Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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	Additional homologs
101	0.003756	0.123	b2972	pppA	-13.47	0.029286	211 -- 222	1 -- 12	bifunctional prepilin leader peptidase/ methylase		_____________210__________223\n_____________\|____________\|\n5'-UAA...UUUUG____________AAUAC...GGC-3'\n______________AUGUUUUUCAGC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACAAAAAGUCG\n3'-UUU...CCCAA____________-5'\n_____________\|___________\|\n_____________13__________1\n	216 -- 222	1 -- 7	-17.018 kcal/mol	2.64154 kcal/mol	0.904394 kcal/mol	210 223@LB@ \| \|@LB@5'-UAA...UUUUG AAUAC...GGC-3'@LB@ AUGUUUUUCAGC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACAAAAAGUCG@LB@3'-UUU...CCCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -17.018 kcal/mol@LB@Unfolding Energy - mRNA 2.64154 kcal/mol@LB@Unfolding Energy - sRNA 0.904394 kcal/mol@LB@@LB@Position - mRNA 211 -- 222@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 1 -- 7@LB@
102	0.003761	0.123	b0928	aspC	-10.71	0.122473	105 -- 118	20 -- 33	aspartate aminotransferase PLP-dependent		_____________104____________119\n_____________\|______________\|\n5'-CGU...CAAAA_____CU_______CAUCA...UUG-3'\n______________ACAGC__GCGUUUU\n______________\|\|\|\|\|__\|\|:\|\|\|\|\n______________UGUCG__CGUAAAA\n3'-UUU...GACCA_____AU_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	112 -- 118	20 -- 26	-14.5276 kcal/mol	2.38321 kcal/mol	1.43447 kcal/mol	104 119@LB@ \| \|@LB@5'-CGU...CAAAA CU CAUCA...UUG-3'@LB@ ACAGC GCGUUUU@LB@ \|\|\|\|\| \|\|:\|\|\|\|@LB@ UGUCG CGUAAAA@LB@3'-UUU...GACCA AU UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -14.5276 kcal/mol@LB@Unfolding Energy - mRNA 2.38321 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 105 -- 118@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 20 -- 26@LB@
103	0.00377	0.123	b2922	yggE	-10.91	0.111523	45 -- 69	24 -- 45	oxidative stress defense protein		_____________44________________________70\n_____________\|_________________________\|\n5'-GCA...GUUAU_______AU__CCU___________AGAGA...CCG-3'\n______________GUGGUUU__UG___UGCAGCUGGCG\n______________\|\|\|\|\|\|:__\|\|___\|:\|\|\|\|\|:\|\|:\n______________CACCAAG__AC___AUGUCGAUCGU\n3'-UUU...UCCUC_______G___C_____________AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________46________________________23\n	63 -- 69	24 -- 30	-26.0515 kcal/mol	10.579 kcal/mol	4.55794 kcal/mol	44 70@LB@ \| \|@LB@5'-GCA...GUUAU AU CCU AGAGA...CCG-3'@LB@ GUGGUUU UG UGCAGCUGGCG@LB@ \|\|\|\|\|\|: \|\| \|:\|\|\|\|\|:\|\|:@LB@ CACCAAG AC AUGUCGAUCGU@LB@3'-UUU...UCCUC G C AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -26.0515 kcal/mol@LB@Unfolding Energy - mRNA 10.579 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 45 -- 69@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 24 -- 30@LB@
104	0.003825	0.1236	b0081	mraZ	-12.90	0.040525	169 -- 210	15 -- 49	RsmH methytransferase inhibitor		_____________168________________________________________211\n_____________\|__________________________________________\|\n5'-GAU...AUUGU____CAAA____GAAUAAGG____A_________GUUCC___GAGCA...AAA-3'\n______________GGGG____GUGG________GGUG_GGCUGGCAU_____GGG\n______________\|\|:\|____\|\|\|\|________\|\|\|:_:\|\|\|:\|\|\|\|_____\|\|\|\n______________CCUC____CACC________CCAU_UCGAUCGUA_____CCC\n3'-UUU...CGAUU____________AAGGA_______G_________AAAUA___AAUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________50_________________________________________14\n	196 -- 202	23 -- 29	-32.8076 kcal/mol	15.3299 kcal/mol	4.57366 kcal/mol	168 211@LB@ \| \|@LB@5'-GAU...AUUGU CAAA GAAUAAGG A GUUCC GAGCA...AAA-3'@LB@ GGGG GUGG GGUG GGCUGGCAU GGG@LB@ \|\|:\| \|\|\|\| \|\|\|: :\|\|\|:\|\|\|\| \|\|\|@LB@ CCUC CACC CCAU UCGAUCGUA CCC@LB@3'-UUU...CGAUU AAGGA G AAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -32.8076 kcal/mol@LB@Unfolding Energy - mRNA 15.3299 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 23 -- 29@LB@
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
106	0.003955	0.1254	b1767	ansA	-7.74	0.383564	250 -- 272	11 -- 34	cytoplasmic L-asparaginase 1		_____________249______________________273\n_____________\|________________________\|\n5'-UGC...CGGGA______GUUCCGAGCA________AUACC...GCC-3'\n______________UGCAGC___________GGGUUAU\n______________\|:\|\|\|\|___________\|\|\|\|\|\|\|\n______________AUGUCG___________CCCAAUA\n3'-UUU...GGACC______AUCGUAAAAUA_______CAAAA...UCG-5'\n_____________\|________________________\|\n_____________35_______________________10\n	266 -- 272	11 -- 17	-16.5796 kcal/mol	7.36686 kcal/mol	1.47152 kcal/mol	249 273@LB@ \| \|@LB@5'-UGC...CGGGA GUUCCGAGCA AUACC...GCC-3'@LB@ UGCAGC GGGUUAU@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|@LB@ AUGUCG CCCAAUA@LB@3'-UUU...GGACC AUCGUAAAAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 35 10@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -16.5796 kcal/mol@LB@Unfolding Energy - mRNA 7.36686 kcal/mol@LB@Unfolding Energy - sRNA 1.47152 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 11 -- 34@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 11 -- 17@LB@
107	0.004137	0.1296	b2164	psuT	-12.74	0.044381	225 -- 254	21 -- 50	putative nucleoside transporter	b2161	_____________224_______________________________255\n_____________\|_________________________________\|\n5'-CUG...UUGUG____U______GUUA________A_________CUGUU...GAG-3'\n______________GGGA_GGUGGU____CUGG__CA__UAGCAUUU\n______________:\|\|\|_\|\|\|\|\|\|____\|\|\|\|__\|\|__\|\|\|\|\|\|\|\|\n______________UCCU_CCACCA____GACC__GU__AUCGUAAA\n3'-UUU...CCGAU___________AG______AU__CG________AUACC...UCG-5'\n_____________\|_________________________________\|\n_____________51________________________________20\n	248 -- 254	21 -- 27	-28.746 kcal/mol	11.392 kcal/mol	4.61445 kcal/mol	224 255@LB@ \| \|@LB@5'-CUG...UUGUG U GUUA A CUGUU...GAG-3'@LB@ GGGA GGUGGU CUGG CA UAGCAUUU@LB@ :\|\|\| \|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UCCU CCACCA GACC GU AUCGUAAA@LB@3'-UUU...CCGAU AG AU CG AUACC...UCG-5'@LB@ \| \|@LB@ 51 20@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.746 kcal/mol@LB@Unfolding Energy - mRNA 11.392 kcal/mol@LB@Unfolding Energy - sRNA 4.61445 kcal/mol@LB@@LB@Position - mRNA 225 -- 254@LB@Position - sRNA 21 -- 50@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 21 -- 27@LB@
108	0.004185	0.1296	b2158	yeiH	-13.47	0.029300	232 -- 260	12 -- 35	UPF0324 family inner membrane protein		_____________231___________________________261\n_____________\|_____________________________\|\n5'-CAC...ACAUC_____CUG___________UCCG______GCCCU...GUG-3'\n______________GUACA___UGGCAUUUUAU____GGGUUA\n______________\|\|\|\|\|___\|:\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\|\n______________CAUGU___AUCGUAAAAUA____CCCAAU\n3'-UUU...AGGAC_____CG______________________ACAAA...UCG-5'\n_____________\|_____________________________\|\n_____________36____________________________11\n	244 -- 250	18 -- 24	-22.9966 kcal/mol	8.07046 kcal/mol	1.45491 kcal/mol	231 261@LB@ \| \|@LB@5'-CAC...ACAUC CUG UCCG GCCCU...GUG-3'@LB@ GUACA UGGCAUUUUAU GGGUUA@LB@ \|\|\|\|\| \|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CAUGU AUCGUAAAAUA CCCAAU@LB@3'-UUU...AGGAC CG ACAAA...UCG-5'@LB@ \| \|@LB@ 36 11@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -22.9966 kcal/mol@LB@Unfolding Energy - mRNA 8.07046 kcal/mol@LB@Unfolding Energy - sRNA 1.45491 kcal/mol@LB@@LB@Position - mRNA 232 -- 260@LB@Position - sRNA 12 -- 35@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 18 -- 24@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB		_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
110	0.004262	0.1302	b1871	cmoB	-11.44	0.086999	165 -- 182	22 -- 44	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent		_____________164______________________183\n_____________\|________________________\|\n5'-CAC...AACUU______A_________________AAAAG...AGC-3'\n______________UGGUUC_CUGG______UGGCAUU\n______________\|\|\|\|\|\|_\|\|\|\|______\|:\|\|\|\|\|\n______________ACCAAG_GACC______AUCGUAA\n3'-UUU...CCUCC___________AUGUCG_______AAUAC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________21\n	176 -- 182	22 -- 28	-20.1895 kcal/mol	4.19283 kcal/mol	4.55859 kcal/mol	164 183@LB@ \| \|@LB@5'-CAC...AACUU A AAAAG...AGC-3'@LB@ UGGUUC CUGG UGGCAUU@LB@ \|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ ACCAAG GACC AUCGUAA@LB@3'-UUU...CCUCC AUGUCG AAUAC...UCG-5'@LB@ \| \|@LB@ 45 21@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.1895 kcal/mol@LB@Unfolding Energy - mRNA 4.19283 kcal/mol@LB@Unfolding Energy - sRNA 4.55859 kcal/mol@LB@@LB@Position - mRNA 165 -- 182@LB@Position - sRNA 22 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 22 -- 28@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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