Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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	Additional homologs
43	0.0008959	0.07003	b3068	mug	-12.52	0.050096	232 -- 248	1 -- 17	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase		_____________231_______________249\n_____________\|_________________\|\n5'-UGG...GUUAC____C_______G____AUCAA...CGG-3'\n______________GGGU_GUGUUUU_CGGU\n______________\|\|\|\|_:\|\|\|\|\|\|_\|:\|:\n______________CCCA_UACAAAA_GUCG\n3'-UUU...AAAUA____A_______A____-5'\n_____________\|________________\|\n_____________18_______________1\n	237 -- 243	6 -- 12	-17.5569 kcal/mol	4.10869 kcal/mol	0.931609 kcal/mol	231 249@LB@ \| \|@LB@5'-UGG...GUUAC C G AUCAA...CGG-3'@LB@ GGGU GUGUUUU CGGU@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|:@LB@ CCCA UACAAAA GUCG@LB@3'-UUU...AAAUA A A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -17.5569 kcal/mol@LB@Unfolding Energy - mRNA 4.10869 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 232 -- 248@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 6 -- 12@LB@
140	0.006493	0.1559	b1916	sdiA	-12.48	0.051059	182 -- 224	1 -- 50	quorum-sensing transcriptional activator		_____________181_________________________________________________225\n_____________\|___________________________________________________\|\n5'-UGU...CUCUC_____C_____G_____U______U___GGAUAA___AU____________UGGCG...AGG-3'\n______________AGGGG___GUU_C_GGU_UA_CUA_GCA_______GG_____UUUUUCAGC\n______________\|\|\|:\|___\|\|\|_\|_\|\|\|_:\|_\|\|\|_\|\|\|_______\|\|_____\|\|\|\|\|\|\|\|\|\n______________UCCUC___CAA_G_CCA_GU_GAU_CGU_______CC_____AAAAAGUCG\n3'-UUU...CCGAU_____CAC___G_A___U__C_______AAAAUAC__AAUAC_________-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	218 -- 224	1 -- 7	-26.3158 kcal/mol	9.17132 kcal/mol	4.6634 kcal/mol	181 225@LB@ \| \|@LB@5'-UGU...CUCUC C G U U GGAUAA AU UGGCG...AGG-3'@LB@ AGGGG GUU C GGU UA CUA GCA GG UUUUUCAGC@LB@ \|\|\|:\| \|\|\| \| \|\|\| :\| \|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUC CAA G CCA GU GAU CGU CC AAAAAGUCG@LB@3'-UUU...CCGAU CAC G A U C AAAAUAC AAUAC -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -26.3158 kcal/mol@LB@Unfolding Energy - mRNA 9.17132 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 182 -- 224@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 1 -- 7@LB@
57	0.001403	0.08147	b0948	rlmL	-12.46	0.051711	286 -- 300	33 -- 47	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent		_____________285____________300\n_____________\|______________\|\n5'-GAC...AUGCC_________AG____-3'\n______________AGGUGGUUC__GGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________UCCACCAAG__CCAU\n3'-UUU...AUUCC_________GA____GUCGA...UCG-5'\n_____________\|_______________\|\n_____________48______________32\n	288 -- 294	39 -- 45	-21.3846 kcal/mol	5.67574 kcal/mol	3.25146 kcal/mol	285 300@LB@ \| \|@LB@5'-GAC...AUGCC AG -3'@LB@ AGGUGGUUC GGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:@LB@ UCCACCAAG CCAU@LB@3'-UUU...AUUCC GA GUCGA...UCG-5'@LB@ \| \|@LB@ 48 32@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.3846 kcal/mol@LB@Unfolding Energy - mRNA 5.67574 kcal/mol@LB@Unfolding Energy - sRNA 3.25146 kcal/mol@LB@@LB@Position - mRNA 286 -- 300@LB@Position - sRNA 33 -- 47@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 39 -- 45@LB@
33	0.0006117	0.0623	b1795	yeaQ	-12.41	0.053010	276 -- 283	42 -- 49	UPF0410 family protein		_____________275______284\n_____________\|________\|\n5'-AUA...AAGAU________AUUCU...UCC-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	277 -- 283	42 -- 48	-16.41 kcal/mol	1.22894 kcal/mol	2.77009 kcal/mol	275 284@LB@ \| \|@LB@5'-AUA...AAGAU AUUCU...UCC-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -16.41 kcal/mol@LB@Unfolding Energy - mRNA 1.22894 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 276 -- 283@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
167	0.00885	0.1781	b0241	phoE	-12.37	0.054121	1 -- 29	1 -- 31	outer membrane phosphoporin protein E	b0929 b2215 b1377	______________1____________________________________30\n______________\|____________________________________\|\n___________5'-___A___________UGCGC___A_____________AAGCC...AUG-3'\n______________AGC_UGGCGUUUUGU_____GGG_________UCAGC\n______________\|\|\|_\|:\|\|:\|\|\|\|:\|_____\|\|\|_________\|\|\|\|\|\n______________UCG_AUCGUAAAAUA_____CCC_________AGUCG\n3'-UUU...CCAUG_______________________AAUACAAAA_____-5'\n_____________\|____________________________________\|\n_____________32___________________________________1\n	9 -- 15	18 -- 24	-21.8929 kcal/mol	8.03382 kcal/mol	1.48722 kcal/mol	1 30@LB@ \| \|@LB@ 5'- A UGCGC A AAGCC...AUG-3'@LB@ AGC UGGCGUUUUGU GGG UCAGC@LB@ \|\|\| \|:\|\|:\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UCG AUCGUAAAAUA CCC AGUCG@LB@3'-UUU...CCAUG AAUACAAAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -21.8929 kcal/mol@LB@Unfolding Energy - mRNA 8.03382 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@LB@
123	0.005173	0.1413	b0839	dacC	-12.36	0.054489	29 -- 38	24 -- 33	D-alanyl-D-alanine carboxypeptidase; penicillin-binding protein 6a		_____________28_________39\n_____________\|__________\|\n5'-AUG...AAGCA__________AAAAA...AAG-3'\n______________ACAGCUGGCA\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	32 -- 38	24 -- 30	-17.0494 kcal/mol	3.2632 kcal/mol	1.42716 kcal/mol	28 39@LB@ \| \|@LB@5'-AUG...AAGCA AAAAA...AAG-3'@LB@ ACAGCUGGCA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -17.0494 kcal/mol@LB@Unfolding Energy - mRNA 3.2632 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 29 -- 38@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 24 -- 30@LB@
158	0.007987	0.1694	b0756	galM	-12.34	0.055034	97 -- 122	25 -- 48	aldose 1-epimerase; type-1 mutarotase; galactose mutarotase		_____________96_________________________123\n_____________\|__________________________\|\n5'-CUG...CGGAA___C____G____CC_______A___UGUCG...GGG-3'\n______________GAG_UGGU_CCUG__GUACAGC_AGC\n______________\|\|\|_\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________CUC_ACCA_GGAC__CAUGUCG_UCG\n3'-UUU...GAUUC___C____A_____________A___UAAAA...UCG-5'\n_____________\|__________________________\|\n_____________49_________________________24\n	112 -- 118	29 -- 35	-29.4823 kcal/mol	12.5844 kcal/mol	4.55759 kcal/mol	96 123@LB@ \| \|@LB@5'-CUG...CGGAA C G CC A UGUCG...GGG-3'@LB@ GAG UGGU CCUG GUACAGC AGC@LB@ \|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ CUC ACCA GGAC CAUGUCG UCG@LB@3'-UUU...GAUUC C A A UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -12.34 kcal/mol@LB@Hybridization Energy -29.4823 kcal/mol@LB@Unfolding Energy - mRNA 12.5844 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 97 -- 122@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 29 -- 35@LB@
39	0.0008004	0.06626	b1533	eamA	-12.23	0.058236	233 -- 264	16 -- 49	cysteine and O-acetyl-L-serine efflux system		_____________232_________________________________265\n_____________\|___________________________________\|\n5'-GUU...CUACU__UA_____CGUA___G_______A__________UCAUC...UGA-3'\n______________GG__GUGGU____UGG___GGCUA__AUUUUGUGG\n______________\|\|__\|\|\|\|\|____\|\|\|___:\|\|\|\|__\|\|\|\|\|:\|\|\|\n______________CC__CACCA____ACC___UCGAU__UAAAAUACC\n3'-UUU...CGAUU__UC_____AGG____AUG_____CG_________CAAUA...UCG-5'\n_____________\|___________________________________\|\n_____________50__________________________________15\n	258 -- 264	16 -- 22	-27.5137 kcal/mol	10.7081 kcal/mol	4.57266 kcal/mol	232 265@LB@ \| \|@LB@5'-GUU...CUACU UA CGUA G A UCAUC...UGA-3'@LB@ GG GUGGU UGG GGCUA AUUUUGUGG@LB@ \|\| \|\|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CC CACCA ACC UCGAU UAAAAUACC@LB@3'-UUU...CGAUU UC AGG AUG CG CAAUA...UCG-5'@LB@ \| \|@LB@ 50 15@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.5137 kcal/mol@LB@Unfolding Energy - mRNA 10.7081 kcal/mol@LB@Unfolding Energy - sRNA 4.57266 kcal/mol@LB@@LB@Position - mRNA 233 -- 264@LB@Position - sRNA 16 -- 49@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
159	0.008045	0.1694	b1780	yeaD	-12.23	0.058242	44 -- 57	32 -- 44	D-hexose-6-phosphate epimerase-like protein		_____________43_____________58\n_____________\|______________\|\n5'-GAU...GAAAC____A_________GACAA...AUC-3'\n______________UGGU_UCCUGGUAC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________ACCA_AGGACCAUG\n3'-UUU...CCUCC______________UCGAU...UCG-5'\n_____________\|______________\|\n_____________45_____________31\n	51 -- 57	32 -- 38	-20.6656 kcal/mol	5.17692 kcal/mol	3.25604 kcal/mol	43 58@LB@ \| \|@LB@5'-GAU...GAAAC A GACAA...AUC-3'@LB@ UGGU UCCUGGUAC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ ACCA AGGACCAUG@LB@3'-UUU...CCUCC UCGAU...UCG-5'@LB@ \| \|@LB@ 45 31@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -20.6656 kcal/mol@LB@Unfolding Energy - mRNA 5.17692 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 32 -- 44@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 32 -- 38@LB@
44	0.0009392	0.07174	b3453	ugpB	-12.21	0.059079	239 -- 268	1 -- 32	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein		_____________238_______________________________269\n_____________\|_________________________________\|\n5'-UUC...GCGCU___A________A______GA___CACA_____AGUGA...UGG-3'\n______________CGG_CUGGCGUU__AUGGG__AUG______GGC\n______________\|:\|_\|\|:\|\|:\|\|__\|\|\|\|\|__\|\|\|______:\|\|\n______________GUC_GAUCGUAA__UACCC__UAC______UCG\n3'-UUU...ACCAU____________AA_____AA___AAAAAG___-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	244 -- 250	22 -- 28	-24.6308 kcal/mol	10.9347 kcal/mol	1.49075 kcal/mol	238 269@LB@ \| \|@LB@5'-UUC...GCGCU A A GA CACA AGUGA...UGG-3'@LB@ CGG CUGGCGUU AUGGG AUG GGC@LB@ \|:\| \|\|:\|\|:\|\| \|\|\|\|\| \|\|\| :\|\|@LB@ GUC GAUCGUAA UACCC UAC UCG@LB@3'-UUU...ACCAU AA AA AAAAAG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.6308 kcal/mol@LB@Unfolding Energy - mRNA 10.9347 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 239 -- 268@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 22 -- 28@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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