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
14	5.486e-05	0.01183	b0420	dxs	-9.76	0.053178	24 -- 31	1 -- 8	1-deoxyxylulose-5-phosphate synthase thiamine triphosphate-binding FAD-requiring	_____________23_______32\n_____________\|________\|\n5'-ACC...GUACC________ACUUC...ACG-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	25 -- 31	1 -- 7	-13.3609 kcal/mol	1.5078 kcal/mol	2.11603 kcal/mol	23 32@LB@ \| \|@LB@5'-ACC...GUACC ACUUC...ACG-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -13.3609 kcal/mol@LB@Unfolding Energy - mRNA 1.5078 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 24 -- 31@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 1 -- 7@LB@
184	0.00812	0.1553	b4371	rsmC	-7.50	0.203534	191 -- 216	4 -- 25	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________190________________________217\n_____________\|__________________________\|\n5'-AUC...AUUGA________CC__G____CAUU_____CGGCA...UGC-3'\n______________GGAGCAUU__AU_UCUG____UACCC\n______________:\|\|:\|\|\|:__\|:_\|\|\|\|____\|\|\|\|\|\n______________UCUUGUAG__UG_AGAC____AUGGG\n3'-AUU...UUCUA________AA__G_____________AUG-5'\n_____________\|__________________________\|\n_____________26_________________________3\n	192 -- 198	18 -- 24	-20.5319 kcal/mol	5.03265 kcal/mol	8.0209 kcal/mol	190 217@LB@ \| \|@LB@5'-AUC...AUUGA CC G CAUU CGGCA...UGC-3'@LB@ GGAGCAUU AU UCUG UACCC@LB@ :\|\|:\|\|\|: \|: \|\|\|\| \|\|\|\|\|@LB@ UCUUGUAG UG AGAC AUGGG@LB@3'-AUU...UUCUA AA G AUG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -20.5319 kcal/mol@LB@Unfolding Energy - mRNA 5.03265 kcal/mol@LB@Unfolding Energy - sRNA 8.0209 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 18 -- 24@LB@
76	0.001511	0.06993	b3465	rsmD	-10.43	0.033857	227 -- 244	49 -- 65	16S rRNA m(2)G966 methyltransferase SAM-dependent	_____________226________________245\n_____________\|__________________\|\n5'-UUG...GGCAG____________C_____UGGCG...GCC-3'\n______________CGGCCAAAUCCG_AUUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________GUCGGUUUAGGC_UAAUG\n3'-AUU...UAUAA__________________CACUU...AUG-5'\n_____________\|__________________\|\n_____________66_________________48\n	232 -- 238	54 -- 60	-22.129 kcal/mol	5.5281 kcal/mol	6.19707 kcal/mol	226 245@LB@ \| \|@LB@5'-UUG...GGCAG C UGGCG...GCC-3'@LB@ CGGCCAAAUCCG AUUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ GUCGGUUUAGGC UAAUG@LB@3'-AUU...UAUAA CACUU...AUG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -22.129 kcal/mol@LB@Unfolding Energy - mRNA 5.5281 kcal/mol@LB@Unfolding Energy - sRNA 6.19707 kcal/mol@LB@@LB@Position - mRNA 227 -- 244@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 54 -- 60@LB@
133	0.004686	0.1239	b3081	fadH	-11.00	0.022420	2 -- 21	1 -- 24	2 4-dienoyl-CoA reductase NADH and FMN-linked	_____________1________________________22\n_____________\|________________________\|\n__________5'-U_____C__________________AUGUG...ACC-3'\n______________GGACG_CUUAUC_C___GCCCUAC\n______________\|:\|\|:_\|\|\|\|:\|_\|___:\|\|\|\|\|\|\n______________CUUGU_GAAUGG_G___UGGGAUG\n3'-AUU...UCUAU_____A______A_ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	15 -- 21	1 -- 7	-21.5738 kcal/mol	2.57038 kcal/mol	8.02158 kcal/mol	1 22@LB@ \| \|@LB@ 5'-U C AUGUG...ACC-3'@LB@ GGACG CUUAUC C GCCCUAC@LB@ \|:\|\|: \|\|\|\|:\| \| :\|\|\|\|\|\|@LB@ CUUGU GAAUGG G UGGGAUG@LB@3'-AUU...UCUAU A A ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -21.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.57038 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 1 -- 7@LB@
4	8.02e-06	0.007054	b0425	panE	-14.83	0.000836	22 -- 49	1 -- 32	2-dehydropantoate reductase NADPH-specific	_____________21________________________________50\n_____________\|_________________________________\|\n5'-AUC...AUAUC_________________UU____________U_AUUUU...CGC-3'\n______________GAAAGAUGG__CAUCUU__CCUCU___CCCU_C\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|__\|\|\|\|\|___\|\|\|\|_\|\n______________CUUUCUAUC__GUAGAA__GGAGA___GGGA_G\n3'-AUU...CCAGA_________UU______U______CAU____U_-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	24 -- 30	24 -- 30	-28.6113 kcal/mol	4.98037 kcal/mol	8.82471 kcal/mol	21 50@LB@ \| \|@LB@5'-AUC...AUAUC UU U AUUUU...CGC-3'@LB@ GAAAGAUGG CAUCUU CCUCU CCCU C@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|@LB@ CUUUCUAUC GUAGAA GGAGA GGGA G@LB@3'-AUU...CCAGA UU U CAU U -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -28.6113 kcal/mol@LB@Unfolding Energy - mRNA 4.98037 kcal/mol@LB@Unfolding Energy - sRNA 8.82471 kcal/mol@LB@@LB@Position - mRNA 22 -- 49@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 24 -- 30@LB@
34	0.0003499	0.03519	b0333	prpC	-9.01	0.085770	169 -- 175	1 -- 7	2-methylcitrate synthase	_____________168_____176\n_____________\|_______\|\n5'-ACU...UCUCG_______AAAUG...GCA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	169 -- 175	1 -- 7	-11.7504 kcal/mol	0.722985 kcal/mol	2.03949 kcal/mol	168 176@LB@ \| \|@LB@5'-ACU...UCUCG AAAUG...GCA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -11.7504 kcal/mol@LB@Unfolding Energy - mRNA 0.722985 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 169 -- 175@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.00315	0.1097	b1822	rlmA	-7.85	0.169074	182 -- 190	1 -- 9	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________181_______191\n_____________\|_________\|\n5'-AAG...CUUUA_________CGGAG...GGU-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	184 -- 190	1 -- 7	-13.1594 kcal/mol	3.20778 kcal/mol	2.12872 kcal/mol	181 191@LB@ \| \|@LB@5'-AAG...CUUUA CGGAG...GGU-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -13.1594 kcal/mol@LB@Unfolding Energy - mRNA 3.20778 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 182 -- 190@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
19	8.831e-05	0.01635	b3389	aroB	-10.54	0.031183	4 -- 17	42 -- 56	3-dehydroquinate synthase	_____________3_______________18\n_____________\|_______________\|\n________5'-ACA___CC__________UCUGG...CGG-3'\n______________CCG___GCGUGAAGU\n______________\|\|\|___:\|\|\|\|\|\|\|\|\n______________GGC___UGCACUUCA\n3'-AUU...GUUUA___UAA_________UUUUC...AUG-5'\n_____________\|_______________\|\n_____________57______________41\n	11 -- 17	42 -- 48	-15.9415 kcal/mol	2.13198 kcal/mol	3.27911 kcal/mol	3 18@LB@ \| \|@LB@ 5'-ACA CC UCUGG...CGG-3'@LB@ CCG GCGUGAAGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|@LB@ GGC UGCACUUCA@LB@3'-AUU...GUUUA UAA UUUUC...AUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.9415 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 3.27911 kcal/mol@LB@@LB@Position - mRNA 4 -- 17@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 42 -- 48@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@
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@

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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