Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
78	0.003218	0.1452	b1641	slyB	-13.21	0.056987	203 -- 235	43 -- 75	outer membrane lipoprotein	_____________202_________________________________236\n_____________\|___________________________________\|\n5'-CCG...UCAAU_____A___________G_________AUGG____UCUGU...AAG-3'\n______________GAUUA_ACGC_GU_AUU_GUUGUUUCA____UAGG\n______________\|\|:\|\|_\|\|:\|_\|:_\|\|\|_\|\|\|\|\|\|\|\|\|____:\|\|\|\n______________CUGAU_UGUG_CG_UAA_CAACAAAGU____GUCC\n3'-UUU...CGUUU_____G____U__U___G_________GA______CCUAA...GCA-5'\n_____________\|___________________________________\|\n_____________76__________________________________42\n	221 -- 227	49 -- 55	-26.1882 kcal/mol	8.63028 kcal/mol	4.35266 kcal/mol	202 236@LB@ \| \|@LB@5'-CCG...UCAAU A G AUGG UCUGU...AAG-3'@LB@ GAUUA ACGC GU AUU GUUGUUUCA UAGG@LB@ \|\|:\|\| \|\|:\| \|: \|\|\| \|\|\|\|\|\|\|\|\| :\|\|\|@LB@ CUGAU UGUG CG UAA CAACAAAGU GUCC@LB@3'-UUU...CGUUU G U U G GA CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.1882 kcal/mol@LB@Unfolding Energy - mRNA 8.63028 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 203 -- 235@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 49 -- 55@LB@
105	0.004683	0.1538	b3349	slyD	-10.61	0.192215	166 -- 197	39 -- 73	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________165_________________________________198\n_____________\|___________________________________\|\n5'-UGU...ACAAU___________U____UUCCCAU________A___AUCAU...ACU-3'\n______________CUGCGC_CA_C_AUUC________GCUCAGG_GAU\n______________\|\|:\|:\|_\|\|_\|_\|\|\|\|________:\|\|\|\|\|\|_\|\|\|\n______________GAUGUG_GU_G_UAAG________UGAGUCC_CUA\n3'-UUU...UUUCU______U__C_U____CAACAAAG_______C___AAGGU...GCA-5'\n_____________\|___________________________________\|\n_____________74__________________________________38\n	187 -- 193	43 -- 49	-23.2642 kcal/mol	7.88699 kcal/mol	4.77295 kcal/mol	165 198@LB@ \| \|@LB@5'-UGU...ACAAU U UUCCCAU A AUCAU...ACU-3'@LB@ CUGCGC CA C AUUC GCUCAGG GAU@LB@ \|\|:\|:\| \|\| \| \|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ GAUGUG GU G UAAG UGAGUCC CUA@LB@3'-UUU...UUUCU U C U CAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 74 38@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -23.2642 kcal/mol@LB@Unfolding Energy - mRNA 7.88699 kcal/mol@LB@Unfolding Energy - sRNA 4.77295 kcal/mol@LB@@LB@Position - mRNA 166 -- 197@LB@Position - sRNA 39 -- 73@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
16	0.00012	0.02638	b3089	sstT	-15.87	0.012233	203 -- 224	42 -- 75	sodium:serine/threonine symporter	_____________202________________________________225\n_____________\|__________________________________\|\n5'-CAC...AAAAU_________ACG______________________CUAUU...CAU-3'\n______________GACUACGCA______________UUCAC_CGGGG\n______________\|\|\|\|\|\|:\|\|______________\|\|\|\|\|_\|:\|\|\|\n______________CUGAUGUGU______________AAGUG_GUCCC\n3'-UUU...CGUUU_________GUCGUUAAGCAACA_____A_____CUAAA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________41\n	205 -- 211	67 -- 73	-24.6329 kcal/mol	4.00159 kcal/mol	4.76397 kcal/mol	202 225@LB@ \| \|@LB@5'-CAC...AAAAU ACG CUAUU...CAU-3'@LB@ GACUACGCA UUCAC CGGGG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\| \|:\|\|\|@LB@ CUGAUGUGU AAGUG GUCCC@LB@3'-UUU...CGUUU GUCGUUAAGCAACA A CUAAA...GCA-5'@LB@ \| \|@LB@ 76 41@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -24.6329 kcal/mol@LB@Unfolding Energy - mRNA 4.00159 kcal/mol@LB@Unfolding Energy - sRNA 4.76397 kcal/mol@LB@@LB@Position - mRNA 203 -- 224@LB@Position - sRNA 42 -- 75@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 67 -- 73@LB@
149	0.006962	0.1638	b0935	ssuD	-8.45	0.421381	102 -- 123	48 -- 71	alkanesulfonate monooxygenase FMNH(2)-dependent	_____________101______________________124\n_____________\|________________________\|\n5'-AAA...CAGCA___A_______A____________GAAAA...AAC-3'\n______________GCA_ACGGCAG_UC__UGUUUUAU\n______________:\|\|_\|\|:\|\|\|:_\|\|__\|\|\|\|\|:\|:\n______________UGU_UGUCGUU_AG__ACAAAGUG\n3'-UUU...UCUGA___G_______A__CA________AGUCC...GCA-5'\n_____________\|________________________\|\n_____________72_______________________47\n	117 -- 123	48 -- 54	-17.2917 kcal/mol	5.19453 kcal/mol	3.65243 kcal/mol	101 124@LB@ \| \|@LB@5'-AAA...CAGCA A A GAAAA...AAC-3'@LB@ GCA ACGGCAG UC UGUUUUAU@LB@ :\|\| \|\|:\|\|\|: \|\| \|\|\|\|\|:\|:@LB@ UGU UGUCGUU AG ACAAAGUG@LB@3'-UUU...UCUGA G A CA AGUCC...GCA-5'@LB@ \| \|@LB@ 72 47@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -17.2917 kcal/mol@LB@Unfolding Energy - mRNA 5.19453 kcal/mol@LB@Unfolding Energy - sRNA 3.65243 kcal/mol@LB@@LB@Position - mRNA 102 -- 123@LB@Position - sRNA 48 -- 71@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 48 -- 54@LB@
181	0.009071	0.1747	b3962	sthA	-14.30	0.031527	83 -- 114	34 -- 76	pyridine nucleotide transhydrogenase soluble	_____________82___________________________________________115\n_____________\|____________________________________________\|\n5'-UAC...GAAAC____AAA___AA_______________________AU__AG___GAUAA...CAG-3'\n______________AGAC___GCA__GGC____________CGCUCAGG__AU__CCA\n______________\|\|\|\|___:\|\|__:\|\|____________\|:\|\|\|\|\|\|__\|\|__\|\|\|\n______________UCUG___UGU__UCG____________GUGAGUCC__UA__GGU\n3'-UUU...CCGUU____AUG___G____UUAAGCAACAAA________CC__AA___ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________77___________________________________________33\n	99 -- 105	43 -- 49	-23.8174 kcal/mol	4.70621 kcal/mol	4.816 kcal/mol	82 115@LB@ \| \|@LB@5'-UAC...GAAAC AAA AA AU AG GAUAA...CAG-3'@LB@ AGAC GCA GGC CGCUCAGG AU CCA@LB@ \|\|\|\| :\|\| :\|\| \|:\|\|\|\|\|\| \|\| \|\|\|@LB@ UCUG UGU UCG GUGAGUCC UA GGU@LB@3'-UUU...CCGUU AUG G UUAAGCAACAAA CC AA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -23.8174 kcal/mol@LB@Unfolding Energy - mRNA 4.70621 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 83 -- 114@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 43 -- 49@LB@
29	0.0004091	0.04965	b0958	sulA	-15.92	0.011809	212 -- 243	48 -- 76	SOS cell division inhibitor	_____________211______________________________244\n_____________\|________________________________\|\n5'-AUA...ACUUC____________UC__UC_____C___C____CCGCA...UCA-3'\n______________AGGCUAUGCACA__GU__UUCGU_GUU_UCAU\n______________\|\|:\|\|\|::\|\|\|\|__\|:__\|\|\|\|\|_\|\|\|_\|\|\|:\n______________UCUGAUGUGUGU__CG__AAGCA_CAA_AGUG\n3'-UUU...CCGUU________________UU_____A________AGUCC...GCA-5'\n_____________\|________________________________\|\n_____________77_______________________________47\n	217 -- 223	65 -- 71	-24.9625 kcal/mol	5.35271 kcal/mol	3.68714 kcal/mol	211 244@LB@ \| \|@LB@5'-AUA...ACUUC UC UC C C CCGCA...UCA-3'@LB@ AGGCUAUGCACA GU UUCGU GUU UCAU@LB@ \|\|:\|\|\|::\|\|\|\| \|: \|\|\|\|\| \|\|\| \|\|\|:@LB@ UCUGAUGUGUGU CG AAGCA CAA AGUG@LB@3'-UUU...CCGUU UU A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -24.9625 kcal/mol@LB@Unfolding Energy - mRNA 5.35271 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 212 -- 243@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 65 -- 71@LB@
93	0.004161	0.1538	b4221	tamB	-11.98	0.104509	154 -- 185	44 -- 78	translocation and assembly module for autotransporter export inner membrane subunit	_____________153__________________________________186\n_____________\|____________________________________\|\n5'-ACC...CGGAU______GA____________ACA________A____UCUGG...AUC-3'\n______________AAAGAC___ACACGG__GUU____GUUUUAC_UCGG\n______________\|\|\|\|\|\|___\|\|\|\|:\|__:\|\|____\|\|\|\|:\|\|_\|\|:\|\n______________UUUCUG___UGUGUC__UAA____CAAAGUG_AGUC\n3'-UUU...ACCCG______AUG______GU___GCAA____________CCCUA...GCA-5'\n_____________\|____________________________________\|\n_____________79___________________________________43\n	174 -- 180	48 -- 54	-22.2219 kcal/mol	6.10136 kcal/mol	4.13875 kcal/mol	153 186@LB@ \| \|@LB@5'-ACC...CGGAU GA ACA A UCUGG...AUC-3'@LB@ AAAGAC ACACGG GUU GUUUUAC UCGG@LB@ \|\|\|\|\|\| \|\|\|\|:\| :\|\| \|\|\|\|:\|\| \|\|:\|@LB@ UUUCUG UGUGUC UAA CAAAGUG AGUC@LB@3'-UUU...ACCCG AUG GU GCAA CCCUA...GCA-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -22.2219 kcal/mol@LB@Unfolding Energy - mRNA 6.10136 kcal/mol@LB@Unfolding Energy - sRNA 4.13875 kcal/mol@LB@@LB@Position - mRNA 154 -- 185@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 48 -- 54@LB@
110	0.004806	0.1538	b1429	tehA	-12.16	0.096068	32 -- 62	44 -- 75	potassium-tellurite ethidium and proflavin transporter	_____________31_________________________________63\n_____________\|__________________________________\|\n5'-AAU...UUCCU___A__UAAA_________C___UC_________ACGAU...UUU-3'\n______________GAU_AC____GGC___UCG_UGU__UUCACUUAG\n______________\|\|:_\|\|____:\|\|___\|\|\|_\|\|\|__\|\|\|\|\|\|:\|\|\n______________CUG_UG____UCG___AGC_ACA__AAGUGAGUC\n3'-UUU...CGUUU___A__UGUG___UUA___A______________CCCUA...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________43\n	56 -- 62	44 -- 50	-20.5577 kcal/mol	4.26011 kcal/mol	4.13839 kcal/mol	31 63@LB@ \| \|@LB@5'-AAU...UUCCU A UAAA C UC ACGAU...UUU-3'@LB@ GAU AC GGC UCG UGU UUCACUUAG@LB@ \|\|: \|\| :\|\| \|\|\| \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UG UCG AGC ACA AAGUGAGUC@LB@3'-UUU...CGUUU A UGUG UUA A CCCUA...GCA-5'@LB@ \| \|@LB@ 76 43@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -20.5577 kcal/mol@LB@Unfolding Energy - mRNA 4.26011 kcal/mol@LB@Unfolding Energy - sRNA 4.13839 kcal/mol@LB@@LB@Position - mRNA 32 -- 62@LB@Position - sRNA 44 -- 75@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 44 -- 50@LB@
45	0.001296	0.1014	b2465	tktB	-16.90	0.006168	210 -- 248	39 -- 78	transketolase 2 thiamine triphosphate-binding	_____________209__________________________________________249\n_____________\|____________________________________________\|\n5'-AGU...CCCGA______CU______AU________CG___________UAU____GCGGU...CUG-3'\n______________AAAGAC__UGC_CA__GCGAUUCG______CACUCAG___GGAU\n______________\|\|\|\|\|\|__\|:\|_\|\|__\|\|:\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|\|\n______________UUUCUG__AUG_GU__CGUUAAGC______GUGAGUC___CCUA\n3'-UUU...ACCCG___________U__GU________AACAAA_______C______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	235 -- 241	44 -- 50	-32.1578 kcal/mol	10.4844 kcal/mol	4.77966 kcal/mol	209 249@LB@ \| \|@LB@5'-AGU...CCCGA CU AU CG UAU GCGGU...CUG-3'@LB@ AAAGAC UGC CA GCGAUUCG CACUCAG GGAU@LB@ \|\|\|\|\|\| \|:\| \|\| \|\|:\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUG AUG GU CGUUAAGC GUGAGUC CCUA@LB@3'-UUU...ACCCG U GU AACAAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.90 kcal/mol@LB@Hybridization Energy -32.1578 kcal/mol@LB@Unfolding Energy - mRNA 10.4844 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 210 -- 248@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 44 -- 50@LB@
141	0.006483	0.1605	b2474	tmcA	-12.94	0.065378	86 -- 105	35 -- 54	elongator methionine tRNA (ac4C34) acetyltransferase	_____________85___________________106\n_____________\|____________________\|\n5'-GAU...AGACA__________U__CAC____CAGCA...UUG-3'\n______________GUUUCACUCA_GG___UUCU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|:\n______________CAAAGUGAGU_CC___AAGG\n3'-UUU...AGCAA__________C__CUA____UACGA...GCA-5'\n_____________\|____________________\|\n_____________55___________________34\n	89 -- 95	45 -- 51	-18.4772 kcal/mol	3.58569 kcal/mol	1.95269 kcal/mol	85 106@LB@ \| \|@LB@5'-GAU...AGACA U CAC CAGCA...UUG-3'@LB@ GUUUCACUCA GG UUCU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ CAAAGUGAGU CC AAGG@LB@3'-UUU...AGCAA C CUA UACGA...GCA-5'@LB@ \| \|@LB@ 55 34@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -18.4772 kcal/mol@LB@Unfolding Energy - mRNA 3.58569 kcal/mol@LB@Unfolding Energy - sRNA 1.95269 kcal/mol@LB@@LB@Position - mRNA 86 -- 105@LB@Position - sRNA 35 -- 54@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 45 -- 51@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