGUCA A UA UUAUU...UUG-5'@LB@ \| \|@LB@ 66 31@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -34.0772 kcal/mol@LB@Unfolding Energy - mRNA 8.3902 kcal/mol@LB@Unfolding Energy - sRNA 10.9649 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 32 -- 65@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 33 -- 39@LB@
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
13	0.0005138	0.1268	b0055	djlA	-16.40	0.003186	213 -- 240	39 -- 65	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________212__________________________241\n_____________\|____________________________\|\n5'-GAC...AUUGG__A_______U_____UG__C_______UACUG...UUG-3'\n______________GG_AAAAUCA_UGGCG__GC_GUGGCCU\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|\|:__\|\|_:\|\|\|\|\|:\n______________CC_UUUUAGU_ACCGU__CG_UACCGGG\n3'-UUU...UACAA__________C_____UA__U_______UUGUC...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________38\n	234 -- 240	39 -- 45	-30.8595 kcal/mol	7.7929 kcal/mol	6.66922 kcal/mol	212 241@LB@ \| \|@LB@5'-GAC...AUUGG A U UG C UACUG...UUG-3'@LB@ GG AAAAUCA UGGCG GC GUGGCCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|: \|\| :\|\|\|\|\|:@LB@ CC UUUUAGU ACCGU CG UACCGGG@LB@3'-UUU...UACAA C UA U UUGUC...UUG-5'@LB@ \| \|@LB@ 66 38@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 7.7929 kcal/mol@LB@Unfolding Energy - sRNA 6.66922 kcal/mol@LB@@LB@Position - mRNA 213 -- 240@LB@Position - sRNA 39 -- 65@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 39 -- 45@LB@
14	0.0005336	0.1268	b0178	skp	-14.43	0.011083	94 -- 112	46 -- 65	periplasmic chaperone	_____________93___________________113\n_____________\|____________________\|\n5'-CUC...ACAAA____UG______________GCGAU...UCC-3'\n______________GGAA___UAGUGGUAGUGUA\n______________\|\|\|\|___:\|\|\|\|\|:\|:\|\|:\|\n______________CCUU___GUCACCGUUACGU\n3'-UUU...UACAA____UUA_____________UACCG...UUG-5'\n_____________\|____________________\|\n_____________66___________________45\n	105 -- 111	47 -- 53	-21.6303 kcal/mol	3.11688 kcal/mol	4.07994 kcal/mol	93 113@LB@ \| \|@LB@5'-CUC...ACAAA UG GCGAU...UCC-3'@LB@ GGAA UAGUGGUAGUGUA@LB@ \|\|\|\| :\|\|\|\|\|:\|:\|\|:\|@LB@ CCUU GUCACCGUUACGU@LB@3'-UUU...UACAA UUA UACCG...UUG-5'@LB@ \| \|@LB@ 66 45@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -21.6303 kcal/mol@LB@Unfolding Energy - mRNA 3.11688 kcal/mol@LB@Unfolding Energy - sRNA 4.07994 kcal/mol@LB@@LB@Position - mRNA 94 -- 112@LB@Position - sRNA 46 -- 65@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 47 -- 53@LB@
15	0.0005657	0.1268	b3715	yieH	-7.91	0.301098	195 -- 204	4 -- 13	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________194________205\n_____________\|__________\|\n5'-CUG...AAAGG__________CCCGG...UUG-3'\n______________AAAGGCAUGU\n______________\|\|\|\|\|\|\|\|:\|\n______________UUUCCGUAUA\n3'-UUU...UGUUA__________UUG-5'\n_____________\|__________\|\n_____________14_________3\n	198 -- 204	4 -- 10	-12.382 kcal/mol	1.66065 kcal/mol	2.80714 kcal/mol	194 205@LB@ \| \|@LB@5'-CUG...AAAGG CCCGG...UUG-3'@LB@ AAAGGCAUGU@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUUCCGUAUA@LB@3'-UUU...UGUUA UUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -7.91 kcal/mol@LB@Hybridization Energy -12.382 kcal/mol@LB@Unfolding Energy - mRNA 1.66065 kcal/mol@LB@Unfolding Energy - sRNA 2.80714 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 4 -- 10@LB@
16	0.0007379	0.1438	b3838	tatB	-12.16	0.040760	131 -- 190	7 -- 68	TatABCE protein translocation system subunit	_____________130___________________________________________________________________191\n_____________\|_____________________________________________________________________\|\n5'-UCG...AAGCA_GC___UAC_______GAA_____________AA_________CGC______GCC__________A___GGUGU...CGG-3'\n______________G__GGA___GAAUCAG___CA_______GGCU__AACAGAAGA___GAAG_C____ACGAUAAAG_GCA\n______________\|__\|\|\|___:\|\|\|\|\|\|___\|\|_______\|\|\|:__\|\|\|\|\|\|\|:\|___:\|\|:_\|____\|\|:\|\|\|\|\|\|_\|\|\|\n______________C__CCU___UUUAGUC___GU_______CCGG__UUGUCUUUU___UUUU_G____UGUUAUUUC_CGU\n3'-UUU...AUAUA_AA_____________ACC__UACGUUA____G__________A______A_ACAC_____________AUAUUG-5'\n_____________\|_____________________________________________________________________\|\n_____________69____________________________________________________________________6\n	180 -- 186	10 -- 16	-35.021 kcal/mol	10.7079 kcal/mol	12.1575 kcal/mol	130 191@LB@ \| \|@LB@5'-UCG...AAGCA GC UAC GAA AA CGC GCC A GGUGU...CGG-3'@LB@ G GGA GAAUCAG CA GGCU AACAGAAGA GAAG C ACGAUAAAG GCA@LB@ \| \|\|\| :\|\|\|\|\|\| \|\| \|\|\|: \|\|\|\|\|\|\|:\| :\|\|: \| \|\|:\|\|\|\|\|\| \|\|\|@LB@ C CCU UUUAGUC GU CCGG UUGUCUUUU UUUU G UGUUAUUUC CGU@LB@3'-UUU...AUAUA AA ACC UACGUUA G A A ACAC AUAUUG-5'@LB@ \| \|@LB@ 69 6@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -35.021 kcal/mol@LB@Unfolding Energy - mRNA 10.7079 kcal/mol@LB@Unfolding Energy - sRNA 12.1575 kcal/mol@LB@@LB@Position - mRNA 131 -- 190@LB@Position - sRNA 7 -- 68@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 10 -- 16@LB@
17	0.0007572	0.1438	b2512	bamB	-10.25	0.108120	60 -- 97	8 -- 56	BamABCDE complex OM biogenesis lipoprotein	_____________59________________________________________________98\n_____________\|_________________________________________________\|\n5'-GCU...CCUGC_______A___U_____G____AAG_________________GC_____GCGCG...CCC-3'\n______________GUGGUGA_GCA_U_GCU_AGCA_____________GUGAUAA__AAGGU\n______________\|\|\|\|::\|_\|\|\|_\|_\|\|:_\|:\|\|_____________\|\|\|\|:\|\|__\|\|\|\|:\n______________CACCGUU_CGU_A_CGG_UUGU_____________CACUGUU__UUCCG\n3'-UUU...UUAGU_______A___U_C___G____CUUUUAUUUUAGA_______AU_____UAUAUUG-5'\n_____________\|_________________________________________________\|\n_____________57________________________________________________7\n	84 -- 90	15 -- 21	-31.6141 kcal/mol	9.34469 kcal/mol	12.0216 kcal/mol	59 98@LB@ \| \|@LB@5'-GCU...CCUGC A U G AAG GC GCGCG...CCC-3'@LB@ GUGGUGA GCA U GCU AGCA GUGAUAA AAGGU@LB@ \|\|\|\|::\| \|\|\| \| \|\|: \|:\|\| \|\|\|\|:\|\| \|\|\|\|:@LB@ CACCGUU CGU A CGG UUGU CACUGUU UUCCG@LB@3'-UUU...UUAGU A U C G CUUUUAUUUUAGA AU UAUAUUG-5'@LB@ \| \|@LB@ 57 7@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -31.6141 kcal/mol@LB@Unfolding Energy - mRNA 9.34469 kcal/mol@LB@Unfolding Energy - sRNA 12.0216 kcal/mol@LB@@LB@Position - mRNA 60 -- 97@LB@Position - sRNA 8 -- 56@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 15 -- 21@LB@
18	0.0007704	0.1438	b4526	ydaE	-7.35	0.372707	186 -- 222	21 -- 54	conserved protein Rac prophage	_____________185___________________________________223\n_____________\|_____________________________________\|\n5'-ACU...GUAAA_____A__C_____GA____UA____________G__CUUAC...UAU-3'\n______________GGCGG_GU_AUGGU__UGAC__AGAAAAUAAAAU_UG\n______________\|\|\|::_\|:_\|\|\|\|:__::\|\|__\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________CCGUU_CG_UACCG__GUUG__UCUUUUAUUUUA_AC\n3'-UUU...AGUCA_____A__U_____G___________________G__ACUGU...UUG-5'\n_____________\|_____________________________________\|\n_____________55____________________________________20\n	212 -- 218	25 -- 31	-28.7009 kcal/mol	12.2907 kcal/mol	9.06413 kcal/mol	185 223@LB@ \| \|@LB@5'-ACU...GUAAA A C GA UA G CUUAC...UAU-3'@LB@ GGCGG GU AUGGU UGAC AGAAAAUAAAAU UG@LB@ \|\|\|:: \|: \|\|\|\|: ::\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ CCGUU CG UACCG GUUG UCUUUUAUUUUA AC@LB@3'-UUU...AGUCA A U G G ACUGU...UUG-5'@LB@ \| \|@LB@ 55 20@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -28.7009 kcal/mol@LB@Unfolding Energy - mRNA 12.2907 kcal/mol@LB@Unfolding Energy - sRNA 9.06413 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 21 -- 54@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 25 -- 31@LB@
19	0.0008126	0.1438	b1205	ychH	-14.60	0.010030	245 -- 269	40 -- 68	DUF2583 family putative inner membrane protein	_____________244____________________________270\n_____________\|______________________________\|\n5'-CAA...AUGGG___________U__________________GGCGU...UAC-3'\n______________GUUGG___GUC_GGUGGUAAUG__GUGGUC\n______________\|\|\|\|\|___:\|\|_:\|\|\|\|:\|\|\|\|__:\|\|\|:\|\n______________CAACC___UAG_UCACCGUUAC__UACCGG\n3'-UUU...AUAUA_____UUU______________GU______GUUGU...UUG-5'\n_____________\|______________________________\|\n_____________69_____________________________39\n	257 -- 263	48 -- 54	-27.4871 kcal/mol	6.07036 kcal/mol	6.81885 kcal/mol	244 270@LB@ \| \|@LB@5'-CAA...AUGGG U GGCGU...UAC-3'@LB@ GUUGG GUC GGUGGUAAUG GUGGUC@LB@ \|\|\|\|\| :\|\| :\|\|\|\|:\|\|\|\| :\|\|\|:\|@LB@ CAACC UAG UCACCGUUAC UACCGG@LB@3'-UUU...AUAUA UUU GU GUUGU...UUG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -14.60 kcal/mol@LB@Hybridization Energy -27.4871 kcal/mol@LB@Unfolding Energy - mRNA 6.07036 kcal/mol@LB@Unfolding Energy - sRNA 6.81885 kcal/mol@LB@@LB@Position - mRNA 245 -- 269@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 48 -- 54@LB@
20	0.0008987	0.1511	b2597	raiA	-11.08	0.071670	189 -- 211	11 -- 33	cold shock protein associated with 30S ribosomal subunit	_____________188_____________________212\n_____________\|_______________________\|\n5'-GCG...GACAA____________A__________CAUUA...AUC-3'\n______________GAGGUAAAAUUU_UGACAAUGAA\n______________:\|::\|\|\|\|\|\|:\|_\|\|\|\|\|\|\|:\|\|\n______________UUUUAUUUUAGA_ACUGUUAUUU\n3'-UUU...UUGUC____________C__________CCGUA...UUG-5'\n_____________\|_______________________\|\n_____________34______________________10\n	205 -- 211	11 -- 17	-19.0558 kcal/mol	3.03608 kcal/mol	4.94152 kcal/mol	188 212@LB@ \| \|@LB@5'-GCG...GACAA A CAUUA...AUC-3'@LB@ GAGGUAAAAUUU UGACAAUGAA@LB@ :\|::\|\|\|\|\|\|:\| \|\|\|\|\|\|\|:\|\|@LB@ UUUUAUUUUAGA ACUGUUAUUU@LB@3'-UUU...UUGUC C CCGUA...UUG-5'@LB@ \| \|@LB@ 34 10@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.0558 kcal/mol@LB@Unfolding Energy - mRNA 3.03608 kcal/mol@LB@Unfolding Energy - sRNA 4.94152 kcal/mol@LB@@LB@Position - mRNA 189 -- 211@LB@Position - sRNA 11 -- 33@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 11 -- 17@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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