Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
184	0.00937	0.1776	b2467	nudK	-13.30	0.054361	69 -- 94	38 -- 78	GDP-mannose pyrophosphatase	_____________68________________________________________95\n_____________\|_________________________________________\|\n5'-CAA...GGCAG______GU_________________________________AUUGA...AAG-3'\n______________AAGGAC__CAUGCGGCA_______________CAGGGGAUU\n______________\|\|:\|\|\|__\|\|::\|:\|\|\|_______________\|\|\|\|\|\|\|\|\|\n______________UUUCUG__GUGUGUCGU_______________GUCCCCUAA\n3'-UUU...ACCCG______AU_________UAAGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|_________________________________________\|\n_____________79________________________________________37\n	88 -- 94	38 -- 44	-30.5001 kcal/mol	12.4248 kcal/mol	4.77973 kcal/mol	68 95@LB@ \| \|@LB@5'-CAA...GGCAG GU AUUGA...AAG-3'@LB@ AAGGAC CAUGCGGCA CAGGGGAUU@LB@ \|\|:\|\|\| \|\|::\|:\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UUUCUG GUGUGUCGU GUCCCCUAA@LB@3'-UUU...ACCCG AU UAAGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 79 37@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -30.5001 kcal/mol@LB@Unfolding Energy - mRNA 12.4248 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 69 -- 94@LB@Position - sRNA 38 -- 78@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 38 -- 44@LB@
141	0.006483	0.1605	b2474	tmcA	-12.94	0.065378	86 -- 105	35 -- 54	elongator methionine tRNA (ac4C34) acetyltransferase	_____________85___________________106\n_____________\|____________________\|\n5'-GAU...AGACA__________U__CAC____CAGCA...UUG-3'\n______________GUUUCACUCA_GG___UUCU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|:\n______________CAAAGUGAGU_CC___AAGG\n3'-UUU...AGCAA__________C__CUA____UACGA...GCA-5'\n_____________\|____________________\|\n_____________55___________________34\n	89 -- 95	45 -- 51	-18.4772 kcal/mol	3.58569 kcal/mol	1.95269 kcal/mol	85 106@LB@ \| \|@LB@5'-GAU...AGACA U CAC CAGCA...UUG-3'@LB@ GUUUCACUCA GG UUCU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ CAAAGUGAGU CC AAGG@LB@3'-UUU...AGCAA C CUA UACGA...GCA-5'@LB@ \| \|@LB@ 55 34@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -18.4772 kcal/mol@LB@Unfolding Energy - mRNA 3.58569 kcal/mol@LB@Unfolding Energy - sRNA 1.95269 kcal/mol@LB@@LB@Position - mRNA 86 -- 105@LB@Position - sRNA 35 -- 54@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 45 -- 51@LB@
59	0.002304	0.1363	b2508	guaB	-11.36	0.139274	1 -- 26	38 -- 71	IMP dehydrogenase	______________1__________________________________27\n______________\|__________________________________\|\n___________5'-__UA_______AA____________G_________GAGAA...AGC-3'\n______________AC__ACGGUAA___________AUU_CAGGGGAUU\n______________\|\|__\|\|:\|:\|\|___________\|:\|_\|\|\|\|\|\|\|\|\|\n______________UG__UGUCGUU___________UGA_GUCCCCUAA\n3'-UUU...UCUGA__UG_______AAGCAACAAAG_____________AGGUA...GCA-5'\n_____________\|___________________________________\|\n_____________72__________________________________37\n	20 -- 26	38 -- 44	-21.1303 kcal/mol	5.02575 kcal/mol	4.74986 kcal/mol	1 27@LB@ \| \|@LB@ 5'- UA AA G GAGAA...AGC-3'@LB@ AC ACGGUAA AUU CAGGGGAUU@LB@ \|\| \|\|:\|:\|\| \|:\| \|\|\|\|\|\|\|\|\|@LB@ UG UGUCGUU UGA GUCCCCUAA@LB@3'-UUU...UCUGA UG AAGCAACAAAG AGGUA...GCA-5'@LB@ \| \|@LB@ 72 37@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -21.1303 kcal/mol@LB@Unfolding Energy - mRNA 5.02575 kcal/mol@LB@Unfolding Energy - sRNA 4.74986 kcal/mol@LB@@LB@Position - mRNA 1 -- 26@LB@Position - sRNA 38 -- 71@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 38 -- 44@LB@
116	0.005119	0.155	b2513	yfgM	-8.84	0.371642	84 -- 101	60 -- 75	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________83_________________102\n_____________\|__________________\|\n5'-GGC...GAAGU_____ACG__________AGUGA...UUG-3'\n______________GGCUA___GCACAGCAGU\n______________\|:\|\|\|___:\|\|\|\|\|\|\|:\|\n______________CUGAU___UGUGUCGUUA\n3'-UUU...CGUUU_____G____________AGCAA...GCA-5'\n_____________\|__________________\|\n_____________76_________________59\n	95 -- 101	60 -- 66	-19.484 kcal/mol	7.35825 kcal/mol	3.28851 kcal/mol	83 102@LB@ \| \|@LB@5'-GGC...GAAGU ACG AGUGA...UUG-3'@LB@ GGCUA GCACAGCAGU@LB@ \|:\|\|\| :\|\|\|\|\|\|\|:\|@LB@ CUGAU UGUGUCGUUA@LB@3'-UUU...CGUUU G AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -19.484 kcal/mol@LB@Unfolding Energy - mRNA 7.35825 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 84 -- 101@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 60 -- 66@LB@
100	0.004525	0.1538	b2550	yphH	-8.03	0.477033	31 -- 47	39 -- 54	putative DNA-binding transcriptional regulator	_____________30_________________48\n_____________\|__________________\|\n5'-AGG...GCCCG_______A___UC_____CUCAA...UGG-3'\n______________GUUUCAU__GG__GGGAU\n______________\|\|\|\|\|\|:__:\|__\|\|\|\|\|\n______________CAAAGUG__UC__CCCUA\n3'-UUU...AGCAA_______AG_________AAGGU...GCA-5'\n_____________\|__________________\|\n_____________55_________________38\n	31 -- 37	48 -- 54	-12.873 kcal/mol	2.94673 kcal/mol	1.89674 kcal/mol	30 48@LB@ \| \|@LB@5'-AGG...GCCCG A UC CUCAA...UGG-3'@LB@ GUUUCAU GG GGGAU@LB@ \|\|\|\|\|\|: :\| \|\|\|\|\|@LB@ CAAAGUG UC CCCUA@LB@3'-UUU...AGCAA AG AAGGU...GCA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -12.873 kcal/mol@LB@Unfolding Energy - mRNA 2.94673 kcal/mol@LB@Unfolding Energy - sRNA 1.89674 kcal/mol@LB@@LB@Position - mRNA 31 -- 47@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 48 -- 54@LB@
22	0.0001899	0.02926	b2562	yfhL	-14.77	0.023959	28 -- 42	42 -- 56	putative 4Fe-4S cluster-containing protein	_____________27______________43\n_____________\|_______________\|\n5'-AGC...UCUGC____CA_________AAUGU...UUA-3'\n______________UUGU__CGCUCAGGG\n______________\|\|\|\|__\|:\|\|\|\|\|\|\|\n______________AACA__GUGAGUCCC\n3'-UUU...UAAGC____AA_________CUAAA...GCA-5'\n_____________\|_______________\|\n_____________57______________41\n	36 -- 42	42 -- 48	-19.6539 kcal/mol	2.98712 kcal/mol	1.89561 kcal/mol	27 43@LB@ \| \|@LB@5'-AGC...UCUGC CA AAUGU...UUA-3'@LB@ UUGU CGCUCAGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AACA GUGAGUCCC@LB@3'-UUU...UAAGC AA CUAAA...GCA-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -19.6539 kcal/mol@LB@Unfolding Energy - mRNA 2.98712 kcal/mol@LB@Unfolding Energy - sRNA 1.89561 kcal/mol@LB@@LB@Position - mRNA 28 -- 42@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 42 -- 48@LB@
109	0.004772	0.1538	b2580	ung	-9.28	0.319241	25 -- 55	36 -- 70	uracil-DNA-glycosylase	_____________24__________________________________56\n_____________\|___________________________________\|\n5'-UCU...AAAAC______U___GUA____G_____AAAU________AUUGU...CCG-3'\n______________CACACA_CAA_____UG__UCGC_____GGAUUUU\n______________\|\|\|\|\|\|_\|\|\|_____\|\|__\|\|:\|_____\|\|\|\|\|\|:\n______________GUGUGU_GUU_____AC__AGUG_____CCUAAAG\n3'-UUU...CUGAU______C___AAGCA__AA____AGUCC_______GUACG...GCA-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	49 -- 55	36 -- 42	-19.0861 kcal/mol	5.04532 kcal/mol	4.7591 kcal/mol	24 56@LB@ \| \|@LB@5'-UCU...AAAAC U GUA G AAAU AUUGU...CCG-3'@LB@ CACACA CAA UG UCGC GGAUUUU@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|:\| \|\|\|\|\|\|:@LB@ GUGUGU GUU AC AGUG CCUAAAG@LB@3'-UUU...CUGAU C AAGCA AA AGUCC GUACG...GCA-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -19.0861 kcal/mol@LB@Unfolding Energy - mRNA 5.04532 kcal/mol@LB@Unfolding Energy - sRNA 4.7591 kcal/mol@LB@@LB@Position - mRNA 25 -- 55@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 36 -- 42@LB@
108	0.004771	0.1538	b2594	rluD	-7.24	0.588975	189 -- 206	62 -- 78	23S rRNA pseudouridine(1911 1915 1917) synthase	_____________188________________207\n_____________\|__________________\|\n5'-CCC...ACGAA____C_G___________CAACG...GUU-3'\n______________GAAG_A_UAUAUAUGGCA\n______________:\|\|\|_\|_\|\|:\|:\|::\|\|\|\n______________UUUC_U_AUGUGUGUCGU\n3'-UUU...ACCCG______G___________UAAGC...GCA-5'\n_____________\|__________________\|\n_____________79_________________61\n	200 -- 206	62 -- 68	-13.9289 kcal/mol	3.43926 kcal/mol	3.2555 kcal/mol	188 207@LB@ \| \|@LB@5'-CCC...ACGAA C G CAACG...GUU-3'@LB@ GAAG A UAUAUAUGGCA@LB@ :\|\|\| \| \|\|:\|:\|::\|\|\|@LB@ UUUC U AUGUGUGUCGU@LB@3'-UUU...ACCCG G UAAGC...GCA-5'@LB@ \| \|@LB@ 79 61@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.9289 kcal/mol@LB@Unfolding Energy - mRNA 3.43926 kcal/mol@LB@Unfolding Energy - sRNA 3.2555 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 62 -- 78@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@LB@
167	0.008121	0.1711	b2603	yfiR	-9.52	0.293133	262 -- 278	35 -- 51	putative periplasmic inhibitor of YfiN activity	_____________261_______________279\n_____________\|_________________\|\n5'-GUA...AAUAC_________A_CC____GACGU...GUA-3'\n______________UCGCUCAGG_G__UUCU\n______________\|\|:\|\|\|\|\|\|_\|__\|\|\|:\n______________AGUGAGUCC_C__AAGG\n3'-UUU...AACAA_________C_UA____UACGA...GCA-5'\n_____________\|_________________\|\n_____________52________________34\n	264 -- 270	43 -- 49	-18.1931 kcal/mol	6.80204 kcal/mol	1.87111 kcal/mol	261 279@LB@ \| \|@LB@5'-GUA...AAUAC A CC GACGU...GUA-3'@LB@ UCGCUCAGG G UUCU@LB@ \|\|:\|\|\|\|\|\| \| \|\|\|:@LB@ AGUGAGUCC C AAGG@LB@3'-UUU...AACAA C UA UACGA...GCA-5'@LB@ \| \|@LB@ 52 34@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -18.1931 kcal/mol@LB@Unfolding Energy - mRNA 6.80204 kcal/mol@LB@Unfolding Energy - sRNA 1.87111 kcal/mol@LB@@LB@Position - mRNA 262 -- 278@LB@Position - sRNA 35 -- 51@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 43 -- 49@LB@
194	0.009812	0.1776	b2687	luxS	-7.90	0.495572	99 -- 106	42 -- 49	S-ribosylhomocysteine lyase	_____________98_______107\n_____________\|________\|\n5'-GAA...UCUGA________AUGAU...UCA-3'\n______________AUUCAGGG\n______________\|:\|\|\|\|\|\|\n______________UGAGUCCC\n3'-UUU...CAAAG________CUAAA...GCA-5'\n_____________\|________\|\n_____________50_______41\n	100 -- 106	42 -- 48	-12.5942 kcal/mol	3.05922 kcal/mol	1.63991 kcal/mol	98 107@LB@ \| \|@LB@5'-GAA...UCUGA AUGAU...UCA-3'@LB@ AUUCAGGG@LB@ \|:\|\|\|\|\|\|@LB@ UGAGUCCC@LB@3'-UUU...CAAAG CUAAA...GCA-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -12.5942 kcal/mol@LB@Unfolding Energy - mRNA 3.05922 kcal/mol@LB@Unfolding Energy - sRNA 1.63991 kcal/mol@LB@@LB@Position - mRNA 99 -- 106@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 42 -- 48@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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