Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
85	0.002234	0.09158	b0118	acnB	-9.43	0.065848	121 -- 128	1 -- 8	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________120______129\n_____________\|________\|\n5'-GAG...GCAUU________AAACU...UGC-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	122 -- 128	1 -- 7	-13.4001 kcal/mol	1.87598 kcal/mol	2.11603 kcal/mol	120 129@LB@ \| \|@LB@5'-GAG...GCAUU AAACU...UGC-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.4001 kcal/mol@LB@Unfolding Energy - mRNA 1.87598 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 121 -- 128@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.002239	0.09158	b0434	yajG	-10.16	0.040736	167 -- 223	4 -- 56	putative lipoprotein	_____________166____________________________________________________________224\n_____________\|______________________________________________________________\|\n5'-UGG...UUUUA__AAAC___CU_________UC________CCC______G__CAAAAAAAU_____U_____GUUAG...UGC-3'\n______________CC____ACG_____UAAGAG__UCUGAGAG___GAACAU_UU_________CCUCU___CCC\n______________\|\|____\|\|\|_____\|\|\|:\|\|__\|\|\|\|\|:\|\|___\|\|\|\|\|\|_\|\|_________\|\|\|\|\|___\|\|\|\n______________GG____UGC_____AUUUUC__AGACUUUC___CUUGUA_AA_________GGAGA___GGG\n3'-AUU...GUUUA__CUAA___ACUUC______C_________UAU______G__U_____________CAU___AUG-5'\n_____________\|______________________________________________________________\|\n_____________57_____________________________________________________________3\n	187 -- 193	28 -- 34	-29.9553 kcal/mol	7.1187 kcal/mol	12.7017 kcal/mol	166 224@LB@ \| \|@LB@5'-UGG...UUUUA AAAC CU UC CCC G CAAAAAAAU U GUUAG...UGC-3'@LB@ CC ACG UAAGAG UCUGAGAG GAACAU UU CCUCU CCC@LB@ \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ GG UGC AUUUUC AGACUUUC CUUGUA AA GGAGA GGG@LB@3'-AUU...GUUUA CUAA ACUUC C UAU G U CAU AUG-5'@LB@ \| \|@LB@ 57 3@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -29.9553 kcal/mol@LB@Unfolding Energy - mRNA 7.1187 kcal/mol@LB@Unfolding Energy - sRNA 12.7017 kcal/mol@LB@@LB@Position - mRNA 167 -- 223@LB@Position - sRNA 4 -- 56@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 28 -- 34@LB@
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate	_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
89	0.002377	0.09395	b4136	dsbD	-10.47	0.032769	211 -- 231	1 -- 22	thiol:disulfide interchange protein and activator of DsbC	_____________210____________________232\n_____________\|______________________\|\n5'-UGC...UCAAC_______UA_G___________UACUU...CGG-3'\n______________GCAUCUU__C_CUG_AUCCUGC\n______________:\|\|\|\|\|\|__\|_\|\|\|_\|:\|\|\|:\|\n______________UGUAGAA__G_GAC_UGGGAUG\n3'-AUU...UAUCU_______UG_A___A_______-5'\n_____________\|_____________________\|\n_____________23____________________1\n	225 -- 231	1 -- 7	-23.5098 kcal/mol	5.0672 kcal/mol	7.99236 kcal/mol	210 232@LB@ \| \|@LB@5'-UGC...UCAAC UA G UACUU...CGG-3'@LB@ GCAUCUU C CUG AUCCUGC@LB@ :\|\|\|\|\|\| \| \|\|\| \|:\|\|\|:\|@LB@ UGUAGAA G GAC UGGGAUG@LB@3'-AUU...UAUCU UG A A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -23.5098 kcal/mol@LB@Unfolding Energy - mRNA 5.0672 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
90	0.002406	0.09404	b0551	quuD	-13.47	0.003063	177 -- 196	40 -- 58	DLP12 prophage; putative antitermination protein	_____________176__________________197\n_____________\|____________________\|\n5'-ACU...UUCUG________UU__________GUUGA...GAU-3'\n______________GUCUGAUU__UGUGGAGUAA\n______________:\|\|:\|\|\|\|__:\|\|\|:\|\|\|\|\|\n______________UAGGCUAA__GCACUUCAUU\n3'-AUU...CGGUU________U___________UUCCA...AUG-5'\n_____________\|____________________\|\n_____________59___________________39\n	190 -- 196	40 -- 46	-19.625 kcal/mol	2.82746 kcal/mol	3.34877 kcal/mol	176 197@LB@ \| \|@LB@5'-ACU...UUCUG UU GUUGA...GAU-3'@LB@ GUCUGAUU UGUGGAGUAA@LB@ :\|\|:\|\|\|\| :\|\|\|:\|\|\|\|\|@LB@ UAGGCUAA GCACUUCAUU@LB@3'-AUU...CGGUU U UUCCA...AUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -19.625 kcal/mol@LB@Unfolding Energy - mRNA 2.82746 kcal/mol@LB@Unfolding Energy - sRNA 3.34877 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
91	0.002527	0.0977	b4393	trpR	-12.48	0.007130	9 -- 21	43 -- 55	transcriptional repressor tryptophan-binding	_____________8_____________22\n_____________\|_____________\|\n___5'-GAGACGCG_____________AACGU...AUC-3'\n______________CGGUUAUGUGAAG\n______________\|\|:\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUUC\n3'-AUU...UUUAG_____________AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	15 -- 21	43 -- 49	-16.824 kcal/mol	1.08541 kcal/mol	3.2693 kcal/mol	8 22@LB@ \| \|@LB@ 5'-GAGACGCG AACGU...AUC-3'@LB@ CGGUUAUGUGAAG@LB@ \|\|:\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUUC@LB@3'-AUU...UUUAG AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -16.824 kcal/mol@LB@Unfolding Energy - mRNA 1.08541 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 9 -- 21@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 43 -- 49@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter	_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
93	0.002634	0.09947	b2202	napC	-9.04	0.084220	177 -- 197	34 -- 54	quinol dehydrogenase electron source for NapAB	_____________176___________________198\n_____________\|_____________________\|\n5'-ACG...CAAAA_______G___A_________AUUAU...GUU-3'\n______________GGUUACG_GAA_UAAGAGGUU\n______________\|:\|\|\|\|\|_\|\|\|_\|\|\|:\|\|\|\|:\n______________CUAAUGC_CUU_AUUUUCCAG\n3'-AUU...UUAGG_______A___C_________ACUUU...AUG-5'\n_____________\|_____________________\|\n_____________55____________________33\n	177 -- 183	48 -- 54	-21.2793 kcal/mol	4.43682 kcal/mol	7.71857 kcal/mol	176 198@LB@ \| \|@LB@5'-ACG...CAAAA G A AUUAU...GUU-3'@LB@ GGUUACG GAA UAAGAGGUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|:@LB@ CUAAUGC CUU AUUUUCCAG@LB@3'-AUU...UUAGG A C ACUUU...AUG-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.2793 kcal/mol@LB@Unfolding Energy - mRNA 4.43682 kcal/mol@LB@Unfolding Energy - sRNA 7.71857 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
94	0.002669	0.09947	b2659	csiD	-13.62	0.002680	28 -- 48	1 -- 21	carbon starvation protein	_____________27____________________49\n_____________\|_____________________\|\n5'-GUU...UGUCU__C________AA________GUUAA...UGG-3'\n______________CA_UUUGCCUU__UACCCUAC\n______________\|\|_:\|\|:\|\|\|:__\|\|\|\|\|\|\|\|\n______________GU_GAAUGGAG__AUGGGAUG\n3'-AUU...AUCUU__A________AC________-5'\n_____________\|____________________\|\n_____________22___________________1\n	42 -- 48	1 -- 7	-22.7197 kcal/mol	1.13457 kcal/mol	7.99195 kcal/mol	27 49@LB@ \| \|@LB@5'-GUU...UGUCU C AA GUUAA...UGG-3'@LB@ CA UUUGCCUU UACCCUAC@LB@ \|\| :\|\|:\|\|\|: \|\|\|\|\|\|\|\|@LB@ GU GAAUGGAG AUGGGAUG@LB@3'-AUU...AUCUU A AC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -22.7197 kcal/mol@LB@Unfolding Energy - mRNA 1.13457 kcal/mol@LB@Unfolding Energy - sRNA 7.99195 kcal/mol@LB@@LB@Position - mRNA 28 -- 48@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 1 -- 7@LB@
95	0.002686	0.09947	b2419	yfeK	-12.78	0.005552	57 -- 65	1 -- 9	uncharacterized protein	_____________56________66\n_____________\|_________\|\n5'-GUU...CUGCA_________UCUUA...UGG-3'\n______________GUGCCCUAC\n______________\|\|:\|\|\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	59 -- 65	1 -- 7	-16.152 kcal/mol	1.26264 kcal/mol	2.12872 kcal/mol	56 66@LB@ \| \|@LB@5'-GUU...CUGCA UCUUA...UGG-3'@LB@ GUGCCCUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -16.152 kcal/mol@LB@Unfolding Energy - mRNA 1.26264 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 57 -- 65@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 1 -- 7@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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service.

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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