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
181	0.0104	0.1919	b2106	rcnA	-12.10	0.062308	133 -- 155	15 -- 50	membrane protein conferring nickel and cobalt resistance	_____________132__________________________________156\n_____________\|____________________________________\|\n5'-UUC...CUACU_______A__A__A______________________GGGGA...ACU-3'\n______________GGGGGGU_GU_UC_GGUAC_____________UGGG\n______________:\|\|:\|\|\|_\|\|_:\|_\|\|\|\|\|_____________\|\|\|\|\n______________UCCUCCA_CA_GG_CCAUG_____________ACCC\n3'-UUU...CCGAU_______C__A__A_____UCGAUCGUAAAAU____AAUAC...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	133 -- 139	44 -- 50	-22.0891 kcal/mol	5.35824 kcal/mol	4.62773 kcal/mol	132 156@LB@ \| \|@LB@5'-UUC...CUACU A A A GGGGA...ACU-3'@LB@ GGGGGGU GU UC GGUAC UGGG@LB@ :\|\|:\|\|\| \|\| :\| \|\|\|\|\| \|\|\|\|@LB@ UCCUCCA CA GG CCAUG ACCC@LB@3'-UUU...CCGAU C A A UCGAUCGUAAAAU AAUAC...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.0891 kcal/mol@LB@Unfolding Energy - mRNA 5.35824 kcal/mol@LB@Unfolding Energy - sRNA 4.62773 kcal/mol@LB@@LB@Position - mRNA 133 -- 155@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 44 -- 50@LB@
182	0.01043	0.1919	b1235	rssB	-12.59	0.048266	47 -- 57	25 -- 36	PcnB-degradosome interaction factor; response regulator	_____________46___________58\n_____________\|____________\|\n5'-AAU...CGGCC____________AGUGG...CAA-3'\n______________GG_ACAGCUGGC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________CC_UGUCGAUCG\n3'-UUU...AAGGA__A_________UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	51 -- 57	25 -- 31	-17.7308 kcal/mol	3.71782 kcal/mol	1.42738 kcal/mol	46 58@LB@ \| \|@LB@5'-AAU...CGGCC AGUGG...CAA-3'@LB@ GG ACAGCUGGC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ CC UGUCGAUCG@LB@3'-UUU...AAGGA A UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -17.7308 kcal/mol@LB@Unfolding Energy - mRNA 3.71782 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 47 -- 57@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 25 -- 31@LB@
183	0.01048	0.1919	b1250	kch	-17.60	0.001460	228 -- 258	1 -- 33	voltage-gated potassium channel	_____________227_______________________________259\n_____________\|_________________________________\|\n5'-AAC...AACAA_____AACAAA_________GACCC________ACGAC...UUA-3'\n______________ACAGC______UUUAUGGGU_______UUCGGC\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|\|_______\|\|\|:\|\|\n______________UGUCG______AAAUACCCA_______AAGUCG\n3'-UUU...GACCA_____AUCGUA_________AUACAAA______-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	241 -- 247	14 -- 20	-24.8286 kcal/mol	5.73827 kcal/mol	1.49313 kcal/mol	227 259@LB@ \| \|@LB@5'-AAC...AACAA AACAAA GACCC ACGAC...UUA-3'@LB@ ACAGC UUUAUGGGU UUCGGC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ UGUCG AAAUACCCA AAGUCG@LB@3'-UUU...GACCA AUCGUA AUACAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -17.60 kcal/mol@LB@Hybridization Energy -24.8286 kcal/mol@LB@Unfolding Energy - mRNA 5.73827 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 228 -- 258@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@LB@
184	0.01055	0.1919	b2175	mepS	-11.10	0.102353	43 -- 84	9 -- 46	murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase	_____________42____________________________________________85\n_____________\|_____________________________________________\|\n5'-CAA...GCCUC__C___AGAUUA____C_______A__UA________C_______CCACA...CAA-3'\n______________GG_GGU______UCCU___ACAGC_UA__AUUUUGUG_GUUA_GU\n______________\|\|_\|\|\|______\|\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|\|:\|\|_\|\|\|\|_\|\|\n______________CC_CCA______AGGA___UGUCG_AU__UAAAAUAC_CAAU_CA\n3'-UUU...UUCCU__A_____________CCA________CG________C____A__AAAAGUCG-5'\n_____________\|_____________________________________________\|\n_____________47____________________________________________8\n	71 -- 77	17 -- 23	-25.0471 kcal/mol	9.34223 kcal/mol	4.60648 kcal/mol	42 85@LB@ \| \|@LB@5'-CAA...GCCUC C AGAUUA C A UA C CCACA...CAA-3'@LB@ GG GGU UCCU ACAGC UA AUUUUGUG GUUA GU@LB@ \|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\| \|\|\|\|\|:\|\| \|\|\|\| \|\|@LB@ CC CCA AGGA UGUCG AU UAAAAUAC CAAU CA@LB@3'-UUU...UUCCU A CCA CG C A AAAAGUCG-5'@LB@ \| \|@LB@ 47 8@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -25.0471 kcal/mol@LB@Unfolding Energy - mRNA 9.34223 kcal/mol@LB@Unfolding Energy - sRNA 4.60648 kcal/mol@LB@@LB@Position - mRNA 43 -- 84@LB@Position - sRNA 9 -- 46@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 17 -- 23@LB@
185	0.01059	0.1919	b3856	mobB	-14.40	0.016564	123 -- 150	1 -- 31	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________122______________________________151\n_____________\|________________________________\|\n5'-GUG...CGUCU________GUC____C_____A__________GAUCA...CCA-3'\n______________GGCUGGCG____AUG_GGUUG____UUUCAGC\n______________:\|\|\|:\|\|:____\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\n______________UCGAUCGU____UAC_CCAAU____AAAGUCG\n3'-UUU...CCAUG________AAAA_________ACAA_______-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	144 -- 150	1 -- 7	-26.2194 kcal/mol	10.3308 kcal/mol	1.48722 kcal/mol	122 151@LB@ \| \|@LB@5'-GUG...CGUCU GUC C A GAUCA...CCA-3'@LB@ GGCUGGCG AUG GGUUG UUUCAGC@LB@ :\|\|\|:\|\|: \|\|\| \|\|\|\|: \|\|\|\|\|\|\|@LB@ UCGAUCGU UAC CCAAU AAAGUCG@LB@3'-UUU...CCAUG AAAA ACAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -26.2194 kcal/mol@LB@Unfolding Energy - mRNA 10.3308 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 123 -- 150@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 1 -- 7@LB@
186	0.01069	0.1919	b1614	ydgA	-8.85	0.262719	182 -- 191	16 -- 25	DUF945 family protein	_____________181________192\n_____________\|__________\|\n5'-ACA...GAUUU__________AUAAU...UCG-3'\n______________CAUUUUAUGG\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUAAAAUACC\n3'-UUU...CGAUC__________CAAUA...UCG-5'\n_____________\|__________\|\n_____________26_________15\n	185 -- 191	16 -- 22	-11.3536 kcal/mol	2.1555 kcal/mol	0.346409 kcal/mol	181 192@LB@ \| \|@LB@5'-ACA...GAUUU AUAAU...UCG-3'@LB@ CAUUUUAUGG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUAAAAUACC@LB@3'-UUU...CGAUC CAAUA...UCG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -11.3536 kcal/mol@LB@Unfolding Energy - mRNA 2.1555 kcal/mol@LB@Unfolding Energy - sRNA 0.346409 kcal/mol@LB@@LB@Position - mRNA 182 -- 191@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 16 -- 22@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@
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@
189	0.01085	0.1919	b3606	trmL	-8.64	0.283903	120 -- 126	63 -- 69	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________119_____127\n_____________\|_______\|\n5'-UAG...CCUCC_______GGGCC...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	120 -- 126	63 -- 69	-10.8913 kcal/mol	1.31422 kcal/mol	0.939295 kcal/mol	119 127@LB@ \| \|@LB@5'-UAG...CCUCC GGGCC...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -10.8913 kcal/mol@LB@Unfolding Energy - mRNA 1.31422 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 120 -- 126@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 63 -- 69@LB@
190	0.0109	0.1919	b2749	ygbE	-11.00	0.107048	99 -- 107	29 -- 37	DUF3561 family inner membrane protein	_____________98________108\n_____________\|_________\|\n5'-UGC...AAAUU_________AAUUA...UCU-3'\n______________UGGUACAGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACCAUGUCG\n3'-UUU...CAAGG_________AUCGU...UCG-5'\n_____________\|_________\|\n_____________38________28\n	101 -- 107	29 -- 35	-15.5774 kcal/mol	2.20256 kcal/mol	2.37218 kcal/mol	98 108@LB@ \| \|@LB@5'-UGC...AAAUU AAUUA...UCU-3'@LB@ UGGUACAGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACCAUGUCG@LB@3'-UUU...CAAGG AUCGU...UCG-5'@LB@ \| \|@LB@ 38 28@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -15.5774 kcal/mol@LB@Unfolding Energy - mRNA 2.20256 kcal/mol@LB@Unfolding Energy - sRNA 2.37218 kcal/mol@LB@@LB@Position - mRNA 99 -- 107@LB@Position - sRNA 29 -- 37@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 29 -- 35@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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