Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
58	0.008338	0.4523	b2280	nuoJ	-13.62	0.015495	7 -- 16	55 -- 64	NADH:ubiquinone oxidoreductase membrane subunit J	_____________6__________17\n_____________\|__________\|\n_____5'-GAUUUC__________AAUAC...UUA-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	10 -- 16	55 -- 61	-15.5198 kcal/mol	1.86933 kcal/mol	0.0291912 kcal/mol	6 17@LB@ \| \|@LB@ 5'-GAUUUC AAUAC...UUA-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -15.5198 kcal/mol@LB@Unfolding Energy - mRNA 1.86933 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 7 -- 16@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 55 -- 61@LB@
12	0.000426	0.1165	b2331	smrB	-16.71	0.002472	163 -- 205	16 -- 57	putative DNA endonuclease	_____________162____________________________________________206\n_____________\|______________________________________________\|\n5'-UCA...GAGUC________UGUA___AAA________A______A____________AAAGA...GAC-3'\n______________GGGUAAAC____GGA___UUAGAAAU_GA_GAC___GAUAAAUGAA\n______________\|\|\|\|\|\|\|\|____:\|\|___\|:\|\|\|\|\|\|_:\|_\|\|\|___:\|\|\|\|\|\|:\|\|\n______________CCCAUUUG____UCU___AGUCUUUA_UU_CUG___UUAUUUAUUU\n3'-UUU...UUAUC_______________GUA________C__A___CCA__________CAAUU...UCG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________15\n	199 -- 205	16 -- 22	-27.8577 kcal/mol	4.82255 kcal/mol	6.32306 kcal/mol	162 206@LB@ \| \|@LB@5'-UCA...GAGUC UGUA AAA A A AAAGA...GAC-3'@LB@ GGGUAAAC GGA UUAGAAAU GA GAC GAUAAAUGAA@LB@ \|\|\|\|\|\|\|\| :\|\| \|:\|\|\|\|\|\| :\| \|\|\| :\|\|\|\|\|\|:\|\|@LB@ CCCAUUUG UCU AGUCUUUA UU CUG UUAUUUAUUU@LB@3'-UUU...UUAUC GUA C A CCA CAAUU...UCG-5'@LB@ \| \|@LB@ 58 15@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -27.8577 kcal/mol@LB@Unfolding Energy - mRNA 4.82255 kcal/mol@LB@Unfolding Energy - sRNA 6.32306 kcal/mol@LB@@LB@Position - mRNA 163 -- 205@LB@Position - sRNA 16 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
125	0.01993	0.5155	b2347	yfdC	-8.10	0.220050	281 -- 291	15 -- 25	putative inner membrane protein	_____________280_________292\n_____________\|___________\|\n5'-GCA...AUAGA___________ACCGA...UCC-3'\n______________AAUAGAUGAAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________UUAUUUAUUUC\n3'-UUU...UGCCA___________AAUUA...UCG-5'\n_____________\|___________\|\n_____________26__________14\n	285 -- 291	15 -- 21	-8.49349 kcal/mol	0.301625 kcal/mol	0.0943905 kcal/mol	280 292@LB@ \| \|@LB@5'-GCA...AUAGA ACCGA...UCC-3'@LB@ AAUAGAUGAAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ UUAUUUAUUUC@LB@3'-UUU...UGCCA AAUUA...UCG-5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -8.49349 kcal/mol@LB@Unfolding Energy - mRNA 0.301625 kcal/mol@LB@Unfolding Energy - sRNA 0.0943905 kcal/mol@LB@@LB@Position - mRNA 281 -- 291@LB@Position - sRNA 15 -- 25@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 15 -- 21@LB@
165	0.02655	0.526	b2388	glk	-7.68	0.259430	184 -- 233	1 -- 52	glucokinase	_____________183_____________________________________________________234\n_____________\|_______________________________________________________\|\n5'-CUA...ACUUU______G__GUU_____________AAA___UGCAUU_____C_______UG___GGCAC...AUU-3'\n______________AGCGGA_CA____GAA__GAAUGAC___GUA________AGU_GGUGAUG__GGC\n______________\|:\|:\|\|_\|\|____\|\|\|__\|\|\|\|\|\|\|___\|\|\|________\|\|\|_::\|\|\|\|\|__:\|\|\n______________UUGUCU_GU____CUU__CUUACUG___CAU________UCA_UUACUAC__UCG\n3'-UUU...CCCAU_________AAGU___UA_______C_____UAUUUAUU___A_______UA___-5'\n_____________\|______________________________________________________\|\n_____________53_____________________________________________________1\n	222 -- 228	6 -- 12	-28.455 kcal/mol	14.4434 kcal/mol	6.33555 kcal/mol	183 234@LB@ \| \|@LB@5'-CUA...ACUUU G GUU AAA UGCAUU C UG GGCAC...AUU-3'@LB@ AGCGGA CA GAA GAAUGAC GUA AGU GGUGAUG GGC@LB@ \|:\|:\|\| \|\| \|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\| ::\|\|\|\|\| :\|\|@LB@ UUGUCU GU CUU CUUACUG CAU UCA UUACUAC UCG@LB@3'-UUU...CCCAU AAGU UA C UAUUUAUU A UA -5'@LB@ \| \|@LB@ 53 1@LB@@LB@@LB@Energy -7.68 kcal/mol@LB@Hybridization Energy -28.455 kcal/mol@LB@Unfolding Energy - mRNA 14.4434 kcal/mol@LB@Unfolding Energy - sRNA 6.33555 kcal/mol@LB@@LB@Position - mRNA 184 -- 233@LB@Position - sRNA 1 -- 52@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 6 -- 12@LB@
106	0.01645	0.5059	b2416	ptsI	-13.93	0.013056	96 -- 143	1 -- 59	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________95__________________________________________________________144\n_____________\|___________________________________________________________\|\n5'-GUG...GCAGA___CGA_________AG_________________UGAACAUCU______AC________GGAAC...CCG-3'\n______________AGG_______AGACG__CAGAAA______GCGGU_________GGUUAA___UGAUGGC\n______________\|\|\|_______\|\|\|\|:__\|\|\|\|\|\|______:\|\|\|\|_________:\|\|\|\|\|___\|\|\|\|:\|\|\n______________UCC_______UCUGU__GUCUUU______UGCCA_________UCAAUU___ACUAUCG\n3'-UUU...CUUUA___CCAUUUG_____AA______ACUUAC_____UUAUUUAUU______ACU_______-5'\n_____________\|__________________________________________________________\|\n_____________60_________________________________________________________1\n	137 -- 143	1 -- 7	-30.8595 kcal/mol	10.5928 kcal/mol	6.33764 kcal/mol	95 144@LB@ \| \|@LB@5'-GUG...GCAGA CGA AG UGAACAUCU AC GGAAC...CCG-3'@LB@ AGG AGACG CAGAAA GCGGU GGUUAA UGAUGGC@LB@ \|\|\| \|\|\|\|: \|\|\|\|\|\| :\|\|\|\| :\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCC UCUGU GUCUUU UGCCA UCAAUU ACUAUCG@LB@3'-UUU...CUUUA CCAUUUG AA ACUUAC UUAUUUAUU ACU -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 10.5928 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 96 -- 143@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 1 -- 7@LB@
126	0.01995	0.5155	b2452	eutH	-9.16	0.141344	190 -- 206	5 -- 22	ethanolamine transporter	_____________189________________207\n_____________\|__________________\|\n5'-UUG...ACAGG________GC________AUUAA...UCC-3'\n______________GAGUAAAG__GAUGG_GA\n______________:\|:\|\|\|\|\|__:\|\|\|:_\|\|\n______________UUUAUUUC__UUACU_CU\n3'-UUU...CAUUA________AA_____A__AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	191 -- 197	15 -- 21	-11.7395 kcal/mol	2.48279 kcal/mol	0.0977783 kcal/mol	189 207@LB@ \| \|@LB@5'-UUG...ACAGG GC AUUAA...UCC-3'@LB@ GAGUAAAG GAUGG GA@LB@ :\|:\|\|\|\|\| :\|\|\|: \|\|@LB@ UUUAUUUC UUACU CU@LB@3'-UUU...CAUUA AA A AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -11.7395 kcal/mol@LB@Unfolding Energy - mRNA 2.48279 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
132	0.0212	0.526	b2455	eutE	-9.17	0.140915	224 -- 235	1 -- 12	aldehyde oxidoreductase ethanolamine utilization protein	_____________223__________236\n_____________\|____________\|\n5'-GGU...GAACA________A___GGUAC...UCG-3'\n______________GGUGGUGA_AGC\n______________::\|\|:\|\|\|_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	225 -- 231	5 -- 11	-12.5804 kcal/mol	3.3751 kcal/mol	0.0394463 kcal/mol	223 236@LB@ \| \|@LB@5'-GGU...GAACA A GGUAC...UCG-3'@LB@ GGUGGUGA AGC@LB@ ::\|\|:\|\|\| \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.5804 kcal/mol@LB@Unfolding Energy - mRNA 3.3751 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 224 -- 235@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
159	0.02583	0.526	b2572	rseA	-12.83	0.023837	184 -- 236	1 -- 63	anti-sigma factor	_____________183_____________________________________________________________237\n_____________\|_______________________________________________________________\|\n5'-UCC...AUACU_____A_____U________G__________CA__UUUCCGCU____________________GAAAC...GGG-3'\n______________GGAUA_GGGUA__UAGGCAU_CAGAAA_GAA__AC______________UUAAUGG__AUGGC\n______________::\|\|\|_\|\|\|\|\|__:\|\|:\|\|\|_\|\|\|\|\|\|_\|\|\|__\|\|______________\|\|\|\|\|\|:__\|\|:\|\|\n______________UUUAU_CCCAU__GUCUGUA_GUCUUU_CUU__UG______________AAUUACU__UAUCG\n3'-UUU...CCAAC_____C_____UU_______A______A___AC__CCAUUAUUUAUUUC_______AC_____-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________1\n	225 -- 231	8 -- 14	-31.1691 kcal/mol	11.9981 kcal/mol	6.344 kcal/mol	183 237@LB@ \| \|@LB@5'-UCC...AUACU A U G CA UUUCCGCU GAAAC...GGG-3'@LB@ GGAUA GGGUA UAGGCAU CAGAAA GAA AC UUAAUGG AUGGC@LB@ ::\|\|\| \|\|\|\|\| :\|\|:\|\|\| \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|:\|\|@LB@ UUUAU CCCAU GUCUGUA GUCUUU CUU UG AAUUACU UAUCG@LB@3'-UUU...CCAAC C UU A A AC CCAUUAUUUAUUUC AC -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -31.1691 kcal/mol@LB@Unfolding Energy - mRNA 11.9981 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 184 -- 236@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 8 -- 14@LB@
47	0.005156	0.3601	b2614	grpE	-12.03	0.036099	152 -- 179	1 -- 26	heat shock protein	_____________151__________________________180\n_____________\|____________________________\|\n5'-GAG...CCCCA_______C________CGA_____AU__GAAAA...CUG-3'\n______________UAAUAAG_GAAGUUAG___GAUGA__GC\n______________\|\|\|\|\|\|:_:\|\|\|\|\|\|:___\|\|\|\|\|__\|\|\n______________AUUAUUU_UUUCAAUU___CUACU__CG\n3'-UUU...CUGCC_______A________A_______AU__-5'\n_____________\|___________________________\|\n_____________27__________________________1\n	161 -- 167	11 -- 17	-17.6467 kcal/mol	5.03361 kcal/mol	0.580494 kcal/mol	151 180@LB@ \| \|@LB@5'-GAG...CCCCA C CGA AU GAAAA...CUG-3'@LB@ UAAUAAG GAAGUUAG GAUGA GC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|: \|\|\|\|\| \|\|@LB@ AUUAUUU UUUCAAUU CUACU CG@LB@3'-UUU...CUGCC A A AU -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -17.6467 kcal/mol@LB@Unfolding Energy - mRNA 5.03361 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 152 -- 179@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@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