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
157	0.0114	0.2504	b3833	ubiE	-14.57	0.035245	198 -- 236	1 -- 30	bifunctional 2-octaprenyl-6-methoxy-1 4-benzoquinone methylase/ S-adenosylmethionine:2-DMK methyltransferase	_____________197_____________________________________237\n_____________\|_______________________________________\|\n5'-ACA...GCAUU_______U____AA____C______CGAC___CUU____UUUCA...CAU-3'\n______________GAGAUGG_GGAU__GUCA_AAGAAA____GCA___UGGU\n______________:\|:\|\|\|\|_\|\|\|:__:\|\|\|_\|\|\|\|\|\|____\|\|\|___\|\|\|:\n______________UUUUACC_CCUG__UAGU_UUCUUU____CGU___ACCG\n3'-UUU...AGGUG_________________________U______C______-5'\n_____________\|______________________________________\|\n_____________31_____________________________________1\n	198 -- 204	24 -- 30	-23.6374 kcal/mol	6.55293 kcal/mol	2.51911 kcal/mol	197 237@LB@ \| \|@LB@5'-ACA...GCAUU U AA C CGAC CUU UUUCA...CAU-3'@LB@ GAGAUGG GGAU GUCA AAGAAA GCA UGGU@LB@ :\|:\|\|\|\| \|\|\|: :\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|:@LB@ UUUUACC CCUG UAGU UUCUUU CGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -23.6374 kcal/mol@LB@Unfolding Energy - mRNA 6.55293 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 236@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@LB@
39	0.001912	0.1648	b2532	trmJ	-14.54	0.035636	97 -- 121	1 -- 23	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent	_____________96________________________122\n_____________\|_________________________\|\n5'-CGU...UCACU_____________C__G_AAAC___GCAGA...UGU-3'\n______________GGAUGUUAAAGAA_GG_A____GGC\n______________\|\|\|::\|:\|\|\|\|\|\|_:\|_\|____\|\|\|\n______________CCUGUAGUUUCUU_UC_U____CCG\n3'-UUU...UUACC_____________U__G_CA_____-5'\n_____________\|________________________\|\n_____________24_______________________1\n	103 -- 109	11 -- 17	-19.8008 kcal/mol	3.67656 kcal/mol	1.57928 kcal/mol	96 122@LB@ \| \|@LB@5'-CGU...UCACU C G AAAC GCAGA...UGU-3'@LB@ GGAUGUUAAAGAA GG A GGC@LB@ \|\|\|::\|:\|\|\|\|\|\| :\| \| \|\|\|@LB@ CCUGUAGUUUCUU UC U CCG@LB@3'-UUU...UUACC U G CA -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -19.8008 kcal/mol@LB@Unfolding Energy - mRNA 3.67656 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 97 -- 121@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 11 -- 17@LB@
107	0.007146	0.2343	b0085	murE	-14.50	0.036427	193 -- 205	1 -- 25	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase	_____________192_______________________206\n_____________\|_________________________\|\n5'-UGC...GGCGA_________________________AGAUC...CGG-3'\n______________GGGGACA____________GGUGGC\n______________\|\|\|\|\|\|\|____________:\|\|\|\|\|\n______________CCCCUGU____________UCACCG\n3'-UUU...UUUUA_______AGUUUCUUUUCG______-5'\n_____________\|________________________\|\n_____________26_______________________1\n	193 -- 199	19 -- 25	-21.3886 kcal/mol	4.36682 kcal/mol	2.51748 kcal/mol	192 206@LB@ \| \|@LB@5'-UGC...GGCGA AGAUC...CGG-3'@LB@ GGGGACA GGUGGC@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CCCCUGU UCACCG@LB@3'-UUU...UUUUA AGUUUCUUUUCG -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -21.3886 kcal/mol@LB@Unfolding Energy - mRNA 4.36682 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 19 -- 25@LB@
195	0.01413	0.2529	b2527	hscB	-14.38	0.038945	62 -- 81	1 -- 21	HscA co-chaperone J domain-containing protein Hsc56; IscU-specific chaperone HscAB	_____________61____________________82\n_____________\|_____________________\|\n5'-GGU...CCCGA__________U__________UGCGG...CUG-3'\n______________ACGUCAAAGA_GAGU_GUGGU\n______________\|\|:\|\|\|\|\|\|\|_:\|\|:_\|\|\|\|:\n______________UGUAGUUUCU_UUCG_CACCG\n3'-UUU...ACCCC__________U____U_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	65 -- 71	12 -- 18	-23.3701 kcal/mol	7.47956 kcal/mol	1.51103 kcal/mol	61 82@LB@ \| \|@LB@5'-GGU...CCCGA U UGCGG...CUG-3'@LB@ ACGUCAAAGA GAGU GUGGU@LB@ \|\|:\|\|\|\|\|\|\| :\|\|: \|\|\|\|:@LB@ UGUAGUUUCU UUCG CACCG@LB@3'-UUU...ACCCC U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.3701 kcal/mol@LB@Unfolding Energy - mRNA 7.47956 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 12 -- 18@LB@
31	0.001481	0.1635	b3468	yhhN	-14.35	0.039524	32 -- 52	1 -- 21	TMEM86 family putative inner membrane protein	_____________31____________________53\n_____________\|_____________________\|\n5'-CGA...UGAUA___A__________A______UUGCU...UAA-3'\n______________ACA_UAAAGAAAAG_GGUGGU\n______________\|\|\|_:\|\|\|\|\|\|\|\|\|_:\|\|\|\|:\n______________UGU_GUUUCUUUUC_UCACCG\n3'-UUU...ACCCC___A__________G______-5'\n_____________\|____________________\|\n_____________22___________________1\n	39 -- 45	8 -- 14	-21.1877 kcal/mol	5.32481 kcal/mol	1.51103 kcal/mol	31 53@LB@ \| \|@LB@5'-CGA...UGAUA A A UUGCU...UAA-3'@LB@ ACA UAAAGAAAAG GGUGGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| :\|\|\|\|:@LB@ UGU GUUUCUUUUC UCACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -21.1877 kcal/mol@LB@Unfolding Energy - mRNA 5.32481 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 32 -- 52@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 8 -- 14@LB@
83	0.005101	0.2147	b2610	ffh	-14.32	0.040245	57 -- 74	4 -- 21	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________56_________________75\n_____________\|__________________\|\n5'-AGG...GAGCA___AG_____________AUAGC...AAG-3'\n______________AUA__AAAGAGAAGCAGU\n______________\|:\|__\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__UUUCUUUUCGUCA\n3'-UUU...ACCCC___AG_____________CCG-5'\n_____________\|__________________\|\n_____________22_________________3\n	68 -- 74	4 -- 10	-18.2522 kcal/mol	2.42435 kcal/mol	1.51 kcal/mol	56 75@LB@ \| \|@LB@5'-AGG...GAGCA AG AUAGC...AAG-3'@LB@ AUA AAAGAGAAGCAGU@LB@ \|:\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU UUUCUUUUCGUCA@LB@3'-UUU...ACCCC AG CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -18.2522 kcal/mol@LB@Unfolding Energy - mRNA 2.42435 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 57 -- 74@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 4 -- 10@LB@
119	0.008338	0.2459	b0123	cueO	-14.31	0.040489	47 -- 61	9 -- 24	multicopper oxidase (laccase)	_____________46_______________62\n_____________\|________________\|\n5'-CUG...UACCA________________UAAAC...CGU-3'\n______________GGGGC_UUAAAGAAGA\n______________\|\|\|:\|_\|:\|\|\|\|\|\|:\|\n______________CCCUG_AGUUUCUUUU\n3'-UUU...UUUAC_____U__________CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	55 -- 61	9 -- 15	-17.0719 kcal/mol	2.10565 kcal/mol	0.659805 kcal/mol	46 62@LB@ \| \|@LB@5'-CUG...UACCA UAAAC...CGU-3'@LB@ GGGGC UUAAAGAAGA@LB@ \|\|\|:\| \|:\|\|\|\|\|\|:\|@LB@ CCCUG AGUUUCUUUU@LB@3'-UUU...UUUAC U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -17.0719 kcal/mol@LB@Unfolding Energy - mRNA 2.10565 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 47 -- 61@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 9 -- 15@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)	_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
36	0.001784	0.1648	b0785	moaE	-14.28	0.040953	241 -- 264	1 -- 21	molybdopterin synthase large subunit	_____________240______________________265\n_____________\|________________________\|\n5'-AGA...GUUCA____A___________CCC_____UGGCG...CCU-3'\n______________GCGU_GGAGAAGAGUA___GUGGC\n______________:\|:\|_::\|\|\|\|:\|\|:\|___\|\|\|\|\|\n______________UGUA_UUUCUUUUCGU___CACCG\n3'-UUU...ACCCC____G___________________-5'\n_____________\|_______________________\|\n_____________22______________________1\n	250 -- 256	6 -- 12	-21.7367 kcal/mol	5.94077 kcal/mol	1.51103 kcal/mol	240 265@LB@ \| \|@LB@5'-AGA...GUUCA A CCC UGGCG...CCU-3'@LB@ GCGU GGAGAAGAGUA GUGGC@LB@ :\|:\| ::\|\|\|\|:\|\|:\| \|\|\|\|\|@LB@ UGUA UUUCUUUUCGU CACCG@LB@3'-UUU...ACCCC G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.28 kcal/mol@LB@Hybridization Energy -21.7367 kcal/mol@LB@Unfolding Energy - mRNA 5.94077 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 241 -- 264@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 6 -- 12@LB@
189	0.01393	0.2529	b0934	ssuC	-14.25	0.041816	137 -- 153	1 -- 17	aliphatic sulfonate ABC transporter permease	_____________136_______________154\n_____________\|_________________\|\n5'-UGC...AUCCG_____C___________GAAUG...GGC-3'\n______________CAAGG_GAAGCGGUGGC\n______________\|\|\|:\|_:\|\|\|\|:\|\|\|\|\|\n______________GUUUC_UUUCGUCACCG\n3'-UUU...CUGUA_____U___________-5'\n_____________\|________________\|\n_____________18_______________1\n	147 -- 153	1 -- 7	-24.8998 kcal/mol	9.21593 kcal/mol	1.43853 kcal/mol	136 154@LB@ \| \|@LB@5'-UGC...AUCCG C GAAUG...GGC-3'@LB@ CAAGG GAAGCGGUGGC@LB@ \|\|\|:\| :\|\|\|\|:\|\|\|\|\|@LB@ GUUUC UUUCGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -24.8998 kcal/mol@LB@Unfolding Energy - mRNA 9.21593 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 137 -- 153@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 147 -- 153@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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