Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein	______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
170	0.02787	0.531	b3184	yhbE	-10.77	0.067448	1 -- 31	11 -- 53	EamA family inner membrane putative transporter	______________1__________________________________________32\n______________\|__________________________________________\|\n___________5'-_________GUA_________AUU___________________AGGCC...UGG-3'\n______________AAGCAGACG_____AAGUGAA___CG__________AAGUUAA\n______________\|\|:\|\|\|\|\|:_____\|\|:\|\|\|\|___\|\|__________\|\|\|\|\|\|\|\n______________UUUGUCUGU_____UUUACUU___GC__________UUCAAUU\n3'-UUU...CCCCA_________AAGUC_______ACU__CAUUAUUUAU_______ACUAC...UCG-5'\n_____________\|___________________________________________\|\n_____________54__________________________________________10\n	25 -- 31	11 -- 17	-18.1985 kcal/mol	1.09209 kcal/mol	6.3325 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GUA AUU AGGCC...UGG-3'@LB@ AAGCAGACG AAGUGAA CG AAGUUAA@LB@ \|\|:\|\|\|\|\|: \|\|:\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUGUCUGU UUUACUU GC UUCAAUU@LB@3'-UUU...CCCCA AAGUC ACU CAUUAUUUAU ACUAC...UCG-5'@LB@ \| \|@LB@ 54 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -18.1985 kcal/mol@LB@Unfolding Energy - mRNA 1.09209 kcal/mol@LB@Unfolding Energy - sRNA 6.3325 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 11 -- 53@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 11 -- 17@LB@
44	0.004782	0.3568	b3243	aaeR	-11.65	0.043804	4 -- 44	1 -- 57	transcriptional regulator for aaeXAB operon	_____________3_________________________________________________________45\n_____________\|_________________________________________________________\|\n________5'-AAC_________________UGU____CCU_____U_____G__________________AGGCG...UCA-3'\n______________GGG_AAACAGAC__UCA____UGA____UGGU_GUAAA_AGAG___________AGC\n______________\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|____\|\|\|____:\|\|\|_:\|\|\|\|_\|:\|\|___________\|\|\|\n______________CCC_UUUGUCUG__AGU____ACU____GCCA_UAUUU_UUUC___________UCG\n3'-UUU...UUAUC___A________UA___CUUU___UACU____U_____A____AAUUACUACUA___-5'\n_____________\|________________________________________________________\|\n_____________58_______________________________________________________1\n	8 -- 14	46 -- 52	-26.9604 kcal/mol	8.9713 kcal/mol	6.33758 kcal/mol	3 45@LB@ \| \|@LB@ 5'-AAC UGU CCU U G AGGCG...UCA-3'@LB@ GGG AAACAGAC UCA UGA UGGU GUAAA AGAG AGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\| :\|\|\|\| \|:\|\| \|\|\|@LB@ CCC UUUGUCUG AGU ACU GCCA UAUUU UUUC UCG@LB@3'-UUU...UUAUC A UA CUUU UACU U A AAUUACUACUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -26.9604 kcal/mol@LB@Unfolding Energy - mRNA 8.9713 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 4 -- 44@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 46 -- 52@LB@
86	0.013	0.4962	b0451	amtB	-9.48	0.122870	5 -- 23	1 -- 22	ammonium transporter	_____________4______________________24\n_____________\|______________________\|\n_______5'-CCAA_______AAU____________GAUUG...CGU-3'\n______________AAGUAAA_____UGAUG_UGGC\n______________\|\|:\|\|\|\|_____\|\|\|\|\|_\|:\|\|\n______________UUUAUUU_____ACUAC_AUCG\n3'-UUU...CAUUA_______CAAUU_____U____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	16 -- 22	-11.4865 kcal/mol	1.90989 kcal/mol	0.0989066 kcal/mol	4 24@LB@ \| \|@LB@ 5'-CCAA AAU GAUUG...CGU-3'@LB@ AAGUAAA UGAUG UGGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|:\|\|@LB@ UUUAUUU ACUAC AUCG@LB@3'-UUU...CAUUA CAAUU U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.4865 kcal/mol@LB@Unfolding Energy - mRNA 1.90989 kcal/mol@LB@Unfolding Energy - sRNA 0.0989066 kcal/mol@LB@@LB@Position - mRNA 5 -- 23@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 16 -- 22@LB@
109	0.01701	0.5123	b2075	mdtB	-10.10	0.092694	6 -- 26	38 -- 56	multidrug efflux system subunit B	_____________5_____________________27\n_____________\|_____________________\|\n______5'-CAUCU_____CGC_____________CAGUC...CCG-3'\n______________GGUGA___CGGGCAUUCAGGA\n______________\|\|\|:\|___\|:\|:\|\|\|\|\|\|\|:\|\n______________CCAUU___GUCUGUAAGUCUU\n3'-UUU...UAUCC_____U_______________UACUU...UCG-5'\n_____________\|_____________________\|\n_____________57____________________37\n	18 -- 24	40 -- 46	-22.2525 kcal/mol	5.90254 kcal/mol	6.25055 kcal/mol	5 27@LB@ \| \|@LB@ 5'-CAUCU CGC CAGUC...CCG-3'@LB@ GGUGA CGGGCAUUCAGGA@LB@ \|\|\|:\| \|:\|:\|\|\|\|\|\|\|:\|@LB@ CCAUU GUCUGUAAGUCUU@LB@3'-UUU...UAUCC U UACUU...UCG-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -22.2525 kcal/mol@LB@Unfolding Energy - mRNA 5.90254 kcal/mol@LB@Unfolding Energy - sRNA 6.25055 kcal/mol@LB@@LB@Position - mRNA 6 -- 26@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 40 -- 46@LB@
58	0.008338	0.4523	b2280	nuoJ	-13.62	0.015495	7 -- 16	55 -- 64	NADH:ubiquinone oxidoreductase membrane subunit J	_____________6__________17\n_____________\|__________\|\n_____5'-GAUUUC__________AAUAC...UUA-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	10 -- 16	55 -- 61	-15.5198 kcal/mol	1.86933 kcal/mol	0.0291912 kcal/mol	6 17@LB@ \| \|@LB@ 5'-GAUUUC AAUAC...UUA-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -15.5198 kcal/mol@LB@Unfolding Energy - mRNA 1.86933 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 7 -- 16@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 55 -- 61@LB@
36	0.003415	0.3114	b1849	purT	-10.41	0.080237	8 -- 43	29 -- 56	phosphoribosylglycinamide formyltransferase 2	_____________7_____________________________________44\n_____________\|_____________________________________\|\n____5'-UUUUGCU_______________UCUCUUCGCCCUCAC_______UACGU...GUC-3'\n______________GGUAAAC_GACAUUU_______________GAAUGAC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:_______________\|\|\|\|\|\|\|\n______________CCAUUUG_CUGUAAG_______________CUUACUG\n3'-UUU...UAUCC_______U_______UCUUUA________________CCAUU...UCG-5'\n_____________\|_____________________________________\|\n_____________57____________________________________28\n	37 -- 43	29 -- 35	-21.896 kcal/mol	5.20104 kcal/mol	6.28612 kcal/mol	7 44@LB@ \| \|@LB@ 5'-UUUUGCU UCUCUUCGCCCUCAC UACGU...GUC-3'@LB@ GGUAAAC GACAUUU GAAUGAC@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCAUUUG CUGUAAG CUUACUG@LB@3'-UUU...UAUCC U UCUUUA CCAUU...UCG-5'@LB@ \| \|@LB@ 57 28@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.896 kcal/mol@LB@Unfolding Energy - mRNA 5.20104 kcal/mol@LB@Unfolding Energy - sRNA 6.28612 kcal/mol@LB@@LB@Position - mRNA 8 -- 43@LB@Position - sRNA 29 -- 56@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 29 -- 35@LB@
96	0.01578	0.5059	b3283	yrdD	-12.59	0.027007	10 -- 20	2 -- 12	ssDNA-binding protein function unknown	_____________9___________21\n_____________\|___________\|\n5'-AAC...CGUGA___________AGCGA...UUG-3'\n______________AAUGGUGAUAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________UUACUACUAUC\n3'-UUU...UUCAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	14 -- 20	2 -- 8	-13.6612 kcal/mol	1.03146 kcal/mol	0.0386655 kcal/mol	9 21@LB@ \| \|@LB@5'-AAC...CGUGA AGCGA...UUG-3'@LB@ AAUGGUGAUAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ UUACUACUAUC@LB@3'-UUU...UUCAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -13.6612 kcal/mol@LB@Unfolding Energy - mRNA 1.03146 kcal/mol@LB@Unfolding Energy - sRNA 0.0386655 kcal/mol@LB@@LB@Position - mRNA 10 -- 20@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 2 -- 8@LB@
139	0.0229	0.526	b3958	argC	-10.25	0.086580	11 -- 36	23 -- 56	N-acetyl-gamma-glutamylphosphate reductase NAD(P)-binding	_____________10___________________________________37\n_____________\|____________________________________\|\n5'-AUC...AGCGC_______CUC__________________________UUGUU...CUG-3'\n______________GGUAAAU___GAUA__________AAUGGCGGUAAU\n______________\|\|\|\|\|\|:___\|\|:\|__________\|\|\|\|:\|\|\|\|\|\|\|\n______________CCAUUUG___CUGU__________UUACUGCCAUUA\n3'-UUU...UAUCC_______U______AAGUCUUUAC____________UUUAU...UCG-5'\n_____________\|____________________________________\|\n_____________57___________________________________22\n	30 -- 36	23 -- 29	-21.8632 kcal/mol	5.30467 kcal/mol	6.31216 kcal/mol	10 37@LB@ \| \|@LB@5'-AUC...AGCGC CUC UUGUU...CUG-3'@LB@ GGUAAAU GAUA AAUGGCGGUAAU@LB@ \|\|\|\|\|\|: \|\|:\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ CCAUUUG CUGU UUACUGCCAUUA@LB@3'-UUU...UAUCC U AAGUCUUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 57 22@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.8632 kcal/mol@LB@Unfolding Energy - mRNA 5.30467 kcal/mol@LB@Unfolding Energy - sRNA 6.31216 kcal/mol@LB@@LB@Position - mRNA 11 -- 36@LB@Position - sRNA 23 -- 56@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 23 -- 29@LB@
2	1.932e-06	0.003171	b1243	oppA	-16.40	0.003005	12 -- 82	1 -- 59	oligopeptide ABC transporter periplasmic binding protein	_____________11__________________________________________________________________________83\n_____________\|___________________________________________________________________________\|\n5'-UGU...UCGAC___________CAGUACGAAUC_____AA__U__UCGUC_____C__CAG____________C____________AAUAC...UCA-3'\n______________AGGGG_AGACA___________GACAU__GG_GA_____UGAAU_AC___AAUAAAUAAAGU____GGUGAUAGU\n______________\|\|\|\|\|_\|:\|\|\|___________\|\|\|\|\|__:\|_:\|_____\|\|\|\|\|_\|\|___\|\|\|\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|\|:\n______________UCCCC_UUUGU___________CUGUA__UC_UU_____ACUUA_UG___UUAUUUAUUUCA____CUACUAUCG\n3'-UUU...CUUUA_____A_____________________AG__U____________C__CCA____________AUUA_________-5'\n_____________\|__________________________________________________________________________\|\n_____________60_________________________________________________________________________1\n	76 -- 82	1 -- 7	-40.1642 kcal/mol	17.4223 kcal/mol	6.33764 kcal/mol	11 83@LB@ \| \|@LB@5'-UGU...UCGAC CAGUACGAAUC AA U UCGUC C CAG C AAUAC...UCA-3'@LB@ AGGGG AGACA GACAU GG GA UGAAU AC AAUAAAUAAAGU GGUGAUAGU@LB@ \|\|\|\|\| \|:\|\|\| \|\|\|\|\| :\| :\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|:@LB@ UCCCC UUUGU CUGUA UC UU ACUUA UG UUAUUUAUUUCA CUACUAUCG@LB@3'-UUU...CUUUA A AG U C CCA AUUA -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -40.1642 kcal/mol@LB@Unfolding Energy - mRNA 17.4223 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 12 -- 82@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 76 -- 82@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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