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
129	0.005449	0.142	b2502	ppx	-11.35	0.090652	145 -- 164	17 -- 36	exopolyphosphatase		_____________144__________________165\n_____________\|____________________\|\n5'-GGC...GUACG__C__________A______ACUAC...GUG-3'\n______________GG_GCAGUUGGCG_UUUAUG\n______________\|\|_:\|\|\|:\|:\|\|:_\|\|\|\|\|\|\n______________CC_UGUCGAUCGU_AAAUAC\n3'-UUU...AAGGA__A__________A______CCAAU...UCG-5'\n_____________\|____________________\|\n_____________37___________________16\n	151 -- 157	24 -- 30	-21.6291 kcal/mol	8.82633 kcal/mol	1.44969 kcal/mol	144 165@LB@ \| \|@LB@5'-GGC...GUACG C A ACUAC...GUG-3'@LB@ GG GCAGUUGGCG UUUAUG@LB@ \|\| :\|\|\|:\|:\|\|: \|\|\|\|\|\|@LB@ CC UGUCGAUCGU AAAUAC@LB@3'-UUU...AAGGA A A CCAAU...UCG-5'@LB@ \| \|@LB@ 37 16@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -21.6291 kcal/mol@LB@Unfolding Energy - mRNA 8.82633 kcal/mol@LB@Unfolding Energy - sRNA 1.44969 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 17 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 24 -- 30@LB@
72	0.001945	0.09081	b3024	ygiW	-9.51	0.204072	108 -- 126	18 -- 35	hydrogen peroxide and cadmium resistance periplasmic protein; stress-induced OB-fold protein		_____________107_________________127\n_____________\|___________________\|\n5'-UGA...GCUCU_______ACUAA_______UUUUU...AAA-3'\n______________GUACAGC_____AUUUUAU\n______________\|\|\|\|\|\|\|_____\|\|\|\|\|\|\|\n______________CAUGUCG_____UAAAAUA\n3'-UUU...AGGAC_______AUCG________CCCAA...UCG-5'\n_____________\|___________________\|\n_____________36__________________17\n	120 -- 126	18 -- 24	-13.5355 kcal/mol	2.57979 kcal/mol	1.44471 kcal/mol	107 127@LB@ \| \|@LB@5'-UGA...GCUCU ACUAA UUUUU...AAA-3'@LB@ GUACAGC AUUUUAU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CAUGUCG UAAAAUA@LB@3'-UUU...AGGAC AUCG CCCAA...UCG-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -9.51 kcal/mol@LB@Hybridization Energy -13.5355 kcal/mol@LB@Unfolding Energy - mRNA 2.57979 kcal/mol@LB@Unfolding Energy - sRNA 1.44471 kcal/mol@LB@@LB@Position - mRNA 108 -- 126@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 18 -- 24@LB@
79	0.002261	0.09621	b2556	glrK	-15.72	0.006745	240 -- 258	20 -- 38	sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR		_____________239_________________259\n_____________\|___________________\|\n5'-CUA...GACAA______AU___________UGCUG...CCU-3'\n______________CUGGUA__GCUGGCAUUUU\n______________\|\|\|\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACCAU__CGAUCGUAAAA\n3'-UUU...CCAAG______GU___________UACCC...UCG-5'\n_____________\|___________________\|\n_____________39__________________19\n	252 -- 258	20 -- 26	-25.6316 kcal/mol	5.4283 kcal/mol	4.48821 kcal/mol	239 259@LB@ \| \|@LB@5'-CUA...GACAA AU UGCUG...CCU-3'@LB@ CUGGUA GCUGGCAUUUU@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACCAU CGAUCGUAAAA@LB@3'-UUU...CCAAG GU UACCC...UCG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -25.6316 kcal/mol@LB@Unfolding Energy - mRNA 5.4283 kcal/mol@LB@Unfolding Energy - sRNA 4.48821 kcal/mol@LB@@LB@Position - mRNA 240 -- 258@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 20 -- 26@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@
179	0.01003	0.1882	b0619	citA	-9.15	0.235039	224 -- 237	20 -- 33	sensory histidine kinase in two-component regulatory system with CitB		_____________223____________238\n_____________\|______________\|\n5'-CAU...AAUAA______U_______UCCAA...UCA-3'\n______________ACAGUU_GCAUUUU\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\n______________UGUCGA_CGUAAAA\n3'-UUU...GACCA______U_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	231 -- 237	20 -- 26	-13.7934 kcal/mol	3.21006 kcal/mol	1.43447 kcal/mol	223 238@LB@ \| \|@LB@5'-CAU...AAUAA U UCCAA...UCA-3'@LB@ ACAGUU GCAUUUU@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|@LB@ UGUCGA CGUAAAA@LB@3'-UUU...GACCA U UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -13.7934 kcal/mol@LB@Unfolding Energy - mRNA 3.21006 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 224 -- 237@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 20 -- 26@LB@
81	0.002689	0.1082	b1498	ydeN	-15.88	0.005981	253 -- 275	21 -- 44	putative Ser-type periplasmic non-aryl sulfatase	b3678 b3801	_____________252______________________276\n_____________\|________________________\|\n5'-AUU...GAUAC___CA___________________GCUGC...UAA-3'\n______________UGG__UCUGGUAUGGCU_GCAUUU\n______________\|\|\|__:\|\|\|\|\|\|::\|\|\|_\|\|\|\|\|\|\n______________ACC__GGACCAUGUCGA_CGUAAA\n3'-UUU...CCUCC___AA____________U______AUACC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________20\n	263 -- 269	28 -- 34	-26.8614 kcal/mol	6.42389 kcal/mol	4.55918 kcal/mol	252 276@LB@ \| \|@LB@5'-AUU...GAUAC CA GCUGC...UAA-3'@LB@ UGG UCUGGUAUGGCU GCAUUU@LB@ \|\|\| :\|\|\|\|\|\|::\|\|\| \|\|\|\|\|\|@LB@ ACC GGACCAUGUCGA CGUAAA@LB@3'-UUU...CCUCC AA U AUACC...UCG-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -15.88 kcal/mol@LB@Hybridization Energy -26.8614 kcal/mol@LB@Unfolding Energy - mRNA 6.42389 kcal/mol@LB@Unfolding Energy - sRNA 4.55918 kcal/mol@LB@@LB@Position - mRNA 253 -- 275@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@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@
120	0.005024	0.1407	b2564	pdxJ	-10.23	0.151404	275 -- 296	21 -- 43	pyridoxine 5'-phosphate synthase		_____________274_____________________297\n_____________\|_______________________\|\n5'-AAA...UACCC__A___________GCC______AUUG-3'\n______________GG_UCC_GGUGCAG___GCGUUU\n______________\|\|_\|\|\|_\|\|\|:\|\|\|___\|\|:\|\|\|\n______________CC_AGG_CCAUGUC___CGUAAA\n3'-UUU...CUCCA__A___A_______GAU______AUACC...UCG-5'\n_____________\|_______________________\|\n_____________44______________________20\n	281 -- 287	30 -- 36	-24.4803 kcal/mol	9.69131 kcal/mol	4.55861 kcal/mol	274 297@LB@ \| \|@LB@5'-AAA...UACCC A GCC AUUG-3'@LB@ GG UCC GGUGCAG GCGUUU@LB@ \|\| \|\|\| \|\|\|:\|\|\| \|\|:\|\|\|@LB@ CC AGG CCAUGUC CGUAAA@LB@3'-UUU...CUCCA A A GAU AUACC...UCG-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -24.4803 kcal/mol@LB@Unfolding Energy - mRNA 9.69131 kcal/mol@LB@Unfolding Energy - sRNA 4.55861 kcal/mol@LB@@LB@Position - mRNA 275 -- 296@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 30 -- 36@LB@
23	0.0002818	0.04118	b1813	nudL	-13.86	0.023273	1 -- 17	22 -- 39	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		______________1_________________18\n______________\|_________________\|\n___________5'-__________________GGCUA...CUG-3'\n______________CCUGGUGCGGC_AGCAUU\n______________\|\|\|\|\|\|:\|:\|\|_\|\|\|\|\|\|\n______________GGACCAUGUCG_UCGUAA\n3'-UUU...ACCAA___________A______AAUAC...UCG-5'\n_____________\|__________________\|\n_____________40_________________21\n	5 -- 11	29 -- 35	-27.845 kcal/mol	9.43444 kcal/mol	4.55392 kcal/mol	1 18@LB@ \| \|@LB@ 5'- GGCUA...CUG-3'@LB@ CCUGGUGCGGC AGCAUU@LB@ \|\|\|\|\|\|:\|:\|\| \|\|\|\|\|\|@LB@ GGACCAUGUCG UCGUAA@LB@3'-UUU...ACCAA A AAUAC...UCG-5'@LB@ \| \|@LB@ 40 21@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -27.845 kcal/mol@LB@Unfolding Energy - mRNA 9.43444 kcal/mol@LB@Unfolding Energy - sRNA 4.55392 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 22 -- 39@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase		_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@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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