Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
168	0.008282	0.1723	b3822	recQ	-12.50	0.081546	124 -- 155	43 -- 77	ATP-dependent DNA helicase	_____________123___________________________________156\n_____________\|_____________________________________\|\n5'-CGC...UCUCA_______AAA____U_______C_________G____CGCUG...UUA-3'\n______________GAGACUA___GCAU_GCAGUUU______UCGC_CAGG\n______________:\|\|\|\|\|\|___:\|\|:_\|\|\|:\|\|:______\|\|:\|_\|\|\|\|\n______________UUCUGAU___UGUG_CGUUAAG______AGUG_GUCC\n3'-UUU...CCCGU_______G______U_______CAACAA____A____CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________78____________________________________42\n	139 -- 145	58 -- 64	-25.7534 kcal/mol	8.90299 kcal/mol	4.3531 kcal/mol	123 156@LB@ \| \|@LB@5'-CGC...UCUCA AAA U C G CGCUG...UUA-3'@LB@ GAGACUA GCAU GCAGUUU UCGC CAGG@LB@ :\|\|\|\|\|\| :\|\|: \|\|\|:\|\|: \|\|:\| \|\|\|\|@LB@ UUCUGAU UGUG CGUUAAG AGUG GUCC@LB@3'-UUU...CCCGU G U CAACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 78 42@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -25.7534 kcal/mol@LB@Unfolding Energy - mRNA 8.90299 kcal/mol@LB@Unfolding Energy - sRNA 4.3531 kcal/mol@LB@@LB@Position - mRNA 124 -- 155@LB@Position - sRNA 43 -- 77@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
23	0.0001955	0.02926	b3846	fadB	-13.56	0.047358	39 -- 83	35 -- 77	fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase	_____________38________________________________________________84\n_____________\|_________________________________________________\|\n5'-AGU...ACCUU___U__C_____CUU____CA____________C___A_C_U_______GCCGA...CUG-3'\n______________AAG_CU_CGCAU___AGCA__UCGU____UCAU_CAG_G_G_GAUUUCU\n______________\|\|\|_\|\|_\|:\|\|:___\|\|\|\|__\|\|\|\|____\|\|\|:_\|\|\|_\|_\|_\|\|\|\|\|\|:\n______________UUC_GA_GUGUG___UCGU__AGCA____AGUG_GUC_C_C_CUAAAGG\n3'-UUU...CCCGU___U__U____________UA____ACAA____A_______________UACGA...GCA-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________34\n	77 -- 83	35 -- 41	-27.7125 kcal/mol	9.35112 kcal/mol	4.80542 kcal/mol	38 84@LB@ \| \|@LB@5'-AGU...ACCUU U C CUU CA C A C U GCCGA...CUG-3'@LB@ AAG CU CGCAU AGCA UCGU UCAU CAG G G GAUUUCU@LB@ \|\|\| \|\| \|:\|\|: \|\|\|\| \|\|\|\| \|\|\|: \|\|\| \| \| \|\|\|\|\|\|:@LB@ UUC GA GUGUG UCGU AGCA AGUG GUC C C CUAAAGG@LB@3'-UUU...CCCGU U U UA ACAA A UACGA...GCA-5'@LB@ \| \|@LB@ 78 34@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -27.7125 kcal/mol@LB@Unfolding Energy - mRNA 9.35112 kcal/mol@LB@Unfolding Energy - sRNA 4.80542 kcal/mol@LB@@LB@Position - mRNA 39 -- 83@LB@Position - sRNA 35 -- 77@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 35 -- 41@LB@
192	0.00979	0.1776	b3879	yihR	-14.50	0.028125	239 -- 282	38 -- 72	putative sulphoquinovose mutarotase	_____________238__________________________________________283\n_____________\|____________________________________________\|\n5'-CAU...ACCAA_______U_____GGACAGACC________UGCCG_________AUCAC...UGA-3'\n______________UAUGCAU_GCAGU_________GUUUCACU_____CGGGGGAUU\n______________\|\|::\|\|:_\|\|\|:\|_________\|\|\|\|\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________AUGUGUG_CGUUA_________CAAAGUGA_____GUCCCCUAA\n3'-UUU...UUCUG_______U_____AGCAA__________________________AGGUA...GCA-5'\n_____________\|____________________________________________\|\n_____________73___________________________________________37\n	276 -- 282	38 -- 44	-32.397 kcal/mol	13.138 kcal/mol	4.76382 kcal/mol	238 283@LB@ \| \|@LB@5'-CAU...ACCAA U GGACAGACC UGCCG AUCAC...UGA-3'@LB@ UAUGCAU GCAGU GUUUCACU CGGGGGAUU@LB@ \|\|::\|\|: \|\|\|:\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGUGUG CGUUA CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUCUG U AGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 73 37@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -32.397 kcal/mol@LB@Unfolding Energy - mRNA 13.138 kcal/mol@LB@Unfolding Energy - sRNA 4.76382 kcal/mol@LB@@LB@Position - mRNA 239 -- 282@LB@Position - sRNA 38 -- 72@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 38 -- 44@LB@
142	0.006549	0.1605	b3902	rhaD	-9.93	0.251242	192 -- 218	44 -- 69	rhamnulose-1-phosphate aldolase	_____________191_________________________219\n_____________\|___________________________\|\n5'-AGA...CAGGA______AACAUGCAAAACA________UCCUG...UGA-3'\n______________ACACAG_____________UUACUCAG\n______________\|\|\|\|\|\|_____________\|:\|\|\|\|\|\|\n______________UGUGUC_____________AGUGAGUC\n3'-UUU...UGAUG______GUUAAGCAACAA_________CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	212 -- 218	44 -- 50	-16.231 kcal/mol	2.20309 kcal/mol	4.09554 kcal/mol	191 219@LB@ \| \|@LB@5'-AGA...CAGGA AACAUGCAAAACA UCCUG...UGA-3'@LB@ ACACAG UUACUCAG@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UGUGUC AGUGAGUC@LB@3'-UUU...UGAUG GUUAAGCAACAA CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -16.231 kcal/mol@LB@Unfolding Energy - mRNA 2.20309 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 192 -- 218@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 44 -- 50@LB@
92	0.004122	0.1538	b3912	cpxR	-15.13	0.019325	106 -- 130	39 -- 76	response regulator in two-component regulatory system with CpxA	_____________105_____________________________________131\n_____________\|_______________________________________\|\n5'-UGA...GAUUC________A___U__________________________GUAAA...AUG-3'\n______________AGGCUGCA_ACA_GCG______________UCAGGGGGU\n______________\|\|:\|\|:\|\|_\|\|\|_\|\|:______________\|\|\|\|\|\|\|:\|\n______________UCUGAUGU_UGU_CGU______________AGUCCCCUA\n3'-UUU...CCGUU________G_______UAAGCAACAAAGUG_________AAGGU...GCA-5'\n_____________\|_______________________________________\|\n_____________77______________________________________38\n	124 -- 130	39 -- 45	-28.779 kcal/mol	8.86764 kcal/mol	4.77949 kcal/mol	105 131@LB@ \| \|@LB@5'-UGA...GAUUC A U GUAAA...AUG-3'@LB@ AGGCUGCA ACA GCG UCAGGGGGU@LB@ \|\|:\|\|:\|\| \|\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ UCUGAUGU UGU CGU AGUCCCCUA@LB@3'-UUU...CCGUU G UAAGCAACAAAGUG AAGGU...GCA-5'@LB@ \| \|@LB@ 77 38@LB@@LB@@LB@Energy -15.13 kcal/mol@LB@Hybridization Energy -28.779 kcal/mol@LB@Unfolding Energy - mRNA 8.86764 kcal/mol@LB@Unfolding Energy - sRNA 4.77949 kcal/mol@LB@@LB@Position - mRNA 106 -- 130@LB@Position - sRNA 39 -- 76@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 39 -- 45@LB@
181	0.009071	0.1747	b3962	sthA	-14.30	0.031527	83 -- 114	34 -- 76	pyridine nucleotide transhydrogenase soluble	_____________82___________________________________________115\n_____________\|____________________________________________\|\n5'-UAC...GAAAC____AAA___AA_______________________AU__AG___GAUAA...CAG-3'\n______________AGAC___GCA__GGC____________CGCUCAGG__AU__CCA\n______________\|\|\|\|___:\|\|__:\|\|____________\|:\|\|\|\|\|\|__\|\|__\|\|\|\n______________UCUG___UGU__UCG____________GUGAGUCC__UA__GGU\n3'-UUU...CCGUU____AUG___G____UUAAGCAACAAA________CC__AA___ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________77___________________________________________33\n	99 -- 105	43 -- 49	-23.8174 kcal/mol	4.70621 kcal/mol	4.816 kcal/mol	82 115@LB@ \| \|@LB@5'-UAC...GAAAC AAA AA AU AG GAUAA...CAG-3'@LB@ AGAC GCA GGC CGCUCAGG AU CCA@LB@ \|\|\|\| :\|\| :\|\| \|:\|\|\|\|\|\| \|\| \|\|\|@LB@ UCUG UGU UCG GUGAGUCC UA GGU@LB@3'-UUU...CCGUU AUG G UUAAGCAACAAA CC AA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -23.8174 kcal/mol@LB@Unfolding Energy - mRNA 4.70621 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 83 -- 114@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 43 -- 49@LB@
183	0.009087	0.1747	b3965	trmA	-11.75	0.116675	18 -- 52	35 -- 74	tRNA m(5)U54 methyltransferase SAM-dependent; tmRNA m(5)U341 methyltransferase	_____________17____________________________________________53\n_____________\|_____________________________________________\|\n5'-UCG...UUACC________U____UCCA_________________________C__UAUUA...UUC-3'\n______________GCUGCGCG_CAGC____GAUUCG______CACU____GGAUU_CC\n______________:\|\|:\|:\|:_\|\|\|\|____:\|\|\|\|\|______\|\|\|\|____\|\|\|\|\|_\|\|\n______________UGAUGUGU_GUCG____UUAAGC______GUGA____CCUAA_GG\n3'-UUU...GUUUC_______________________AACAAA____GUCC_____A__UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________34\n	18 -- 24	68 -- 74	-28.5766 kcal/mol	12.0258 kcal/mol	4.80541 kcal/mol	17 53@LB@ \| \|@LB@5'-UCG...UUACC U UCCA C UAUUA...UUC-3'@LB@ GCUGCGCG CAGC GAUUCG CACU GGAUU CC@LB@ :\|\|:\|:\|: \|\|\|\| :\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UGAUGUGU GUCG UUAAGC GUGA CCUAA GG@LB@3'-UUU...GUUUC AACAAA GUCC A UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -28.5766 kcal/mol@LB@Unfolding Energy - mRNA 12.0258 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 18 -- 52@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
148	0.006951	0.1638	b3995	rsd	-9.56	0.289012	16 -- 28	58 -- 70	stationary phase protein binds sigma 70 RNA polymerase subunit	_____________15____________29\n_____________\|_____________\|\n5'-AAU...UUCGC_____________UCCCU...ACU-3'\n______________CAUAUGGCAAUUC\n______________\|\|:\|::\|\|\|\|\|\|\|\n______________GUGUGUCGUUAAG\n3'-UUU...CUGAU_____________CAACA...GCA-5'\n_____________\|_____________\|\n_____________71____________57\n	22 -- 28	58 -- 64	-15.8606 kcal/mol	3.09015 kcal/mol	3.21169 kcal/mol	15 29@LB@ \| \|@LB@5'-AAU...UUCGC UCCCU...ACU-3'@LB@ CAUAUGGCAAUUC@LB@ \|\|:\|::\|\|\|\|\|\|\|@LB@ GUGUGUCGUUAAG@LB@3'-UUU...CUGAU CAACA...GCA-5'@LB@ \| \|@LB@ 71 57@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -15.8606 kcal/mol@LB@Unfolding Energy - mRNA 3.09015 kcal/mol@LB@Unfolding Energy - sRNA 3.21169 kcal/mol@LB@@LB@Position - mRNA 16 -- 28@LB@Position - sRNA 58 -- 70@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 58 -- 64@LB@
182	0.009082	0.1747	b3998	nfi	-11.38	0.137700	53 -- 76	45 -- 75	endonuclease V; deoxyinosine 3' endonuclease	_____________52______________________________77\n_____________\|_______________________________\|\n5'-UGG...GUAGC________UU_________________G___CGGCG...GAG-3'\n______________GACUAUAC___GCAG______GUUUCG_UCA\n______________\|\|\|\|\|:\|\|___\|\|\|:______\|\|\|\|\|:_\|\|\|\n______________CUGAUGUG___CGUU______CAAAGU_AGU\n3'-UUU...CGUUU________UGU____AAGCAA______G___CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	54 -- 60	68 -- 74	-21.6188 kcal/mol	6.49773 kcal/mol	3.74078 kcal/mol	52 77@LB@ \| \|@LB@5'-UGG...GUAGC UU G CGGCG...GAG-3'@LB@ GACUAUAC GCAG GUUUCG UCA@LB@ \|\|\|\|\|:\|\| \|\|\|: \|\|\|\|\|: \|\|\|@LB@ CUGAUGUG CGUU CAAAGU AGU@LB@3'-UUU...CGUUU UGU AAGCAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.38 kcal/mol@LB@Hybridization Energy -21.6188 kcal/mol@LB@Unfolding Energy - mRNA 6.49773 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 53 -- 76@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 68 -- 74@LB@
5	9.512e-06	0.006694	b4006	purH	-17.40	0.004319	188 -- 204	31 -- 46	IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase	_____________187_______________205\n_____________\|_________________\|\n5'-GUA...AAAUC__________A______AACAA...AGC-3'\n______________CAGGGGAUUU_CCAUGC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________GUCCCCUAAA_GGUACG\n3'-UUU...AGUGA_________________AAUAU...GCA-5'\n_____________\|_________________\|\n_____________47________________30\n	191 -- 197	37 -- 43	-27.6893 kcal/mol	6.33421 kcal/mol	3.95768 kcal/mol	187 205@LB@ \| \|@LB@5'-GUA...AAAUC A AACAA...AGC-3'@LB@ CAGGGGAUUU CCAUGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCCCCUAAA GGUACG@LB@3'-UUU...AGUGA AAUAU...GCA-5'@LB@ \| \|@LB@ 47 30@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -27.6893 kcal/mol@LB@Unfolding Energy - mRNA 6.33421 kcal/mol@LB@Unfolding Energy - sRNA 3.95768 kcal/mol@LB@@LB@Position - mRNA 188 -- 204@LB@Position - sRNA 31 -- 46@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@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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service.

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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