Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein		_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@LB@
115	0.007886	0.2401	b2890	lysS	-11.64	0.144658	161 -- 186	1 -- 20	lysine tRNA synthetase constitutive	b4129	_____________160_________________________187\n_____________\|___________________________\|\n5'-AAA...CAAUU________CAAGUUU____________UAUGA...GGA-3'\n______________UAUCGAAG_______GAAAGCAG_GGU\n______________:\|\|\|:\|\|\|_______:\|\|\|\|\|\|\|_\|\|:\n______________GUAGUUUC_______UUUUCGUC_CCG\n3'-UUU...CCCCU_______________________A___-5'\n_____________\|__________________________\|\n_____________21_________________________1\n	177 -- 183	5 -- 11	-18.6981 kcal/mol	5.60124 kcal/mol	1.45855 kcal/mol	160 187@LB@ \| \|@LB@5'-AAA...CAAUU CAAGUUU UAUGA...GGA-3'@LB@ UAUCGAAG GAAAGCAG GGU@LB@ :\|\|\|:\|\|\| :\|\|\|\|\|\|\| \|\|:@LB@ GUAGUUUC UUUUCGUC CCG@LB@3'-UUU...CCCCU A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -18.6981 kcal/mol@LB@Unfolding Energy - mRNA 5.60124 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 161 -- 186@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 5 -- 11@LB@
184	0.0132	0.2504	b2897	sdhE	-10.91	0.194803	203 -- 220	7 -- 23	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair		_____________202________________221\n_____________\|__________________\|\n5'-GUA...AAGAU_________CAAC_____CCGCA...ACA-3'\n______________GGACAUUAA____AAAGC\n______________\|\|\|\|\|\|:\|\|____\|\|\|\|\|\n______________CCUGUAGUU____UUUCG\n3'-UUU...UUACC_________UCU______UCACCG-5'\n_____________\|__________________\|\n_____________24_________________6\n	205 -- 211	15 -- 21	-14.6885 kcal/mol	3.17611 kcal/mol	0.599063 kcal/mol	202 221@LB@ \| \|@LB@5'-GUA...AAGAU CAAC CCGCA...ACA-3'@LB@ GGACAUUAA AAAGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUGUAGUU UUUCG@LB@3'-UUU...UUACC UCU UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -14.6885 kcal/mol@LB@Unfolding Energy - mRNA 3.17611 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 203 -- 220@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 15 -- 21@LB@
57	0.003017	0.1789	b2950	yggR	-13.19	0.071427	205 -- 223	1 -- 21	putative PilT family AAA+ ATPase		_____________204___________________224\n_____________\|_____________________\|\n5'-UUC...UAUGA____G_______UU_______CCUUA...GAA-3'\n______________AUAU_GAAGAAA____GUGGC\n______________\|:\|\|_:\|\|\|\|\|\|____\|\|\|\|\|\n______________UGUA_UUUCUUU____CACCG\n3'-UUU...ACCCC____G_______UCGU_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	210 -- 216	10 -- 16	-17.7325 kcal/mol	3.03326 kcal/mol	1.51103 kcal/mol	204 224@LB@ \| \|@LB@5'-UUC...UAUGA G UU CCUUA...GAA-3'@LB@ AUAU GAAGAAA GUGGC@LB@ \|:\|\| :\|\|\|\|\|\| \|\|\|\|\|@LB@ UGUA UUUCUUU CACCG@LB@3'-UUU...ACCCC G UCGU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -17.7325 kcal/mol@LB@Unfolding Energy - mRNA 3.03326 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 205 -- 223@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 10 -- 16@LB@
117	0.008014	0.2404	b3052	hldE	-12.77	0.087254	132 -- 161	1 -- 30	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase		_____________131______________________________162\n_____________\|________________________________\|\n5'-GCG...UGGCA_______CUG___G_____AU___________AUUAU...CGC-3'\n______________GAAGUGG____GU_GAAGA__GAAGUA_UGGU\n______________:\|\|:\|\|\|____:\|_:\|\|\|\|__:\|\|\|:\|_\|\|\|:\n______________UUUUACC____UA_UUUCU__UUUCGU_ACCG\n3'-UUU...AGGUG_______CCUG__G_____________C____-5'\n_____________\|_______________________________\|\n_____________31______________________________1\n	132 -- 138	24 -- 30	-21.0542 kcal/mol	5.76621 kcal/mol	2.51911 kcal/mol	131 162@LB@ \| \|@LB@5'-GCG...UGGCA CUG G AU AUUAU...CGC-3'@LB@ GAAGUGG GU GAAGA GAAGUA UGGU@LB@ :\|\|:\|\|\| :\| :\|\|\|\| :\|\|\|:\| \|\|\|:@LB@ UUUUACC UA UUUCU UUUCGU ACCG@LB@3'-UUU...AGGUG CCUG G C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.76621 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 132 -- 161@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 24 -- 30@LB@
21	0.0007937	0.1243	b3055	ygiM	-17.78	0.004866	75 -- 99	1 -- 23	SH3 domain protein		_____________74________________________100\n_____________\|_________________________\|\n5'-GGC...UUGAC______A____UUU___________AAGAC...AUA-3'\n______________GGGCGU_AAAG___GAAGCAGUGGC\n______________\|\|:\|:\|_\|\|\|\|___:\|\|\|\|\|\|\|\|\|\|\n______________CCUGUA_UUUC___UUUCGUCACCG\n3'-UUU...UUACC______G____U_____________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	93 -- 99	1 -- 7	-29.8569 kcal/mol	10.4968 kcal/mol	1.57928 kcal/mol	74 100@LB@ \| \|@LB@5'-GGC...UUGAC A UUU AAGAC...AUA-3'@LB@ GGGCGU AAAG GAAGCAGUGGC@LB@ \|\|:\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ CCUGUA UUUC UUUCGUCACCG@LB@3'-UUU...UUACC G U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.78 kcal/mol@LB@Hybridization Energy -29.8569 kcal/mol@LB@Unfolding Energy - mRNA 10.4968 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 75 -- 99@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 1 -- 7@LB@
175	0.01275	0.2504	b3057	bacA	-10.43	0.234919	238 -- 261	5 -- 26	undecaprenyl pyrophosphate phosphatase		_____________237______________________262\n_____________\|________________________\|\n5'-UUC...AAUAU____U_UG_________UU_A___AAUUU...UUG-3'\n______________UGGG_G__GUCGAAGGA__G_CAG\n______________\|\|\|\|_\|__:\|\|:\|\|\|:\|__\|_\|\|\|\n______________ACCC_C__UAGUUUCUU__C_GUC\n3'-UUU...GUUUU______UG_________UU_____ACCG-5'\n_____________\|________________________\|\n_____________27_______________________4\n	248 -- 254	11 -- 17	-20.3624 kcal/mol	7.43347 kcal/mol	2.50108 kcal/mol	237 262@LB@ \| \|@LB@5'-UUC...AAUAU U UG UU A AAUUU...UUG-3'@LB@ UGGG G GUCGAAGGA G CAG@LB@ \|\|\|\| \| :\|\|:\|\|\|:\| \| \|\|\|@LB@ ACCC C UAGUUUCUU C GUC@LB@3'-UUU...GUUUU UG UU ACCG-5'@LB@ \| \|@LB@ 27 4@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -20.3624 kcal/mol@LB@Unfolding Energy - mRNA 7.43347 kcal/mol@LB@Unfolding Energy - sRNA 2.50108 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 5 -- 26@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 11 -- 17@LB@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon		_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
139	0.01022	0.2504	b3163	nlpI	-13.31	0.067339	19 -- 42	4 -- 21	lipoprotein involved in osmotic sensitivity and filamentation		_____________18_______________________43\n_____________\|________________________\|\n5'-AGG...UCUGA___________GCGACU_______CUCAA...CAU-3'\n______________GCAUUAAAGAA______GAGCAGU\n______________:\|\|\|:\|\|\|\|\|\|______:\|\|\|\|\|\|\n______________UGUAGUUUCUU______UUCGUCA\n3'-UUU...ACCCC________________________CCG-5'\n_____________\|________________________\|\n_____________22_______________________3\n	36 -- 42	4 -- 10	-18.4935 kcal/mol	3.67449 kcal/mol	1.51 kcal/mol	18 43@LB@ \| \|@LB@5'-AGG...UCUGA GCGACU CUCAA...CAU-3'@LB@ GCAUUAAAGAA GAGCAGU@LB@ :\|\|\|:\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCUU UUCGUCA@LB@3'-UUU...ACCCC CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -18.4935 kcal/mol@LB@Unfolding Energy - mRNA 3.67449 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 19 -- 42@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 4 -- 10@LB@
47	0.002271	0.1648	b3169	nusA	-13.61	0.058009	55 -- 79	4 -- 28	transcription termination/antitermination L factor		_____________54__________________________80\n_____________\|___________________________\|\n5'-UUG...UCGUA_____CA________UC__________AGACG...CAG-3'\n______________AAUGG__GGGCGUUA____AAAGCGGU\n______________\|\|\|\|\|__\|\|:\|:\|:\|____\|\|\|\|\|:\|\|\n______________UUACC__CCUGUAGU____UUUCGUCA\n3'-UUU...GUGUU_______________UUCU________CCG-5'\n_____________\|___________________________\|\n_____________29__________________________3\n	73 -- 79	4 -- 10	-21.8237 kcal/mol	5.69952 kcal/mol	2.51457 kcal/mol	54 80@LB@ \| \|@LB@5'-UUG...UCGUA CA UC AGACG...CAG-3'@LB@ AAUGG GGGCGUUA AAAGCGGU@LB@ \|\|\|\|\| \|\|:\|:\|:\| \|\|\|\|\|:\|\|@LB@ UUACC CCUGUAGU UUUCGUCA@LB@3'-UUU...GUGUU UUCU CCG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -21.8237 kcal/mol@LB@Unfolding Energy - mRNA 5.69952 kcal/mol@LB@Unfolding Energy - sRNA 2.51457 kcal/mol@LB@@LB@Position - mRNA 55 -- 79@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@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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