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
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@
32	0.001499	0.1635	b0661	miaB	-12.88	0.082685	213 -- 250	6 -- 36	tRNA-i(6)A37 methylthiotransferase	_____________212____________________________________251\n_____________\|______________________________________\|\n5'-CGC...AAAAA_______UU_AAACC_____C_______U___C_____CGAUU...AAC-3'\n______________CUCCAUA__A_____UGGGG_UGUCAGA_GAA_GAGUA\n______________\|\|\|\|\|:\|__\|_____\|\|\|\|\|_::\|\|\|:\|_\|\|\|_:\|\|:\|\n______________GAGGUGU__U_____ACCCC_GUAGUUU_CUU_UUCGU\n3'-UUU...UACCC_______UU___________U_________________CACCG-5'\n_____________\|______________________________________\|\n_____________37_____________________________________5\n	234 -- 240	14 -- 20	-26.1374 kcal/mol	6.57825 kcal/mol	6.67617 kcal/mol	212 251@LB@ \| \|@LB@5'-CGC...AAAAA UU AAACC C U C CGAUU...AAC-3'@LB@ CUCCAUA A UGGGG UGUCAGA GAA GAGUA@LB@ \|\|\|\|\|:\| \| \|\|\|\|\| ::\|\|\|:\| \|\|\| :\|\|:\|@LB@ GAGGUGU U ACCCC GUAGUUU CUU UUCGU@LB@3'-UUU...UACCC UU U CACCG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -26.1374 kcal/mol@LB@Unfolding Energy - mRNA 6.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.67617 kcal/mol@LB@@LB@Position - mRNA 213 -- 250@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 14 -- 20@LB@
33	0.001538	0.1635	b4141	yjeH	-13.95	0.048780	254 -- 275	1 -- 22	putative transporter	_____________253____________________276\n_____________\|______________________\|\n5'-CAG...CUAUC_______UUAUU_____C____GUGUU...CUG-3'\n______________GACGUCA_____AGGCA_UGGC\n______________\|\|\|:\|\|\|_____\|:\|\|\|_\|\|\|\|\n______________CUGUAGU_____UUCGU_ACCG\n3'-UUU...UACCC_______UUCUU_____C____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	254 -- 260	16 -- 22	-22.2624 kcal/mol	6.77205 kcal/mol	1.54023 kcal/mol	253 276@LB@ \| \|@LB@5'-CAG...CUAUC UUAUU C GUGUU...CUG-3'@LB@ GACGUCA AGGCA UGGC@LB@ \|\|\|:\|\|\| \|:\|\|\| \|\|\|\|@LB@ CUGUAGU UUCGU ACCG@LB@3'-UUU...UACCC UUCUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -22.2624 kcal/mol@LB@Unfolding Energy - mRNA 6.77205 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 16 -- 22@LB@
34	0.001647	0.1648	b1218	chaC	-13.74	0.054411	171 -- 189	1 -- 17	cation transport regulator	_____________170_________________190\n_____________\|___________________\|\n5'-AUA...UGUCG________UAU________GGAAG...CGC-3'\n______________CAGGGAAG___GCAGUGGC\n______________\|\|::\|\|\|:___\|\|\|\|\|\|\|\|\n______________GUUUCUUU___CGUCACCG\n3'-UUU...CUGUA________U__________-5'\n_____________\|__________________\|\n_____________18_________________1\n	183 -- 189	1 -- 7	-23.3292 kcal/mol	8.15416 kcal/mol	1.43853 kcal/mol	170 190@LB@ \| \|@LB@5'-AUA...UGUCG UAU GGAAG...CGC-3'@LB@ CAGGGAAG GCAGUGGC@LB@ \|\|::\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.74 kcal/mol@LB@Hybridization Energy -23.3292 kcal/mol@LB@Unfolding Energy - mRNA 8.15416 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 171 -- 189@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 1 -- 7@LB@
35	0.00168	0.1648	b2231	gyrA	-15.33	0.023033	230 -- 249	7 -- 25	DNA gyrase (type II topoisomerase) subunit A	_____________229__________________250\n_____________\|____________________\|\n5'-AGC...ACACC__UCA_______________UGAAG...CGC-3'\n______________GG___ACAUUGAGGAAGAGC\n______________\|\|___\|\|\|\|::\|:\|\|\|:\|\|\|\n______________CC___UGUAGUUUCUUUUCG\n3'-UUU...UUUUA__CC________________UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	243 -- 249	7 -- 13	-19.3394 kcal/mol	3.30418 kcal/mol	0.70626 kcal/mol	229 250@LB@ \| \|@LB@5'-AGC...ACACC UCA UGAAG...CGC-3'@LB@ GG ACAUUGAGGAAGAGC@LB@ \|\| \|\|\|\|::\|:\|\|\|:\|\|\|@LB@ CC UGUAGUUUCUUUUCG@LB@3'-UUU...UUUUA CC UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -19.3394 kcal/mol@LB@Unfolding Energy - mRNA 3.30418 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 230 -- 249@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 7 -- 13@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@
37	0.001785	0.1648	b3933	ftsN	-15.64	0.019200	24 -- 52	1 -- 29	essential cell division protein	_____________23______________________________53\n_____________\|_______________________________\|\n5'-AGC...UGAUC_____CA______A__CGUU___________UCUCG...CUC-3'\n______________AAAUG__GGGGCA_CA______GGCAGUGGC\n______________\|\|\|\|\|__\|\|\|:\|\|_\|\|______:\|\|\|\|\|\|\|\|\n______________UUUAC__CCCUGU_GU______UCGUCACCG\n3'-UUU...GGUGU_____________A__UUCUUU_________-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	46 -- 52	1 -- 7	-29.0551 kcal/mol	10.8938 kcal/mol	2.51907 kcal/mol	23 53@LB@ \| \|@LB@5'-AGC...UGAUC CA A CGUU UCUCG...CUC-3'@LB@ AAAUG GGGGCA CA GGCAGUGGC@LB@ \|\|\|\|\| \|\|\|:\|\| \|\| :\|\|\|\|\|\|\|\|@LB@ UUUAC CCCUGU GU UCGUCACCG@LB@3'-UUU...GGUGU A UUCUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -29.0551 kcal/mol@LB@Unfolding Energy - mRNA 10.8938 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 24 -- 52@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
38	0.001836	0.1648	b3188	sfsB	-13.60	0.058336	253 -- 274	1 -- 32	malPQ operon transcriptional activator	_____________252______________________________275\n_____________\|________________________________\|\n5'-CGG...UUUGC______A___A_____________________GGCGG...UGA-3'\n______________GCAAGA_GGG_ACGUCAA__________UGGC\n______________:\|\|\|:\|_\|\|\|_\|\|:\|\|\|\|__________\|\|\|\|\n______________UGUUUU_CCC_UGUAGUU__________ACCG\n3'-UUU...CGAGG______A___C_______UCUUUUCGUC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	264 -- 270	15 -- 21	-21.5209 kcal/mol	5.38314 kcal/mol	2.53929 kcal/mol	252 275@LB@ \| \|@LB@5'-CGG...UUUGC A A GGCGG...UGA-3'@LB@ GCAAGA GGG ACGUCAA UGGC@LB@ :\|\|\|:\| \|\|\| \|\|:\|\|\|\| \|\|\|\|@LB@ UGUUUU CCC UGUAGUU ACCG@LB@3'-UUU...CGAGG A C UCUUUUCGUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -21.5209 kcal/mol@LB@Unfolding Energy - mRNA 5.38314 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 253 -- 274@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 15 -- 21@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@
40	0.001973	0.1648	b1823	cspC	-10.89	0.196769	199 -- 231	1 -- 29	stress protein member of the CspA-family	_____________198_______________________________232\n_____________\|_________________________________\|\n5'-UAU...UUUUC______CAA_G________UC____UA______UCAAC...UCU-3'\n______________AAAUGG___A_AUUAAAGG__AGGU__AGUGGU\n______________\|\|\|\|\|\|___\|_\|\|:\|\|\|\|:__\|:\|:__\|\|\|\|\|:\n______________UUUACC___U_UAGUUUCU__UUCG__UCACCG\n3'-UUU...GGUGU______CC__G________U_____________-5'\n_____________\|________________________________\|\n_____________30_______________________________1\n	210 -- 216	13 -- 19	-20.1954 kcal/mol	6.78842 kcal/mol	2.51907 kcal/mol	198 232@LB@ \| \|@LB@5'-UAU...UUUUC CAA G UC UA UCAAC...UCU-3'@LB@ AAAUGG A AUUAAAGG AGGU AGUGGU@LB@ \|\|\|\|\|\| \| \|\|:\|\|\|\|: \|:\|: \|\|\|\|\|:@LB@ UUUACC U UAGUUUCU UUCG UCACCG@LB@3'-UUU...GGUGU CC G U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -10.89 kcal/mol@LB@Hybridization Energy -20.1954 kcal/mol@LB@Unfolding Energy - mRNA 6.78842 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 199 -- 231@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 13 -- 19@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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