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
127	0.01387	0.3627	b1224	narG	-12.01	0.089072	151 -- 160	37 -- 46	nitrate reductase 1 alpha subunit	_____________150________161\n_____________\|__________\|\n5'-UAA...ACAUU__________AUUUA...AGG-3'\n______________AGCAAUGUCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGUUACAGC\n3'-UUU...UACAC__________ACGAA...GCG-5'\n_____________\|__________\|\n_____________47_________36\n	154 -- 160	37 -- 43	-14.8133 kcal/mol	1.65076 kcal/mol	1.15554 kcal/mol	150 161@LB@ \| \|@LB@5'-UAA...ACAUU AUUUA...AGG-3'@LB@ AGCAAUGUCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGUUACAGC@LB@3'-UUU...UACAC ACGAA...GCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -14.8133 kcal/mol@LB@Unfolding Energy - mRNA 1.65076 kcal/mol@LB@Unfolding Energy - sRNA 1.15554 kcal/mol@LB@@LB@Position - mRNA 151 -- 160@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 37 -- 43@LB@
5	0.0002772	0.1521	b3365	nirB	-15.55	0.022306	192 -- 212	38 -- 57	nitrite reductase large subunit NAD(P)H-binding	_____________191___________________213\n_____________\|_____________________\|\n5'-AUC...AAAUC_______AAA_______A___AGACU...UUA-3'\n______________GAGGCAA___UGAGCAA_GUC\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\n______________CUUCGUU___ACUCGUU_CAG\n3'-UUU...AUGAC_______AC________A___CACGA...GCG-5'\n_____________\|_____________________\|\n_____________58____________________37\n	202 -- 208	42 -- 48	-22.0527 kcal/mol	3.28811 kcal/mol	3.2161 kcal/mol	191 213@LB@ \| \|@LB@5'-AUC...AAAUC AAA A AGACU...UUA-3'@LB@ GAGGCAA UGAGCAA GUC@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ CUUCGUU ACUCGUU CAG@LB@3'-UUU...AUGAC AC A CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -22.0527 kcal/mol@LB@Unfolding Energy - mRNA 3.28811 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 192 -- 212@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
97	0.0101	0.3393	b0192	nlpE	-13.07	0.059097	192 -- 230	40 -- 68	lipoprotein involved with copper homeostasis and adhesion	_____________191_____________________________________231\n_____________\|_______________________________________\|\n5'-UCA...AAAAG___GA___GA___UGAAAA_______A____CA______GCUGU...CGC-3'\n______________AAG__AUG__UGG______AAGCGAU_GUGA__GCGAUG\n______________\|\|\|__\|\|:__\|\|\|______\|\|\|\|:\|\|_\|\|\|\|__\|\|:\|\|\|\n______________UUC__UAU__ACC______UUCGUUA_CACU__CGUUAC\n3'-UUU...ACCGA___AU___G______________________________AGCAC...GCG-5'\n_____________\|_______________________________________\|\n_____________69______________________________________39\n	211 -- 217	50 -- 56	-20.8621 kcal/mol	4.48665 kcal/mol	3.30507 kcal/mol	191 231@LB@ \| \|@LB@5'-UCA...AAAAG GA GA UGAAAA A CA GCUGU...CGC-3'@LB@ AAG AUG UGG AAGCGAU GUGA GCGAUG@LB@ \|\|\| \|\|: \|\|\| \|\|\|\|:\|\| \|\|\|\| \|\|:\|\|\|@LB@ UUC UAU ACC UUCGUUA CACU CGUUAC@LB@3'-UUU...ACCGA AU G AGCAC...GCG-5'@LB@ \| \|@LB@ 69 39@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -20.8621 kcal/mol@LB@Unfolding Energy - mRNA 4.48665 kcal/mol@LB@Unfolding Energy - sRNA 3.30507 kcal/mol@LB@@LB@Position - mRNA 192 -- 230@LB@Position - sRNA 40 -- 68@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 50 -- 56@LB@
25	0.002073	0.2692	b3163	nlpI	-16.34	0.016289	1 -- 45	38 -- 89	lipoprotein involved in osmotic sensitivity and filamentation	______________1____________________________________________________46\n______________\|____________________________________________________\|\n___________5'-______________U___A__AUUAAA_____________C_________C__AACCU...CAU-3'\n______________AGGGCC_GUAUCCG_CUG_GC____________GAAGCGA__UGAGCAGU_UC\n______________\|::\|\|\|_\|:\|:\|\|\|_\|\|\|_\|\|____________\|\|\|\|\|:\|__\|\|\|\|\|\|:\|_\|\|\n______________UUUCGG_CGUGGGC_GAC_CG____________CUUCGUU__ACUCGUUA_AG\n__________3'-U______U_______C______AUUCAUUAUGAC_______AC________C__CACGA...GCG-5'\n_____________\|_____________________________________________________\|\n_____________90____________________________________________________37\n	36 -- 42	41 -- 47	-40.4977 kcal/mol	9.24688 kcal/mol	14.9106 kcal/mol	1 46@LB@ \| \|@LB@ 5'- U A AUUAAA C C AACCU...CAU-3'@LB@ AGGGCC GUAUCCG CUG GC GAAGCGA UGAGCAGU UC@LB@ \|::\|\|\| \|:\|:\|\|\| \|\|\| \|\| \|\|\|\|\|:\| \|\|\|\|\|\|:\| \|\|@LB@ UUUCGG CGUGGGC GAC CG CUUCGUU ACUCGUUA AG@LB@ 3'-U U C AUUCAUUAUGAC AC C CACGA...GCG-5'@LB@ \| \|@LB@ 90 37@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -40.4977 kcal/mol@LB@Unfolding Energy - mRNA 9.24688 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 1 -- 45@LB@Position - sRNA 38 -- 89@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 41 -- 47@LB@
103	0.0104	0.3393	b2711	norW	-11.75	0.098250	192 -- 208	42 -- 58	NADH:flavorubredoxin oxidoreductase	_____________191_______________209\n_____________\|_________________\|\n5'-GAA...GCAUC________AA_______CGGCA...UUG-3'\n______________GGAGGCAA__UGAGUAA\n______________\|\|\|:\|\|\|\|__\|\|\|\|:\|\|\n______________CCUUCGUU__ACUCGUU\n3'-UUU...UAUGA________AC_______ACAGC...GCG-5'\n_____________\|_________________\|\n_____________59________________41\n	202 -- 208	42 -- 48	-20.2467 kcal/mol	5.28663 kcal/mol	3.2101 kcal/mol	191 209@LB@ \| \|@LB@5'-GAA...GCAUC AA CGGCA...UUG-3'@LB@ GGAGGCAA UGAGUAA@LB@ \|\|\|:\|\|\|\| \|\|\|\|:\|\|@LB@ CCUUCGUU ACUCGUU@LB@3'-UUU...UAUGA AC ACAGC...GCG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -20.2467 kcal/mol@LB@Unfolding Energy - mRNA 5.28663 kcal/mol@LB@Unfolding Energy - sRNA 3.2101 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
186	0.02299	0.4113	b3996	nudC	-11.58	0.104830	175 -- 203	40 -- 67	NADH pyrophosphatase	_____________174____________________________204\n_____________\|______________________________\|\n5'-GAU...AUGCC________AA_________CAA____U___GAUCG...CGG-3'\n______________AGUGAUGC___AGGUAGUG___GAGC_AUG\n______________\|\|\|:\|\|:\|___\|:\|:\|:\|\|___\|\|\|\|_\|\|\|\n______________UCAUUAUG___UUCGUUAC___CUCG_UAC\n3'-UUU...CCGAU________ACC________A______U___AGCAC...GCG-5'\n_____________\|______________________________\|\n_____________68_____________________________39\n	186 -- 192	49 -- 55	-21.6638 kcal/mol	6.77954 kcal/mol	3.30504 kcal/mol	174 204@LB@ \| \|@LB@5'-GAU...AUGCC AA CAA U GAUCG...CGG-3'@LB@ AGUGAUGC AGGUAGUG GAGC AUG@LB@ \|\|\|:\|\|:\| \|:\|:\|:\|\| \|\|\|\| \|\|\|@LB@ UCAUUAUG UUCGUUAC CUCG UAC@LB@3'-UUU...CCGAU ACC A U AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -21.6638 kcal/mol@LB@Unfolding Energy - mRNA 6.77954 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 49 -- 55@LB@
170	0.02096	0.4072	b2283	nuoG	-12.68	0.068788	186 -- 195	52 -- 61	NADH:ubiquinone oxidoreductase chain G	_____________185________196\n_____________\|__________\|\n5'-CUG...AGAAA__________UGCUA...UUU-3'\n______________ACUGGAAGCA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UGACCUUCGU\n3'-UUU...CAUUA__________UACAC...GCG-5'\n_____________\|__________\|\n_____________62_________51\n	189 -- 195	52 -- 58	-16.7738 kcal/mol	1.20687 kcal/mol	2.88813 kcal/mol	185 196@LB@ \| \|@LB@5'-CUG...AGAAA UGCUA...UUU-3'@LB@ ACUGGAAGCA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UGACCUUCGU@LB@3'-UUU...CAUUA UACAC...GCG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.68 kcal/mol@LB@Hybridization Energy -16.7738 kcal/mol@LB@Unfolding Energy - mRNA 1.20687 kcal/mol@LB@Unfolding Energy - sRNA 2.88813 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
135	0.0153	0.379	b1245	oppC	-10.91	0.134968	184 -- 214	42 -- 65	oligopeptide ABC transporter permease	_____________183_____________________________215\n_____________\|_______________________________\|\n5'-GGU...GUUAC___________CUC______A__UUA_____GAAAA...UUA-3'\n______________UGAUACUGGAG___GCGAUG_UG___AGUAA\n______________\|:\|\|\|\|\|\|\|\|:___\|\|:\|\|\|_\|\|___\|\|:\|\|\n______________AUUAUGACCUU___CGUUAC_AC___UCGUU\n3'-UUU...GAUUC_______________________________ACAGC...GCG-5'\n_____________\|_______________________________\|\n_____________66______________________________41\n	188 -- 194	55 -- 61	-22.5581 kcal/mol	8.34668 kcal/mol	3.30456 kcal/mol	183 215@LB@ \| \|@LB@5'-GGU...GUUAC CUC A UUA GAAAA...UUA-3'@LB@ UGAUACUGGAG GCGAUG UG AGUAA@LB@ \|:\|\|\|\|\|\|\|\|: \|\|:\|\|\| \|\| \|\|:\|\|@LB@ AUUAUGACCUU CGUUAC AC UCGUU@LB@3'-UUU...GAUUC ACAGC...GCG-5'@LB@ \| \|@LB@ 66 41@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -22.5581 kcal/mol@LB@Unfolding Energy - mRNA 8.34668 kcal/mol@LB@Unfolding Energy - sRNA 3.30456 kcal/mol@LB@@LB@Position - mRNA 184 -- 214@LB@Position - sRNA 42 -- 65@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 55 -- 61@LB@
85	0.008408	0.3323	b1246	oppD	-9.75	0.205761	38 -- 64	37 -- 61	oligopeptide ABC transporter ATPase	_____________37__________________________65\n_____________\|___________________________\|\n5'-AGC...AAGCA_______U___U__C_________G__CGAAC...ACG-3'\n______________GCUGGGG_GCA_UG_UGAGUGAUG_CG\n______________:\|\|\|\|::_\|\|\|_\|\|_\|\|\|\|::\|\|\|_\|\|\n______________UGACCUU_CGU_AC_ACUCGUUAC_GC\n3'-UUU...CAUUA___________U____________A__ACGAA...GCG-5'\n_____________\|___________________________\|\n_____________62__________________________36\n	55 -- 61	40 -- 46	-27.1525 kcal/mol	14.0993 kcal/mol	3.30158 kcal/mol	37 65@LB@ \| \|@LB@5'-AGC...AAGCA U U C G CGAAC...ACG-3'@LB@ GCUGGGG GCA UG UGAGUGAUG CG@LB@ :\|\|\|\|:: \|\|\| \|\| \|\|\|\|::\|\|\| \|\|@LB@ UGACCUU CGU AC ACUCGUUAC GC@LB@3'-UUU...CAUUA U A ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -27.1525 kcal/mol@LB@Unfolding Energy - mRNA 14.0993 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 38 -- 64@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 40 -- 46@LB@
163	0.02026	0.4072	b1283	osmB	-10.88	0.136535	231 -- 259	38 -- 61	osmotically and stress inducible lipoprotein	_____________230___________________________260\n_____________\|_____________________________\|\n5'-UAA...CCGCG____UUCU______UACUUU_________UCUGA...ACA-3'\n______________GCUG____GGCAAU______GGCAAUGUC\n______________:\|\|\|____:\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________UGAC____UCGUUA______UCGUUACAG\n3'-UUU...CAUUA____CU________CAC____________CACGA...GCG-5'\n_____________\|_____________________________\|\n_____________62____________________________37\n	253 -- 259	38 -- 44	-21.4164 kcal/mol	7.23917 kcal/mol	3.30134 kcal/mol	230 260@LB@ \| \|@LB@5'-UAA...CCGCG UUCU UACUUU UCUGA...ACA-3'@LB@ GCUG GGCAAU GGCAAUGUC@LB@ :\|\|\| :\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UGAC UCGUUA UCGUUACAG@LB@3'-UUU...CAUUA CU CAC CACGA...GCG-5'@LB@ \| \|@LB@ 62 37@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -21.4164 kcal/mol@LB@Unfolding Energy - mRNA 7.23917 kcal/mol@LB@Unfolding Energy - sRNA 3.30134 kcal/mol@LB@@LB@Position - mRNA 231 -- 259@LB@Position - sRNA 38 -- 61@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 38 -- 44@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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