Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
18	0.001289	0.2406	b3930	menA	-10.08	0.182848	73 -- 82	42 -- 51	1 4-dihydroxy-2-naphthoate octaprenyltransferase	_____________72_________83\n_____________\|__________\|\n5'-AGC...AGAUU__________ACAUC...CGC-3'\n______________AUGUGAGCAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UACACUCGUU\n3'-UUU...UUCGU__________ACAGC...GCG-5'\n_____________\|__________\|\n_____________52_________41\n	76 -- 82	42 -- 48	-14.1762 kcal/mol	2.92742 kcal/mol	1.16834 kcal/mol	72 83@LB@ \| \|@LB@5'-AGC...AGAUU ACAUC...CGC-3'@LB@ AUGUGAGCAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UACACUCGUU@LB@3'-UUU...UUCGU ACAGC...GCG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -14.1762 kcal/mol@LB@Unfolding Energy - mRNA 2.92742 kcal/mol@LB@Unfolding Energy - sRNA 1.16834 kcal/mol@LB@@LB@Position - mRNA 73 -- 82@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 42 -- 48@LB@
171	0.02102	0.4072	b1747	astA	-10.86	0.137376	74 -- 103	34 -- 65	arginine succinyltransferase	_____________73_______________________________104\n_____________\|________________________________\|\n5'-GGC...CGUGA________AUU_____________C__G____GUUUU...AAG-3'\n______________UGGUACUG___GCGG_GUG_GCAA_GU_GUGC\n______________\|::\|\|\|\|\|___\|\|::_\|\|\|_\|\|\|\|_\|\|_\|\|\|\|\n______________AUUAUGAC___CGUU_CAC_CGUU_CA_CACG\n3'-UUU...GAUUC________CUU____A___U____A__G____AAAGU...GCG-5'\n_____________\|________________________________\|\n_____________66_______________________________33\n	75 -- 81	58 -- 64	-29.9398 kcal/mol	12.3081 kcal/mol	6.77229 kcal/mol	73 104@LB@ \| \|@LB@5'-GGC...CGUGA AUU C G GUUUU...AAG-3'@LB@ UGGUACUG GCGG GUG GCAA GU GUGC@LB@ \|::\|\|\|\|\| \|\|:: \|\|\| \|\|\|\| \|\| \|\|\|\|@LB@ AUUAUGAC CGUU CAC CGUU CA CACG@LB@3'-UUU...GAUUC CUU A U A G AAAGU...GCG-5'@LB@ \| \|@LB@ 66 33@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -29.9398 kcal/mol@LB@Unfolding Energy - mRNA 12.3081 kcal/mol@LB@Unfolding Energy - sRNA 6.77229 kcal/mol@LB@@LB@Position - mRNA 74 -- 103@LB@Position - sRNA 34 -- 65@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 58 -- 64@LB@
64	0.005632	0.2905	b3005	exbD	-12.96	0.061586	76 -- 96	37 -- 56	membrane spanning protein in TonB-ExbB-ExbD complex	_____________75____________________97\n_____________\|_____________________\|\n5'-CGG...CUUUA________C____________CAGCG...UCU-3'\n______________AAGCGAUG_UGGGUGAUGUUG\n______________\|\|\|\|:\|\|\|_\|\|:\|::\|\|\|\|:\|\n______________UUCGUUAC_ACUCGUUACAGC\n3'-UUU...UGACC_____________________ACGAA...GCG-5'\n_____________\|_____________________\|\n_____________57____________________36\n	90 -- 96	37 -- 43	-25.0811 kcal/mol	8.89195 kcal/mol	3.22494 kcal/mol	75 97@LB@ \| \|@LB@5'-CGG...CUUUA C CAGCG...UCU-3'@LB@ AAGCGAUG UGGGUGAUGUUG@LB@ \|\|\|\|:\|\|\| \|\|:\|::\|\|\|\|:\|@LB@ UUCGUUAC ACUCGUUACAGC@LB@3'-UUU...UGACC ACGAA...GCG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -25.0811 kcal/mol@LB@Unfolding Energy - mRNA 8.89195 kcal/mol@LB@Unfolding Energy - sRNA 3.22494 kcal/mol@LB@@LB@Position - mRNA 76 -- 96@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 37 -- 43@LB@
182	0.02236	0.4113	b2206	napA	-12.10	0.085901	76 -- 101	42 -- 66	nitrate reductase periplasmic large subunit	_____________75_________________________102\n_____________\|__________________________\|\n5'-GAC...UGAUU______G_________AAGAC_____AACGC...UUG-3'\n______________GUGGUG_UGGAAGCAG_____AGCGA\n______________\|\|::\|:_\|\|\|\|\|\|\|\|:_____\|\|\|:\|\n______________CAUUAU_ACCUUCGUU_____UCGUU\n3'-UUU...CGAUU______G_________ACAC______ACAGC...GCG-5'\n_____________\|__________________________\|\n_____________67_________________________41\n	85 -- 91	51 -- 57	-24.6932 kcal/mol	9.28668 kcal/mol	3.30477 kcal/mol	75 102@LB@ \| \|@LB@5'-GAC...UGAUU G AAGAC AACGC...UUG-3'@LB@ GUGGUG UGGAAGCAG AGCGA@LB@ \|\|::\|: \|\|\|\|\|\|\|\|: \|\|\|:\|@LB@ CAUUAU ACCUUCGUU UCGUU@LB@3'-UUU...CGAUU G ACAC ACAGC...GCG-5'@LB@ \| \|@LB@ 67 41@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -24.6932 kcal/mol@LB@Unfolding Energy - mRNA 9.28668 kcal/mol@LB@Unfolding Energy - sRNA 3.30477 kcal/mol@LB@@LB@Position - mRNA 76 -- 101@LB@Position - sRNA 42 -- 66@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 51 -- 57@LB@
185	0.02285	0.4113	b0920	elyC	-11.60	0.104081	77 -- 89	66 -- 78	envelope biogenesis factor; DUF218 superfamily protein	_____________76____________90\n_____________\|_____________\|\n5'-UUG...CUCCA_____________ACGUU...GCC-3'\n______________CCGGUUGGCUAAG\n______________\|\|\|\|:\|\|\|\|\|\|\|\|\n______________GGCCGACCGAUUC\n3'-UUU...UCGUG_____________AUUAU...GCG-5'\n_____________\|_____________\|\n_____________79____________65\n	83 -- 89	66 -- 72	-24.3939 kcal/mol	5.56302 kcal/mol	7.23276 kcal/mol	76 90@LB@ \| \|@LB@5'-UUG...CUCCA ACGUU...GCC-3'@LB@ CCGGUUGGCUAAG@LB@ \|\|\|\|:\|\|\|\|\|\|\|\|@LB@ GGCCGACCGAUUC@LB@3'-UUU...UCGUG AUUAU...GCG-5'@LB@ \| \|@LB@ 79 65@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -24.3939 kcal/mol@LB@Unfolding Energy - mRNA 5.56302 kcal/mol@LB@Unfolding Energy - sRNA 7.23276 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 66 -- 78@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 66 -- 72@LB@
138	0.01576	0.3813	b3361	fic	-10.85	0.137765	79 -- 110	27 -- 60	stationary phase-induced protein putative toxin	_____________78__________________________________111\n_____________\|___________________________________\|\n5'-CGC...CGUCU________UUC_______UAA____AA________CCAGU...AAC-3'\n______________CUGGGAGC______AGCG___UCGU__UUUUCAGG\n______________\|\|\|\|:\|\|\|______\|\|\|:___\|\|\|\|__:\|\|\|\|\|\|\|\n______________GACCUUCG______UCGU___AGCA__GAAAGUCC\n3'-UUU...AUUAU________UUACAC____UAC____C_________AAGAG...GCG-5'\n_____________\|___________________________________\|\n_____________61__________________________________26\n	104 -- 110	27 -- 33	-28.8548 kcal/mol	10.0238 kcal/mol	7.97931 kcal/mol	78 111@LB@ \| \|@LB@5'-CGC...CGUCU UUC UAA AA CCAGU...AAC-3'@LB@ CUGGGAGC AGCG UCGU UUUUCAGG@LB@ \|\|\|\|:\|\|\| \|\|\|: \|\|\|\| :\|\|\|\|\|\|\|@LB@ GACCUUCG UCGU AGCA GAAAGUCC@LB@3'-UUU...AUUAU UUACAC UAC C AAGAG...GCG-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -28.8548 kcal/mol@LB@Unfolding Energy - mRNA 10.0238 kcal/mol@LB@Unfolding Energy - sRNA 7.97931 kcal/mol@LB@@LB@Position - mRNA 79 -- 110@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 27 -- 33@LB@
54	0.00511	0.2905	b0487	cueR	-8.71	0.294876	81 -- 102	6 -- 25	copper-responsive regulon transcriptional regulator	_____________80_____________________103\n_____________\|______________________\|\n5'-GUU...ACAUC________C_CA__A_______UAUUA...AAA-3'\n______________UCUCUGUG_G__GU_CUUCCUG\n______________\|\|\|\|:\|:\|_\|__\|\|_\|\|\|\|\|\|\|\n______________AGAGGCGC_C__CA_GAAGGAC\n3'-UUU...GUCCA________U_C___________UAGCG-5'\n_____________\|______________________\|\n_____________26_____________________5\n	96 -- 102	6 -- 12	-22.4921 kcal/mol	6.07455 kcal/mol	7.70509 kcal/mol	80 103@LB@ \| \|@LB@5'-GUU...ACAUC C CA A UAUUA...AAA-3'@LB@ UCUCUGUG G GU CUUCCUG@LB@ \|\|\|\|:\|:\| \| \|\| \|\|\|\|\|\|\|@LB@ AGAGGCGC C CA GAAGGAC@LB@3'-UUU...GUCCA U C UAGCG-5'@LB@ \| \|@LB@ 26 5@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -22.4921 kcal/mol@LB@Unfolding Energy - mRNA 6.07455 kcal/mol@LB@Unfolding Energy - sRNA 7.70509 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 6 -- 25@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 6 -- 12@LB@
140	0.01604	0.3851	b4022	rluF	-13.68	0.046602	82 -- 103	39 -- 60	23S rRNA pseudouridine(2604) synthase	_____________81______________________104\n_____________\|_______________________\|\n5'-UUA...UGCUU____A_______U__________AACGA...UGU-3'\n______________CUGG_AAGUGAU_UGAGCAG_GU\n______________\|\|\|\|_\|\|\|::\|\|_\|\|\|\|\|\|:_\|\|\n______________GACC_UUCGUUA_ACUCGUU_CA\n3'-UUU...AUUAU____________C_______A__GCACG...GCG-5'\n_____________\|_______________________\|\n_____________61______________________38\n	95 -- 101	42 -- 48	-22.0004 kcal/mol	5.021 kcal/mol	3.3001 kcal/mol	81 104@LB@ \| \|@LB@5'-UUA...UGCUU A U AACGA...UGU-3'@LB@ CUGG AAGUGAU UGAGCAG GU@LB@ \|\|\|\| \|\|\|::\|\| \|\|\|\|\|\|: \|\|@LB@ GACC UUCGUUA ACUCGUU CA@LB@3'-UUU...AUUAU C A GCACG...GCG-5'@LB@ \| \|@LB@ 61 38@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -22.0004 kcal/mol@LB@Unfolding Energy - mRNA 5.021 kcal/mol@LB@Unfolding Energy - sRNA 3.3001 kcal/mol@LB@@LB@Position - mRNA 82 -- 103@LB@Position - sRNA 39 -- 60@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 42 -- 48@LB@
16	0.00116	0.2406	b0221	fadE	-14.73	0.030789	87 -- 104	36 -- 53	acyl coenzyme A dehydrogenase	_____________86_________________105\n_____________\|__________________\|\n5'-GUG...AGCAA__________UU______AAUUA...GGA-3'\n______________CAAUGUGAGC__UGUUGU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|:\|\|\n______________GUUACACUCG__ACAGCA\n3'-UUU...CCUUC__________UU______CGAAA...GCG-5'\n_____________\|__________________\|\n_____________54_________________35\n	90 -- 96	44 -- 50	-23.2381 kcal/mol	5.2956 kcal/mol	3.20883 kcal/mol	86 105@LB@ \| \|@LB@5'-GUG...AGCAA UU AAUUA...GGA-3'@LB@ CAAUGUGAGC UGUUGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ GUUACACUCG ACAGCA@LB@3'-UUU...CCUUC UU CGAAA...GCG-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -14.73 kcal/mol@LB@Hybridization Energy -23.2381 kcal/mol@LB@Unfolding Energy - mRNA 5.2956 kcal/mol@LB@Unfolding Energy - sRNA 3.20883 kcal/mol@LB@@LB@Position - mRNA 87 -- 104@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 44 -- 50@LB@
30	0.002864	0.2776	b1863	ruvC	-10.04	0.185852	89 -- 98	54 -- 63	component of RuvABC resolvasome endonuclease	_____________88_________99\n_____________\|__________\|\n5'-AGC...UCGAU__________AUUGC...GCA-3'\n______________AUGCUGGAAG\n______________\|\|:\|\|\|\|\|\|\|\n______________UAUGACCUUC\n3'-UUU...UUCAU__________GUUAC...GCG-5'\n_____________\|__________\|\n_____________64_________53\n	92 -- 98	54 -- 60	-14.3659 kcal/mol	1.62427 kcal/mol	2.70635 kcal/mol	88 99@LB@ \| \|@LB@5'-AGC...UCGAU AUUGC...GCA-3'@LB@ AUGCUGGAAG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ UAUGACCUUC@LB@3'-UUU...UUCAU GUUAC...GCG-5'@LB@ \| \|@LB@ 64 53@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -14.3659 kcal/mol@LB@Unfolding Energy - mRNA 1.62427 kcal/mol@LB@Unfolding Energy - sRNA 2.70635 kcal/mol@LB@@LB@Position - mRNA 89 -- 98@LB@Position - sRNA 54 -- 63@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 54 -- 60@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)

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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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