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
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@
176	0.008803	0.1747	b1242	ychE	-11.39	0.137124	41 -- 64	45 -- 75	UPF0056 family inner membrane protein	_____________40______________________________65\n_____________\|_______________________________\|\n5'-CAU...UUGGU____________________________A__ACUAG...GCA-3'\n______________GGCUACAU_UAGCA______UGUUUUGC_CA\n______________\|:\|\|\|\|\|:_:\|\|\|\|______\|\|\|\|\|::\|_\|\|\n______________CUGAUGUG_GUCGU______ACAAAGUG_GU\n3'-UUU...CGUUU________U_____UAAGCA________A__CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	55 -- 61	48 -- 54	-19.9041 kcal/mol	4.77357 kcal/mol	3.74078 kcal/mol	40 65@LB@ \| \|@LB@5'-CAU...UUGGU A ACUAG...GCA-3'@LB@ GGCUACAU UAGCA UGUUUUGC CA@LB@ \|:\|\|\|\|\|: :\|\|\|\| \|\|\|\|\|::\| \|\|@LB@ CUGAUGUG GUCGU ACAAAGUG GU@LB@3'-UUU...CGUUU U UAAGCA A CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -19.9041 kcal/mol@LB@Unfolding Energy - mRNA 4.77357 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 41 -- 64@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 48 -- 54@LB@
79	0.00332	0.1462	b1845	ptrB	-10.90	0.169644	42 -- 70	35 -- 70	protease II	_____________41____________________________________71\n_____________\|_____________________________________\|\n5'-UCU...AGAAU________C_____AA____________CU_______UCUGU...AGC-3'\n______________CGCACAGC_AUUUG__________CAGG__GAUUUUC\n______________\|:\|\|\|\|\|\|_\|\|\|:\|__________\|\|\|\|__\|\|\|\|\|:\|\n______________GUGUGUCG_UAAGC__________GUCC__CUAAAGG\n3'-UUU...CUGAU________U_____AACAAAGUGA____C________UACGA...GCA-5'\n_____________\|_____________________________________\|\n_____________71____________________________________34\n	64 -- 70	35 -- 41	-24.5069 kcal/mol	8.82337 kcal/mol	4.7817 kcal/mol	41 71@LB@ \| \|@LB@5'-UCU...AGAAU C AA CU UCUGU...AGC-3'@LB@ CGCACAGC AUUUG CAGG GAUUUUC@LB@ \|:\|\|\|\|\|\| \|\|\|:\| \|\|\|\| \|\|\|\|\|:\|@LB@ GUGUGUCG UAAGC GUCC CUAAAGG@LB@3'-UUU...CUGAU U AACAAAGUGA C UACGA...GCA-5'@LB@ \| \|@LB@ 71 34@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -24.5069 kcal/mol@LB@Unfolding Energy - mRNA 8.82337 kcal/mol@LB@Unfolding Energy - sRNA 4.7817 kcal/mol@LB@@LB@Position - mRNA 42 -- 70@LB@Position - sRNA 35 -- 70@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 35 -- 41@LB@
66	0.002697	0.1417	b1306	pspC	-11.06	0.158336	44 -- 64	55 -- 75	psp operon transcription co-activator	_____________43_____________________65\n_____________\|______________________\|\n5'-CCG...GUUAU_______U______________CUGGU...CGG-3'\n______________GGCUGCA_UACAGCAAU_CGUU\n______________\|:\|\|:\|\|_:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUGAUGU_GUGUCGUUA_GCAA\n3'-UUU...CGUUU_________________A____CAAAG...GCA-5'\n_____________\|______________________\|\n_____________76_____________________54\n	54 -- 60	60 -- 66	-24.9269 kcal/mol	10.2549 kcal/mol	3.6092 kcal/mol	43 65@LB@ \| \|@LB@5'-CCG...GUUAU U CUGGU...CGG-3'@LB@ GGCUGCA UACAGCAAU CGUU@LB@ \|:\|\|:\|\| :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGAUGU GUGUCGUUA GCAA@LB@3'-UUU...CGUUU A CAAAG...GCA-5'@LB@ \| \|@LB@ 76 54@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -24.9269 kcal/mol@LB@Unfolding Energy - mRNA 10.2549 kcal/mol@LB@Unfolding Energy - sRNA 3.6092 kcal/mol@LB@@LB@Position - mRNA 44 -- 64@LB@Position - sRNA 55 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 60 -- 66@LB@
133	0.006126	0.1605	b0387	yaiI	-9.01	0.350598	46 -- 81	33 -- 74	UPF0178 family protein	_____________45_________________________________________82\n_____________\|__________________________________________\|\n5'-CAC...CCCAU____________CAAUAAAACCG______UCU__________UGCCU...CAA-3'\n______________AUUGC_CGCAGC_____________AUUU______UUUCCAU\n______________\|:\|:\|_\|:\|\|\|\|_____________\|:\|:______\|\|\|\|\|\|\|\n______________UGAUG_GUGUCG_____________UGAG______AAAGGUA\n3'-UUU...GUUUC_____U______UUAAGCAACAAAG____UCCCCU_______CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	75 -- 81	33 -- 39	-16.9561 kcal/mol	3.12923 kcal/mol	4.81602 kcal/mol	45 82@LB@ \| \|@LB@5'-CAC...CCCAU CAAUAAAACCG UCU UGCCU...CAA-3'@LB@ AUUGC CGCAGC AUUU UUUCCAU@LB@ \|:\|:\| \|:\|\|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ UGAUG GUGUCG UGAG AAAGGUA@LB@3'-UUU...GUUUC U UUAAGCAACAAAG UCCCCU CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -16.9561 kcal/mol@LB@Unfolding Energy - mRNA 3.12923 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 46 -- 81@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 33 -- 39@LB@
90	0.004009	0.1538	b3152	yraR	-13.99	0.037452	47 -- 72	45 -- 75	putative nucleoside-diphosphate-sugar epimerase	_____________46______________________________73\n_____________\|_______________________________\|\n5'-ACU...UCAGU_____AA___________UC___________UGCUU...CGA-3'\n______________GAUUA___ACGGCAAUUU______UUACUCA\n______________\|\|:\|\|___\|\|:\|\|\|\|\|\|:______\|:\|\|\|\|\|\n______________CUGAU___UGUCGUUAAG______AGUGAGU\n3'-UUU...CGUUU_____GUG__________CAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	66 -- 72	45 -- 51	-19.6514 kcal/mol	1.92306 kcal/mol	3.74078 kcal/mol	46 73@LB@ \| \|@LB@5'-ACU...UCAGU AA UC UGCUU...CGA-3'@LB@ GAUUA ACGGCAAUUU UUACUCA@LB@ \|\|:\|\| \|\|:\|\|\|\|\|\|: \|:\|\|\|\|\|@LB@ CUGAU UGUCGUUAAG AGUGAGU@LB@3'-UUU...CGUUU GUG CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -19.6514 kcal/mol@LB@Unfolding Energy - mRNA 1.92306 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 47 -- 72@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 45 -- 51@LB@
185	0.009421	0.1776	b3094	exuR	-10.10	0.235203	51 -- 95	35 -- 75	hexuronate regulon transcriptional repressor; autorepressor	_____________50____________________________________________96\n_____________\|_____________________________________________\|\n5'-CCG...AUAAC___CC_____C____CAUUAAC_______GUA__UUUUA______CUUCA...CUG-3'\n______________GAU__CGCAC_GCAA_______GUUUCGU___AG_____GUUUCC\n______________\|\|:__\|:\|\|\|_\|\|\|\|_______\|\|\|\|\|::___\|\|_____:\|\|\|\|\|\n______________CUG__GUGUG_CGUU_______CAAAGUG___UC_____UAAAGG\n3'-UUU...CGUUU___AU_____U____AAGCAA________AG___CCC________UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________76____________________________________________34\n	73 -- 79	48 -- 54	-21.0703 kcal/mol	6.16224 kcal/mol	4.80541 kcal/mol	50 96@LB@ \| \|@LB@5'-CCG...AUAAC CC C CAUUAAC GUA UUUUA CUUCA...CUG-3'@LB@ GAU CGCAC GCAA GUUUCGU AG GUUUCC@LB@ \|\|: \|:\|\|\| \|\|\|\| \|\|\|\|\|:: \|\| :\|\|\|\|\|@LB@ CUG GUGUG CGUU CAAAGUG UC UAAAGG@LB@3'-UUU...CGUUU AU U AAGCAA AG CCC UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -21.0703 kcal/mol@LB@Unfolding Energy - mRNA 6.16224 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 51 -- 95@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 48 -- 54@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@
38	0.0006674	0.0618	b2069	yegD	-11.14	0.153468	57 -- 84	48 -- 76	Hsp70 chaperone family protein	_____________56____________________________85\n_____________\|_____________________________\|\n5'-CAC...AGUUC___G_______C___UC__CUUA______CCGCU...UGC-3'\n______________AGG_UAUACAU_GCA__UC_____UUCAU\n______________\|\|:_\|\|:\|\|\|:_\|\|\|__\|\|_____\|\|\|\|:\n______________UCU_AUGUGUG_CGU__AG_____AAGUG\n3'-UUU...CCGUU___G_______U___UA__CAACA_____AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	61 -- 67	66 -- 72	-18.1339 kcal/mol	3.31217 kcal/mol	3.68714 kcal/mol	56 85@LB@ \| \|@LB@5'-CAC...AGUUC G C UC CUUA CCGCU...UGC-3'@LB@ AGG UAUACAU GCA UC UUCAU@LB@ \|\|: \|\|:\|\|\|: \|\|\| \|\| \|\|\|\|:@LB@ UCU AUGUGUG CGU AG AAGUG@LB@3'-UUU...CCGUU G U UA CAACA AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1339 kcal/mol@LB@Unfolding Energy - mRNA 3.31217 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 57 -- 84@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 66 -- 72@LB@
169	0.008352	0.1723	b1222	narX	-15.18	0.018797	58 -- 74	61 -- 75	sensory histidine kinase in two-component regulatory system with NarL	_____________57________________75\n_____________\|_________________\|\n5'-AAA...AAAGC_____AC__________AUAAG...CUG-3'\n______________GACUA__CACACGGCAA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________CUGAU__GUGUGUCGUU\n3'-UUU...CGUUU_________________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________76________________60\n	68 -- 74	61 -- 67	-20.5903 kcal/mol	2.1582 kcal/mol	3.25399 kcal/mol	57 75@LB@ \| \|@LB@5'-AAA...AAAGC AC AUAAG...CUG-3'@LB@ GACUA CACACGGCAA@LB@ \|\|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGAU GUGUGUCGUU@LB@3'-UUU...CGUUU AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -20.5903 kcal/mol@LB@Unfolding Energy - mRNA 2.1582 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 58 -- 74@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 61 -- 67@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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