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
86	0.005461	0.2147	b0002	thrA	-11.41	0.159352	219 -- 235	1 -- 25	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________218_________________________236\n_____________\|___________________________\|\n5'-CCA...AGUUC__C__U_____________________AAAUG...UGG-3'\n______________GG_GG_ACAU__________CAGUGGC\n______________\|\|_\|\|_\|\|\|\|__________\|\|\|\|\|\|\|\n______________CC_CC_UGUA__________GUCACCG\n3'-UUU...UUUUA__________GUUUCUUUUC_______-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	229 -- 235	1 -- 7	-18.4664 kcal/mol	4.54068 kcal/mol	2.51748 kcal/mol	218 236@LB@ \| \|@LB@5'-CCA...AGUUC C U AAAUG...UGG-3'@LB@ GG GG ACAU CAGUGGC@LB@ \|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CC CC UGUA GUCACCG@LB@3'-UUU...UUUUA GUUUCUUUUC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -18.4664 kcal/mol@LB@Unfolding Energy - mRNA 4.54068 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
116	0.007938	0.2401	b0008	talB	-12.38	0.104625	254 -- 276	7 -- 26	transaldolase B	_____________253_____________________277\n_____________\|_______________________\|\n5'-AGG...GACAC___________C__CAAU_____UGUAU...CAA-3'\n______________UGGGGACAUCG_GG____GAAGC\n______________\|\|\|\|\|\|\|\|\|\|:_:\|____:\|\|\|\|\n______________ACCCCUGUAGU_UC____UUUCG\n3'-UUU...GUUUU___________U__U________UCACCG-5'\n_____________\|_______________________\|\n_____________27______________________6\n	258 -- 264	16 -- 22	-23.5048 kcal/mol	10.4229 kcal/mol	0.706388 kcal/mol	253 277@LB@ \| \|@LB@5'-AGG...GACAC C CAAU UGUAU...CAA-3'@LB@ UGGGGACAUCG GG GAAGC@LB@ \|\|\|\|\|\|\|\|\|\|: :\| :\|\|\|\|@LB@ ACCCCUGUAGU UC UUUCG@LB@3'-UUU...GUUUU U U UCACCG-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -23.5048 kcal/mol@LB@Unfolding Energy - mRNA 10.4229 kcal/mol@LB@Unfolding Energy - sRNA 0.706388 kcal/mol@LB@@LB@Position - mRNA 254 -- 276@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@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@
160	0.0118	0.2504	b0078	ilvH	-13.58	0.059018	151 -- 175	1 -- 25	acetolactate synthase 3 small subunit valine-sensitive	_____________150_______________________176\n_____________\|_________________________\|\n5'-GCC...UUCGC_______GAAU___UGAAAU_____UAAGC...UGA-3'\n______________GGGGGCG____GGA______GUGGU\n______________\|\|\|\|:\|:____:\|\|______\|\|\|\|:\n______________CCCCUGU____UCU______CACCG\n3'-UUU...UUUUA_______AGUU___UUUCGU_____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	151 -- 157	19 -- 25	-21.9405 kcal/mol	5.84786 kcal/mol	2.51748 kcal/mol	150 176@LB@ \| \|@LB@5'-GCC...UUCGC GAAU UGAAAU UAAGC...UGA-3'@LB@ GGGGGCG GGA GUGGU@LB@ \|\|\|\|:\|: :\|\| \|\|\|\|:@LB@ CCCCUGU UCU CACCG@LB@3'-UUU...UUUUA AGUU UUUCGU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -21.9405 kcal/mol@LB@Unfolding Energy - mRNA 5.84786 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 151 -- 175@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 19 -- 25@LB@
3	3.973e-07	0.0004647	b0081	mraZ	-16.47	0.011640	172 -- 200	1 -- 32	RsmH methytransferase inhibitor	_____________171______________________________201\n_____________\|________________________________\|\n5'-GAU...GUGGG__________A___A_____U___________AUGUU...AAA-3'\n______________GCAAAGUGGG_AUA__GGGG_GAGGC__UGGC\n______________:\|\|\|\|:\|\|\|\|_\|:\|__:::\|_:\|:\|\|__\|\|\|\|\n______________UGUUUUACCC_UGU__UUUC_UUUCG__ACCG\n3'-UUU...CGAGG__________C___AG____U_____UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	175 -- 181	23 -- 29	-28.2943 kcal/mol	9.28897 kcal/mol	2.53929 kcal/mol	171 201@LB@ \| \|@LB@5'-GAU...GUGGG A A U AUGUU...AAA-3'@LB@ GCAAAGUGGG AUA GGGG GAGGC UGGC@LB@ :\|\|\|\|:\|\|\|\| \|:\| :::\| :\|:\|\| \|\|\|\|@LB@ UGUUUUACCC UGU UUUC UUUCG ACCG@LB@3'-UUU...CGAGG C AG U UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -16.47 kcal/mol@LB@Hybridization Energy -28.2943 kcal/mol@LB@Unfolding Energy - mRNA 9.28897 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 172 -- 200@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 23 -- 29@LB@
148	0.01095	0.2504	b0082	rsmH	-17.59	0.005541	130 -- 156	1 -- 25	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________129_________________________157\n_____________\|___________________________\|\n5'-UGG...GUCAA__AA________C_C________U___UACCG...GUC-3'\n______________GG__GAUAUCGA_G_AGAGCAGU_GGC\n______________\|\|__\|\|:\|\|\|:\|_\|_\|:\|\|\|\|\|\|_\|\|\|\n______________CC__CUGUAGUU_C_UUUCGUCA_CCG\n3'-UUU...UUUUA__C_________U_U____________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	146 -- 152	4 -- 10	-26.6505 kcal/mol	6.5392 kcal/mol	2.51748 kcal/mol	129 157@LB@ \| \|@LB@5'-UGG...GUCAA AA C C U UACCG...GUC-3'@LB@ GG GAUAUCGA G AGAGCAGU GGC@LB@ \|\| \|\|:\|\|\|:\| \| \|:\|\|\|\|\|\| \|\|\|@LB@ CC CUGUAGUU C UUUCGUCA CCG@LB@3'-UUU...UUUUA C U U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -17.59 kcal/mol@LB@Hybridization Energy -26.6505 kcal/mol@LB@Unfolding Energy - mRNA 6.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 130 -- 156@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 4 -- 10@LB@
87	0.005508	0.2147	b0083	ftsL	-13.20	0.070894	129 -- 146	1 -- 23	membrane bound cell division leucine zipper septum protein	_____________128_____________________147\n_____________\|_______________________\|\n5'-CGU...AUGCC_______________________UGAGA...UGC-3'\n______________GGGC___GAAGAAGAG__GUGGC\n______________\|\|:\|___:\|\|\|\|\|:\|\|__\|\|\|\|\|\n______________CCUG___UUUCUUUUC__CACCG\n3'-UUU...UUACC____UAG_________GU_____-5'\n_____________\|______________________\|\n_____________24_____________________1\n	135 -- 141	8 -- 14	-20.4792 kcal/mol	5.69631 kcal/mol	1.57928 kcal/mol	128 147@LB@ \| \|@LB@5'-CGU...AUGCC UGAGA...UGC-3'@LB@ GGGC GAAGAAGAG GUGGC@LB@ \|\|:\| :\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUG UUUCUUUUC CACCG@LB@3'-UUU...UUACC UAG GU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -20.4792 kcal/mol@LB@Unfolding Energy - mRNA 5.69631 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 8 -- 14@LB@
186	0.01333	0.2514	b0084	ftsI	-11.80	0.135121	196 -- 214	1 -- 22	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________195____________________215\n_____________\|______________________\|\n5'-GUU...AACGC_______U__________C___GAAAA...UGG-3'\n______________GACG_CA___GAAAGCAG_GGC\n______________\|\|\|:_\|\|___:\|\|\|\|\|\|\|_\|\|\|\n______________CUGU_GU___UUUUCGUC_CCG\n3'-UUU...UACCC____A__UUC________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	204 -- 210	5 -- 11	-21.3841 kcal/mol	8.04628 kcal/mol	1.54023 kcal/mol	195 215@LB@ \| \|@LB@5'-GUU...AACGC U C GAAAA...UGG-3'@LB@ GACG CA GAAAGCAG GGC@LB@ \|\|\|: \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CUGU GU UUUUCGUC CCG@LB@3'-UUU...UACCC A UUC A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -21.3841 kcal/mol@LB@Unfolding Energy - mRNA 8.04628 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
107	0.007146	0.2343	b0085	murE	-14.50	0.036427	193 -- 205	1 -- 25	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase	_____________192_______________________206\n_____________\|_________________________\|\n5'-UGC...GGCGA_________________________AGAUC...CGG-3'\n______________GGGGACA____________GGUGGC\n______________\|\|\|\|\|\|\|____________:\|\|\|\|\|\n______________CCCCUGU____________UCACCG\n3'-UUU...UUUUA_______AGUUUCUUUUCG______-5'\n_____________\|________________________\|\n_____________26_______________________1\n	193 -- 199	19 -- 25	-21.3886 kcal/mol	4.36682 kcal/mol	2.51748 kcal/mol	192 206@LB@ \| \|@LB@5'-UGC...GGCGA AGAUC...CGG-3'@LB@ GGGGACA GGUGGC@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CCCCUGU UCACCG@LB@3'-UUU...UUUUA AGUUUCUUUUCG -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -21.3886 kcal/mol@LB@Unfolding Energy - mRNA 4.36682 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 19 -- 25@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@

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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