Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
189	0.02313	0.4113	b2438	eutK	-12.08	0.086588	220 -- 243	37 -- 62	putative ethanol utilization carboxysome structural protein	_____________219________________________244\n_____________\|__________________________\|\n5'-CGA...GGGAU____________AC______UG____CCGCG...GUC-3'\n______________UGCUGGAAGUGG____GGCA__GUCG\n______________\|:\|\|\|\|\|\|\|:::____:\|\|\|__\|\|\|\|\n______________AUGACCUUCGUU____UCGU__CAGC\n3'-UUU...UCAUU____________ACAC____UA____ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	224 -- 230	52 -- 58	-25.7957 kcal/mol	10.4122 kcal/mol	3.3026 kcal/mol	219 244@LB@ \| \|@LB@5'-CGA...GGGAU AC UG CCGCG...GUC-3'@LB@ UGCUGGAAGUGG GGCA GUCG@LB@ \|:\|\|\|\|\|\|\|::: :\|\|\| \|\|\|\|@LB@ AUGACCUUCGUU UCGU CAGC@LB@3'-UUU...UCAUU ACAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -25.7957 kcal/mol@LB@Unfolding Energy - mRNA 10.4122 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 220 -- 243@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 52 -- 58@LB@
105	0.01075	0.3439	b2457	eutM	-13.65	0.047053	202 -- 241	1 -- 59	ethanolamine utilization protein putative carboxysome structural protein	_____________201__________________________________________________________242\n_____________\|____________________________________________________________\|\n5'-UAU...CACAA________UU_____G____A___AAA_________________________________ACUGA...UUA-3'\n______________UGGAAGCA_____AG_AAUG_UCG______________CC_CGGGG_____CCUGGUUGC\n______________\|\|\|\|\|\|\|\|_____\|\|_\|\|\|\|_\|\|\|______________\|\|_\|\|:\|\|_____\|\|\|\|:\|:\|\|\n______________ACCUUCGU_____UC_UUAC_AGC______________GG_GCUCC_____GGACUAGCG\n3'-UUU...UUAUG________UACAC__G________ACGAAAGUCCAAGA__C_____CAGAA_________-5'\n_____________\|___________________________________________________________\|\n_____________60__________________________________________________________1\n	235 -- 241	1 -- 7	-38.4359 kcal/mol	10.6717 kcal/mol	14.1095 kcal/mol	201 242@LB@ \| \|@LB@5'-UAU...CACAA UU G A AAA ACUGA...UUA-3'@LB@ UGGAAGCA AG AAUG UCG CC CGGGG CCUGGUUGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\| \|\|\| \|\| \|\|:\|\| \|\|\|\|:\|:\|\|@LB@ ACCUUCGU UC UUAC AGC GG GCUCC GGACUAGCG@LB@3'-UUU...UUAUG UACAC G ACGAAAGUCCAAGA C CAGAA -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -38.4359 kcal/mol@LB@Unfolding Energy - mRNA 10.6717 kcal/mol@LB@Unfolding Energy - sRNA 14.1095 kcal/mol@LB@@LB@Position - mRNA 202 -- 241@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
17	0.001256	0.2406	b2496	hda	-13.91	0.042623	63 -- 79	52 -- 68	ATPase regulatory factor involved in DnaA inactivation	_____________62________________80\n_____________\|_________________\|\n5'-GAC...UGAAG_____________C___GAAGA...CGC-3'\n______________AAGUGGUGCUGGA_GCA\n______________\|\|\|\|::\|:\|\|\|\|\|_\|\|\|\n______________UUCAUUAUGACCU_CGU\n3'-UUU...ACCGA_____________U___UACAC...GCG-5'\n_____________\|_________________\|\n_____________69________________51\n	69 -- 75	56 -- 62	-21.6495 kcal/mol	4.84804 kcal/mol	2.8943 kcal/mol	62 80@LB@ \| \|@LB@5'-GAC...UGAAG C GAAGA...CGC-3'@LB@ AAGUGGUGCUGGA GCA@LB@ \|\|\|\|::\|:\|\|\|\|\| \|\|\|@LB@ UUCAUUAUGACCU CGU@LB@3'-UUU...ACCGA U UACAC...GCG-5'@LB@ \| \|@LB@ 69 51@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -21.6495 kcal/mol@LB@Unfolding Energy - mRNA 4.84804 kcal/mol@LB@Unfolding Energy - sRNA 2.8943 kcal/mol@LB@@LB@Position - mRNA 63 -- 79@LB@Position - sRNA 52 -- 68@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 56 -- 62@LB@
184	0.02284	0.4113	b2512	bamB	-14.63	0.032048	112 -- 136	38 -- 58	BamABCDE complex OM biogenesis lipoprotein	_____________111_______________________137\n_____________\|_________________________\|\n5'-GCU...GCAUG________GC____AAA________ACUCC...CCC-3'\n______________GGAAGCAG__GUGA___GCGAUGUU\n______________\|\|\|\|\|\|\|:__\|\|\|\|___\|\|:\|\|\|\|:\n______________CCUUCGUU__CACU___CGUUACAG\n3'-UUU...UAUGA________A________________CACGA...GCG-5'\n_____________\|_________________________\|\n_____________59________________________37\n	130 -- 136	38 -- 44	-25.7462 kcal/mol	7.89766 kcal/mol	3.21639 kcal/mol	111 137@LB@ \| \|@LB@5'-GCU...GCAUG GC AAA ACUCC...CCC-3'@LB@ GGAAGCAG GUGA GCGAUGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|\|:\|\|\|\|:@LB@ CCUUCGUU CACU CGUUACAG@LB@3'-UUU...UAUGA A CACGA...GCG-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -14.63 kcal/mol@LB@Hybridization Energy -25.7462 kcal/mol@LB@Unfolding Energy - mRNA 7.89766 kcal/mol@LB@Unfolding Energy - sRNA 3.21639 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 38 -- 44@LB@
87	0.008915	0.3393	b2530	iscS	-12.30	0.079567	175 -- 203	40 -- 68	cysteine desulfurase (tRNA sulfurtransferase) PLP-dependent	_____________174___________________________204\n_____________\|_____________________________\|\n5'-AAG...GCAUU________UAC_____UUAUA________AAAUU...UUG-3'\n______________GAGUGAUG___GGAGU_____GAGCAAUG\n______________:\|\|\|:\|\|:___\|:\|\|:_____\|\|\|\|\|\|\|\|\n______________UUCAUUAU___CUUCG_____CUCGUUAC\n3'-UUU...ACCGA________GAC_____UUACA________AGCAC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________39\n	197 -- 203	40 -- 46	-22.6486 kcal/mol	7.04226 kcal/mol	3.30507 kcal/mol	174 204@LB@ \| \|@LB@5'-AAG...GCAUU UAC UUAUA AAAUU...UUG-3'@LB@ GAGUGAUG GGAGU GAGCAAUG@LB@ :\|\|\|:\|\|: \|:\|\|: \|\|\|\|\|\|\|\|@LB@ UUCAUUAU CUUCG CUCGUUAC@LB@3'-UUU...ACCGA GAC UUACA AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -12.30 kcal/mol@LB@Hybridization Energy -22.6486 kcal/mol@LB@Unfolding Energy - mRNA 7.04226 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@LB@
198	0.02503	0.4226	b2544	yphB	-11.73	0.099011	68 -- 80	47 -- 61	mutarotase superfamily protein YphB family	_____________67______________81\n_____________\|_______________\|\n5'-CGG...GACGG_______________GCCGC...UAC-3'\n______________ACUGGAAGC__UGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGACCUUCG__ACAC\n3'-UUU...CAUUA_________UU____UCGUU...GCG-5'\n_____________\|_______________\|\n_____________62______________46\n	70 -- 76	53 -- 59	-17.6322 kcal/mol	2.81046 kcal/mol	3.09217 kcal/mol	67 81@LB@ \| \|@LB@5'-CGG...GACGG GCCGC...UAC-3'@LB@ ACUGGAAGC UGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACCUUCG ACAC@LB@3'-UUU...CAUUA UU UCGUU...GCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.6322 kcal/mol@LB@Unfolding Energy - mRNA 2.81046 kcal/mol@LB@Unfolding Energy - sRNA 3.09217 kcal/mol@LB@@LB@Position - mRNA 68 -- 80@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 53 -- 59@LB@
27	0.002163	0.2692	b2563	acpS	-16.12	0.017802	179 -- 203	40 -- 65	holo-[acyl-carrier-protein] synthase 1	_____________178_________________________204\n_____________\|___________________________\|\n5'-GCC...GCGUC______________C_______U____GCAAU...GCG-3'\n______________UGAUGCUGGAAGCG__GUG_GC_AAUG\n______________\|:\|\|:\|\|\|\|\|\|\|\|:__\|\|\|_\|\|_\|\|\|\|\n______________AUUAUGACCUUCGU__CAC_CG_UUAC\n3'-UUU...GAUUC______________UA___U_______AGCAC...GCG-5'\n_____________\|___________________________\|\n_____________66__________________________39\n	186 -- 192	52 -- 58	-28.0575 kcal/mol	8.63593 kcal/mol	3.30476 kcal/mol	178 204@LB@ \| \|@LB@5'-GCC...GCGUC C U GCAAU...GCG-3'@LB@ UGAUGCUGGAAGCG GUG GC AAUG@LB@ \|:\|\|:\|\|\|\|\|\|\|\|: \|\|\| \|\| \|\|\|\|@LB@ AUUAUGACCUUCGU CAC CG UUAC@LB@3'-UUU...GAUUC UA U AGCAC...GCG-5'@LB@ \| \|@LB@ 66 39@LB@@LB@@LB@Energy -16.12 kcal/mol@LB@Hybridization Energy -28.0575 kcal/mol@LB@Unfolding Energy - mRNA 8.63593 kcal/mol@LB@Unfolding Energy - sRNA 3.30476 kcal/mol@LB@@LB@Position - mRNA 179 -- 203@LB@Position - sRNA 40 -- 65@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 52 -- 58@LB@
200	0.02516	0.4226	b2566	era	-10.17	0.177109	195 -- 210	37 -- 61	membrane-associated 16S rRNA-binding GTPase	_____________194_______________________211\n_____________\|_________________________\|\n5'-UUG...CUGGA_________________________AUAAA...UCU-3'\n______________GCUGGAA______UGAGCA___UCG\n______________:\|\|\|\|\|\|______\|\|\|\|\|\|___\|\|\|\n______________UGACCUU______ACUCGU___AGC\n3'-UUU...CAUUA_______CGUUAC______UAC___ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	195 -- 201	55 -- 61	-17.979 kcal/mol	4.50899 kcal/mol	3.30158 kcal/mol	194 211@LB@ \| \|@LB@5'-UUG...CUGGA AUAAA...UCU-3'@LB@ GCUGGAA UGAGCA UCG@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UGACCUU ACUCGU AGC@LB@3'-UUU...CAUUA CGUUAC UAC ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -17.979 kcal/mol@LB@Unfolding Energy - mRNA 4.50899 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 195 -- 210@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 55 -- 61@LB@
192	0.02457	0.4226	b2689	yqaA	-16.30	0.016522	258 -- 300	44 -- 85	COG1238 family inner membrane protein	_____________257_________________________________________300\n_____________\|___________________________________________\|\n5'-CAC...CUACA___U________AACUCCG____C_______U________U___-3'\n______________CUA_UACCCGGC_______AAGU_GUGCUGG_GGCAAUGU__GC\n______________\|:\|_:\|\|\|\|\|\|\|_______\|\|\|\|_:\|:\|\|\|\|_:\|\|\|\|\|\|\|__\|\|\n______________GGU_GUGGGCCG_______UUCA_UAUGACC_UCGUUACA__CG\n______3'-UUUUC___C________ACCGA______U_______U________CU__UUACA...GCG-5'\n_____________\|____________________________________________\|\n_____________86___________________________________________43\n	291 -- 297	48 -- 54	-43.3701 kcal/mol	12.1561 kcal/mol	14.9093 kcal/mol	257 300@LB@ \| \|@LB@5'-CAC...CUACA U AACUCCG C U U -3'@LB@ CUA UACCCGGC AAGU GUGCUGG GGCAAUGU GC@LB@ \|:\| :\|\|\|\|\|\|\| \|\|\|\| :\|:\|\|\|\| :\|\|\|\|\|\|\| \|\|@LB@ GGU GUGGGCCG UUCA UAUGACC UCGUUACA CG@LB@ 3'-UUUUC C ACCGA U U CU UUACA...GCG-5'@LB@ \| \|@LB@ 86 43@LB@@LB@@LB@Energy -16.30 kcal/mol@LB@Hybridization Energy -43.3701 kcal/mol@LB@Unfolding Energy - mRNA 12.1561 kcal/mol@LB@Unfolding Energy - sRNA 14.9093 kcal/mol@LB@@LB@Position - mRNA 258 -- 300@LB@Position - sRNA 44 -- 85@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 48 -- 54@LB@
149	0.01819	0.4072	b2708	srlQ	-10.57	0.153166	157 -- 203	40 -- 61	D-arabinose 5-phosphate isomerase	_____________156_____________________________________________204\n_____________\|_______________________________________________\|\n5'-UAC...CAGGC________AGAAAGGGAU______GAUCAUAACCGGAGA________AGUGA...GCG-3'\n______________GCUGGAAG__________CGAUGU_______________GAGCAAUG\n______________:\|\|\|\|\|\|\|__________\|:\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UGACCUUC__________GUUACA_______________CUCGUUAC\n3'-UUU...CAUUA_______________________________________________AGCAC...GCG-5'\n_____________\|_______________________________________________\|\n_____________62______________________________________________39\n	197 -- 203	40 -- 46	-23.3244 kcal/mol	9.45822 kcal/mol	3.30075 kcal/mol	156 204@LB@ \| \|@LB@5'-UAC...CAGGC AGAAAGGGAU GAUCAUAACCGGAGA AGUGA...GCG-3'@LB@ GCUGGAAG CGAUGU GAGCAAUG@LB@ :\|\|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACCUUC GUUACA CUCGUUAC@LB@3'-UUU...CAUUA AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -23.3244 kcal/mol@LB@Unfolding Energy - mRNA 9.45822 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 157 -- 203@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 40 -- 46@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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