Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
119	0.006508	0.1913	b3834	ubiJ	-9.73	0.156135	145 -- 181	28 -- 78	aerobic ubiquinone synthesis protein SCP2 family protein		_____________144_________________________________________________182\n_____________\|___________________________________________________\|\n5'-GCU...AAUCU____G______UUGUGGC_____A___________________________UUCUG...UGG-3'\n______________GACG_CAGGGG_______GCUGC_UCGU______________GGUUAUAAG\n______________:\|\|:_\|\|\|\|\|:_______\|\|\|\|\|_:\|\|\|______________:\|\|\|\|:\|\|\|\n______________UUGU_GUCCCU_______CGACG_GGCA______________UCAAUGUUC\n3'-UUU...CGCGG____G______UUAGAAC_____C____UUUAAUAAUACUAC_________CCGUG...GUG-5'\n_____________\|___________________________________________________\|\n_____________79__________________________________________________27\n	175 -- 181	28 -- 34	-33.2852 kcal/mol	14.1676 kcal/mol	9.38606 kcal/mol	144 182@LB@ \| \|@LB@5'-GCU...AAUCU G UUGUGGC A UUCUG...UGG-3'@LB@ GACG CAGGGG GCUGC UCGU GGUUAUAAG@LB@ :\|\|: \|\|\|\|\|: \|\|\|\|\| :\|\|\| :\|\|\|\|:\|\|\|@LB@ UUGU GUCCCU CGACG GGCA UCAAUGUUC@LB@3'-UUU...CGCGG G UUAGAAC C UUUAAUAAUACUAC CCGUG...GUG-5'@LB@ \| \|@LB@ 79 27@LB@@LB@@LB@Energy -9.73 kcal/mol@LB@Hybridization Energy -33.2852 kcal/mol@LB@Unfolding Energy - mRNA 14.1676 kcal/mol@LB@Unfolding Energy - sRNA 9.38606 kcal/mol@LB@@LB@Position - mRNA 145 -- 181@LB@Position - sRNA 28 -- 78@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 28 -- 34@LB@
6	0.0001378	0.08054	b3860	dsbA	-12.69	0.042007	89 -- 111	55 -- 75	periplasmic protein disulfide isomerase I		_____________88______________________112\n_____________\|_______________________\|\n5'-UUU...GGUUA_______A_____AC________ACAGA...AAC-3'\n______________ACCGGGG_AGAUU__UGGCUGCG\n______________\|\|\|:\|\|\|_\|:\|\|:__\|\|\|\|\|\|\|\|\n______________UGGUCCC_UUUAG__ACCGACGC\n3'-UUU...GGUUG_____________A_________GGCAU...GUG-5'\n_____________\|_______________________\|\n_____________76______________________54\n	105 -- 111	55 -- 61	-30.5184 kcal/mol	9.58616 kcal/mol	8.24199 kcal/mol	88 112@LB@ \| \|@LB@5'-UUU...GGUUA A AC ACAGA...AAC-3'@LB@ ACCGGGG AGAUU UGGCUGCG@LB@ \|\|\|:\|\|\| \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UGGUCCC UUUAG ACCGACGC@LB@3'-UUU...GGUUG A GGCAU...GUG-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -30.5184 kcal/mol@LB@Unfolding Energy - mRNA 9.58616 kcal/mol@LB@Unfolding Energy - sRNA 8.24199 kcal/mol@LB@@LB@Position - mRNA 89 -- 111@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 55 -- 61@LB@
170	0.01004	0.2071	b3887	dtd	-7.24	0.420466	57 -- 66	52 -- 62	D-tyr-tRNA(Tyr) deacylase		_____________56__________67\n_____________\|___________\|\n5'-GGA...AUUUA___________GCGGU...UCG-3'\n______________UGG_UGUGCUG\n______________\|\|\|_\|\|:\|\|:\|\n______________ACC_ACGCGGC\n3'-UUU...UUAGA___G_______AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	60 -- 66	52 -- 58	-13.8062 kcal/mol	1.68508 kcal/mol	4.8804 kcal/mol	56 67@LB@ \| \|@LB@5'-GGA...AUUUA GCGGU...UCG-3'@LB@ UGG UGUGCUG@LB@ \|\|\| \|\|:\|\|:\|@LB@ ACC ACGCGGC@LB@3'-UUU...UUAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.8062 kcal/mol@LB@Unfolding Energy - mRNA 1.68508 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 57 -- 66@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 52 -- 58@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@LB@
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit		_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3		_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
71	0.003482	0.1727	b4046	zur	-8.96	0.216158	254 -- 300	53 -- 94	transcriptional repressor Zn(II)-binding		_____________253__________________________________________________300\n_____________\|____________________________________________________\|\n5'-UAA...UGCGC__A___U___________UGACCCCAC______U___________________-3'\n______________GC_GCG_AAUG_UGCGCC_________AGCGCC__GGAAGU____GUUGCGCC\n______________\|\|_\|\|\|_\|\|\|:_\|\|\|\|\|\|_________\|:\|:\|\|__\|\|\|\|:\|____\|:\|\|\|\|\|\|\n______________CG_CGC_UUAU_ACGCGG_________UUGUGG__CCUUUA____CGACGCGG\n3'-UUU...CCCCA___________G_____________________UC______GAAC________CAUUU...GUG-5'\n_____________\|_____________________________________________________\|\n_____________95____________________________________________________52\n	294 -- 300	53 -- 59	-43.5981 kcal/mol	17.5702 kcal/mol	17.0684 kcal/mol	253 300@LB@ \| \|@LB@5'-UAA...UGCGC A U UGACCCCAC U -3'@LB@ GC GCG AAUG UGCGCC AGCGCC GGAAGU GUUGCGCC@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\|\| \|:\|:\|\| \|\|\|\|:\| \|:\|\|\|\|\|\|@LB@ CG CGC UUAU ACGCGG UUGUGG CCUUUA CGACGCGG@LB@3'-UUU...CCCCA G UC GAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 95 52@LB@@LB@@LB@Energy -8.96 kcal/mol@LB@Hybridization Energy -43.5981 kcal/mol@LB@Unfolding Energy - mRNA 17.5702 kcal/mol@LB@Unfolding Energy - sRNA 17.0684 kcal/mol@LB@@LB@Position - mRNA 254 -- 300@LB@Position - sRNA 53 -- 94@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 53 -- 59@LB@
127	0.007097	0.1961	b4065	yjcE	-10.62	0.105957	81 -- 91	51 -- 62	putative cation/proton antiporter		_____________80___________92\n_____________\|____________\|\n5'-UAU...GGCAA____________UUUUA...UGC-3'\n______________UGGCUGC_CCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\n______________ACCGACG_GGCA\n3'-UUU...UUAGA_______C____UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	81 -- 87	56 -- 62	-18.8543 kcal/mol	3.34811 kcal/mol	4.8826 kcal/mol	80 92@LB@ \| \|@LB@5'-UAU...GGCAA UUUUA...UGC-3'@LB@ UGGCUGC CCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ ACCGACG GGCA@LB@3'-UUU...UUAGA C UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -18.8543 kcal/mol@LB@Unfolding Energy - mRNA 3.34811 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 81 -- 91@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 56 -- 62@LB@
171	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease		_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
163	0.009572	0.2068	b4126	yjdI	-8.84	0.226749	182 -- 194	26 -- 41	putative 4Fe-4S mono-cluster protein		_____________181______________195\n_____________\|________________\|\n5'-UAG...CAUAC_______A________AAGGU...GCG-3'\n______________UGAUGAG____GAGGG\n______________\|\|\|\|\|\|\|____:\|\|\|\|\n______________ACUACUC____UUCCC\n3'-UUU...AUAAU_______AAUG_____GUGUC...GUG-5'\n_____________\|________________\|\n_____________42_______________25\n	182 -- 188	35 -- 41	-13.4129 kcal/mol	1.87738 kcal/mol	2.69216 kcal/mol	181 195@LB@ \| \|@LB@5'-UAG...CAUAC A AAGGU...GCG-3'@LB@ UGAUGAG GAGGG@LB@ \|\|\|\|\|\|\| :\|\|\|\|@LB@ ACUACUC UUCCC@LB@3'-UUU...AUAAU AAUG GUGUC...GUG-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.4129 kcal/mol@LB@Unfolding Energy - mRNA 1.87738 kcal/mol@LB@Unfolding Energy - sRNA 2.69216 kcal/mol@LB@@LB@Position - mRNA 182 -- 194@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 35 -- 41@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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