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
157	0.007641	0.1668	b3154	yhbP	-10.32	0.216043	188 -- 213	45 -- 78	UPF0306 family protein	_____________187________________________________214\n_____________\|__________________________________\|\n5'-AAA...GUAUA_____GA____________GGAAA__________UCGCC...UUU-3'\n______________AAAGA______ACAGCAAU_________CACUCA\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|_________\|\|\|\|\|\|\n______________UUUCU______UGUCGUUA_________GUGAGU\n3'-UUU...ACCCG_____GAUGUG________AGCAACAAA______CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________44\n	196 -- 202	60 -- 66	-17.2265 kcal/mol	3.1682 kcal/mol	3.741 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...GUAUA GA GGAAA UCGCC...UUU-3'@LB@ AAAGA ACAGCAAU CACUCA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUCU UGUCGUUA GUGAGU@LB@3'-UUU...ACCCG GAUGUG AGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.2265 kcal/mol@LB@Unfolding Energy - mRNA 3.1682 kcal/mol@LB@Unfolding Energy - sRNA 3.741 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 60 -- 66@LB@
176	0.008803	0.1747	b1242	ychE	-11.39	0.137124	41 -- 64	45 -- 75	UPF0056 family inner membrane protein	_____________40______________________________65\n_____________\|_______________________________\|\n5'-CAU...UUGGU____________________________A__ACUAG...GCA-3'\n______________GGCUACAU_UAGCA______UGUUUUGC_CA\n______________\|:\|\|\|\|\|:_:\|\|\|\|______\|\|\|\|\|::\|_\|\|\n______________CUGAUGUG_GUCGU______ACAAAGUG_GU\n3'-UUU...CGUUU________U_____UAAGCA________A__CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	55 -- 61	48 -- 54	-19.9041 kcal/mol	4.77357 kcal/mol	3.74078 kcal/mol	40 65@LB@ \| \|@LB@5'-CAU...UUGGU A ACUAG...GCA-3'@LB@ GGCUACAU UAGCA UGUUUUGC CA@LB@ \|:\|\|\|\|\|: :\|\|\|\| \|\|\|\|\|::\| \|\|@LB@ CUGAUGUG GUCGU ACAAAGUG GU@LB@3'-UUU...CGUUU U UAAGCA A CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -19.9041 kcal/mol@LB@Unfolding Energy - mRNA 4.77357 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 41 -- 64@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 48 -- 54@LB@
182	0.009082	0.1747	b3998	nfi	-11.38	0.137700	53 -- 76	45 -- 75	endonuclease V; deoxyinosine 3' endonuclease	_____________52______________________________77\n_____________\|_______________________________\|\n5'-UGG...GUAGC________UU_________________G___CGGCG...GAG-3'\n______________GACUAUAC___GCAG______GUUUCG_UCA\n______________\|\|\|\|\|:\|\|___\|\|\|:______\|\|\|\|\|:_\|\|\|\n______________CUGAUGUG___CGUU______CAAAGU_AGU\n3'-UUU...CGUUU________UGU____AAGCAA______G___CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	54 -- 60	68 -- 74	-21.6188 kcal/mol	6.49773 kcal/mol	3.74078 kcal/mol	52 77@LB@ \| \|@LB@5'-UGG...GUAGC UU G CGGCG...GAG-3'@LB@ GACUAUAC GCAG GUUUCG UCA@LB@ \|\|\|\|\|:\|\| \|\|\|: \|\|\|\|\|: \|\|\|@LB@ CUGAUGUG CGUU CAAAGU AGU@LB@3'-UUU...CGUUU UGU AAGCAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.38 kcal/mol@LB@Hybridization Energy -21.6188 kcal/mol@LB@Unfolding Energy - mRNA 6.49773 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 53 -- 76@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 68 -- 74@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@
198	0.01016	0.1776	b1764	selD	-10.66	0.187945	118 -- 146	45 -- 71	selenophosphate synthase	_____________117___________________________147\n_____________\|_____________________________\|\n5'-UUU...AGCAA_G______G_____AGACACUC_______UCACU...AGC-3'\n______________A_GCGCAG_AAUUC________UCACUUA\n______________\|_:\|:\|\|\|_\|\|\|\|\|________\|\|\|\|\|:\|\n______________U_UGUGUC_UUAAG________AGUGAGU\n3'-UUU...UCUGA_G______G_____CAACAA_________CCCCU...GCA-5'\n_____________\|_____________________________\|\n_____________72____________________________44\n	140 -- 146	45 -- 51	-20.1282 kcal/mol	5.75637 kcal/mol	3.71323 kcal/mol	117 147@LB@ \| \|@LB@5'-UUU...AGCAA G G AGACACUC UCACU...AGC-3'@LB@ A GCGCAG AAUUC UCACUUA@LB@ \| :\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|@LB@ U UGUGUC UUAAG AGUGAGU@LB@3'-UUU...UCUGA G G CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 72 44@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -20.1282 kcal/mol@LB@Unfolding Energy - mRNA 5.75637 kcal/mol@LB@Unfolding Energy - sRNA 3.71323 kcal/mol@LB@@LB@Position - mRNA 118 -- 146@LB@Position - sRNA 45 -- 71@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 45 -- 51@LB@
199	0.01026	0.1776	b2324	mnmC	-11.15	0.152427	29 -- 45	45 -- 74	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme	_____________28_____________________________46\n_____________\|______________________________\|\n5'-GCU...UAAUC______________________________AUACC...ACG-3'\n______________ACUGCAC_____________GUUUCAUUCA\n______________\|\|\|:\|\|\|_____________\|\|\|\|\|\|:\|\|\|\n______________UGAUGUG_____________CAAAGUGAGU\n3'-UUU...GUUUC_______UGUCGUUAAGCAA__________CCCCU...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________44\n	39 -- 45	45 -- 51	-17.885 kcal/mol	2.99426 kcal/mol	3.74056 kcal/mol	28 46@LB@ \| \|@LB@5'-GCU...UAAUC AUACC...ACG-3'@LB@ ACUGCAC GUUUCAUUCA@LB@ \|\|\|:\|\|\| \|\|\|\|\|\|:\|\|\|@LB@ UGAUGUG CAAAGUGAGU@LB@3'-UUU...GUUUC UGUCGUUAAGCAA CCCCU...GCA-5'@LB@ \| \|@LB@ 75 44@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -17.885 kcal/mol@LB@Unfolding Energy - mRNA 2.99426 kcal/mol@LB@Unfolding Energy - sRNA 3.74056 kcal/mol@LB@@LB@Position - mRNA 29 -- 45@LB@Position - sRNA 45 -- 74@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 45 -- 51@LB@
50	0.001668	0.1153	b2821	ptrA	-10.19	0.227412	3 -- 12	46 -- 55	protease III	_____________2__________13\n_____________\|__________\|\n_________5'-GC__________UAAUC...CCA-3'\n______________UGUUUCGCUU\n______________\|\|\|\|\|\|:\|\|:\n______________ACAAAGUGAG\n3'-UUU...AAGCA__________UCCCC...GCA-5'\n_____________\|__________\|\n_____________56_________45\n	6 -- 12	46 -- 52	-11.8599 kcal/mol	0.772948 kcal/mol	0.89782 kcal/mol	2 13@LB@ \| \|@LB@ 5'-GC UAAUC...CCA-3'@LB@ UGUUUCGCUU@LB@ \|\|\|\|\|\|:\|\|:@LB@ ACAAAGUGAG@LB@3'-UUU...AAGCA UCCCC...GCA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -11.8599 kcal/mol@LB@Unfolding Energy - mRNA 0.772948 kcal/mol@LB@Unfolding Energy - sRNA 0.89782 kcal/mol@LB@@LB@Position - mRNA 3 -- 12@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 46 -- 52@LB@
103	0.004595	0.1538	b3554	yiaF	-10.61	0.191588	8 -- 38	46 -- 75	barrier effect co-colonization resistance factor; DUF3053 family lipoprotein	_____________7_________________________________39\n_____________\|_________________________________\|\n____5'-AAUCUCU_______AAAAA_________GCACUA______UUUAA...AGC-3'\n______________GGCUACA_____GGCAA__CG______UCAUUU\n______________\|:\|\|\|\|\|_____:\|\|\|\|__\|\|______\|\|\|:\|:\n______________CUGAUGU_____UCGUU__GC______AGUGAG\n3'-UUU...CGUUU_______GUG_______AA__AACAA_______UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________76________________________________45\n	8 -- 14	69 -- 75	-17.9003 kcal/mol	3.5618 kcal/mol	3.72616 kcal/mol	7 39@LB@ \| \|@LB@ 5'-AAUCUCU AAAAA GCACUA UUUAA...AGC-3'@LB@ GGCUACA GGCAA CG UCAUUU@LB@ \|:\|\|\|\|\| :\|\|\|\| \|\| \|\|\|:\|:@LB@ CUGAUGU UCGUU GC AGUGAG@LB@3'-UUU...CGUUU GUG AA AACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 76 45@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -17.9003 kcal/mol@LB@Unfolding Energy - mRNA 3.5618 kcal/mol@LB@Unfolding Energy - sRNA 3.72616 kcal/mol@LB@@LB@Position - mRNA 8 -- 38@LB@Position - sRNA 46 -- 75@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 69 -- 75@LB@
130	0.005881	0.1577	b0965	yccU	-10.68	0.186123	93 -- 125	46 -- 74	putative CoA-binding protein	_____________92________________________________126\n_____________\|_________________________________\|\n5'-UCA...UACUU___A________A__UAU___CCGC________UCAUU...UGA-3'\n______________ACU_ACAUAUAG_CA___UUC____UUUUGCUC\n______________\|\|\|_\|\|\|:\|:\|\|_\|\|___\|\|\|____\|\|\|::\|\|\|\n______________UGA_UGUGUGUC_GU___AAG____AAAGUGAG\n3'-UUU...GUUUC_______________U_____CAAC________UCCCC...GCA-5'\n_____________\|_________________________________\|\n_____________75________________________________45\n	119 -- 125	46 -- 52	-18.0647 kcal/mol	3.65669 kcal/mol	3.72594 kcal/mol	92 126@LB@ \| \|@LB@5'-UCA...UACUU A A UAU CCGC UCAUU...UGA-3'@LB@ ACU ACAUAUAG CA UUC UUUUGCUC@LB@ \|\|\| \|\|\|:\|:\|\| \|\| \|\|\| \|\|\|::\|\|\|@LB@ UGA UGUGUGUC GU AAG AAAGUGAG@LB@3'-UUU...GUUUC U CAAC UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.0647 kcal/mol@LB@Unfolding Energy - mRNA 3.65669 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 93 -- 125@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 46 -- 52@LB@
131	0.005914	0.1577	b2360	yfdQ	-15.68	0.013816	114 -- 143	46 -- 74	CPS-53 (KpLE1) prophage; uncharacterized protein	_____________113____________________________144\n_____________\|______________________________\|\n5'-UCC...GGAAA___C__________G__AUUAAUA______UUAAU...CUG-3'\n______________ACU_CGCGCAGCAG_UC_______UCAUUC\n______________\|\|\|_\|:\|:\|\|\|\|\|:_\|\|_______\|\|\|:\|\|\n______________UGA_GUGUGUCGUU_AG_______AGUGAG\n3'-UUU...GUUUC___U__________A__CAACAA_______UCCCC...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________45\n	121 -- 127	61 -- 67	-23.4619 kcal/mol	4.06011 kcal/mol	3.72594 kcal/mol	113 144@LB@ \| \|@LB@5'-UCC...GGAAA C G AUUAAUA UUAAU...CUG-3'@LB@ ACU CGCGCAGCAG UC UCAUUC@LB@ \|\|\| \|:\|:\|\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UGA GUGUGUCGUU AG AGUGAG@LB@3'-UUU...GUUUC U A CAACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -23.4619 kcal/mol@LB@Unfolding Energy - mRNA 4.06011 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 114 -- 143@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 61 -- 67@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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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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