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
51	0.00253	0.1729	b0699	ybfA	-18.06	0.004001	182 -- 204	2 -- 32	DUF2517 family protein	_____________181_____________________________205\n_____________\|_______________________________\|\n5'-AUG...UAGAU_______________________________AACUC...GGA-3'\n______________ACAAAA_GGGG______GAGAAAAGUA_UGG\n______________\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|:\|_\|\|\|\n______________UGUUUU_CCCC______UUCUUUUCGU_ACC\n3'-UUU...CGAGG______A____UGUAGU__________C___G-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	195 -- 201	6 -- 12	-23.7835 kcal/mol	3.18782 kcal/mol	2.53929 kcal/mol	181 205@LB@ \| \|@LB@5'-AUG...UAGAU AACUC...GGA-3'@LB@ ACAAAA GGGG GAGAAAAGUA UGG@LB@ \|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|:\| \|\|\|@LB@ UGUUUU CCCC UUCUUUUCGU ACC@LB@3'-UUU...CGAGG A UGUAGU C G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -23.7835 kcal/mol@LB@Unfolding Energy - mRNA 3.18782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 204@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
52	0.002562	0.1729	b0881	clpS	-16.21	0.013666	11 -- 25	5 -- 25	regulatory protein for ClpA substrate specificity	_____________10____________________26\n_____________\|_____________________\|\n5'-GCA...UGACA_____________________GUAUG...UCA-3'\n______________GGGGACA______AGGGGCAG\n______________\|\|\|\|\|\|\|______\|:::\|\|\|\|\n______________CCCCUGU______UUUUCGUC\n3'-UUU...UUUUA_______AGUUUC________ACCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	19 -- 25	5 -- 11	-21.27 kcal/mol	2.56205 kcal/mol	2.50017 kcal/mol	10 26@LB@ \| \|@LB@5'-GCA...UGACA GUAUG...UCA-3'@LB@ GGGGACA AGGGGCAG@LB@ \|\|\|\|\|\|\| \|:::\|\|\|\|@LB@ CCCCUGU UUUUCGUC@LB@3'-UUU...UUUUA AGUUUC ACCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -21.27 kcal/mol@LB@Unfolding Energy - mRNA 2.56205 kcal/mol@LB@Unfolding Energy - sRNA 2.50017 kcal/mol@LB@@LB@Position - mRNA 11 -- 25@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
53	0.002642	0.1735	b0055	djlA	-12.56	0.096184	186 -- 227	1 -- 31	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________185________________________________________228\n_____________\|__________________________________________\|\n5'-GAC...UGUGU___UU______AUAUAUGCAG____________AU__U____GUGGC...UUG-3'\n______________CGA__UGGGGA__________UAUUGGGGAAAA__CA_UGGC\n______________\|:\|__\|\|\|\|\|\|__________:\|\|::::\|\|\|\|\|__\|\|_\|\|\|\|\n______________GUU__ACCCCU__________GUAGUUUCUUUU__GU_ACCG\n3'-UUU...GAGGU___UU____________________________C___C____-5'\n_____________\|_________________________________________\|\n_____________32________________________________________1\n	212 -- 218	9 -- 15	-25.7115 kcal/mol	10.6128 kcal/mol	2.53929 kcal/mol	185 228@LB@ \| \|@LB@5'-GAC...UGUGU UU AUAUAUGCAG AU U GUGGC...UUG-3'@LB@ CGA UGGGGA UAUUGGGGAAAA CA UGGC@LB@ \|:\| \|\|\|\|\|\| :\|\|::::\|\|\|\|\| \|\| \|\|\|\|@LB@ GUU ACCCCU GUAGUUUCUUUU GU ACCG@LB@3'-UUU...GAGGU UU C C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -25.7115 kcal/mol@LB@Unfolding Energy - mRNA 10.6128 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 227@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 9 -- 15@LB@
54	0.00267	0.1735	b0131	panD	-12.96	0.079905	178 -- 195	5 -- 22	aspartate 1-decarboxylase	_____________177________________196\n_____________\|__________________\|\n5'-AUU...UUAAC____GGGU__________AAGUU...UUG-3'\n______________GACA____AGAAAGGUAG\n______________\|\|\|\|____\|\|\|\|\|:\|:\|\|\n______________CUGU____UCUUUUCGUC\n3'-UUU...UACCC____AGUU__________ACCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	189 -- 195	5 -- 11	-16.4376 kcal/mol	1.9462 kcal/mol	1.53637 kcal/mol	177 196@LB@ \| \|@LB@5'-AUU...UUAAC GGGU AAGUU...UUG-3'@LB@ GACA AGAAAGGUAG@LB@ \|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CUGU UCUUUUCGUC@LB@3'-UUU...UACCC AGUU ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -16.4376 kcal/mol@LB@Unfolding Energy - mRNA 1.9462 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 5 -- 11@LB@
55	0.002823	0.1778	b3319	rplD	-12.54	0.096993	18 -- 45	1 -- 32	50S ribosomal subunit protein L4	_____________17________________________________46\n_____________\|_________________________________\|\n5'-UCA...UCCGG________U____________C___AAAA____AGGUC...UUG-3'\n______________GCAAAGUG______UCAAAGG_AAG____UGGC\n______________:\|\|\|\|:\|\|______\|\|\|\|\|\|:_\|\|\|____\|\|\|\|\n______________UGUUUUAC______AGUUUCU_UUC____ACCG\n3'-UUU...CGAGG________CCCUGU_______U___GUC_____-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	27 -- 33	12 -- 18	-19.13 kcal/mol	4.04955 kcal/mol	2.53929 kcal/mol	17 46@LB@ \| \|@LB@5'-UCA...UCCGG U C AAAA AGGUC...UUG-3'@LB@ GCAAAGUG UCAAAGG AAG UGGC@LB@ :\|\|\|\|:\|\| \|\|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UGUUUUAC AGUUUCU UUC ACCG@LB@3'-UUU...CGAGG CCCUGU U GUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -19.13 kcal/mol@LB@Unfolding Energy - mRNA 4.04955 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 12 -- 18@LB@
56	0.002838	0.1778	b3371	frlB	-17.11	0.007704	196 -- 228	2 -- 32	fructoselysine-6-P-deglycase	_____________195________________________________229\n_____________\|__________________________________\|\n5'-ACU...AGAAA________UU_________U________CC____ACUUU...ACG-3'\n______________AUAAAAUG__GGAUAUUGA__AAAAGCA__GUGG\n______________\|:\|\|\|\|\|\|__\|\|\|:\|\|::\|__\|\|\|\|\|\|\|__\|\|\|\|\n______________UGUUUUAC__CCUGUAGUU__UUUUCGU__CACC\n3'-UUU...CGAGG________C__________UC_____________G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	216 -- 222	6 -- 12	-25.2618 kcal/mol	5.61622 kcal/mol	2.53929 kcal/mol	195 229@LB@ \| \|@LB@5'-ACU...AGAAA UU U CC ACUUU...ACG-3'@LB@ AUAAAAUG GGAUAUUGA AAAAGCA GUGG@LB@ \|:\|\|\|\|\|\| \|\|\|:\|\|::\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UGUUUUAC CCUGUAGUU UUUUCGU CACC@LB@3'-UUU...CGAGG C UC G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -17.11 kcal/mol@LB@Hybridization Energy -25.2618 kcal/mol@LB@Unfolding Energy - mRNA 5.61622 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 196 -- 228@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
57	0.003017	0.1789	b2950	yggR	-13.19	0.071427	205 -- 223	1 -- 21	putative PilT family AAA+ ATPase	_____________204___________________224\n_____________\|_____________________\|\n5'-UUC...UAUGA____G_______UU_______CCUUA...GAA-3'\n______________AUAU_GAAGAAA____GUGGC\n______________\|:\|\|_:\|\|\|\|\|\|____\|\|\|\|\|\n______________UGUA_UUUCUUU____CACCG\n3'-UUU...ACCCC____G_______UCGU_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	210 -- 216	10 -- 16	-17.7325 kcal/mol	3.03326 kcal/mol	1.51103 kcal/mol	204 224@LB@ \| \|@LB@5'-UUC...UAUGA G UU CCUUA...GAA-3'@LB@ AUAU GAAGAAA GUGGC@LB@ \|:\|\| :\|\|\|\|\|\| \|\|\|\|\|@LB@ UGUA UUUCUUU CACCG@LB@3'-UUU...ACCCC G UCGU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -17.7325 kcal/mol@LB@Unfolding Energy - mRNA 3.03326 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 205 -- 223@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 10 -- 16@LB@
58	0.00302	0.1789	b0556	rzpD	-16.79	0.009474	64 -- 103	3 -- 36	DLP12 prophage; putative murein endopeptidase	_____________63_________________________________________104\n_____________\|__________________________________________\|\n5'-CGC...CGCUU___________AAACCA___C___________C_____U___AUCAG...ACA-3'\n______________CUUCGCAAAAU______GGG_GAUAUCAAAGG___GCA_GUG\n______________\|\|:\|:\|\|\|\|\|\|______\|\|\|_\|\|:\|\|\|\|\|\|\|:___\|\|\|_\|\|\|\n______________GAGGUGUUUUA______CCC_CUGUAGUUUCU___CGU_CAC\n3'-UUU...UACCC________________________________UUU_______CG-5'\n_____________\|__________________________________________\|\n_____________37_________________________________________2\n	89 -- 95	12 -- 18	-34.1904 kcal/mol	10.724 kcal/mol	6.67685 kcal/mol	63 104@LB@ \| \|@LB@5'-CGC...CGCUU AAACCA C C U AUCAG...ACA-3'@LB@ CUUCGCAAAAU GGG GAUAUCAAAGG GCA GUG@LB@ \|\|:\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\|\|\|\|\|: \|\|\| \|\|\|@LB@ GAGGUGUUUUA CCC CUGUAGUUUCU CGU CAC@LB@3'-UUU...UACCC UUU CG-5'@LB@ \| \|@LB@ 37 2@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -34.1904 kcal/mol@LB@Unfolding Energy - mRNA 10.724 kcal/mol@LB@Unfolding Energy - sRNA 6.67685 kcal/mol@LB@@LB@Position - mRNA 64 -- 103@LB@Position - sRNA 3 -- 36@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 12 -- 18@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter	_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@LB@
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2	_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@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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