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	Additional homologs
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein		_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
118	0.003907	0.1165	b3827	yigM	-8.32	0.129405	260 -- 268	1 -- 9	putative inner membrane EamA-like transporter		_____________259_______269\n_____________\|_________\|\n5'-GGA...GGCGA_________GGGGC...UGG-3'\n______________GUACCUUGC\n______________\|\|\|\|\|:\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	262 -- 268	1 -- 7	-12.9582 kcal/mol	2.53078 kcal/mol	2.12872 kcal/mol	259 269@LB@ \| \|@LB@5'-GGA...GGCGA GGGGC...UGG-3'@LB@ GUACCUUGC@LB@ \|\|\|\|\|:\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -12.9582 kcal/mol@LB@Unfolding Energy - mRNA 2.53078 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 260 -- 268@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 1 -- 7@LB@
123	0.004171	0.1178	b2989	yghU	-8.31	0.130595	46 -- 54	49 -- 57	putative S-transferase		_____________45________55\n_____________\|_________\|\n5'-UUA...UGUGC_________CUGCU...CGC-3'\n______________UCUGAUUAC\n______________\|\|:\|\|\|\|\|\|\n______________AGGCUAAUG\n3'-AUU...GGUUU_________CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	48 -- 54	49 -- 55	-9.38135 kcal/mol	0.766517 kcal/mol	0.318327 kcal/mol	45 55@LB@ \| \|@LB@5'-UUA...UGUGC CUGCU...CGC-3'@LB@ UCUGAUUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ AGGCUAAUG@LB@3'-AUU...GGUUU CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -9.38135 kcal/mol@LB@Unfolding Energy - mRNA 0.766517 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 46 -- 54@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 49 -- 55@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@
100	0.003115	0.1096	b0353	mhpT	-8.28	0.132596	137 -- 146	48 -- 57	3-hydroxyphenylpropionic transporter		_____________136________147\n_____________\|__________\|\n5'-CGG...AUAGU__________CGGCU...CGG-3'\n______________UCUGAUUACG\n______________\|\|:\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	140 -- 146	48 -- 54	-13.4725 kcal/mol	3.61374 kcal/mol	1.55976 kcal/mol	136 147@LB@ \| \|@LB@5'-CGG...AUAGU CGGCU...CGG-3'@LB@ UCUGAUUACG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -8.28 kcal/mol@LB@Hybridization Energy -13.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.61374 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 137 -- 146@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 48 -- 54@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@
168	0.006917	0.1448	b3070	yqjH	-8.25	0.134865	172 -- 181	49 -- 58	putative siderophore interacting protein		_____________171________182\n_____________\|__________\|\n5'-ACU...GAUAU__________CAUCA...AGC-3'\n______________AUCUGAUUAC\n______________\|\|\|:\|\|\|\|\|\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	175 -- 181	49 -- 55	-10.8722 kcal/mol	2.31397 kcal/mol	0.318367 kcal/mol	171 182@LB@ \| \|@LB@5'-ACU...GAUAU CAUCA...AGC-3'@LB@ AUCUGAUUAC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -10.8722 kcal/mol@LB@Unfolding Energy - mRNA 2.31397 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 172 -- 181@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@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@
175	0.007291	0.1466	b1498	ydeN	-8.19	0.139530	95 -- 124	45 -- 67	putative Ser-type periplasmic non-aryl sulfatase	b3678 b3801	_____________94_____________________________125\n_____________\|______________________________\|\n5'-AUU...CUUUU______________CUAUCUCU________CUAAC...UAA-3'\n______________UUUAGCUAAAUCUG________UUAUGUGA\n______________\|\|:\|\|\|:\|\|\|\|\|:\|________\|\|\|:\|\|\|\|\n______________AAGUCGGUUUAGGC________AAUGCACU\n3'-AUU...UUUAU______________U_______________UCAUU...AUG-5'\n_____________\|______________________________\|\n_____________68_____________________________44\n	118 -- 124	45 -- 51	-22.2428 kcal/mol	5.90754 kcal/mol	8.16749 kcal/mol	94 125@LB@ \| \|@LB@5'-AUU...CUUUU CUAUCUCU CUAAC...UAA-3'@LB@ UUUAGCUAAAUCUG UUAUGUGA@LB@ \|\|:\|\|\|:\|\|\|\|\|:\| \|\|\|:\|\|\|\|@LB@ AAGUCGGUUUAGGC AAUGCACU@LB@3'-AUU...UUUAU U UCAUU...AUG-5'@LB@ \| \|@LB@ 68 44@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -22.2428 kcal/mol@LB@Unfolding Energy - mRNA 5.90754 kcal/mol@LB@Unfolding Energy - sRNA 8.16749 kcal/mol@LB@@LB@Position - mRNA 95 -- 124@LB@Position - sRNA 45 -- 67@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 45 -- 51@LB@
79	0.001698	0.07533	b2890	lysS	-8.16	0.142186	53 -- 64	54 -- 65	lysine tRNA synthetase constitutive	b4129	_____________52___________65\n_____________\|____________\|\n5'-AAA...UGGGG____________UUCUU...GGA-3'\n______________CAGCCAGAUUCG\n______________\|\|\|\|\|\|:\|\|:\|\|\n______________GUCGGUUUAGGC\n3'-AUU...UAUAA____________UAAUG...AUG-5'\n_____________\|____________\|\n_____________66___________53\n	58 -- 64	54 -- 60	-18.439 kcal/mol	4.14677 kcal/mol	6.15795 kcal/mol	52 65@LB@ \| \|@LB@5'-AAA...UGGGG UUCUU...GGA-3'@LB@ CAGCCAGAUUCG@LB@ \|\|\|\|\|\|:\|\|:\|\|@LB@ GUCGGUUUAGGC@LB@3'-AUU...UAUAA UAAUG...AUG-5'@LB@ \| \|@LB@ 66 53@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -18.439 kcal/mol@LB@Unfolding Energy - mRNA 4.14677 kcal/mol@LB@Unfolding Energy - sRNA 6.15795 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 54 -- 65@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 54 -- 60@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)

Job resubmission

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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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