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
187	0.009506	0.1776	b1243	oppA	-10.52	0.199375	11 -- 17	40 -- 46	oligopeptide ABC transporter periplasmic binding protein	_____________10______18\n_____________\|_______\|\n5'-UGU...CUCGA_______GACAC...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	11 -- 17	40 -- 46	-13.6251 kcal/mol	1.75344 kcal/mol	1.35582 kcal/mol	10 18@LB@ \| \|@LB@5'-UGU...CUCGA GACAC...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -13.6251 kcal/mol@LB@Unfolding Energy - mRNA 1.75344 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 40 -- 46@LB@
132	0.005915	0.1577	b3356	yhfA	-11.83	0.112173	273 -- 293	39 -- 71	OsmC family protein	_____________272_______________________________294\n_____________\|_________________________________\|\n5'-CUG...UUUUA___G_________________________C___AAAGCAC-3'\n______________AUG_ACGGCA____________ACUCAGG_GAU\n______________\|::_\|\|:\|\|\|____________\|\|\|\|\|\|\|_\|\|\|\n______________UGU_UGUCGU____________UGAGUCC_CUA\n3'-UUU...UCUGA___G______UAAGCAACAAAG_______C___AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	283 -- 289	43 -- 49	-20.9729 kcal/mol	4.393 kcal/mol	4.74947 kcal/mol	272 294@LB@ \| \|@LB@5'-CUG...UUUUA G C AAAGCAC-3'@LB@ AUG ACGGCA ACUCAGG GAU@LB@ \|:: \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UGU UGUCGU UGAGUCC CUA@LB@3'-UUU...UCUGA G UAAGCAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -20.9729 kcal/mol@LB@Unfolding Energy - mRNA 4.393 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 273 -- 293@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 43 -- 49@LB@
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@
24	0.0002076	0.02926	b3459	panM	-18.00	0.002751	9 -- 48	38 -- 75	PanD autocleavage accelerator panothenate synthesis	_____________8___________________________________________49\n_____________\|___________________________________________\|\n___5'-AAAAUAAC_______A_G___GGAAU_____ACUA________________AUGCU...UUG-3'\n______________GGC_ACA_A_GGC_____AAUUC______UCAUUCAGGGGAUU\n______________\|:\|_\|\|\|_\|_:\|\|_____\|\|\|\|\|______\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________CUG_UGU_U_UCG_____UUAAG______AGUGAGUCCCCUAA\n3'-UUU...CGUUU___A___G_G_____________CAACAA______________AGGUA...GCA-5'\n_____________\|___________________________________________\|\n_____________76__________________________________________37\n	42 -- 48	38 -- 44	-31.5918 kcal/mol	8.81239 kcal/mol	4.77946 kcal/mol	8 49@LB@ \| \|@LB@ 5'-AAAAUAAC A G GGAAU ACUA AUGCU...UUG-3'@LB@ GGC ACA A GGC AAUUC UCAUUCAGGGGAUU@LB@ \|:\| \|\|\| \| :\|\| \|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ CUG UGU U UCG UUAAG AGUGAGUCCCCUAA@LB@3'-UUU...CGUUU A G G CAACAA AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -31.5918 kcal/mol@LB@Unfolding Energy - mRNA 8.81239 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 9 -- 48@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 38 -- 44@LB@
46	0.001357	0.1038	b1235	rssB	-13.33	0.053430	184 -- 194	40 -- 50	PcnB-degradosome interaction factor; response regulator	_____________183_________195\n_____________\|___________\|\n5'-AAU...AAAGC__G________GAGAA...CAA-3'\n______________CA_UCAGGGGA\n______________\|\|_\|\|\|\|\|\|\|\|\n______________GU_AGUCCCCU\n3'-UUU...ACAAA__G________AAAGG...GCA-5'\n_____________\|___________\|\n_____________51__________39\n	188 -- 194	40 -- 46	-19.1981 kcal/mol	4.11697 kcal/mol	1.75243 kcal/mol	183 195@LB@ \| \|@LB@5'-AAU...AAAGC G GAGAA...CAA-3'@LB@ CA UCAGGGGA@LB@ \|\| \|\|\|\|\|\|\|\|@LB@ GU AGUCCCCU@LB@3'-UUU...ACAAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -19.1981 kcal/mol@LB@Unfolding Energy - mRNA 4.11697 kcal/mol@LB@Unfolding Energy - sRNA 1.75243 kcal/mol@LB@@LB@Position - mRNA 184 -- 194@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 40 -- 46@LB@
191	0.009733	0.1776	b0190	yaeQ	-9.83	0.261410	113 -- 128	45 -- 75	PDDEXK superfamily protein	_____________112_____________________________129\n_____________\|_______________________________\|\n5'-UAC...AAGGU_______________________________UUUCU...CUU-3'\n______________GACUAUAC_CA______________CACUCA\n______________\|\|\|\|\|:\|\|_\|\|______________\|\|\|\|\|\|\n______________CUGAUGUG_GU______________GUGAGU\n3'-UUU...CGUUU________U__CGUUAAGCAACAAA______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	114 -- 120	68 -- 74	-15.3898 kcal/mol	1.82074 kcal/mol	3.74078 kcal/mol	112 129@LB@ \| \|@LB@5'-UAC...AAGGU UUUCU...CUU-3'@LB@ GACUAUAC CA CACUCA@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CUGAUGUG GU GUGAGU@LB@3'-UUU...CGUUU U CGUUAAGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -15.3898 kcal/mol@LB@Unfolding Energy - mRNA 1.82074 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 68 -- 74@LB@
15	0.0001044	0.0245	b0741	pal	-16.61	0.007509	30 -- 75	30 -- 71	peptidoglycan-associated outer membrane lipoprotein	_____________29_____________________________________________76\n_____________\|______________________________________________\|\n5'-GGA...UAACG____U________CUACAGCUCUU__________GGGA________GAAUU...GCG-3'\n______________GCAC_AUGGUAAU___________CUCAGGGGAU____UCCGUGCU\n______________:\|\|\|_\|::\|:\|\|\|___________\|\|\|\|\|\|\|\|\|\|____\|\|\|:\|\|\|\|\n______________UGUG_UGUCGUUA___________GAGUCCCCUA____AGGUACGA\n3'-UUU...UCUGA_____________AGCAACAAAGU__________A___________AUAUU...GCA-5'\n_____________\|______________________________________________\|\n_____________72_____________________________________________29\n	69 -- 75	30 -- 36	-38.4662 kcal/mol	13.7923 kcal/mol	8.066 kcal/mol	29 76@LB@ \| \|@LB@5'-GGA...UAACG U CUACAGCUCUU GGGA GAAUU...GCG-3'@LB@ GCAC AUGGUAAU CUCAGGGGAU UCCGUGCU@LB@ :\|\|\| \|::\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|\|@LB@ UGUG UGUCGUUA GAGUCCCCUA AGGUACGA@LB@3'-UUU...UCUGA AGCAACAAAGU A AUAUU...GCA-5'@LB@ \| \|@LB@ 72 29@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -38.4662 kcal/mol@LB@Unfolding Energy - mRNA 13.7923 kcal/mol@LB@Unfolding Energy - sRNA 8.066 kcal/mol@LB@@LB@Position - mRNA 30 -- 75@LB@Position - sRNA 30 -- 71@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 30 -- 36@LB@
40	0.0008945	0.07693	b0525	ppiB	-7.31	0.578113	284 -- 298	61 -- 76	peptidyl-prolyl cis-trans isomerase B (rotamase B)	_____________283______________299\n_____________\|________________\|\n5'-UGU...UUCCU___________C____AG-3'\n______________GGACUAC_UGC_GCGA\n______________:\|\|\|\|\|\|_::\|_\|\|:\|\n______________UCUGAUG_GUG_CGUU\n3'-UUU...CCGUU_______U___U____AAGCA...GCA-5'\n_____________\|________________\|\n_____________77_______________60\n	284 -- 290	70 -- 76	-14.2171 kcal/mol	3.65067 kcal/mol	3.25604 kcal/mol	283 299@LB@ \| \|@LB@5'-UGU...UUCCU C AG-3'@LB@ GGACUAC UGC GCGA@LB@ :\|\|\|\|\|\| ::\| \|\|:\|@LB@ UCUGAUG GUG CGUU@LB@3'-UUU...CCGUU U U AAGCA...GCA-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -14.2171 kcal/mol@LB@Unfolding Energy - mRNA 3.65067 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 70 -- 76@LB@
9	4.743e-05	0.01855	b1204	pth	-17.38	0.004387	162 -- 190	43 -- 74	peptidyl-tRNA hydrolase	_____________161_______________________________191\n_____________\|_________________________________\|\n5'-UGG...AGUAA________________A_____ACA________ACAAA...AGC-3'\n______________ACUACGCGC__CAGUU___UGU___CACUCAGG\n______________\|\|\|\|\|:\|:\|__\|\|:\|\|___\|\|\|___\|\|\|\|\|\|\|\|\n______________UGAUGUGUG__GUUAA___ACA___GUGAGUCC\n3'-UUU...GUUUC_________UC_____GCA___AA_________CCUAA...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________42\n	184 -- 190	43 -- 49	-27.969 kcal/mol	6.24318 kcal/mol	4.35222 kcal/mol	161 191@LB@ \| \|@LB@5'-UGG...AGUAA A ACA ACAAA...AGC-3'@LB@ ACUACGCGC CAGUU UGU CACUCAGG@LB@ \|\|\|\|\|:\|:\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAUGUGUG GUUAA ACA GUGAGUCC@LB@3'-UUU...GUUUC UC GCA AA CCUAA...GCA-5'@LB@ \| \|@LB@ 75 42@LB@@LB@@LB@Energy -17.38 kcal/mol@LB@Hybridization Energy -27.969 kcal/mol@LB@Unfolding Energy - mRNA 6.24318 kcal/mol@LB@Unfolding Energy - sRNA 4.35222 kcal/mol@LB@@LB@Position - mRNA 162 -- 190@LB@Position - sRNA 43 -- 74@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 43 -- 49@LB@
172	0.008479	0.1735	b4395	ytjC	-10.99	0.163500	244 -- 268	34 -- 71	phosphatase	_____________243____________________________________269\n_____________\|______________________________________\|\n5'-UCC...GUGGA____CG________________________________GUCUG...AGC-3'\n______________ACGC__AGCGA__CGU______AUUCAGGG_____CCA\n______________\|\|:\|__\|\|\|:\|__\|\|\|______\|:\|\|\|\|\|\|_____\|\|\|\n______________UGUG__UCGUU__GCA______UGAGUCCC_____GGU\n3'-UUU...UCUGA____UG_____AA___ACAAAG________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	259 -- 265	42 -- 48	-22.1302 kcal/mol	6.3498 kcal/mol	4.79237 kcal/mol	243 269@LB@ \| \|@LB@5'-UCC...GUGGA CG GUCUG...AGC-3'@LB@ ACGC AGCGA CGU AUUCAGGG CCA@LB@ \|\|:\| \|\|\|:\| \|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGUG UCGUU GCA UGAGUCCC GGU@LB@3'-UUU...UCUGA UG AA ACAAAG CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -22.1302 kcal/mol@LB@Unfolding Energy - mRNA 6.3498 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 244 -- 268@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@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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