Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
33	0.0003369	0.03519	b0523	purE	-12.01	0.010423	150 -- 160	3 -- 13	N5-carboxyaminoimidazole ribonucleotide mutase	_____________149__________161\n_____________\|____________\|\n5'-UGG...GCUAU____________CUAAA...UGA-3'\n______________UCUCUGUGCCCU\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GGAGACAUGGGA\n3'-AUU...AGAAU____________UG-5'\n_____________\|____________\|\n_____________14___________2\n	154 -- 160	3 -- 9	-20.2448 kcal/mol	2.89849 kcal/mol	5.35591 kcal/mol	149 161@LB@ \| \|@LB@5'-UGG...GCUAU CUAAA...UGA-3'@LB@ UCUCUGUGCCCU@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GGAGACAUGGGA@LB@3'-AUU...AGAAU UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -20.2448 kcal/mol@LB@Unfolding Energy - mRNA 2.89849 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 150 -- 160@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
60	0.0009057	0.0531	b2740	ygbN	-7.72	0.181404	16 -- 72	3 -- 58	putative transporter	_____________15__________________________________________________________73\n_____________\|___________________________________________________________\|\n5'-GUG...CGCCU_______G_G_____A__UC___G_____UC___UGU______AA__________G___CACCG...UCC-3'\n______________GUUCGAU_A_GUGGG_UA__AGG_CUGGA__GGU___GAAUAU___ACCUC_GUG_CCU\n______________:\|:\|\|\|\|_\|_\|\|\|::_\|\|__\|\|\|_\|\|\|:\|__\|:\|___\|\|\|:\|\|___\|\|\|\|\|_\|\|:_\|\|\|\n______________UAGGCUA_U_CACUU_AU__UCC_GACUU__CUA___CUUGUA___UGGAG_CAU_GGA\n3'-AUU...CGGUU_______A_G_____C__UU___A_____U____U________GAA_____A___G___UG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	16 -- 22	52 -- 58	-40.891 kcal/mol	20.495 kcal/mol	12.7026 kcal/mol	15 73@LB@ \| \|@LB@5'-GUG...CGCCU G G A UC G UC UGU AA G CACCG...UCC-3'@LB@ GUUCGAU A GUGGG UA AGG CUGGA GGU GAAUAU ACCUC GUG CCU@LB@ :\|:\|\|\|\| \| \|\|\|:: \|\| \|\|\| \|\|\|:\| \|:\| \|\|\|:\|\| \|\|\|\|\| \|\|: \|\|\|@LB@ UAGGCUA U CACUU AU UCC GACUU CUA CUUGUA UGGAG CAU GGA@LB@3'-AUU...CGGUU A G C UU A U U GAA A G UG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -40.891 kcal/mol@LB@Unfolding Energy - mRNA 20.495 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 16 -- 72@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 52 -- 58@LB@
68	0.001174	0.05856	b1253	yciA	-8.30	0.130708	128 -- 145	3 -- 21	acyl-CoA esterase	_____________127__________________146\n_____________\|____________________\|\n5'-UUU...CGCUG______________UC____CAGGA...GGU-3'\n______________UAUCU__CCUCUGU__UCCU\n______________:\|\|\|\|__\|\|\|\|\|\|\|__:\|\|\|\n______________GUAGA__GGAGACA__GGGA\n3'-AUU...AUCUU_____AU_______U_____UG-5'\n_____________\|____________________\|\n_____________22___________________2\n	133 -- 139	8 -- 14	-17.321 kcal/mol	1.04882 kcal/mol	7.99052 kcal/mol	127 146@LB@ \| \|@LB@5'-UUU...CGCUG UC CAGGA...GGU-3'@LB@ UAUCU CCUCUGU UCCU@LB@ :\|\|\|\| \|\|\|\|\|\|\| :\|\|\|@LB@ GUAGA GGAGACA GGGA@LB@3'-AUU...AUCUU AU U UG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -8.30 kcal/mol@LB@Hybridization Energy -17.321 kcal/mol@LB@Unfolding Energy - mRNA 1.04882 kcal/mol@LB@Unfolding Energy - sRNA 7.99052 kcal/mol@LB@@LB@Position - mRNA 128 -- 145@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 8 -- 14@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)	_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@LB@
136	0.004892	0.1265	b2349	intS	-8.19	0.139381	273 -- 281	3 -- 11	CPS-53 (KpLE1) prophage; putative prophage CPS-53 integrase	_____________272_______282\n_____________\|_________\|\n5'-AAG...AUGGC_________UAUGU...GGA-3'\n______________CUGUACCUU\n______________\|\|\|\|\|\|\|:\|\n______________GACAUGGGA\n3'-AUU...AUGGA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	275 -- 281	3 -- 9	-13.0022 kcal/mol	1.37836 kcal/mol	3.45478 kcal/mol	272 282@LB@ \| \|@LB@5'-AAG...AUGGC UAUGU...GGA-3'@LB@ CUGUACCUU@LB@ \|\|\|\|\|\|\|:\|@LB@ GACAUGGGA@LB@3'-AUU...AUGGA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -13.0022 kcal/mol@LB@Unfolding Energy - mRNA 1.37836 kcal/mol@LB@Unfolding Energy - sRNA 3.45478 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
149	0.005967	0.1406	b0472	recR	-13.66	0.002580	134 -- 160	3 -- 29	gap repair protein	_____________133_________________________161\n_____________\|___________________________\|\n5'-GUG...AACGC___A____AAAAUG_____________CCGGA...UUC-3'\n______________AGA_AGAA______GCCUCUGUAUCCU\n______________\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|\|:\|\|\|\n______________UCU_UCUU______UGGAGACAUGGGA\n3'-AUU...GACUU___A____GUAGAA_____________UG-5'\n_____________\|___________________________\|\n_____________30__________________________2\n	154 -- 160	3 -- 9	-27.6106 kcal/mol	5.92472 kcal/mol	8.05021 kcal/mol	133 161@LB@ \| \|@LB@5'-GUG...AACGC A AAAAUG CCGGA...UUC-3'@LB@ AGA AGAA GCCUCUGUAUCCU@LB@ \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|:\|\|\|@LB@ UCU UCUU UGGAGACAUGGGA@LB@3'-AUU...GACUU A GUAGAA UG-5'@LB@ \| \|@LB@ 30 2@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -27.6106 kcal/mol@LB@Unfolding Energy - mRNA 5.92472 kcal/mol@LB@Unfolding Energy - sRNA 8.05021 kcal/mol@LB@@LB@Position - mRNA 134 -- 160@LB@Position - sRNA 3 -- 29@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
198	0.008802	0.1558	b1905	ftnA	-8.07	0.149574	234 -- 260	3 -- 24	ferritin iron storage protein (cytoplasmic)	_____________233_________________________261\n_____________\|___________________________\|\n5'-CAU...UUAAU_____GA_GA____GGAA_________UCACU...AUC-3'\n______________GAGCA__U__ACCU____CUGUACUCU\n______________\|\|:\|\|__\|__\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CUUGU__A__UGGA____GACAUGGGA\n3'-AUU...UCUAU_____AG_A__________________UG-5'\n_____________\|___________________________\|\n_____________25__________________________2\n	254 -- 260	3 -- 9	-20.546 kcal/mol	4.48094 kcal/mol	8.02061 kcal/mol	233 261@LB@ \| \|@LB@5'-CAU...UUAAU GA GA GGAA UCACU...AUC-3'@LB@ GAGCA U ACCU CUGUACUCU@LB@ \|\|:\|\| \| \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CUUGU A UGGA GACAUGGGA@LB@3'-AUU...UCUAU AG A UG-5'@LB@ \| \|@LB@ 25 2@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.546 kcal/mol@LB@Unfolding Energy - mRNA 4.48094 kcal/mol@LB@Unfolding Energy - sRNA 8.02061 kcal/mol@LB@@LB@Position - mRNA 234 -- 260@LB@Position - sRNA 3 -- 24@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 3 -- 9@LB@
5	1.055e-05	0.007422	b1287	yciW	-9.98	0.045809	266 -- 289	4 -- 27	putative oxidoreductase	_____________265______________________290\n_____________\|________________________\|\n5'-GUC...ACGGA___U______C________GU___GGAAG...CAA-3'\n______________GUA_GACGUU_UGCCUCUG__CCC\n______________:\|\|_:\|\|:\|:_\|:\|\|\|\|\|\|__\|\|\|\n______________UAU_UUGUAG_AUGGAGAC__GGG\n3'-AUU...CUUUC___C______A________AU___AUG-5'\n_____________\|________________________\|\n_____________28_______________________3\n	278 -- 284	9 -- 15	-26.8114 kcal/mol	8.80708 kcal/mol	8.0435 kcal/mol	265 290@LB@ \| \|@LB@5'-GUC...ACGGA U C GU GGAAG...CAA-3'@LB@ GUA GACGUU UGCCUCUG CCC@LB@ :\|\| :\|\|:\|: \|:\|\|\|\|\|\| \|\|\|@LB@ UAU UUGUAG AUGGAGAC GGG@LB@3'-AUU...CUUUC C A AU AUG-5'@LB@ \| \|@LB@ 28 3@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -26.8114 kcal/mol@LB@Unfolding Energy - mRNA 8.80708 kcal/mol@LB@Unfolding Energy - sRNA 8.0435 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 4 -- 27@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 9 -- 15@LB@
7	1.5e-05	0.00754	b0720	gltA	-8.97	0.087950	70 -- 79	4 -- 13	citrate synthase	_____________69_________80\n_____________\|__________\|\n5'-CGG...CAGAG__________AGGUU...GUA-3'\n______________CUCUGUACCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________GAGACAUGGG\n3'-AUU...GAAUG__________AUG-5'\n_____________\|__________\|\n_____________14_________3\n	73 -- 79	4 -- 10	-18.8657 kcal/mol	4.79377 kcal/mol	5.12835 kcal/mol	69 80@LB@ \| \|@LB@5'-CGG...CAGAG AGGUU...GUA-3'@LB@ CUCUGUACCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GAGACAUGGG@LB@3'-AUU...GAAUG AUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -18.8657 kcal/mol@LB@Unfolding Energy - mRNA 4.79377 kcal/mol@LB@Unfolding Energy - sRNA 5.12835 kcal/mol@LB@@LB@Position - mRNA 70 -- 79@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
10	2.605e-05	0.009165	b3599	mtlA	-16.58	0.000118	1 -- 31	4 -- 28	mannitol-specific PTS enzyme: IIA IIB and IIC components	______________1_______________________________32\n______________\|_______________________________\|\n___________5'-___________ACGUCAA________C_____CCUAU...UCA-3'\n______________GAU_GAACGUC_______UUACCUCU_UACCC\n______________\|\|\|_\|\|\|\|:\|\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUA_CUUGUAG_______AAUGGAGA_AUGGG\n3'-AUU...ACUUU___U______________________C_____AUG-5'\n_____________\|________________________________\|\n_____________29_______________________________3\n	19 -- 25	10 -- 16	-27.7982 kcal/mol	3.19385 kcal/mol	8.04825 kcal/mol	1 32@LB@ \| \|@LB@ 5'- ACGUCAA C CCUAU...UCA-3'@LB@ GAU GAACGUC UUACCUCU UACCC@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUA CUUGUAG AAUGGAGA AUGGG@LB@3'-AUU...ACUUU U C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -27.7982 kcal/mol@LB@Unfolding Energy - mRNA 3.19385 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 10 -- 16@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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