Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
68	0.005347	0.2645	b3184	yhbE	-8.71	0.217326	12 -- 35	8 -- 33	EamA family inner membrane putative transporter	_____________11_________________________36\n_____________\|__________________________\|\n5'-AAG...ACGGU___________C____AGU_______CCGAA...UGG-3'\n______________AAAGUGAAAUU___GA___UAAAGGC\n______________\|\|\|:\|:\|\|\|\|:___\|\|___\|\|\|\|\|\|\|\n______________UUUUAUUUUAG___CU___AUUUCCG\n3'-UUU...UUGUC___________ACA__GUU_______UAUAUUG-5'\n_____________\|__________________________\|\n_____________34_________________________7\n	29 -- 35	8 -- 14	-15.936 kcal/mol	2.19409 kcal/mol	5.02883 kcal/mol	11 36@LB@ \| \|@LB@5'-AAG...ACGGU C AGU CCGAA...UGG-3'@LB@ AAAGUGAAAUU GA UAAAGGC@LB@ \|\|\|:\|:\|\|\|\|: \|\| \|\|\|\|\|\|\|@LB@ UUUUAUUUUAG CU AUUUCCG@LB@3'-UUU...UUGUC ACA GUU UAUAUUG-5'@LB@ \| \|@LB@ 34 7@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -15.936 kcal/mol@LB@Unfolding Energy - mRNA 2.19409 kcal/mol@LB@Unfolding Energy - sRNA 5.02883 kcal/mol@LB@@LB@Position - mRNA 12 -- 35@LB@Position - sRNA 8 -- 33@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 8 -- 14@LB@
69	0.005697	0.2777	b0829	gsiA	-9.42	0.158982	246 -- 287	28 -- 64	glutathione ABC transporter ATPase	_____________245__________________________________________288\n_____________\|____________________________________________\|\n5'-CGG...CGGUU_______UGAAUAUU__CUUU_________A_____________GCUGC...GCA-3'\n______________GAAAAUC________GC____AUGCA__GG_CCAGCAGAAAAUA\n______________\|\|\|\|\|\|\|________\|\|____\|\|\|\|\|__\|\|_\|\|\|:\|\|\|\|\|\|\|\|\|\n______________CUUUUAG________CG____UACGU__CC_GGUUGUCUUUUAU\n3'-UUU...ACAAC_______UCAC______U________UA__G_____________UUUAG...UUG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	246 -- 252	58 -- 64	-27.8415 kcal/mol	7.44564 kcal/mol	10.972 kcal/mol	245 288@LB@ \| \|@LB@5'-CGG...CGGUU UGAAUAUU CUUU A GCUGC...GCA-3'@LB@ GAAAAUC GC AUGCA GG CCAGCAGAAAAUA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ CUUUUAG CG UACGU CC GGUUGUCUUUUAU@LB@3'-UUU...ACAAC UCAC U UA G UUUAG...UUG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -27.8415 kcal/mol@LB@Unfolding Energy - mRNA 7.44564 kcal/mol@LB@Unfolding Energy - sRNA 10.972 kcal/mol@LB@@LB@Position - mRNA 246 -- 287@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
70	0.005852	0.2791	b3524	yhjG	-5.99	0.576071	198 -- 212	7 -- 18	putative inner membrane-anchored periplasmic AsmA family protein	_____________197_____________213\n_____________\|_______________\|\n5'-UUG...AGCGA_______GCA_____GGCAA...GAC-3'\n______________ACGAUGA___AGGCA\n______________\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUUAUU___UCCGU\n3'-UUU...GACAC_______________AUAUUG-5'\n_____________\|_______________\|\n_____________19______________6\n	198 -- 204	12 -- 18	-10.9915 kcal/mol	1.73561 kcal/mol	3.26755 kcal/mol	197 213@LB@ \| \|@LB@5'-UUG...AGCGA GCA GGCAA...GAC-3'@LB@ ACGAUGA AGGCA@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGUUAUU UCCGU@LB@3'-UUU...GACAC AUAUUG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -10.9915 kcal/mol@LB@Unfolding Energy - mRNA 1.73561 kcal/mol@LB@Unfolding Energy - sRNA 3.26755 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
71	0.005918	0.2791	b4348	hsdS	-11.53	0.056880	66 -- 85	42 -- 60	specificity determinant for hsdM and hsdR	_____________65___________________86\n_____________\|____________________\|\n5'-CUG...GAUGU_____C_____AA_______GCGAA...UAA-3'\n______________AUUAG_GGCAG__GCGAUGG\n______________\|\|:\|\|_\|\|\|\|:__\|\|:\|\|\|\|\n______________UAGUC_CCGUU__CGUUACC\n3'-UUU...CCUUU_____A_____A________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________61___________________41\n	79 -- 85	42 -- 48	-21.0522 kcal/mol	5.82821 kcal/mol	3.69672 kcal/mol	65 86@LB@ \| \|@LB@5'-CUG...GAUGU C AA GCGAA...UAA-3'@LB@ AUUAG GGCAG GCGAUGG@LB@ \|\|:\|\| \|\|\|\|: \|\|:\|\|\|\|@LB@ UAGUC CCGUU CGUUACC@LB@3'-UUU...CCUUU A A GGGUU...UUG-5'@LB@ \| \|@LB@ 61 41@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -21.0522 kcal/mol@LB@Unfolding Energy - mRNA 5.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.69672 kcal/mol@LB@@LB@Position - mRNA 66 -- 85@LB@Position - sRNA 42 -- 60@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
72	0.005975	0.2791	b1062	pyrC	-13.01	0.025478	15 -- 31	41 -- 58	dihydro-orotase	_____________14_________________32\n_____________\|__________________\|\n5'-GCG...GCAGC_________A________GAAAA...CCA-3'\n______________CAG_GGCGA_GCAAUGGC\n______________\|\|\|_\|\|\|:\|_\|\|\|\|\|\|\|\|\n______________GUC_CCGUU_CGUUACCG\n3'-UUU...UUUUA___A_____A________GGUUG...UUG-5'\n_____________\|__________________\|\n_____________59_________________40\n	25 -- 31	41 -- 47	-24.8377 kcal/mol	7.56192 kcal/mol	4.26806 kcal/mol	14 32@LB@ \| \|@LB@5'-GCG...GCAGC A GAAAA...CCA-3'@LB@ CAG GGCGA GCAAUGGC@LB@ \|\|\| \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ GUC CCGUU CGUUACCG@LB@3'-UUU...UUUUA A A GGUUG...UUG-5'@LB@ \| \|@LB@ 59 40@LB@@LB@@LB@Energy -13.01 kcal/mol@LB@Hybridization Energy -24.8377 kcal/mol@LB@Unfolding Energy - mRNA 7.56192 kcal/mol@LB@Unfolding Energy - sRNA 4.26806 kcal/mol@LB@@LB@Position - mRNA 15 -- 31@LB@Position - sRNA 41 -- 58@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 41 -- 47@LB@
73	0.006265	0.2822	b2452	eutH	-10.44	0.098342	69 -- 89	40 -- 58	ethanolamine transporter	_____________68____________________90\n_____________\|_____________________\|\n5'-UUG...UCCGC________CG_______U___GGAUG...UCC-3'\n______________CAGUGGCG__GUGCAAU_GCC\n______________\|\|\|\|\|\|\|:__:\|\|\|\|\|\|_\|\|\|\n______________GUCACCGU__UACGUUA_CGG\n3'-UUU...UUUUA_________________C___GUUGU...UUG-5'\n_____________\|_____________________\|\n_____________59____________________39\n	79 -- 85	44 -- 50	-25.8936 kcal/mol	9.38235 kcal/mol	6.06808 kcal/mol	68 90@LB@ \| \|@LB@5'-UUG...UCCGC CG U GGAUG...UCC-3'@LB@ CAGUGGCG GUGCAAU GCC@LB@ \|\|\|\|\|\|\|: :\|\|\|\|\|\| \|\|\|@LB@ GUCACCGU UACGUUA CGG@LB@3'-UUU...UUUUA C GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -25.8936 kcal/mol@LB@Unfolding Energy - mRNA 9.38235 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 69 -- 89@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 44 -- 50@LB@
74	0.006275	0.2822	b3298	rpsM	-14.03	0.014091	187 -- 207	39 -- 57	30S ribosomal subunit protein S13	_____________186___________________208\n_____________\|_____________________\|\n5'-GUC...UAAAU___A_G______UA_______GUAUA...UCC-3'\n______________AGU_G_AGUGCA__GUGGCCC\n______________\|\|\|_\|_\|:\|\|\|\|__:\|\|\|\|\|\|\n______________UCA_C_UUACGU__UACCGGG\n3'-UUU...UUUAG___C_G_______________UUGUC...UUG-5'\n_____________\|_____________________\|\n_____________58____________________38\n	201 -- 207	39 -- 45	-23.7565 kcal/mol	4.54468 kcal/mol	5.17956 kcal/mol	186 208@LB@ \| \|@LB@5'-GUC...UAAAU A G UA GUAUA...UCC-3'@LB@ AGU G AGUGCA GUGGCCC@LB@ \|\|\| \| \|:\|\|\|\| :\|\|\|\|\|\|@LB@ UCA C UUACGU UACCGGG@LB@3'-UUU...UUUAG C G UUGUC...UUG-5'@LB@ \| \|@LB@ 58 38@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -23.7565 kcal/mol@LB@Unfolding Energy - mRNA 4.54468 kcal/mol@LB@Unfolding Energy - sRNA 5.17956 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 39 -- 57@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 39 -- 45@LB@
75	0.006388	0.2822	b2813	mltA	-10.80	0.082551	232 -- 252	47 -- 66	membrane-bound lytic murein transglycosylase A	_____________231____________________253\n_____________\|______________________\|\n5'-UGC...UCUUA____CAC_______________UUGCC...AAG-3'\n______________UGGG___GGUU_GUGGCAAUGC\n______________\|\|\|:___::\|:_\|\|\|\|\|\|\|\|\|\|\n______________ACCU___UUAG_CACCGUUACG\n3'-UUU...AUACA____U______U__________UUACC...UUG-5'\n_____________\|______________________\|\n_____________67_____________________46\n	246 -- 252	47 -- 53	-21.5988 kcal/mol	6.72365 kcal/mol	4.0775 kcal/mol	231 253@LB@ \| \|@LB@5'-UGC...UCUUA CAC UUGCC...AAG-3'@LB@ UGGG GGUU GUGGCAAUGC@LB@ \|\|\|: ::\|: \|\|\|\|\|\|\|\|\|\|@LB@ ACCU UUAG CACCGUUACG@LB@3'-UUU...AUACA U U UUACC...UUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -21.5988 kcal/mol@LB@Unfolding Energy - mRNA 6.72365 kcal/mol@LB@Unfolding Energy - sRNA 4.0775 kcal/mol@LB@@LB@Position - mRNA 232 -- 252@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 47 -- 53@LB@
76	0.006626	0.2822	b1658	purR	-10.59	0.091499	175 -- 205	41 -- 63	transcriptional repressor hypoxanthine-binding	_____________174______________________________206\n_____________\|________________________________\|\n5'-UUU...GAGCU____________CUGGAGUGA____G______AACAA...GCA-3'\n______________GAAGUUAG_GGU_________AAUG_AAUGGC\n______________:\|\|:\|:\|\|_\|\|:_________\|\|\|\|_\|\|\|\|\|\|\n______________UUUUAGUC_CCG_________UUAC_UUACCG\n3'-UUU...CAACC________A________________G______GGUUG...UUG-5'\n_____________\|________________________________\|\n_____________64_______________________________40\n	176 -- 182	56 -- 62	-19.9152 kcal/mol	5.04846 kcal/mol	4.27657 kcal/mol	174 206@LB@ \| \|@LB@5'-UUU...GAGCU CUGGAGUGA G AACAA...GCA-3'@LB@ GAAGUUAG GGU AAUG AAUGGC@LB@ :\|\|:\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|\|@LB@ UUUUAGUC CCG UUAC UUACCG@LB@3'-UUU...CAACC A G GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 5.04846 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 175 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 56 -- 62@LB@
77	0.006658	0.2822	b3347	fkpA	-8.74	0.214444	80 -- 111	4 -- 28	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)	_____________79________________________________112\n_____________\|_________________________________\|\n5'-UGG...CAAAA________AAAAUAGA_________________CUGUA...CAG-3'\n______________AGAGUCUG________UGAUAAU_AGGGCGUGU\n______________\|:\|:\|\|\|\|________\|\|\|:\|\|\|_\|:\|\|\|:\|:\|\n______________UUUUAGAC________ACUGUUA_UUCCGUAUA\n3'-UUU...UUUUA_______________________U_________UUG-5'\n_____________\|_________________________________\|\n_____________29________________________________3\n	104 -- 110	5 -- 11	-22.6947 kcal/mol	9.05802 kcal/mol	4.89231 kcal/mol	79 112@LB@ \| \|@LB@5'-UGG...CAAAA AAAAUAGA CUGUA...CAG-3'@LB@ AGAGUCUG UGAUAAU AGGGCGUGU@LB@ \|:\|:\|\|\|\| \|\|\|:\|\|\| \|:\|\|\|:\|:\|@LB@ UUUUAGAC ACUGUUA UUCCGUAUA@LB@3'-UUU...UUUUA U UUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -22.6947 kcal/mol@LB@Unfolding Energy - mRNA 9.05802 kcal/mol@LB@Unfolding Energy - sRNA 4.89231 kcal/mol@LB@@LB@Position - mRNA 80 -- 111@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 5 -- 11@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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