Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
188	0.01085	0.1919	b1878	flhE	-11.23	0.096033	252 -- 283	16 -- 51	proton seal during flagellar secretion		_____________251__________________________________284\n_____________\|____________________________________\|\n5'-CGU...CCGCC__________A__G___CA____A____GUG_____AAUUA...AUC-3'\n______________GGGGAGG_GG__U_UGG___GGC_AGUA___UA_GG\n______________::\|\|\|\|\|_\|\|__:_\|\|\|___:\|\|_\|\|:\|___\|\|_\|\|\n______________UUCCUCC_CC__G_ACC___UCG_UCGU___AU_CC\n3'-UUU...UCCGA_______A__AA_G___AUG___A____AAA__A__CAAUA...UCG-5'\n_____________\|____________________________________\|\n_____________52___________________________________15\n	252 -- 258	45 -- 51	-25.2373 kcal/mol	9.34808 kcal/mol	4.65624 kcal/mol	251 284@LB@ \| \|@LB@5'-CGU...CCGCC A G CA A GUG AAUUA...AUC-3'@LB@ GGGGAGG GG U UGG GGC AGUA UA GG@LB@ ::\|\|\|\|\| \|\| : \|\|\| :\|\| \|\|:\| \|\| \|\|@LB@ UUCCUCC CC G ACC UCG UCGU AU CC@LB@3'-UUU...UCCGA A AA G AUG A AAA A CAAUA...UCG-5'@LB@ \| \|@LB@ 52 15@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -25.2373 kcal/mol@LB@Unfolding Energy - mRNA 9.34808 kcal/mol@LB@Unfolding Energy - sRNA 4.65624 kcal/mol@LB@@LB@Position - mRNA 252 -- 283@LB@Position - sRNA 16 -- 51@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 45 -- 51@LB@
90	0.002979	0.1113	b3328	gspG	-12.13	0.061461	284 -- 293	37 -- 46	pseudopilin cryptic general secretion pathway		_____________283________294\n_____________\|__________\|\n5'-AAA...AGCCU__________AACCUAA-3'\n______________GGUGGUUCCU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCACCAAGGA\n3'-UUU...UUCCU__________CCAUG...UCG-5'\n_____________\|__________\|\n_____________47_________36\n	287 -- 293	37 -- 43	-18.4741 kcal/mol	3.21142 kcal/mol	3.13317 kcal/mol	283 294@LB@ \| \|@LB@5'-AAA...AGCCU AACCUAA-3'@LB@ GGUGGUUCCU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCACCAAGGA@LB@3'-UUU...UUCCU CCAUG...UCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.4741 kcal/mol@LB@Unfolding Energy - mRNA 3.21142 kcal/mol@LB@Unfolding Energy - sRNA 3.13317 kcal/mol@LB@@LB@Position - mRNA 284 -- 293@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
187	0.01074	0.1919	b2536	hcaT	-7.74	0.383266	275 -- 291	25 -- 41	putative 3-phenylpropionic transporter		_____________274_______________292\n_____________\|_________________\|\n5'-UCG...CUACC_______A___U_____UUAAA...GGA-3'\n______________UUUCUGG_GCG_CUGGC\n______________\|\|:\|\|\|\|_:\|:_\|\|:\|\|\n______________AAGGACC_UGU_GAUCG\n3'-UUU...CCACC_______A___C_____UAAAA...UCG-5'\n_____________\|_________________\|\n_____________42________________24\n	275 -- 281	35 -- 41	-17.8602 kcal/mol	5.56231 kcal/mol	4.55428 kcal/mol	274 292@LB@ \| \|@LB@5'-UCG...CUACC A U UUAAA...GGA-3'@LB@ UUUCUGG GCG CUGGC@LB@ \|\|:\|\|\|\| :\|: \|\|:\|\|@LB@ AAGGACC UGU GAUCG@LB@3'-UUU...CCACC A C UAAAA...UCG-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -17.8602 kcal/mol@LB@Unfolding Energy - mRNA 5.56231 kcal/mol@LB@Unfolding Energy - sRNA 4.55428 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 35 -- 41@LB@
42	0.000828	0.06626	b2129	yehX	-13.83	0.023625	55 -- 85	15 -- 47	putative ABC transporter ATPase		_____________54________________________________86\n_____________\|_________________________________\|\n5'-GGU...GGCGC___C___________________UUUCCAG___CUGCU...UUG-3'\n______________AGG_GGUU_UUGGUGC_GCUGGU_______GGG\n______________\|\|\|_\|\|\|\|_:\|\|\|\|:\|_\|\|\|:\|:_______\|\|\|\n______________UCC_CCAA_GACCAUG_CGAUCG_______CCC\n3'-UUU...AUUCC___A____G_______U______UAAAAUA___AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________48________________________________14\n	63 -- 69	32 -- 38	-32.2293 kcal/mol	13.8239 kcal/mol	4.57348 kcal/mol	54 86@LB@ \| \|@LB@5'-GGU...GGCGC C UUUCCAG CUGCU...UUG-3'@LB@ AGG GGUU UUGGUGC GCUGGU GGG@LB@ \|\|\| \|\|\|\| :\|\|\|\|:\| \|\|\|:\|: \|\|\|@LB@ UCC CCAA GACCAUG CGAUCG CCC@LB@3'-UUU...AUUCC A G U UAAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 48 14@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -32.2293 kcal/mol@LB@Unfolding Energy - mRNA 13.8239 kcal/mol@LB@Unfolding Energy - sRNA 4.57348 kcal/mol@LB@@LB@Position - mRNA 55 -- 85@LB@Position - sRNA 15 -- 47@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 32 -- 38@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease		_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@
161	0.008114	0.1694	b3656	yicI	-11.96	0.067144	124 -- 143	14 -- 37	putative alpha-glucosidase	b3878	_____________123______________________144\n_____________\|________________________\|\n5'-ACA...CGUUA___A_________UCA________AAACG...UGG-3'\n______________UGG_ACAGCUGGC_______GGGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|_______\|\|\|\|\n______________ACC_UGUCGAUCG_______CCCA\n3'-UUU...CAAGG___A_________UAAAAUA____AUACA...UCG-5'\n_____________\|________________________\|\n_____________38_______________________13\n	130 -- 136	25 -- 31	-23.0355 kcal/mol	8.41802 kcal/mol	2.65978 kcal/mol	123 144@LB@ \| \|@LB@5'-ACA...CGUUA A UCA AAACG...UGG-3'@LB@ UGG ACAGCUGGC GGGU@LB@ \|\|\| \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACC UGUCGAUCG CCCA@LB@3'-UUU...CAAGG A UAAAAUA AUACA...UCG-5'@LB@ \| \|@LB@ 38 13@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -23.0355 kcal/mol@LB@Unfolding Energy - mRNA 8.41802 kcal/mol@LB@Unfolding Energy - sRNA 2.65978 kcal/mol@LB@@LB@Position - mRNA 124 -- 143@LB@Position - sRNA 14 -- 37@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 25 -- 31@LB@
38	0.0007298	0.06455	b3196	yrbG	-13.22	0.033821	90 -- 115	1 -- 31	putative calcium/sodium:proton antiporter		_____________89______________________________116\n_____________\|_______________________________\|\n5'-UUC...GCGAA___________________UUAC________CGCAU...UUG-3'\n______________AGCUGGCAUUU_____GUU____UUUUUAGC\n______________\|\|\|\|:\|\|\|\|\|\|_____\|\|\|____\|\|\|\|:\|\|\|\n______________UCGAUCGUAAA_____CAA____AAAAGUCG\n3'-UUU...CCAUG___________AUACC___UACA________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	109 -- 115	1 -- 7	-21.7779 kcal/mol	7.06678 kcal/mol	1.48722 kcal/mol	89 116@LB@ \| \|@LB@5'-UUC...GCGAA UUAC CGCAU...UUG-3'@LB@ AGCUGGCAUUU GUU UUUUUAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ UCGAUCGUAAA CAA AAAAGUCG@LB@3'-UUU...CCAUG AUACC UACA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -21.7779 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 90 -- 115@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 1 -- 7@LB@
3	2.088e-07	0.000234	b2077	iceT	-18.53	0.000593	226 -- 254	1 -- 30	putative citrate/iron-citrate/zinc-citrate efflux transporter		_____________225____________________________255\n_____________\|______________________________\|\n5'-CGG...CACCC_______A_______A_____GC_______UUCUU...UUC-3'\n______________GUUGGCA__UUGUGG_UUGUG__UUUCGGC\n______________\|:\|:\|\|\|__\|\|:\|\|\|_\|\|:\|\|__\|\|\|\|:\|\|\n______________CGAUCGU__AAUACC_AAUAC__AAAGUCG\n3'-UUU...CAUGU_______AA______C_____AA_______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	248 -- 254	1 -- 7	-30.4381 kcal/mol	10.4245 kcal/mol	1.48556 kcal/mol	225 255@LB@ \| \|@LB@5'-CGG...CACCC A A GC UUCUU...UUC-3'@LB@ GUUGGCA UUGUGG UUGUG UUUCGGC@LB@ \|:\|:\|\|\| \|\|:\|\|\| \|\|:\|\| \|\|\|\|:\|\|@LB@ CGAUCGU AAUACC AAUAC AAAGUCG@LB@3'-UUU...CAUGU AA C AA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -18.53 kcal/mol@LB@Hybridization Energy -30.4381 kcal/mol@LB@Unfolding Energy - mRNA 10.4245 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 226 -- 254@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 1 -- 7@LB@
23	0.0002818	0.04118	b1813	nudL	-13.86	0.023273	1 -- 17	22 -- 39	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		______________1_________________18\n______________\|_________________\|\n___________5'-__________________GGCUA...CUG-3'\n______________CCUGGUGCGGC_AGCAUU\n______________\|\|\|\|\|\|:\|:\|\|_\|\|\|\|\|\|\n______________GGACCAUGUCG_UCGUAA\n3'-UUU...ACCAA___________A______AAUAC...UCG-5'\n_____________\|__________________\|\n_____________40_________________21\n	5 -- 11	29 -- 35	-27.845 kcal/mol	9.43444 kcal/mol	4.55392 kcal/mol	1 18@LB@ \| \|@LB@ 5'- GGCUA...CUG-3'@LB@ CCUGGUGCGGC AGCAUU@LB@ \|\|\|\|\|\|:\|:\|\| \|\|\|\|\|\|@LB@ GGACCAUGUCG UCGUAA@LB@3'-UUU...ACCAA A AAUAC...UCG-5'@LB@ \| \|@LB@ 40 21@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -27.845 kcal/mol@LB@Unfolding Energy - mRNA 9.43444 kcal/mol@LB@Unfolding Energy - sRNA 4.55392 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 22 -- 39@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
20	0.0001678	0.0282	b2056	wcaD	-17.66	0.001373	77 -- 104	24 -- 48	putative colanic acid polymerase		_____________76___________________________105\n_____________\|____________________________\|\n5'-GCC...AAGAA______CUGCAA____________A___AACCG...UCA-3'\n______________GAGGUG______CUGGUGCAGUUA_GCA\n______________\|\|\|\|\|\|______\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUCCAC______GACCAUGUCGAU_CGU\n3'-UUU...GAUUC______CAAG__________________AAAAU...UCG-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	94 -- 100	27 -- 33	-32.1729 kcal/mol	9.95006 kcal/mol	4.55899 kcal/mol	76 105@LB@ \| \|@LB@5'-GCC...AAGAA CUGCAA A AACCG...UCA-3'@LB@ GAGGUG CUGGUGCAGUUA GCA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUCCAC GACCAUGUCGAU CGU@LB@3'-UUU...GAUUC CAAG AAAAU...UCG-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -17.66 kcal/mol@LB@Hybridization Energy -32.1729 kcal/mol@LB@Unfolding Energy - mRNA 9.95006 kcal/mol@LB@Unfolding Energy - sRNA 4.55899 kcal/mol@LB@@LB@Position - mRNA 77 -- 104@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 27 -- 33@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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