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
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@
122	0.01263	0.3462	b0537	intD	-10.49	0.096065	54 -- 80	48 -- 76	DLP12 prophage; putative phage integrase	_____________53____________________________81\n_____________\|_____________________________\|\n5'-GAG...AUUGG____________________A________ACGCA...AAG-3'\n______________UUUUGUAU_UUGGGGAG_CA_UGGCGAUG\n______________\|\|\|\|:\|\|\|_\|\|\|\|::\|:_\|\|_\|\|\|\|:\|\|\|\n______________AAAAUAUA_AACCUUUU_GU_ACCGUUAC\n3'-UUU...ACAGA________C________A__C________GUUAC...UUG-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	74 -- 80	48 -- 54	-25.3626 kcal/mol	9.83015 kcal/mol	5.0412 kcal/mol	53 81@LB@ \| \|@LB@5'-GAG...AUUGG A ACGCA...AAG-3'@LB@ UUUUGUAU UUGGGGAG CA UGGCGAUG@LB@ \|\|\|\|:\|\|\| \|\|\|\|::\|: \|\| \|\|\|\|:\|\|\|@LB@ AAAAUAUA AACCUUUU GU ACCGUUAC@LB@3'-UUU...ACAGA C A C GUUAC...UUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.3626 kcal/mol@LB@Unfolding Energy - mRNA 9.83015 kcal/mol@LB@Unfolding Energy - sRNA 5.0412 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 48 -- 54@LB@
44	0.002732	0.2088	b3450	ugpC	-10.48	0.096645	106 -- 116	47 -- 57	sn-glycerol-3-phosphate ABC transporter ATPase	_____________105_________117\n_____________\|___________\|\n5'-GUG...GUGAU___________UGUUA...UCG-3'\n______________GGUGGCGAUGU\n______________:\|\|\|\|\|:\|\|\|:\n______________UCACCGUUACG\n3'-UUU...UUUAG___________UUACC...UUG-5'\n_____________\|___________\|\n_____________58__________46\n	110 -- 116	47 -- 53	-17.083 kcal/mol	3.56469 kcal/mol	3.03952 kcal/mol	105 117@LB@ \| \|@LB@5'-GUG...GUGAU UGUUA...UCG-3'@LB@ GGUGGCGAUGU@LB@ :\|\|\|\|\|:\|\|\|:@LB@ UCACCGUUACG@LB@3'-UUU...UUUAG UUACC...UUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.083 kcal/mol@LB@Unfolding Energy - mRNA 3.56469 kcal/mol@LB@Unfolding Energy - sRNA 3.03952 kcal/mol@LB@@LB@Position - mRNA 106 -- 116@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 47 -- 53@LB@
9	0.0003848	0.1262	b2708	srlQ	-10.45	0.097910	5 -- 28	40 -- 60	D-arabinose 5-phosphate isomerase	_____________4_________________________29\n_____________\|_________________________\|\n_______5'-UACC______AA____AU___________GCGCG...GCG-3'\n______________GUCAGU__GGCA__GUGCAAUG_CC\n______________:\|\|\|\|\|__\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\n______________UAGUCA__CCGU__UACGUUAC_GG\n3'-UUU...CCUUU______________________C__GUUGU...UUG-5'\n_____________\|_________________________\|\n_____________61________________________39\n	20 -- 26	43 -- 49	-23.8159 kcal/mol	7.25851 kcal/mol	6.10522 kcal/mol	4 29@LB@ \| \|@LB@ 5'-UACC AA AU GCGCG...GCG-3'@LB@ GUCAGU GGCA GUGCAAUG CC@LB@ :\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ UAGUCA CCGU UACGUUAC GG@LB@3'-UUU...CCUUU C GUUGU...UUG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -23.8159 kcal/mol@LB@Unfolding Energy - mRNA 7.25851 kcal/mol@LB@Unfolding Energy - sRNA 6.10522 kcal/mol@LB@@LB@Position - mRNA 5 -- 28@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 43 -- 49@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@
180	0.02233	0.4143	b0435	bolA	-10.38	0.101210	35 -- 46	39 -- 51	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________34____________47\n_____________\|_____________\|\n5'-UGA...ACACU_____________GUGUU...CCG-3'\n______________GAUGCGA_GGCCU\n______________:\|\|\|\|:\|_\|\|\|\|:\n______________UUACGUU_CCGGG\n3'-UUU...CACCG_______A_____UUGUC...UUG-5'\n_____________\|_____________\|\n_____________52____________38\n	35 -- 41	45 -- 51	-16.689 kcal/mol	1.55914 kcal/mol	4.74571 kcal/mol	34 47@LB@ \| \|@LB@5'-UGA...ACACU GUGUU...CCG-3'@LB@ GAUGCGA GGCCU@LB@ :\|\|\|\|:\| \|\|\|\|:@LB@ UUACGUU CCGGG@LB@3'-UUU...CACCG A UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.689 kcal/mol@LB@Unfolding Energy - mRNA 1.55914 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@LB@
135	0.01531	0.3774	b3224	nanT	-10.34	0.103537	56 -- 77	28 -- 54	sialic acid transporter	_____________55__________________________78\n_____________\|___________________________\|\n5'-CGC...CUGAA_____________________UU____CAAGA...GUU-3'\n______________GGC___GC__UGGCCCAGCAG__GAUG\n______________\|\|\|___\|\|__\|\|\|\|\|\|\|:\|\|\|__:\|\|:\n______________CCG___CG__ACCGGGUUGUC__UUAU\n3'-UUU...AGUCA___UUA__UU___________UU____UUUAG...UUG-5'\n_____________\|___________________________\|\n_____________55__________________________27\n	63 -- 69	36 -- 42	-28.0045 kcal/mol	8.68418 kcal/mol	8.98285 kcal/mol	55 78@LB@ \| \|@LB@5'-CGC...CUGAA UU CAAGA...GUU-3'@LB@ GGC GC UGGCCCAGCAG GAUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|:\|\|\| :\|\|:@LB@ CCG CG ACCGGGUUGUC UUAU@LB@3'-UUU...AGUCA UUA UU UU UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -28.0045 kcal/mol@LB@Unfolding Energy - mRNA 8.68418 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 56 -- 77@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 36 -- 42@LB@
131	0.01428	0.3654	b2099	yegU	-10.27	0.106798	246 -- 258	42 -- 54	ADP-ribosylglycohydrolase family protein	_____________245___________259\n_____________\|_____________\|\n5'-GUG...CGUUA__G__________GGAUG...CAC-3'\n______________GG_GAUGCGAUGG\n______________\|\|_:\|\|\|\|:\|\|\|\|\n______________CC_UUACGUUACC\n3'-UUU...AGUCA__G__________GGGUU...UUG-5'\n_____________\|_____________\|\n_____________55____________41\n	252 -- 258	42 -- 48	-19.8763 kcal/mol	6.10373 kcal/mol	3.49932 kcal/mol	245 259@LB@ \| \|@LB@5'-GUG...CGUUA G GGAUG...CAC-3'@LB@ GG GAUGCGAUGG@LB@ \|\| :\|\|\|\|:\|\|\|\|@LB@ CC UUACGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -19.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.10373 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 42 -- 48@LB@
17	0.0007572	0.1438	b2512	bamB	-10.25	0.108120	60 -- 97	8 -- 56	BamABCDE complex OM biogenesis lipoprotein	_____________59________________________________________________98\n_____________\|_________________________________________________\|\n5'-GCU...CCUGC_______A___U_____G____AAG_________________GC_____GCGCG...CCC-3'\n______________GUGGUGA_GCA_U_GCU_AGCA_____________GUGAUAA__AAGGU\n______________\|\|\|\|::\|_\|\|\|_\|_\|\|:_\|:\|\|_____________\|\|\|\|:\|\|__\|\|\|\|:\n______________CACCGUU_CGU_A_CGG_UUGU_____________CACUGUU__UUCCG\n3'-UUU...UUAGU_______A___U_C___G____CUUUUAUUUUAGA_______AU_____UAUAUUG-5'\n_____________\|_________________________________________________\|\n_____________57________________________________________________7\n	84 -- 90	15 -- 21	-31.6141 kcal/mol	9.34469 kcal/mol	12.0216 kcal/mol	59 98@LB@ \| \|@LB@5'-GCU...CCUGC A U G AAG GC GCGCG...CCC-3'@LB@ GUGGUGA GCA U GCU AGCA GUGAUAA AAGGU@LB@ \|\|\|\|::\| \|\|\| \| \|\|: \|:\|\| \|\|\|\|:\|\| \|\|\|\|:@LB@ CACCGUU CGU A CGG UUGU CACUGUU UUCCG@LB@3'-UUU...UUAGU A U C G CUUUUAUUUUAGA AU UAUAUUG-5'@LB@ \| \|@LB@ 57 7@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -31.6141 kcal/mol@LB@Unfolding Energy - mRNA 9.34469 kcal/mol@LB@Unfolding Energy - sRNA 12.0216 kcal/mol@LB@@LB@Position - mRNA 60 -- 97@LB@Position - sRNA 8 -- 56@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 15 -- 21@LB@
108	0.01004	0.3126	b2422	cysA	-10.23	0.108830	144 -- 158	52 -- 72	sulfate/thiosulfate transporter subunit	_____________143___________________159\n_____________\|_____________________\|\n5'-GGU...AAAAA_____________________GCCUG...UGC-3'\n______________GUAUGUUG______CAGUGGC\n______________:\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________UAUACAAC______GUCACCG\n3'-UUU...AAAAA________CUUUUA_______UUACG...UUG-5'\n_____________\|_____________________\|\n_____________73____________________51\n	152 -- 158	52 -- 58	-18.4697 kcal/mol	5.08596 kcal/mol	3.1495 kcal/mol	143 159@LB@ \| \|@LB@5'-GGU...AAAAA GCCUG...UGC-3'@LB@ GUAUGUUG CAGUGGC@LB@ :\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UAUACAAC GUCACCG@LB@3'-UUU...AAAAA CUUUUA UUACG...UUG-5'@LB@ \| \|@LB@ 73 51@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -18.4697 kcal/mol@LB@Unfolding Energy - mRNA 5.08596 kcal/mol@LB@Unfolding Energy - sRNA 3.1495 kcal/mol@LB@@LB@Position - mRNA 144 -- 158@LB@Position - sRNA 52 -- 72@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 52 -- 58@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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