Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
48	0.009918	0.5385	b0641	lptE	-9.88	0.110832	177 -- 184	74 -- 81	LPS assembly OM complex LptDE lipoprotein component	_____________176______185\n_____________\|________\|\n5'-ACG...CUGGU________AAGCG...UGA-3'\n______________CGUUGGCU\n______________\|\|\|\|\|\|\|\|\n______________GCAACCGA\n3'-CGC...CAAGU________AAUCA...AAG-5'\n_____________\|________\|\n_____________82_______73\n	178 -- 184	74 -- 80	-13.2047 kcal/mol	2.99134 kcal/mol	0.332056 kcal/mol	176 185@LB@ \| \|@LB@5'-ACG...CUGGU AAGCG...UGA-3'@LB@ CGUUGGCU@LB@ \|\|\|\|\|\|\|\|@LB@ GCAACCGA@LB@3'-CGC...CAAGU AAUCA...AAG-5'@LB@ \| \|@LB@ 82 73@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.2047 kcal/mol@LB@Unfolding Energy - mRNA 2.99134 kcal/mol@LB@Unfolding Energy - sRNA 0.332056 kcal/mol@LB@@LB@Position - mRNA 177 -- 184@LB@Position - sRNA 74 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 74 -- 80@LB@
42	0.008798	0.5385	b0087	mraY	-9.88	0.111048	142 -- 153	79 -- 90	phospho-N-acetylmuramoyl-pentapeptide transferase	_____________141__________154\n_____________\|____________\|\n5'-GAC...UAGUU____________AGUGC...CGC-3'\n______________AAGGGUUCACGU\n______________\|\|::\|\|\|\|\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	147 -- 153	79 -- 85	-14.1224 kcal/mol	3.73912 kcal/mol	0.506924 kcal/mol	141 154@LB@ \| \|@LB@5'-GAC...UAGUU AGUGC...CGC-3'@LB@ AAGGGUUCACGU@LB@ \|\|::\|\|\|\|\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -14.1224 kcal/mol@LB@Unfolding Energy - mRNA 3.73912 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 79 -- 85@LB@
124	0.02124	0.5385	b0198	metI	-9.85	0.112177	270 -- 285	71 -- 87	DL-methionine transporter subunit	_____________269_______________286\n_____________\|_________________\|\n5'-UCA...UAUCC_____UU__________UGAUU...CGG-3'\n______________GGUUU___UUGGCUUUG\n______________:\|\|\|:___\|\|\|\|\|\|\|\|:\n______________UCAAG___AACCGAAAU\n3'-CGC...CGUUU_____UGC_________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	279 -- 285	71 -- 77	-13.0228 kcal/mol	2.60961 kcal/mol	0.562376 kcal/mol	269 286@LB@ \| \|@LB@5'-UCA...UAUCC UU UGAUU...CGG-3'@LB@ GGUUU UUGGCUUUG@LB@ :\|\|\|: \|\|\|\|\|\|\|\|:@LB@ UCAAG AACCGAAAU@LB@3'-CGC...CGUUU UGC CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.0228 kcal/mol@LB@Unfolding Energy - mRNA 2.60961 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 270 -- 285@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 71 -- 77@LB@
100	0.01671	0.5385	b3211	yhcC	-9.80	0.114390	283 -- 295	70 -- 82	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________282___________296\n_____________\|_____________\|\n5'-UGC...GCUGC___GC________CUGCC-3'\n______________ACG__GGUUUUAG\n______________\|\|\|__\|\|:\|\|\|\|\|\n______________UGC__CCGAAAUC\n3'-CGC...UCAAG___AA________AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	289 -- 295	70 -- 76	-11.7424 kcal/mol	1.55142 kcal/mol	0.389672 kcal/mol	282 296@LB@ \| \|@LB@5'-UGC...GCUGC GC CUGCC-3'@LB@ ACG GGUUUUAG@LB@ \|\|\| \|\|:\|\|\|\|\|@LB@ UGC CCGAAAUC@LB@3'-CGC...UCAAG AA AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -11.7424 kcal/mol@LB@Unfolding Energy - mRNA 1.55142 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
76	0.01392	0.5385	b0066	thiQ	-9.74	0.117374	220 -- 232	71 -- 84	thiamine/thiamine pyrophosphate ABC transporter ATPase	_____________219____________233\n_____________\|______________\|\n5'-GCU...UGAUA____C_________CCACC...CAA-3'\n______________UCAC__UGGCUUUA\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________AGUG__ACCGAAAU\n3'-CGC...UUUCA____CA________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	226 -- 232	71 -- 77	-13.9563 kcal/mol	3.66363 kcal/mol	0.5567 kcal/mol	219 233@LB@ \| \|@LB@5'-GCU...UGAUA C CCACC...CAA-3'@LB@ UCAC UGGCUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGUG ACCGAAAU@LB@3'-CGC...UUUCA CA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.9563 kcal/mol@LB@Unfolding Energy - mRNA 3.66363 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 220 -- 232@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 71 -- 77@LB@
110	0.0189	0.5385	b3175	secG	-9.72	0.118042	86 -- 106	67 -- 90	preprotein translocase membrane subunit	_____________85_______________________107\n_____________\|________________________\|\n5'-GCG...CUUGC__________UC____________GUAUU...CCU-3'\n______________GAAGG_UCAU____GCUUUGGUUA\n______________:\|\|:\|_\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________UUUUC_AGUG____CGAAAUCAAU\n3'-CGC...AGGCG_____A____CAAC__________AAGCU...AAG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	100 -- 106	67 -- 73	-15.607 kcal/mol	5.31183 kcal/mol	0.573552 kcal/mol	85 107@LB@ \| \|@LB@5'-GCG...CUUGC UC GUAUU...CCU-3'@LB@ GAAGG UCAU GCUUUGGUUA@LB@ :\|\|:\| \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ UUUUC AGUG CGAAAUCAAU@LB@3'-CGC...AGGCG A CAAC AAGCU...AAG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -9.72 kcal/mol@LB@Hybridization Energy -15.607 kcal/mol@LB@Unfolding Energy - mRNA 5.31183 kcal/mol@LB@Unfolding Energy - sRNA 0.573552 kcal/mol@LB@@LB@Position - mRNA 86 -- 106@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 67 -- 73@LB@
165	0.02909	0.5559	b3283	yrdD	-9.69	0.119373	265 -- 285	52 -- 72	ssDNA-binding protein function unknown	_____________264___________________286\n_____________\|_____________________\|\n5'-AAC...UGAAC___________UCC_______ACGGU...UUG-3'\n______________UGGUUAUUCGA___GGGAAAC\n______________\|:\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________AUCAAUAAGCU___CUCUUUG\n3'-CGC...CCGAA___________CAA_______AGAGC...AAG-5'\n_____________\|_____________________\|\n_____________73____________________51\n	279 -- 285	52 -- 58	-20.8466 kcal/mol	6.85358 kcal/mol	4.29991 kcal/mol	264 286@LB@ \| \|@LB@5'-AAC...UGAAC UCC ACGGU...UUG-3'@LB@ UGGUUAUUCGA GGGAAAC@LB@ \|:\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ AUCAAUAAGCU CUCUUUG@LB@3'-CGC...CCGAA CAA AGAGC...AAG-5'@LB@ \| \|@LB@ 73 51@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -20.8466 kcal/mol@LB@Unfolding Energy - mRNA 6.85358 kcal/mol@LB@Unfolding Energy - sRNA 4.29991 kcal/mol@LB@@LB@Position - mRNA 265 -- 285@LB@Position - sRNA 52 -- 72@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 52 -- 58@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
167	0.02971	0.5559	b3062	ttdB	-9.65	0.121251	224 -- 260	75 -- 106	L-tartrate dehydratase beta subunit	_____________223___________________________________261\n_____________\|_____________________________________\|\n5'-GGA...ACCCC____AAAG___A____________UA_______C___GAUGU...GCG-3'\n______________GAUC____CUG_AGAUCUGCAAGA__UUCGCGU_GGC\n______________\|\|\|\|____\|\|\|_\|\|\|\|\|:\|\|\|\|:\|__\|\|\|:\|\|\|_\|\|\|\n______________CUAG____GAC_UCUAGGCGUUUU__AAGUGCA_CCG\n________3'-CGC___________C____________C________A___AAAUC...AAG-5'\n_____________\|_____________________________________\|\n_____________107___________________________________74\n	250 -- 256	79 -- 85	-36.8095 kcal/mol	15.2774 kcal/mol	11.8787 kcal/mol	223 261@LB@ \| \|@LB@5'-GGA...ACCCC AAAG A UA C GAUGU...GCG-3'@LB@ GAUC CUG AGAUCUGCAAGA UUCGCGU GGC@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\|\|\|\|:\| \|\|\|:\|\|\| \|\|\|@LB@ CUAG GAC UCUAGGCGUUUU AAGUGCA CCG@LB@ 3'-CGC C C A AAAUC...AAG-5'@LB@ \| \|@LB@ 107 74@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -36.8095 kcal/mol@LB@Unfolding Energy - mRNA 15.2774 kcal/mol@LB@Unfolding Energy - sRNA 11.8787 kcal/mol@LB@@LB@Position - mRNA 224 -- 260@LB@Position - sRNA 75 -- 106@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 79 -- 85@LB@
184	0.03259	0.5559	b0811	glnH	-9.61	0.123139	215 -- 230	74 -- 90	glutamine transporter subunit	_____________214________________231\n_____________\|__________________\|\n5'-AUC...GUAUU_______U__________GCACU...CCG-3'\n______________AAAAGUU_CAC__UGGCU\n______________\|\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________UUUUCAA_GUG__ACCGA\n3'-CGC...AGGCG___________CA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	215 -- 221	84 -- 90	-14.2101 kcal/mol	4.07847 kcal/mol	0.517587 kcal/mol	214 231@LB@ \| \|@LB@5'-AUC...GUAUU U GCACU...CCG-3'@LB@ AAAAGUU CAC UGGCU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUCAA GUG ACCGA@LB@3'-CGC...AGGCG CA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -14.2101 kcal/mol@LB@Unfolding Energy - mRNA 4.07847 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 84 -- 90@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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