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
195	0.008707	0.1558	b3318	rplW	-7.58	0.194751	202 -- 213	43 -- 55	50S ribosomal subunit protein L23	_____________201___________214\n_____________\|_____________\|\n5'-GCA...UGGCA_____________AACGU...AAG-3'\n______________UGAUU_CGUGAAG\n______________:\|\|\|\|_\|\|\|\|\|\|\|\n______________GCUAA_GCACUUC\n3'-AUU...UUUAG_____U_______AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	207 -- 213	43 -- 49	-13.4464 kcal/mol	2.60751 kcal/mol	3.2693 kcal/mol	201 214@LB@ \| \|@LB@5'-GCA...UGGCA AACGU...AAG-3'@LB@ UGAUU CGUGAAG@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ GCUAA GCACUUC@LB@3'-AUU...UUUAG U AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -13.4464 kcal/mol@LB@Unfolding Energy - mRNA 2.60751 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 43 -- 49@LB@
67	0.001147	0.05856	b2319	usg	-10.96	0.023185	203 -- 221	18 -- 36	putative semialdehyde dehydrogenase	_____________202_________________222\n_____________\|___________________\|\n5'-GAG...ACCAU_________C_________GCCGU...AAA-3'\n______________GUCUGAAGG_UGGAACAUU\n______________\|\|\|\|\|\|\|:\|_\|:\|\|\|\|\|\|:\n______________CAGACUUUC_AUCUUGUAG\n3'-AUU...UUUUC_________U_________AAUGG...AUG-5'\n_____________\|___________________\|\n_____________37__________________17\n	215 -- 221	18 -- 24	-22.956 kcal/mol	5.32254 kcal/mol	6.60045 kcal/mol	202 222@LB@ \| \|@LB@5'-GAG...ACCAU C GCCGU...AAA-3'@LB@ GUCUGAAGG UGGAACAUU@LB@ \|\|\|\|\|\|\|:\| \|:\|\|\|\|\|\|:@LB@ CAGACUUUC AUCUUGUAG@LB@3'-AUU...UUUUC U AAUGG...AUG-5'@LB@ \| \|@LB@ 37 17@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.956 kcal/mol@LB@Unfolding Energy - mRNA 5.32254 kcal/mol@LB@Unfolding Energy - sRNA 6.60045 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 18 -- 36@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 18 -- 24@LB@
144	0.005273	0.1288	b1652	rnt	-8.26	0.134019	203 -- 213	48 -- 58	RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair	_____________202_________214\n_____________\|___________\|\n5'-AAG...CAGAU_______A___CUCAA...CCG-3'\n______________GUCCGAU_ACG\n______________:\|\|\|\|\|\|_\|\|\|\n______________UAGGCUA_UGC\n3'-AUU...CGGUU_______A___ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	203 -- 209	52 -- 58	-12.2442 kcal/mol	2.4043 kcal/mol	1.55987 kcal/mol	202 214@LB@ \| \|@LB@5'-AAG...CAGAU A CUCAA...CCG-3'@LB@ GUCCGAU ACG@LB@ :\|\|\|\|\|\| \|\|\|@LB@ UAGGCUA UGC@LB@3'-AUU...CGGUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -12.2442 kcal/mol@LB@Unfolding Energy - mRNA 2.4043 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 203 -- 213@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 52 -- 58@LB@
164	0.006623	0.1421	b2278	nuoL	-8.77	0.099276	203 -- 221	5 -- 24	NADH:ubiquinone oxidoreductase membrane subunit L	_____________202___________________222\n_____________\|_____________________\|\n5'-GGU...CGGAU______G________A_____AUUAU...UCG-3'\n______________GAACAU_CUUGCCUU___ACC\n______________\|\|\|\|\|\|_\|\|\|:\|\|\|:___\|\|\|\n______________CUUGUA_GAAUGGAG___UGG\n3'-AUU...UCUAU_______________ACA___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	211 -- 217	11 -- 17	-20.7037 kcal/mol	3.94864 kcal/mol	8.01095 kcal/mol	202 222@LB@ \| \|@LB@5'-GGU...CGGAU G A AUUAU...UCG-3'@LB@ GAACAU CUUGCCUU ACC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|: \|\|\|@LB@ CUUGUA GAAUGGAG UGG@LB@3'-AUU...UCUAU ACA GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -20.7037 kcal/mol@LB@Unfolding Energy - mRNA 3.94864 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
38	0.0004278	0.03766	b3092	uxaC	-12.53	0.006845	206 -- 269	1 -- 57	uronate isomerase	_____________205_________________________________________________________________270\n_____________\|___________________________________________________________________\|\n5'-UUG...AUGAC____U_____AC_____AUUUC______UU_____CC____UUGCCC___G________ACGA____GCAAA...AUU-3'\n______________UCCG_UUAUG__UGAAG________CUG__AGAUA__GAAU______GCC_UCUGUAUC____CUAC\n______________\|\|\|\|_\|\|\|:\|__\|\|\|\|\|________\|\|\|__\|\|\|\|\|__\|\|\|:______:\|\|_\|\|\|\|\|\|:\|____\|\|\|\|\n______________AGGC_AAUGC__ACUUC________GAC__UCUAU__CUUG______UGG_AGACAUGG____GAUG\n3'-AUU...GGUUU____U____________AUUUUCCA___UU___________UAGAA_____________________-5'\n_____________\|__________________________________________________________________\|\n_____________58_________________________________________________________________1\n	255 -- 261	5 -- 11	-36.5836 kcal/mol	11.3711 kcal/mol	12.7026 kcal/mol	205 270@LB@ \| \|@LB@5'-UUG...AUGAC U AC AUUUC UU CC UUGCCC G ACGA GCAAA...AUU-3'@LB@ UCCG UUAUG UGAAG CUG AGAUA GAAU GCC UCUGUAUC CUAC@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|\| \|\|\| \|\|\|\|\| \|\|\|: :\|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ AGGC AAUGC ACUUC GAC UCUAU CUUG UGG AGACAUGG GAUG@LB@3'-AUU...GGUUU U AUUUUCCA UU UAGAA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -36.5836 kcal/mol@LB@Unfolding Energy - mRNA 11.3711 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 206 -- 269@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
120	0.003999	0.1172	b2582	trxC	-9.28	0.072721	206 -- 219	4 -- 16	thioredoxin 2	_____________205____________220\n_____________\|______________\|\n5'-CUC...AUGAA____G_________AUUGU...UUG-3'\n______________UACC_UUUGUACCC\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________AUGG_AGACAUGGG\n3'-AUU...GUAGA______________AUG-5'\n_____________\|______________\|\n_____________17_____________3\n	213 -- 219	4 -- 10	-18.1109 kcal/mol	2.27225 kcal/mol	6.59015 kcal/mol	205 220@LB@ \| \|@LB@5'-CUC...AUGAA G AUUGU...UUG-3'@LB@ UACC UUUGUACCC@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGG AGACAUGGG@LB@3'-AUU...GUAGA AUG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -18.1109 kcal/mol@LB@Unfolding Energy - mRNA 2.27225 kcal/mol@LB@Unfolding Energy - sRNA 6.59015 kcal/mol@LB@@LB@Position - mRNA 206 -- 219@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 4 -- 10@LB@
161	0.006501	0.1413	b2682	ygaZ	-8.47	0.118892	208 -- 214	1 -- 7	putative L-valine exporter norvaline resistance protein	_____________207_____215\n_____________\|_______\|\n5'-UGG...GGAAA_______UCCAC...CCU-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	208 -- 214	1 -- 7	-11.2451 kcal/mol	0.761293 kcal/mol	2.03949 kcal/mol	207 215@LB@ \| \|@LB@5'-UGG...GGAAA UCCAC...CCU-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.2451 kcal/mol@LB@Unfolding Energy - mRNA 0.761293 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 208 -- 214@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
23	0.0001777	0.02687	b0774	bioA	-12.72	0.005870	209 -- 228	5 -- 24	7 8-diaminopelargonic acid synthase PLP-dependent	_____________208___________________229\n_____________\|_____________________\|\n5'-ACG...ACAAC____G________________AACGC...AAG-3'\n______________GGAC_AUCUUGCCUUUG_ACC\n______________\|:\|\|_\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUUG_UAGAAUGGAGAC_UGG\n3'-AUU...UCUAU_________________A___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	219 -- 225	9 -- 15	-24.4474 kcal/mol	3.74608 kcal/mol	8.01095 kcal/mol	208 229@LB@ \| \|@LB@5'-ACG...ACAAC G AACGC...AAG-3'@LB@ GGAC AUCUUGCCUUUG ACC@LB@ \|:\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUUG UAGAAUGGAGAC UGG@LB@3'-AUU...UCUAU A GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -24.4474 kcal/mol@LB@Unfolding Energy - mRNA 3.74608 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 9 -- 15@LB@
89	0.002377	0.09395	b4136	dsbD	-10.47	0.032769	211 -- 231	1 -- 22	thiol:disulfide interchange protein and activator of DsbC	_____________210____________________232\n_____________\|______________________\|\n5'-UGC...UCAAC_______UA_G___________UACUU...CGG-3'\n______________GCAUCUU__C_CUG_AUCCUGC\n______________:\|\|\|\|\|\|__\|_\|\|\|_\|:\|\|\|:\|\n______________UGUAGAA__G_GAC_UGGGAUG\n3'-AUU...UAUCU_______UG_A___A_______-5'\n_____________\|_____________________\|\n_____________23____________________1\n	225 -- 231	1 -- 7	-23.5098 kcal/mol	5.0672 kcal/mol	7.99236 kcal/mol	210 232@LB@ \| \|@LB@5'-UGC...UCAAC UA G UACUU...CGG-3'@LB@ GCAUCUU C CUG AUCCUGC@LB@ :\|\|\|\|\|\| \| \|\|\| \|:\|\|\|:\|@LB@ UGUAGAA G GAC UGGGAUG@LB@3'-AUU...UAUCU UG A A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -23.5098 kcal/mol@LB@Unfolding Energy - mRNA 5.0672 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@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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