Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
134	0.01184	0.2883	bsu01450	cbiO	-8.85	0.304208	221 -- 231	32 -- 43	energy-coupling factor transporter ATP-binding protein EcfA1	_____________220__________232\n_____________\|____________\|\n5'-AUA...UUGAU____________AUAUC...AUG-3'\n______________AUC_GGUAGAGG\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	225 -- 231	32 -- 38	-12.7681 kcal/mol	2.95776 kcal/mol	0.959872 kcal/mol	220 232@LB@ \| \|@LB@5'-AUA...UUGAU AUAUC...AUG-3'@LB@ AUC GGUAGAGG@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.7681 kcal/mol@LB@Unfolding Energy - mRNA 2.95776 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 221 -- 231@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 32 -- 38@LB@
137	0.01211	0.2883	bsu27850	nadA	-8.79	0.309443	168 -- 191	32 -- 52	quinolinate synthase A	_____________167_______________________192\n_____________\|_________________________\|\n5'-UAC...UGUUA__UU___AAA__A____________AAUGC...UUA-3'\n______________CG__AUC___UG_AUCU_GUGGAGG\n______________\|\|__\|\|\|___\|\|_\|\|\|\|_:\|:\|\|\|\|\n______________GC__UAG___AC_UAGA_UAUCUCC\n3'-UUU...AAAAA__C____A_________C_______CCAAC...AUA-5'\n_____________\|_________________________\|\n_____________53________________________31\n	185 -- 191	32 -- 38	-13.8724 kcal/mol	4.10431 kcal/mol	0.976384 kcal/mol	167 192@LB@ \| \|@LB@5'-UAC...UGUUA UU AAA A AAUGC...UUA-3'@LB@ CG AUC UG AUCU GUGGAGG@LB@ \|\| \|\|\| \|\| \|\|\|\| :\|:\|\|\|\|@LB@ GC UAG AC UAGA UAUCUCC@LB@3'-UUU...AAAAA C A C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -8.79 kcal/mol@LB@Hybridization Energy -13.8724 kcal/mol@LB@Unfolding Energy - mRNA 4.10431 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 32 -- 38@LB@
156	0.0141	0.3008	bsu23600	yqxK	-15.33	0.025853	66 -- 91	32 -- 51	Evidence 4: Homologs of previously reported genes of unknown function	_____________65_________________________92\n_____________\|__________________________\|\n5'-GAA...GAUGA___CGAGUU_G____AG_________UGACG...GAA-3'\n______________GGA______U_UUGA__UGAUGGAGG\n______________\|\|\|______\|_\|\|\|\|__\|\|\|\|:\|\|\|\|\n______________CCU______A_AACU__ACUAUCUCC\n3'-UUU...AAAAG__________G____AG_________CCAAC...AUA-5'\n_____________\|__________________________\|\n_____________52_________________________31\n	85 -- 91	32 -- 38	-19.9693 kcal/mol	3.66503 kcal/mol	0.97021 kcal/mol	65 92@LB@ \| \|@LB@5'-GAA...GAUGA CGAGUU G AG UGACG...GAA-3'@LB@ GGA U UUGA UGAUGGAGG@LB@ \|\|\| \| \|\|\|\| \|\|\|\|:\|\|\|\|@LB@ CCU A AACU ACUAUCUCC@LB@3'-UUU...AAAAG G AG CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -19.9693 kcal/mol@LB@Unfolding Energy - mRNA 3.66503 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 66 -- 91@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 32 -- 38@LB@
172	0.01654	0.3152	bsu29680	acsA	-11.36	0.133506	267 -- 288	32 -- 52	acetyl-CoA synthetase	_____________266____________________289\n_____________\|______________________\|\n5'-UUU...CGUAC___C_________G__CC____CAGAG...AUU-3'\n______________CGG_AUUUUGAUU_GG__GAGG\n______________\|\|\|_\|\|:\|\|\|\|\|:_\|:__\|\|\|\|\n______________GCC_UAGAACUAG_CU__CUCC\n3'-UUU...AAAAA_____________A__AU____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	273 -- 279	41 -- 47	-18.8322 kcal/mol	6.49419 kcal/mol	0.976384 kcal/mol	266 289@LB@ \| \|@LB@5'-UUU...CGUAC C G CC CAGAG...AUU-3'@LB@ CGG AUUUUGAUU GG GAGG@LB@ \|\|\| \|\|:\|\|\|\|\|: \|: \|\|\|\|@LB@ GCC UAGAACUAG CU CUCC@LB@3'-UUU...AAAAA A AU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -18.8322 kcal/mol@LB@Unfolding Energy - mRNA 6.49419 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 267 -- 288@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 41 -- 47@LB@
180	0.01704	0.3152	bsu28380	gerM	-9.54	0.246988	269 -- 291	32 -- 52	spore germination protein GerM	_____________268______________________292\n_____________\|________________________\|\n5'-AGU...GGAUG___UUU____CA____________CAGCC...AGG-3'\n______________CGG___GUUU__AUCUGAUA_AGG\n______________\|\|\|___:\|:\|__\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC___UAGA__UAGACUAU_UCC\n3'-UUU...AAAAA__________AC________C___CCAAC...AUA-5'\n_____________\|________________________\|\n_____________53_______________________31\n	282 -- 288	36 -- 42	-15.6565 kcal/mol	5.13957 kcal/mol	0.976384 kcal/mol	268 292@LB@ \| \|@LB@5'-AGU...GGAUG UUU CA CAGCC...AGG-3'@LB@ CGG GUUU AUCUGAUA AGG@LB@ \|\|\| :\|:\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC UAGA UAGACUAU UCC@LB@3'-UUU...AAAAA AC C CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -15.6565 kcal/mol@LB@Unfolding Energy - mRNA 5.13957 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 269 -- 291@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 36 -- 42@LB@
187	0.01872	0.3269	bsu10530	ntdC	-12.62	0.082941	177 -- 192	32 -- 53	NTD biosynthesis operon putative oxidoreductase NtdC	_____________176____________________193\n_____________\|______________________\|\n5'-CCU...AUUAA_______A______________AAAUA...ACA-3'\n______________UUGGAUC_UGA______GGAGG\n______________\|:\|\|\|\|\|_\|\|\|______:\|\|\|\|\n______________AGCCUAG_ACU______UCUCC\n3'-UUU...AAAAA_______A___AGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	177 -- 183	47 -- 53	-16.8717 kcal/mol	3.27102 kcal/mol	0.981755 kcal/mol	176 193@LB@ \| \|@LB@5'-CCU...AUUAA A AAAUA...ACA-3'@LB@ UUGGAUC UGA GGAGG@LB@ \|:\|\|\|\|\| \|\|\| :\|\|\|\|@LB@ AGCCUAG ACU UCUCC@LB@3'-UUU...AAAAA A AGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -16.8717 kcal/mol@LB@Unfolding Energy - mRNA 3.27102 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 47 -- 53@LB@
59	0.003314	0.1874	bsu01560	kbaA	-8.60	0.327174	11 -- 30	33 -- 52	kinB-signaling pathway activation protein	_____________10___________________31\n_____________\|____________________\|\n5'-AGU...AUAUC__CUG________UU_____CGCAA...AUA-3'\n______________CG___CUUGGUCU__UGGAG\n______________\|\|___\|\|\|\|:\|\|\|__\|:\|\|\|\n______________GC___GAACUAGA__AUCUC\n3'-UUU...AAAAA__CUA________CU_____CCCAA...AUA-5'\n_____________\|____________________\|\n_____________53___________________32\n	17 -- 23	40 -- 46	-17.5678 kcal/mol	7.9942 kcal/mol	0.976367 kcal/mol	10 31@LB@ \| \|@LB@5'-AGU...AUAUC CUG UU CGCAA...AUA-3'@LB@ CG CUUGGUCU UGGAG@LB@ \|\| \|\|\|\|:\|\|\| \|:\|\|\|@LB@ GC GAACUAGA AUCUC@LB@3'-UUU...AAAAA CUA CU CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.5678 kcal/mol@LB@Unfolding Energy - mRNA 7.9942 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 11 -- 30@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 40 -- 46@LB@
86	0.006791	0.2588	bsu17010	ymcB	-10.99	0.152529	169 -- 190	33 -- 52	(dimethylallyl)adenosine tRNA methylthiotransferase MiaB	_____________168____________________191\n_____________\|______________________\|\n5'-AUC...AAGGG____AG__________AA____AAAAU...CGC-3'\n______________UGGA__UUUGGUUUGA__GGAG\n______________:\|\|\|__:\|\|\|:\|:\|\|\|__:\|\|\|\n______________GCCU__GAACUAGACU__UCUC\n3'-UUU...AAAAA____A___________A_____CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	178 -- 184	38 -- 44	-16.81 kcal/mol	4.84464 kcal/mol	0.976367 kcal/mol	168 191@LB@ \| \|@LB@5'-AUC...AAGGG AG AA AAAAU...CGC-3'@LB@ UGGA UUUGGUUUGA GGAG@LB@ :\|\|\| :\|\|\|:\|:\|\|\| :\|\|\|@LB@ GCCU GAACUAGACU UCUC@LB@3'-UUU...AAAAA A A CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.81 kcal/mol@LB@Unfolding Energy - mRNA 4.84464 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 169 -- 190@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 38 -- 44@LB@
114	0.009837	0.2871	bsu30580	ytmA	-11.73	0.116519	193 -- 212	33 -- 52	peptidase YtmA	_____________192____________________213\n_____________\|______________________\|\n5'-AGA...GGAGG___CU_________________AAAAG...UGG-3'\n______________CGG__GUUUUGAUU__GUAGAG\n______________\|\|\|__:\|:\|\|\|\|\|:__:\|\|\|\|\|\n______________GCC__UAGAACUAG__UAUCUC\n3'-UUU...AAAAA______________AC______CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	200 -- 206	41 -- 47	-17.5653 kcal/mol	4.85678 kcal/mol	0.976367 kcal/mol	192 213@LB@ \| \|@LB@5'-AGA...GGAGG CU AAAAG...UGG-3'@LB@ CGG GUUUUGAUU GUAGAG@LB@ \|\|\| :\|:\|\|\|\|\|: :\|\|\|\|\|@LB@ GCC UAGAACUAG UAUCUC@LB@3'-UUU...AAAAA AC CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.5653 kcal/mol@LB@Unfolding Energy - mRNA 4.85678 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@LB@
60	0.003464	0.1926	bsu03300	nasD	-15.33	0.025906	190 -- 205	34 -- 52	nitrite reductase	_____________189_________________206\n_____________\|___________________\|\n5'-UUU...AGGAG___________________AAAAA...CAA-3'\n______________CGGAUC___AUCUGAUGGG\n______________\|\|\|\|\|\|___\|\|\|\|\|\|\|:\|:\n______________GCCUAG___UAGACUAUCU\n3'-UUU...AAAAA______AAC__________CCCCA...AUA-5'\n_____________\|___________________\|\n_____________53__________________33\n	199 -- 205	34 -- 40	-21.0079 kcal/mol	4.70189 kcal/mol	0.976339 kcal/mol	189 206@LB@ \| \|@LB@5'-UUU...AGGAG AAAAA...CAA-3'@LB@ CGGAUC AUCUGAUGGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|:\|:@LB@ GCCUAG UAGACUAUCU@LB@3'-UUU...AAAAA AAC CCCCA...AUA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -21.0079 kcal/mol@LB@Unfolding Energy - mRNA 4.70189 kcal/mol@LB@Unfolding Energy - sRNA 0.976339 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 34 -- 40@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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