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
63	0.002639	0.1417	b2751	cysN	-11.35	0.139541	181 -- 198	34 -- 49	sulfate adenylyltransferase subunit 1	_____________180________________199\n_____________\|__________________\|\n5'-AGU...AAAAA__G_______U_______AGAUG...GUG-3'\n______________AC_UCAGGGG_AUUUUUA\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|\|::\|\n______________UG_AGUCCCC_UAAAGGU\n3'-UUU...CAAAG__________________ACGAA...GCA-5'\n_____________\|__________________\|\n_____________50_________________33\n	184 -- 190	41 -- 47	-17.8149 kcal/mol	4.64155 kcal/mol	1.82276 kcal/mol	180 199@LB@ \| \|@LB@5'-AGU...AAAAA G U AGAUG...GUG-3'@LB@ AC UCAGGGG AUUUUUA@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|::\|@LB@ UG AGUCCCC UAAAGGU@LB@3'-UUU...CAAAG ACGAA...GCA-5'@LB@ \| \|@LB@ 50 33@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -17.8149 kcal/mol@LB@Unfolding Energy - mRNA 4.64155 kcal/mol@LB@Unfolding Energy - sRNA 1.82276 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 34 -- 49@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 41 -- 47@LB@
75	0.003119	0.1452	b0871	poxB	-11.12	0.154817	181 -- 203	32 -- 50	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________180_____________________204\n_____________\|_______________________\|\n5'-CCG...UAUCA________AGAU___GAA_____AAACA...GUG-3'\n______________CAUUCAGG____GGA___CCAUG\n______________\|\|:\|\|\|\|\|____\|\|\|___\|\|\|\|\|\n______________GUGAGUCC____CCU___GGUAC\n3'-UUU...ACAAA_______________AAA_____GAAUA...GCA-5'\n_____________\|_______________________\|\n_____________51______________________31\n	182 -- 188	43 -- 49	-21.2585 kcal/mol	5.84423 kcal/mol	4.29868 kcal/mol	180 204@LB@ \| \|@LB@5'-CCG...UAUCA AGAU GAA AAACA...GUG-3'@LB@ CAUUCAGG GGA CCAUG@LB@ \|\|:\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GUGAGUCC CCU GGUAC@LB@3'-UUU...ACAAA AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 51 31@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -21.2585 kcal/mol@LB@Unfolding Energy - mRNA 5.84423 kcal/mol@LB@Unfolding Energy - sRNA 4.29868 kcal/mol@LB@@LB@Position - mRNA 181 -- 203@LB@Position - sRNA 32 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
46	0.001357	0.1038	b1235	rssB	-13.33	0.053430	184 -- 194	40 -- 50	PcnB-degradosome interaction factor; response regulator	_____________183_________195\n_____________\|___________\|\n5'-AAU...AAAGC__G________GAGAA...CAA-3'\n______________CA_UCAGGGGA\n______________\|\|_\|\|\|\|\|\|\|\|\n______________GU_AGUCCCCU\n3'-UUU...ACAAA__G________AAAGG...GCA-5'\n_____________\|___________\|\n_____________51__________39\n	188 -- 194	40 -- 46	-19.1981 kcal/mol	4.11697 kcal/mol	1.75243 kcal/mol	183 195@LB@ \| \|@LB@5'-AAU...AAAGC G GAGAA...CAA-3'@LB@ CA UCAGGGGA@LB@ \|\| \|\|\|\|\|\|\|\|@LB@ GU AGUCCCCU@LB@3'-UUU...ACAAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -19.1981 kcal/mol@LB@Unfolding Energy - mRNA 4.11697 kcal/mol@LB@Unfolding Energy - sRNA 1.75243 kcal/mol@LB@@LB@Position - mRNA 184 -- 194@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 40 -- 46@LB@
43	0.00107	0.08759	b4036	lamB	-10.48	0.202041	185 -- 197	39 -- 51	maltose outer membrane porin (maltoporin)	_____________184___________198\n_____________\|_____________\|\n5'-CGC...AGCAA_G_______A___AGAAU...GUU-3'\n______________U_ACUCAGG_GAU\n______________\|_\|\|\|\|\|\|\|_\|\|\|\n______________A_UGAGUCC_CUA\n3'-UUU...AACAA_G_______C___AAGGU...GCA-5'\n_____________\|_____________\|\n_____________52____________38\n	187 -- 193	43 -- 49	-14.6452 kcal/mol	2.36402 kcal/mol	1.79807 kcal/mol	184 198@LB@ \| \|@LB@5'-CGC...AGCAA G A AGAAU...GUU-3'@LB@ U ACUCAGG GAU@LB@ \| \|\|\|\|\|\|\| \|\|\|@LB@ A UGAGUCC CUA@LB@3'-UUU...AACAA G C AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -14.6452 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
88	0.003962	0.1538	b3084	rlmG	-11.78	0.115170	185 -- 197	40 -- 51	23S rRNA m(2)G1835 methyltransferase SAM-dependent	_____________184___________198\n_____________\|_____________\|\n5'-UGU...UUUUA_________A___CCGAU...AAU-3'\n______________UCAUUCAGG_GGG\n______________\|\|\|:\|\|\|\|\|_\|\|:\n______________AGUGAGUCC_CCU\n3'-UUU...AACAA_____________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	187 -- 193	43 -- 49	-16.9089 kcal/mol	3.37488 kcal/mol	1.76028 kcal/mol	184 198@LB@ \| \|@LB@5'-UGU...UUUUA A CCGAU...AAU-3'@LB@ UCAUUCAGG GGG@LB@ \|\|\|:\|\|\|\|\| \|\|:@LB@ AGUGAGUCC CCU@LB@3'-UUU...AACAA AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -16.9089 kcal/mol@LB@Unfolding Energy - mRNA 3.37488 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
12	9.939e-05	0.0245	b2308	hisQ	-13.21	0.056865	186 -- 218	34 -- 75	histidine ABC transporter permease	_____________185__________________________________________219\n_____________\|____________________________________________\|\n5'-GAU...CACAC___AGG___G_______________AU_________________GGUGU...UUG-3'\n______________GAC___ACA_GCAGCA___UGUUGU__________GGGUUUUCA\n______________\|\|\|___\|\|\|_:\|\|\|\|\|___:\|\|\|\|\|__________\|\|:\|\|\|:\|\|\n______________CUG___UGU_UGUCGU___GCAACA__________CCUAAAGGU\n3'-UUU...CGUUU___A_____G______UAA______AAGUGAGUCC_________ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________33\n	212 -- 218	34 -- 40	-26.3199 kcal/mol	8.29445 kcal/mol	4.816 kcal/mol	185 219@LB@ \| \|@LB@5'-GAU...CACAC AGG G AU GGUGU...UUG-3'@LB@ GAC ACA GCAGCA UGUUGU GGGUUUUCA@LB@ \|\|\| \|\|\| :\|\|\|\|\| :\|\|\|\|\| \|\|:\|\|\|:\|\|@LB@ CUG UGU UGUCGU GCAACA CCUAAAGGU@LB@3'-UUU...CGUUU A G UAA AAGUGAGUCC ACGAA...GCA-5'@LB@ \| \|@LB@ 76 33@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -26.3199 kcal/mol@LB@Unfolding Energy - mRNA 8.29445 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 186 -- 218@LB@Position - sRNA 34 -- 75@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 34 -- 40@LB@
5	9.512e-06	0.006694	b4006	purH	-17.40	0.004319	188 -- 204	31 -- 46	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase	_____________187_______________205\n_____________\|_________________\|\n5'-GUA...AAAUC__________A______AACAA...AGC-3'\n______________CAGGGGAUUU_CCAUGC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GUCCCCUAAA_GGUACG\n3'-UUU...AGUGA_________________AAUAU...GCA-5'\n_____________\|_________________\|\n_____________47________________30\n	191 -- 197	37 -- 43	-27.6893 kcal/mol	6.33421 kcal/mol	3.95768 kcal/mol	187 205@LB@ \| \|@LB@5'-GUA...AAAUC A AACAA...AGC-3'@LB@ CAGGGGAUUU CCAUGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCCCCUAAA GGUACG@LB@3'-UUU...AGUGA AAUAU...GCA-5'@LB@ \| \|@LB@ 47 30@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -27.6893 kcal/mol@LB@Unfolding Energy - mRNA 6.33421 kcal/mol@LB@Unfolding Energy - sRNA 3.95768 kcal/mol@LB@@LB@Position - mRNA 188 -- 204@LB@Position - sRNA 31 -- 46@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
157	0.007641	0.1668	b3154	yhbP	-10.32	0.216043	188 -- 213	45 -- 78	UPF0306 family protein	_____________187________________________________214\n_____________\|__________________________________\|\n5'-AAA...GUAUA_____GA____________GGAAA__________UCGCC...UUU-3'\n______________AAAGA______ACAGCAAU_________CACUCA\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|_________\|\|\|\|\|\|\n______________UUUCU______UGUCGUUA_________GUGAGU\n3'-UUU...ACCCG_____GAUGUG________AGCAACAAA______CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________44\n	196 -- 202	60 -- 66	-17.2265 kcal/mol	3.1682 kcal/mol	3.741 kcal/mol	187 214@LB@ \| \|@LB@5'-AAA...GUAUA GA GGAAA UCGCC...UUU-3'@LB@ AAAGA ACAGCAAU CACUCA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUCU UGUCGUUA GUGAGU@LB@3'-UUU...ACCCG GAUGUG AGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.2265 kcal/mol@LB@Unfolding Energy - mRNA 3.1682 kcal/mol@LB@Unfolding Energy - sRNA 3.741 kcal/mol@LB@@LB@Position - mRNA 188 -- 213@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 60 -- 66@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@
117	0.005152	0.155	b2235	nrdB	-9.05	0.346139	190 -- 222	48 -- 77	ribonucleoside-diphosphate reductase 1 beta subunit ferritin-like protein	_____________189_______________________________223\n_____________\|_________________________________\|\n5'-UCC...CCAAC_____AC__U_______UAUACCACCU______AGACG...AAU-3'\n______________AGGAC__AC_CAUGGCA__________UUUCAC\n______________\|:\|\|\|__\|\|_\|\|::\|\|\|__________\|\|\|\|\|\|\n______________UUCUG__UG_GUGUCGU__________AAAGUG\n3'-UUU...CCCGU_____A___U_______UAAGCAAC________AGUCC...GCA-5'\n_____________\|_________________________________\|\n_____________78________________________________47\n	200 -- 206	62 -- 68	-18.188 kcal/mol	5.45206 kcal/mol	3.68729 kcal/mol	189 223@LB@ \| \|@LB@5'-UCC...CCAAC AC U UAUACCACCU AGACG...AAU-3'@LB@ AGGAC AC CAUGGCA UUUCAC@LB@ \|:\|\|\| \|\| \|\|::\|\|\| \|\|\|\|\|\|@LB@ UUCUG UG GUGUCGU AAAGUG@LB@3'-UUU...CCCGU A U UAAGCAAC AGUCC...GCA-5'@LB@ \| \|@LB@ 78 47@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -18.188 kcal/mol@LB@Unfolding Energy - mRNA 5.45206 kcal/mol@LB@Unfolding Energy - sRNA 3.68729 kcal/mol@LB@@LB@Position - mRNA 190 -- 222@LB@Position - sRNA 48 -- 77@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 62 -- 68@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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