Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter		_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
68	0.01422	0.6177	b3826	yigL	-7.04	0.159921	44 -- 50	49 -- 55	pyridoxal phosphate phosphatase		_____________43______51\n_____________\|_______\|\n5'-GCA...AUCCU_______GAGGA...CGC-3'\n______________GUCGAAG\n______________\|\|\|:\|\|\|\n______________CAGUUUC\n3'-UUU...CCGGG_______UCCUU...ACA-5'\n_____________\|_______\|\n_____________56______48\n	44 -- 50	49 -- 55	-7.68974 kcal/mol	0.331193 kcal/mol	0.314364 kcal/mol	43 51@LB@ \| \|@LB@5'-GCA...AUCCU GAGGA...CGC-3'@LB@ GUCGAAG@LB@ \|\|\|:\|\|\|@LB@ CAGUUUC@LB@3'-UUU...CCGGG UCCUU...ACA-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -7.68974 kcal/mol@LB@Unfolding Energy - mRNA 0.331193 kcal/mol@LB@Unfolding Energy - sRNA 0.314364 kcal/mol@LB@@LB@Position - mRNA 44 -- 50@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 49 -- 55@LB@
135	0.02628	0.6177	b3547	yhjX	-9.70	0.047334	158 -- 184	28 -- 55	pyruvate-inducible inner membrane protein putative transporter		_____________157___________________________185\n_____________\|_____________________________\|\n5'-UAA...UGGUU_____C____AUU____C___________CUGCA...UUA-3'\n______________GUCGG_AGAG___UUUC___UUUUUAUUA\n______________\|\|\|::_\|\|\|\|___\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________CAGUU_UCUC___AAAG___AAAAAUAAU\n3'-UUU...CCGGG__________CUU____UAA_________AAUAC...ACA-5'\n_____________\|_____________________________\|\n_____________56____________________________27\n	178 -- 184	28 -- 34	-15.2509 kcal/mol	4.36169 kcal/mol	1.18814 kcal/mol	157 185@LB@ \| \|@LB@5'-UAA...UGGUU C AUU C CUGCA...UUA-3'@LB@ GUCGG AGAG UUUC UUUUUAUUA@LB@ \|\|\|:: \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CAGUU UCUC AAAG AAAAAUAAU@LB@3'-UUU...CCGGG CUU UAA AAUAC...ACA-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -15.2509 kcal/mol@LB@Unfolding Energy - mRNA 4.36169 kcal/mol@LB@Unfolding Energy - sRNA 1.18814 kcal/mol@LB@@LB@Position - mRNA 158 -- 184@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 28 -- 34@LB@
160	0.0322	0.6177	b1550	gnsB	-8.75	0.073686	189 -- 197	44 -- 52	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)	b4517	_____________188_______198\n_____________\|_________\|\n5'-UGG...GACUA_________AUGAU...UUA-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.5466 kcal/mol	1.93458 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-UGG...GACUA AUGAU...UUA-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.5466 kcal/mol@LB@Unfolding Energy - mRNA 1.93458 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
50	0.009706	0.6129	b0109	nadC	-3.48	0.624399	8 -- 15	22 -- 29	quinolinate phosphoribosyltransferase		_____________7________16\n_____________\|________\|\n____5'-AGGCUAA________ACCAC...AAG-3'\n______________UAUUGUGC\n______________\|\|\|\|:\|\|\|\n______________AUAAUACG\n3'-UUU...AAAUA________GCAGU...ACA-5'\n_____________\|________\|\n_____________30_______21\n	9 -- 15	22 -- 28	-7.42611 kcal/mol	1.02369 kcal/mol	2.92038 kcal/mol	7 16@LB@ \| \|@LB@ 5'-AGGCUAA ACCAC...AAG-3'@LB@ UAUUGUGC@LB@ \|\|\|\|:\|\|\|@LB@ AUAAUACG@LB@3'-UUU...AAAUA GCAGU...ACA-5'@LB@ \| \|@LB@ 30 21@LB@@LB@@LB@Energy -3.48 kcal/mol@LB@Hybridization Energy -7.42611 kcal/mol@LB@Unfolding Energy - mRNA 1.02369 kcal/mol@LB@Unfolding Energy - sRNA 2.92038 kcal/mol@LB@@LB@Position - mRNA 8 -- 15@LB@Position - sRNA 22 -- 29@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@LB@
75	0.01577	0.6177	b1345	intR	-9.71	0.047033	139 -- 151	42 -- 53	Rac prophage; integrase		_____________138___________152\n_____________\|_____________\|\n5'-UAA...GACAG____C________AUCUG...GGG-3'\n______________CAAA_GAGGGAUU\n______________\|\|\|\|_\|\|\|\|:\|\|\|\n______________GUUU_CUCCUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	145 -- 151	42 -- 48	-12.4741 kcal/mol	1.8255 kcal/mol	0.933904 kcal/mol	138 152@LB@ \| \|@LB@5'-UAA...GACAG C AUCUG...GGG-3'@LB@ CAAA GAGGGAUU@LB@ \|\|\|\| \|\|\|\|:\|\|\|@LB@ GUUU CUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -12.4741 kcal/mol@LB@Unfolding Energy - mRNA 1.8255 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 139 -- 151@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 42 -- 48@LB@
56	0.01199	0.6177	b0836	bssR	-10.68	0.029916	18 -- 32	42 -- 55	repressor of biofilm formation by indole transport regulation		_____________17______________33\n_____________\|_______________\|\n5'-AUU...GAAAG_______C_______CUACA...ACA-3'\n______________GUCAGGG_AGGGAUU\n______________\|\|\|\|::\|_\|\|\|:\|\|\|\n______________CAGUUUC_UCCUUAA\n3'-UUU...CCGGG_______________AGUAA...ACA-5'\n_____________\|_______________\|\n_____________56______________41\n	26 -- 32	42 -- 48	-16.3055 kcal/mol	4.68166 kcal/mol	0.947316 kcal/mol	17 33@LB@ \| \|@LB@5'-AUU...GAAAG C CUACA...ACA-3'@LB@ GUCAGGG AGGGAUU@LB@ \|\|\|\|::\| \|\|\|:\|\|\|@LB@ CAGUUUC UCCUUAA@LB@3'-UUU...CCGGG AGUAA...ACA-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -16.3055 kcal/mol@LB@Unfolding Energy - mRNA 4.68166 kcal/mol@LB@Unfolding Energy - sRNA 0.947316 kcal/mol@LB@@LB@Position - mRNA 18 -- 32@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 42 -- 48@LB@
40	0.007925	0.6129	b1109	ndh	-7.04	0.160101	187 -- 195	46 -- 54	respiratory NADH dehydrogenase 2/cupric reductase		_____________186_______196\n_____________\|_________\|\n5'-UGU...UAAAU_________UCACG...AAG-3'\n______________UUAAGGGGG\n______________\|:\|\|:\|:\|\|\n______________AGUUUCUCC\n3'-UUU...CGGGC_________UUAAA...ACA-5'\n_____________\|_________\|\n_____________55________45\n	189 -- 195	46 -- 52	-9.48398 kcal/mol	1.51964 kcal/mol	0.922697 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UAAAU UCACG...AAG-3'@LB@ UUAAGGGGG@LB@ \|:\|\|:\|:\|\|@LB@ AGUUUCUCC@LB@3'-UUU...CGGGC UUAAA...ACA-5'@LB@ \| \|@LB@ 55 45@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.48398 kcal/mol@LB@Unfolding Energy - mRNA 1.51964 kcal/mol@LB@Unfolding Energy - sRNA 0.922697 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 46 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
60	0.01286	0.6177	b4113	basR	-8.68	0.076010	6 -- 31	48 -- 75	response regulator in two-component regulatory system with BasS		_____________5____________________________32\n_____________\|____________________________\|\n______5'-CAGGU_______C____________________AUUAU...CGC-3'\n______________GCCGAUG_UGCUG_UGG_CUGUCGGAGG\n______________\|\|\|:\|\|:_:\|\|\|:_\|\|\|_\|:\|\|\|::\|\|:\n______________CGGUUAU_GCGAU_ACC_GGCAGUUUCU\n3'-UUU...UUUAC_______A_____A___G__________CCUUA...ACA-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	25 -- 31	48 -- 54	-31.4034 kcal/mol	11.3837 kcal/mol	11.3355 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAGGU C AUUAU...CGC-3'@LB@ GCCGAUG UGCUG UGG CUGUCGGAGG@LB@ \|\|\|:\|\|: :\|\|\|: \|\|\| \|:\|\|\|::\|\|:@LB@ CGGUUAU GCGAU ACC GGCAGUUUCU@LB@3'-UUU...UUUAC A A G CCUUA...ACA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -8.68 kcal/mol@LB@Hybridization Energy -31.4034 kcal/mol@LB@Unfolding Energy - mRNA 11.3837 kcal/mol@LB@Unfolding Energy - sRNA 11.3355 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 48 -- 54@LB@
88	0.01799	0.6177	b0415	ribE	-8.66	0.076826	57 -- 64	47 -- 54	riboflavin synthase beta chain		_____________56_______65\n_____________\|________\|\n5'-CGG...UAAAU________AUACG...GUG-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	58 -- 64	47 -- 53	-10.4141 kcal/mol	0.855178 kcal/mol	0.897871 kcal/mol	56 65@LB@ \| \|@LB@5'-CGG...UAAAU AUACG...GUG-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -10.4141 kcal/mol@LB@Unfolding Energy - mRNA 0.855178 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 57 -- 64@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 47 -- 53@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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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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