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
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@
106	0.003365	0.1101	b0955	ycbZ	-10.52	0.031644	269 -- 288	48 -- 66	putative peptidase		_____________268__________________289\n_____________\|____________________\|\n5'-UUG...UUUGC_______C_________A__AAAAC...CUU-3'\n______________UCAGCCA_AUUUGAUUG_CG\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|:_\|\|\n______________AGUCGGU_UAGGCUAAU_GC\n3'-AUU...UUAUA_______U____________ACUUC...AUG-5'\n_____________\|____________________\|\n_____________67___________________47\n	279 -- 285	50 -- 56	-21.5915 kcal/mol	3.60671 kcal/mol	7.48271 kcal/mol	268 289@LB@ \| \|@LB@5'-UUG...UUUGC C A AAAAC...CUU-3'@LB@ UCAGCCA AUUUGAUUG CG@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|: \|\|@LB@ AGUCGGU UAGGCUAAU GC@LB@3'-AUU...UUAUA U ACUUC...AUG-5'@LB@ \| \|@LB@ 67 47@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -21.5915 kcal/mol@LB@Unfolding Energy - mRNA 3.60671 kcal/mol@LB@Unfolding Energy - sRNA 7.48271 kcal/mol@LB@@LB@Position - mRNA 269 -- 288@LB@Position - sRNA 48 -- 66@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@LB@
108	0.003398	0.1101	b0973	hyaB	-11.40	0.016694	267 -- 275	48 -- 56	hydrogenase 1 large subunit		_____________266_______276\n_____________\|_________\|\n5'-GGU...UCGAC_________CGCAU...GCG-3'\n______________CCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	269 -- 275	48 -- 54	-14.3171 kcal/mol	1.33562 kcal/mol	1.55919 kcal/mol	266 276@LB@ \| \|@LB@5'-GGU...UCGAC CGCAU...GCG-3'@LB@ CCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -14.3171 kcal/mol@LB@Unfolding Energy - mRNA 1.33562 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 267 -- 275@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
109	0.003426	0.1101	b2280	nuoJ	-6.41	0.346318	31 -- 43	48 -- 59	NADH:ubiquinone oxidoreductase membrane subunit J		_____________30____________44\n_____________\|_____________\|\n5'-GAU...GCCAG_________U___AGAAA...UUA-3'\n______________GAUCUGGUU_ACG\n______________:\|\|\|:\|:\|\|_\|\|\|\n______________UUAGGCUAA_UGC\n3'-AUU...UCGGU_____________ACUUC...AUG-5'\n_____________\|_____________\|\n_____________60____________47\n	33 -- 39	51 -- 57	-11.2654 kcal/mol	3.27917 kcal/mol	1.55995 kcal/mol	30 44@LB@ \| \|@LB@5'-GAU...GCCAG U AGAAA...UUA-3'@LB@ GAUCUGGUU ACG@LB@ :\|\|\|:\|:\|\| \|\|\|@LB@ UUAGGCUAA UGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -11.2654 kcal/mol@LB@Unfolding Energy - mRNA 3.27917 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 31 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 51 -- 57@LB@
131	0.004483	0.1204	b2069	yegD	-6.32	0.360285	213 -- 222	48 -- 57	Hsp70 chaperone family protein		_____________212________223\n_____________\|__________\|\n5'-CAC...UUGGU__________GUACA...UGC-3'\n______________UUUGAUUACG\n______________\|::\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	216 -- 222	48 -- 54	-10.2333 kcal/mol	2.33693 kcal/mol	1.55976 kcal/mol	212 223@LB@ \| \|@LB@5'-CAC...UUGGU GUACA...UGC-3'@LB@ UUUGAUUACG@LB@ \|::\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.2333 kcal/mol@LB@Unfolding Energy - mRNA 2.33693 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 48 -- 54@LB@
138	0.004994	0.127	b3633	waaA	-9.37	0.068643	230 -- 259	48 -- 75	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)		_____________229____________________________260\n_____________\|______________________________\|\n5'-UCG...CUUCU___CCU__________CU_______A____GCUCU...AAC-3'\n______________CUA___UAUUCAGCCG__GAUCUGG_UACG\n______________\|\|\|___\|\|\|\|\|\|\|\|\|:__:\|\|\|:\|:_\|\|\|\|\n______________GAU___AUAAGUCGGU__UUAGGCU_AUGC\n3'-AUU...CCGCC___UUU___________________A____ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	248 -- 254	53 -- 59	-25.3567 kcal/mol	8.33931 kcal/mol	7.67232 kcal/mol	229 260@LB@ \| \|@LB@5'-UCG...CUUCU CCU CU A GCUCU...AAC-3'@LB@ CUA UAUUCAGCCG GAUCUGG UACG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: :\|\|\|:\|: \|\|\|\|@LB@ GAU AUAAGUCGGU UUAGGCU AUGC@LB@3'-AUU...CCGCC UUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -25.3567 kcal/mol@LB@Unfolding Energy - mRNA 8.33931 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 53 -- 59@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@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon		_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@LB@
163	0.006545	0.1413	b0532	sfmD	-7.71	0.181786	104 -- 132	48 -- 76	putative outer membrane export usher protein	b3144 b4317 b0940	_____________103____________________________133\n_____________\|______________________________\|\n5'-UCA...GGAAA______________A___UUAA________GUUCA...GCU-3'\n______________GCUGAAAU_UUCAG_CCG____UGAUUAUG\n______________\|\|\|:\|\|\|\|_\|\|\|\|\|_\|\|:____:\|\|\|\|\|:\|\n______________CGAUUUUA_AAGUC_GGU____GCUAAUGC\n3'-AUU...CCCGC________U_________UUAG________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________77_____________________________47\n	126 -- 132	48 -- 54	-23.9612 kcal/mol	8.59534 kcal/mol	7.67378 kcal/mol	103 133@LB@ \| \|@LB@5'-UCA...GGAAA A UUAA GUUCA...GCU-3'@LB@ GCUGAAAU UUCAG CCG UGAUUAUG@LB@ \|\|\|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|\|:\|@LB@ CGAUUUUA AAGUC GGU GCUAAUGC@LB@3'-AUU...CCCGC U UUAG ACUUC...AUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -23.9612 kcal/mol@LB@Unfolding Energy - mRNA 8.59534 kcal/mol@LB@Unfolding Energy - sRNA 7.67378 kcal/mol@LB@@LB@Position - mRNA 104 -- 132@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 48 -- 54@LB@
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase		_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 49 -- 55@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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usability assessment

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service.

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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