Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
188	0.01388	0.2529	b4198	ulaF	-10.93	0.193396	24 -- 37	2 -- 17	L-ribulose 5-phosphate 4-epimerase		_____________23_______________38\n_____________\|________________\|\n5'-GUC...UUUGG______U_________AUUUC...GCG-3'\n______________CGAAGG___GUAGUGG\n______________\|:\|\|\|:___\|:\|\|\|\|\|\n______________GUUUCU___CGUCACC\n3'-UUU...CUGUA______UUU_______G-5'\n_____________\|________________\|\n_____________18_______________1\n	31 -- 37	2 -- 8	-15.3961 kcal/mol	3.02615 kcal/mol	1.43836 kcal/mol	23 38@LB@ \| \|@LB@5'-GUC...UUUGG U AUUUC...GCG-3'@LB@ CGAAGG GUAGUGG@LB@ \|:\|\|\|: \|:\|\|\|\|\|@LB@ GUUUCU CGUCACC@LB@3'-UUU...CUGUA UUU G-5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -15.3961 kcal/mol@LB@Unfolding Energy - mRNA 3.02615 kcal/mol@LB@Unfolding Energy - sRNA 1.43836 kcal/mol@LB@@LB@Position - mRNA 24 -- 37@LB@Position - sRNA 2 -- 17@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 2 -- 8@LB@
31	0.001481	0.1635	b3468	yhhN	-14.35	0.039524	32 -- 52	1 -- 21	TMEM86 family putative inner membrane protein		_____________31____________________53\n_____________\|_____________________\|\n5'-CGA...UGAUA___A__________A______UUGCU...UAA-3'\n______________ACA_UAAAGAAAAG_GGUGGU\n______________\|\|\|_:\|\|\|\|\|\|\|\|\|_:\|\|\|\|:\n______________UGU_GUUUCUUUUC_UCACCG\n3'-UUU...ACCCC___A__________G______-5'\n_____________\|____________________\|\n_____________22___________________1\n	39 -- 45	8 -- 14	-21.1877 kcal/mol	5.32481 kcal/mol	1.51103 kcal/mol	31 53@LB@ \| \|@LB@5'-CGA...UGAUA A A UUGCU...UAA-3'@LB@ ACA UAAAGAAAAG GGUGGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| :\|\|\|\|:@LB@ UGU GUUUCUUUUC UCACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -21.1877 kcal/mol@LB@Unfolding Energy - mRNA 5.32481 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 32 -- 52@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 8 -- 14@LB@
161	0.01187	0.2504	b0093	ftsQ	-14.15	0.043981	32 -- 43	18 -- 29	divisome assembly protein membrane anchored protein involved in growth of wall at septum		_____________31___________44\n_____________\|____________\|\n5'-GCU...GCAAA____________AUUGA...CCG-3'\n______________GGAUGGGGACGU\n______________::\|\|\|\|\|\|\|\|:\|\n______________UUUACCCCUGUA\n3'-UUU...GGUGU____________GUUUC...CCG-5'\n_____________\|____________\|\n_____________30___________17\n	37 -- 43	18 -- 24	-18.9266 kcal/mol	4.11166 kcal/mol	0.665542 kcal/mol	31 44@LB@ \| \|@LB@5'-GCU...GCAAA AUUGA...CCG-3'@LB@ GGAUGGGGACGU@LB@ ::\|\|\|\|\|\|\|\|:\|@LB@ UUUACCCCUGUA@LB@3'-UUU...GGUGU GUUUC...CCG-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -18.9266 kcal/mol@LB@Unfolding Energy - mRNA 4.11166 kcal/mol@LB@Unfolding Energy - sRNA 0.665542 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 18 -- 24@LB@
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
46	0.002205	0.1648	b1662	ribC	-17.71	0.005126	34 -- 61	2 -- 29	riboflavin synthase alpha subunit		_____________33_____________________________62\n_____________\|______________________________\|\n5'-UUU...CGCCU_______CA___A_____A___________GAAAU...UGG-3'\n______________GAAUGGG__GCA__AAAG_AGAAGCAG_GG\n______________:\|\|\|\|\|\|__:\|\|__\|\|\|\|_\|:\|\|\|\|\|\|_\|\|\n______________UUUACCC__UGU__UUUC_UUUUCGUC_CC\n3'-UUU...GGUGU_______C____AG_____________A__G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	53 -- 59	5 -- 11	-25.8778 kcal/mol	5.65259 kcal/mol	2.51906 kcal/mol	33 62@LB@ \| \|@LB@5'-UUU...CGCCU CA A A GAAAU...UGG-3'@LB@ GAAUGGG GCA AAAG AGAAGCAG GG@LB@ :\|\|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|\| \|\|@LB@ UUUACCC UGU UUUC UUUUCGUC CC@LB@3'-UUU...GGUGU C AG A G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -25.8778 kcal/mol@LB@Unfolding Energy - mRNA 5.65259 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 34 -- 61@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@LB@
100	0.006296	0.2188	b1321	ycjX	-13.69	0.055797	38 -- 45	18 -- 25	DUF463 family protein puatative P-loop NTPase		_____________37_______46\n_____________\|________\|\n5'-UGA...UAGUA________AGGUC...CAG-3'\n______________GGGGACAU\n______________\|\|\|\|\|\|\|\|\n______________CCCCUGUA\n3'-UUU...UUUUA________GUUUC...CCG-5'\n_____________\|________\|\n_____________26_______17\n	39 -- 45	18 -- 24	-15.5505 kcal/mol	1.21152 kcal/mol	0.65218 kcal/mol	37 46@LB@ \| \|@LB@5'-UGA...UAGUA AGGUC...CAG-3'@LB@ GGGGACAU@LB@ \|\|\|\|\|\|\|\|@LB@ CCCCUGUA@LB@3'-UUU...UUUUA GUUUC...CCG-5'@LB@ \| \|@LB@ 26 17@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -15.5505 kcal/mol@LB@Unfolding Energy - mRNA 1.21152 kcal/mol@LB@Unfolding Energy - sRNA 0.65218 kcal/mol@LB@@LB@Position - mRNA 38 -- 45@LB@Position - sRNA 18 -- 25@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 18 -- 24@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)		_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor		_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@LB@
145	0.01066	0.2504	b2153	folE	-11.37	0.162147	44 -- 68	1 -- 21	GTP cyclohydrolase I		_____________43________________________69\n_____________\|_________________________\|\n5'-CUG...UUUUA_____UGCU__U_________C___AAUUA...ACG-3'\n______________ACAUC____GA_GAAAGGCAG_GGC\n______________\|\|\|\|\|____:\|_\|\|\|\|:\|\|\|\|_\|\|\|\n______________UGUAG____UU_CUUUUCGUC_CCG\n3'-UUU...ACCCC___________U_________A___-5'\n_____________\|________________________\|\n_____________22_______________________1\n	58 -- 64	5 -- 11	-23.5216 kcal/mol	10.6442 kcal/mol	1.51103 kcal/mol	43 69@LB@ \| \|@LB@5'-CUG...UUUUA UGCU U C AAUUA...ACG-3'@LB@ ACAUC GA GAAAGGCAG GGC@LB@ \|\|\|\|\| :\| \|\|\|\|:\|\|\|\| \|\|\|@LB@ UGUAG UU CUUUUCGUC CCG@LB@3'-UUU...ACCCC U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -23.5216 kcal/mol@LB@Unfolding Energy - mRNA 10.6442 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 44 -- 68@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@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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