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
85	0.006705	0.2588	bsu28790	araB	-13.91	0.048694	184 -- 192	30 -- 38	ribulokinase	_____________183_______193\n_____________\|_________\|\n5'-GGA...CAAAA_________GAUGU...AAU-3'\n______________GUAGAGGGG\n______________:\|\|\|\|\|\|\|\|\n______________UAUCUCCCC\n3'-UUU...UAGAC_________AACCC...AUA-5'\n_____________\|_________\|\n_____________39________29\n	186 -- 192	30 -- 36	-16.4519 kcal/mol	1.87822 kcal/mol	0.6591 kcal/mol	183 193@LB@ \| \|@LB@5'-GGA...CAAAA GAUGU...AAU-3'@LB@ GUAGAGGGG@LB@ :\|\|\|\|\|\|\|\|@LB@ UAUCUCCCC@LB@3'-UUU...UAGAC AACCC...AUA-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -16.4519 kcal/mol@LB@Unfolding Energy - mRNA 1.87822 kcal/mol@LB@Unfolding Energy - sRNA 0.6591 kcal/mol@LB@@LB@Position - mRNA 184 -- 192@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@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@
87	0.00681	0.2588	bsu29140	citZ	-14.51	0.037644	213 -- 231	27 -- 52	citrate synthase 2	_____________212_________________________232\n_____________\|___________________________\|\n5'-GAG...CGACA__C________________________UAGCA...AUG-3'\n______________CG_GGUCUUGA________AGGGGUUG\n______________\|\|_\|:\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________GC_CUAGAACU________UCCCCAAC\n3'-UUU...AAAAA___________AGACUAUC________CCCUU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________26\n	225 -- 231	27 -- 33	-23.9033 kcal/mol	8.41647 kcal/mol	0.980744 kcal/mol	212 232@LB@ \| \|@LB@5'-GAG...CGACA C UAGCA...AUG-3'@LB@ CG GGUCUUGA AGGGGUUG@LB@ \|\| \|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GC CUAGAACU UCCCCAAC@LB@3'-UUU...AAAAA AGACUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -23.9033 kcal/mol@LB@Unfolding Energy - mRNA 8.41647 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
88	0.006855	0.2588	bsu03770	rapC	-14.27	0.041792	179 -- 211	12 -- 42	response regulator aspartate phosphatase C	_____________178_______________________________212\n_____________\|_________________________________\|\n5'-UCA...CAGUU______G____A____GAA______A_______GGUAA...UAA-3'\n______________UUUGAU_GGAG_GGGU___GGAAUG_AGAGUGG\n______________\|:\|\|\|\|_:\|\|\|_\|\|\|\|___\|\|\|\|::_\|\|\|\|\|:\|\n______________AGACUA_UCUC_CCCA___CCUUGU_UCUCAUC\n3'-UUU...GAACU________________ACC______C_______GAAGA...AUA-5'\n_____________\|_________________________________\|\n_____________43________________________________11\n	205 -- 211	12 -- 18	-33.0113 kcal/mol	8.84839 kcal/mol	9.89449 kcal/mol	178 212@LB@ \| \|@LB@5'-UCA...CAGUU G A GAA A GGUAA...UAA-3'@LB@ UUUGAU GGAG GGGU GGAAUG AGAGUGG@LB@ \|:\|\|\|\| :\|\|\| \|\|\|\| \|\|\|\|:: \|\|\|\|\|:\|@LB@ AGACUA UCUC CCCA CCUUGU UCUCAUC@LB@3'-UUU...GAACU ACC C GAAGA...AUA-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -14.27 kcal/mol@LB@Hybridization Energy -33.0113 kcal/mol@LB@Unfolding Energy - mRNA 8.84839 kcal/mol@LB@Unfolding Energy - sRNA 9.89449 kcal/mol@LB@@LB@Position - mRNA 179 -- 211@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 12 -- 18@LB@
89	0.00694	0.2588	bsu06230	iolT	-9.37	0.260314	174 -- 193	31 -- 49	major myo-inositol transporter IolT	_____________173__________________194\n_____________\|____________________\|\n5'-AAA...UACGC_______AAAA__CU_____AAACA...AUG-3'\n______________AUUUUGA____GA__GGGGG\n______________\|\|:\|\|\|\|____\|\|__\|:\|\|\|\n______________UAGAACU____CU__CUCCC\n3'-UUU...AAGCC_______AGA___AU_____CAACC...AUA-5'\n_____________\|____________________\|\n_____________50___________________30\n	174 -- 180	43 -- 49	-14.1903 kcal/mol	3.84886 kcal/mol	0.970571 kcal/mol	173 194@LB@ \| \|@LB@5'-AAA...UACGC AAAA CU AAACA...AUG-3'@LB@ AUUUUGA GA GGGGG@LB@ \|\|:\|\|\|\| \|\| \|:\|\|\|@LB@ UAGAACU CU CUCCC@LB@3'-UUU...AAGCC AGA AU CAACC...AUA-5'@LB@ \| \|@LB@ 50 30@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -14.1903 kcal/mol@LB@Unfolding Energy - mRNA 3.84886 kcal/mol@LB@Unfolding Energy - sRNA 0.970571 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 31 -- 49@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 43 -- 49@LB@
90	0.006982	0.2588	bsu40920	yyaF	-12.87	0.074972	6 -- 31	25 -- 50	GTP-dependent nucleic acid-binding protein EngD	_____________5___________________________32\n_____________\|___________________________\|\n______5'-CAAAU___ACAAAU_______AU__AA_____AAGUA...CGU-3'\n______________GAU______UCUGAUA__GG___UGGG\n______________\|\|\|______\|\|\|\|\|\|\|__\|\|___\|\|\|\|\n______________CUA______AGACUAU__CC___ACCC\n3'-UUU...AAAGC___GAACU________CU__CCA____CUUGU...AUA-5'\n_____________\|___________________________\|\n_____________51__________________________24\n	15 -- 21	36 -- 42	-17.5884 kcal/mol	3.73957 kcal/mol	0.976057 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAAAU ACAAAU AU AA AAGUA...CGU-3'@LB@ GAU UCUGAUA GG UGGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|@LB@ CUA AGACUAU CC ACCC@LB@3'-UUU...AAAGC GAACU CU CCA CUUGU...AUA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -17.5884 kcal/mol@LB@Unfolding Energy - mRNA 3.73957 kcal/mol@LB@Unfolding Energy - sRNA 0.976057 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 36 -- 42@LB@
91	0.007102	0.2604	bsu36520	glnK	-7.98	0.387566	247 -- 267	32 -- 49	nitrogen regulatory PII-like protein	_____________246____________________268\n_____________\|______________________\|\n5'-GGU...GGCAA_______AAAG_______C___AACUC...CUU-3'\n______________AUUUUGA____CUGA_AG_AGG\n______________\|\|:\|\|\|\|____\|\|\|\|_\|\|_\|\|\|\n______________UAGAACU____GACU_UC_UCC\n3'-UUU...AAGCC_______A_______A______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________50_____________________31\n	247 -- 253	43 -- 49	-11.0905 kcal/mol	2.14263 kcal/mol	0.970192 kcal/mol	246 268@LB@ \| \|@LB@5'-GGU...GGCAA AAAG C AACUC...CUU-3'@LB@ AUUUUGA CUGA AG AGG@LB@ \|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|@LB@ UAGAACU GACU UC UCC@LB@3'-UUU...AAGCC A A CCAAC...AUA-5'@LB@ \| \|@LB@ 50 31@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -11.0905 kcal/mol@LB@Unfolding Energy - mRNA 2.14263 kcal/mol@LB@Unfolding Energy - sRNA 0.970192 kcal/mol@LB@@LB@Position - mRNA 247 -- 267@LB@Position - sRNA 32 -- 49@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 43 -- 49@LB@
92	0.007313	0.2652	bsu34470	yveA	-16.72	0.013215	240 -- 265	25 -- 47	aspartate-proton symporter	_____________239________________________266\n_____________\|__________________________\|\n5'-CCU...CGCUG___________UUU__UU___A____AGCCA...UCA-3'\n______________UUUGAUCUGAU___GA__GGG_UGGG\n______________:\|\|\|\|\|\|\|\|\|\|___\|\|__\|\|\|_\|\|\|\|\n______________GAACUAGACUA___CU__CCC_ACCC\n3'-UUU...GCCUA___________U____C____A____CUUGU...AUA-5'\n_____________\|__________________________\|\n_____________48_________________________24\n	244 -- 250	37 -- 43	-24.6158 kcal/mol	6.92071 kcal/mol	0.975871 kcal/mol	239 266@LB@ \| \|@LB@5'-CCU...CGCUG UUU UU A AGCCA...UCA-3'@LB@ UUUGAUCUGAU GA GGG UGGG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GAACUAGACUA CU CCC ACCC@LB@3'-UUU...GCCUA U C A CUUGU...AUA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -16.72 kcal/mol@LB@Hybridization Energy -24.6158 kcal/mol@LB@Unfolding Energy - mRNA 6.92071 kcal/mol@LB@Unfolding Energy - sRNA 0.975871 kcal/mol@LB@@LB@Position - mRNA 240 -- 265@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 37 -- 43@LB@
93	0.007837	0.2778	bsu33430	yvgQ	-5.79	0.632053	172 -- 180	38 -- 46	sulfite reductase [NADPH] hemoprotein beta-component	_____________171_______181\n_____________\|_________\|\n5'-GCU...GUAUA_________CUUGA...UGA-3'\n______________UUGAUUUGA\n______________\|\|\|\|\|:\|\|\|\n______________AACUAGACU\n3'-UUU...CCUAG_________AUCUC...AUA-5'\n_____________\|_________\|\n_____________47________37\n	174 -- 180	38 -- 44	-9.05403 kcal/mol	2.31378 kcal/mol	0.946105 kcal/mol	171 181@LB@ \| \|@LB@5'-GCU...GUAUA CUUGA...UGA-3'@LB@ UUGAUUUGA@LB@ \|\|\|\|\|:\|\|\|@LB@ AACUAGACU@LB@3'-UUU...CCUAG AUCUC...AUA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -5.79 kcal/mol@LB@Hybridization Energy -9.05403 kcal/mol@LB@Unfolding Energy - mRNA 2.31378 kcal/mol@LB@Unfolding Energy - sRNA 0.946105 kcal/mol@LB@@LB@Position - mRNA 172 -- 180@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 38 -- 44@LB@
94	0.007849	0.2778	bsu27000	yraB	-9.14	0.279232	183 -- 193	29 -- 39	MerR family transcriptional regulator	_____________182_________194\n_____________\|___________\|\n5'-AGU...UACAG_______A___GAAGA...ACA-3'\n______________GAUAGAG_GGU\n______________\|\|\|\|\|\|\|_\|\|\|\n______________CUAUCUC_CCA\n3'-UUU...CUAGA_______C___ACCCC...AUA-5'\n_____________\|___________\|\n_____________40__________28\n	183 -- 189	33 -- 39	-13.977 kcal/mol	4.05751 kcal/mol	0.779471 kcal/mol	182 194@LB@ \| \|@LB@5'-AGU...UACAG A GAAGA...ACA-3'@LB@ GAUAGAG GGU@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ CUAUCUC CCA@LB@3'-UUU...CUAGA C ACCCC...AUA-5'@LB@ \| \|@LB@ 40 28@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -13.977 kcal/mol@LB@Unfolding Energy - mRNA 4.05751 kcal/mol@LB@Unfolding Energy - sRNA 0.779471 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 29 -- 39@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 33 -- 39@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching