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
48	0.002302	0.1648	b3460	livJ	-15.11	0.026091	183 -- 229	1 -- 30	branched-chain amino acid ABC transporter periplasmic binding protein	_____________182_____________________________________________230\n_____________\|_______________________________________________\|\n5'-AAU...CCAGA___________UC___GGAUGAACAUAA____U______UUAC____AGGAU...CAA-3'\n______________AGAAUGGGGAU__UCA____________AGGG_AAAGCG____UGGC\n______________\|:\|\|\|\|\|\|\|\|:__\|\|\|____________\|:\|:_\|\|\|\|\|:____\|\|\|\|\n______________UUUUACCCCUG__AGU____________UUCU_UUUCGU____ACCG\n3'-UUU...AGGUG___________U___________________________C_______-5'\n_____________\|______________________________________________\|\n_____________31_____________________________________________1\n	187 -- 193	20 -- 26	-27.0033 kcal/mol	9.37443 kcal/mol	2.51911 kcal/mol	182 230@LB@ \| \|@LB@5'-AAU...CCAGA UC GGAUGAACAUAA U UUAC AGGAU...CAA-3'@LB@ AGAAUGGGGAU UCA AGGG AAAGCG UGGC@LB@ \|:\|\|\|\|\|\|\|\|: \|\|\| \|:\|: \|\|\|\|\|: \|\|\|\|@LB@ UUUUACCCCUG AGU UUCU UUUCGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -27.0033 kcal/mol@LB@Unfolding Energy - mRNA 9.37443 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 183 -- 229@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@LB@
49	0.002324	0.1648	b1119	nagK	-12.21	0.112661	180 -- 199	1 -- 21	N-acetyl-D-glucosamine kinase	_____________179___________________200\n_____________\|_____________________\|\n5'-UCA...GCAGU________AC____G__C___AAUGU...GUG-3'\n______________ACAUUAAA___AAG_AG_GGC\n______________\|\|\|\|:\|\|\|___\|\|\|_\|\|_\|\|\|\n______________UGUAGUUU___UUC_UC_CCG\n3'-UUU...ACCCC________CUU___G__A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	181 -- 187	14 -- 20	-16.408 kcal/mol	2.6857 kcal/mol	1.51103 kcal/mol	179 200@LB@ \| \|@LB@5'-UCA...GCAGU AC G C AAUGU...GUG-3'@LB@ ACAUUAAA AAG AG GGC@LB@ \|\|\|\|:\|\|\| \|\|\| \|\| \|\|\|@LB@ UGUAGUUU UUC UC CCG@LB@3'-UUU...ACCCC CUU G A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -16.408 kcal/mol@LB@Unfolding Energy - mRNA 2.6857 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 180 -- 199@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 14 -- 20@LB@
53	0.002642	0.1735	b0055	djlA	-12.56	0.096184	186 -- 227	1 -- 31	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________185________________________________________228\n_____________\|__________________________________________\|\n5'-GAC...UGUGU___UU______AUAUAUGCAG____________AU__U____GUGGC...UUG-3'\n______________CGA__UGGGGA__________UAUUGGGGAAAA__CA_UGGC\n______________\|:\|__\|\|\|\|\|\|__________:\|\|::::\|\|\|\|\|__\|\|_\|\|\|\|\n______________GUU__ACCCCU__________GUAGUUUCUUUU__GU_ACCG\n3'-UUU...GAGGU___UU____________________________C___C____-5'\n_____________\|_________________________________________\|\n_____________32________________________________________1\n	212 -- 218	9 -- 15	-25.7115 kcal/mol	10.6128 kcal/mol	2.53929 kcal/mol	185 228@LB@ \| \|@LB@5'-GAC...UGUGU UU AUAUAUGCAG AU U GUGGC...UUG-3'@LB@ CGA UGGGGA UAUUGGGGAAAA CA UGGC@LB@ \|:\| \|\|\|\|\|\| :\|\|::::\|\|\|\|\| \|\| \|\|\|\|@LB@ GUU ACCCCU GUAGUUUCUUUU GU ACCG@LB@3'-UUU...GAGGU UU C C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -25.7115 kcal/mol@LB@Unfolding Energy - mRNA 10.6128 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 227@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 9 -- 15@LB@
55	0.002823	0.1778	b3319	rplD	-12.54	0.096993	18 -- 45	1 -- 32	50S ribosomal subunit protein L4	_____________17________________________________46\n_____________\|_________________________________\|\n5'-UCA...UCCGG________U____________C___AAAA____AGGUC...UUG-3'\n______________GCAAAGUG______UCAAAGG_AAG____UGGC\n______________:\|\|\|\|:\|\|______\|\|\|\|\|\|:_\|\|\|____\|\|\|\|\n______________UGUUUUAC______AGUUUCU_UUC____ACCG\n3'-UUU...CGAGG________CCCUGU_______U___GUC_____-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	27 -- 33	12 -- 18	-19.13 kcal/mol	4.04955 kcal/mol	2.53929 kcal/mol	17 46@LB@ \| \|@LB@5'-UCA...UCCGG U C AAAA AGGUC...UUG-3'@LB@ GCAAAGUG UCAAAGG AAG UGGC@LB@ :\|\|\|\|:\|\| \|\|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UGUUUUAC AGUUUCU UUC ACCG@LB@3'-UUU...CGAGG CCCUGU U GUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -19.13 kcal/mol@LB@Unfolding Energy - mRNA 4.04955 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 12 -- 18@LB@
57	0.003017	0.1789	b2950	yggR	-13.19	0.071427	205 -- 223	1 -- 21	putative PilT family AAA+ ATPase	_____________204___________________224\n_____________\|_____________________\|\n5'-UUC...UAUGA____G_______UU_______CCUUA...GAA-3'\n______________AUAU_GAAGAAA____GUGGC\n______________\|:\|\|_:\|\|\|\|\|\|____\|\|\|\|\|\n______________UGUA_UUUCUUU____CACCG\n3'-UUU...ACCCC____G_______UCGU_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	210 -- 216	10 -- 16	-17.7325 kcal/mol	3.03326 kcal/mol	1.51103 kcal/mol	204 224@LB@ \| \|@LB@5'-UUC...UAUGA G UU CCUUA...GAA-3'@LB@ AUAU GAAGAAA GUGGC@LB@ \|:\|\| :\|\|\|\|\|\| \|\|\|\|\|@LB@ UGUA UUUCUUU CACCG@LB@3'-UUU...ACCCC G UCGU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -17.7325 kcal/mol@LB@Unfolding Energy - mRNA 3.03326 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 205 -- 223@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 10 -- 16@LB@
61	0.00311	0.1789	b0224	yafK	-14.83	0.030578	183 -- 204	1 -- 20	L D-transpeptidase-related protein	_____________182____________________205\n_____________\|______________________\|\n5'-UUA...CGUUU__________U_______AU__GUAAA...AAG-3'\n______________UAUCAAGGAA_AAGCAGU__GC\n______________:\|\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________GUAGUUUCUU_UUCGUCA__CG\n3'-UUU...CCCCU__________________C___-5'\n_____________\|_____________________\|\n_____________21____________________1\n	194 -- 200	4 -- 10	-21.3079 kcal/mol	5.02402 kcal/mol	1.45855 kcal/mol	182 205@LB@ \| \|@LB@5'-UUA...CGUUU U AU GUAAA...AAG-3'@LB@ UAUCAAGGAA AAGCAGU GC@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUAGUUUCUU UUCGUCA CG@LB@3'-UUU...CCCCU C -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -21.3079 kcal/mol@LB@Unfolding Energy - mRNA 5.02402 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 4 -- 10@LB@
62	0.003256	0.1843	b1243	oppA	-14.22	0.042360	208 -- 232	1 -- 21	oligopeptide ABC transporter periplasmic binding protein	_____________207_______________________233\n_____________\|_________________________\|\n5'-UGU...GACCA______CC_________UU___A__AGCUG...UCA-3'\n______________ACAUCA__AAGAGAAGU__AGU_GC\n______________\|\|\|\|\|\|__\|\|\|\|:\|\|\|:__\|\|\|_\|\|\n______________UGUAGU__UUCUUUUCG__UCA_CG\n3'-UUU...ACCCC______________________C__-5'\n_____________\|________________________\|\n_____________22_______________________1\n	218 -- 224	7 -- 13	-18.9529 kcal/mol	3.22094 kcal/mol	1.51103 kcal/mol	207 233@LB@ \| \|@LB@5'-UGU...GACCA CC UU A AGCUG...UCA-3'@LB@ ACAUCA AAGAGAAGU AGU GC@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|: \|\|\| \|\|@LB@ UGUAGU UUCUUUUCG UCA CG@LB@3'-UUU...ACCCC C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -18.9529 kcal/mol@LB@Unfolding Energy - mRNA 3.22094 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 208 -- 232@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 7 -- 13@LB@
63	0.003337	0.1851	b1453	ansP	-14.01	0.047364	263 -- 293	1 -- 34	L-asparagine transporter	_____________262_________________________________294\n_____________\|___________________________________\|\n5'-GUC...AAUGC________A__________C_________AUG___AAUCGCC-3'\n______________CCACGAAG_GGGG_UAUCA____AAAGCG___GGC\n______________\|\|\|\|:\|\|:_\|\|\|\|_:\|\|\|\|____\|\|\|\|\|:___\|\|\|\n______________GGUGUUUU_CCCC_GUAGU____UUUCGU___CCG\n3'-UUU...CCCGA________A____U_____UUCU______CA____-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	263 -- 269	28 -- 34	-31.7064 kcal/mol	13.4305 kcal/mol	4.26884 kcal/mol	262 294@LB@ \| \|@LB@5'-GUC...AAUGC A C AUG AAUCGCC-3'@LB@ CCACGAAG GGGG UAUCA AAAGCG GGC@LB@ \|\|\|\|:\|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|: \|\|\|@LB@ GGUGUUUU CCCC GUAGU UUUCGU CCG@LB@3'-UUU...CCCGA A U UUCU CA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -31.7064 kcal/mol@LB@Unfolding Energy - mRNA 13.4305 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
64	0.003422	0.1851	b4238	nrdD	-18.31	0.003326	69 -- 106	1 -- 34	anaerobic ribonucleoside-triphosphate reductase	_____________68_____________________________________107\n_____________\|______________________________________\|\n5'-UAU...GCUCC________AA__U_C_______U___U______A____GAUUG...UCG-3'\n______________CCACGAAA__GG_G_GGCGUUG_GGA_AAGCGG_UGGC\n______________\|\|\|\|:\|\|\|__\|\|_\|_\|:\|:\|::_:\|\|_\|\|\|\|:\|_\|\|\|\|\n______________GGUGUUUU__CC_C_CUGUAGU_UCU_UUCGUC_ACCG\n3'-UUU...CCCGA________A_____________U___U___________-5'\n_____________\|_____________________________________\|\n_____________35____________________________________1\n	84 -- 90	16 -- 22	-34.2754 kcal/mol	11.6957 kcal/mol	4.26884 kcal/mol	68 107@LB@ \| \|@LB@5'-UAU...GCUCC AA U C U U A GAUUG...UCG-3'@LB@ CCACGAAA GG G GGCGUUG GGA AAGCGG UGGC@LB@ \|\|\|\|:\|\|\| \|\| \| \|:\|:\|:: :\|\| \|\|\|\|:\| \|\|\|\|@LB@ GGUGUUUU CC C CUGUAGU UCU UUCGUC ACCG@LB@3'-UUU...CCCGA A U U -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -18.31 kcal/mol@LB@Hybridization Energy -34.2754 kcal/mol@LB@Unfolding Energy - mRNA 11.6957 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 69 -- 106@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
66	0.003537	0.1858	b0411	tsx	-15.28	0.023631	170 -- 194	1 -- 34	nucleoside channel receptor of phage T6 and colicin K	_____________169_________________________________195\n_____________\|___________________________________\|\n5'-AGG...CACUC_______________UU__________________AUACA...ACU-3'\n______________CCGCAA____GGGAU__UCAAA______CAGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GGUGUU____CCCUG__AGUUU______GUCACCG\n3'-UUU...CCCGA______UUAC_____U______CUUUUC_______-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	188 -- 194	1 -- 7	-27.9509 kcal/mol	8.39787 kcal/mol	4.26884 kcal/mol	169 195@LB@ \| \|@LB@5'-AGG...CACUC UU AUACA...ACU-3'@LB@ CCGCAA GGGAU UCAAA CAGUGGC@LB@ \|\|:\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGUGUU CCCUG AGUUU GUCACCG@LB@3'-UUU...CCCGA UUAC U CUUUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -27.9509 kcal/mol@LB@Unfolding Energy - mRNA 8.39787 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 188 -- 194@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)

Job resubmission

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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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