Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
28	0.005242	0.6024	b0785	moaE	-11.01	0.025514	211 -- 232	52 -- 74	molybdopterin synthase large subunit	_____________210_____________________233\n_____________\|_______________________\|\n5'-AGA...AGAAA____A__________________GCCGU...CCU-3'\n______________CCAA_AUUGUUGUUGGUCCG_CA\n______________\|\|\|\|_\|\|:\|:\|:\|\|\|\|:\|\|\|_\|\|\n______________GGUU_UAGCGAUAACCGGGC_GU\n3'-UUU...UUACC____A_______________A__UUCUC...ACA-5'\n_____________\|_______________________\|\n_____________75______________________51\n	216 -- 222	63 -- 69	-28.4518 kcal/mol	6.10798 kcal/mol	11.3304 kcal/mol	210 233@LB@ \| \|@LB@5'-AGA...AGAAA A GCCGU...CCU-3'@LB@ CCAA AUUGUUGUUGGUCCG CA@LB@ \|\|\|\| \|\|:\|:\|:\|\|\|\|:\|\|\| \|\|@LB@ GGUU UAGCGAUAACCGGGC GU@LB@3'-UUU...UUACC A A UUCUC...ACA-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -28.4518 kcal/mol@LB@Unfolding Energy - mRNA 6.10798 kcal/mol@LB@Unfolding Energy - sRNA 11.3304 kcal/mol@LB@@LB@Position - mRNA 211 -- 232@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 63 -- 69@LB@
170	0.03452	0.6177	b0792	ybhR	-7.08	0.157577	208 -- 236	47 -- 69	putative ABC transporter permease	_____________207____________________________237\n_____________\|______________________________\|\n5'-CAG...GUUUC______UA___ACGUUAA____________UUGCA...AGG-3'\n______________AUCGCU__UGG_______UCCG_CAAAGAG\n______________\|\|\|\|\|\|__\|\|\|_______:\|\|\|_\|\|\|\|\|\|\|\n______________UAGCGA__ACC_______GGGC_GUUUCUC\n3'-UUU...GGUUA______UA______________A_______CUUAA...ACA-5'\n_____________\|______________________________\|\n_____________70_____________________________46\n	230 -- 236	47 -- 53	-23.2437 kcal/mol	4.95079 kcal/mol	11.2154 kcal/mol	207 237@LB@ \| \|@LB@5'-CAG...GUUUC UA ACGUUAA UUGCA...AGG-3'@LB@ AUCGCU UGG UCCG CAAAGAG@LB@ \|\|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ UAGCGA ACC GGGC GUUUCUC@LB@3'-UUU...GGUUA UA A CUUAA...ACA-5'@LB@ \| \|@LB@ 70 46@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -23.2437 kcal/mol@LB@Unfolding Energy - mRNA 4.95079 kcal/mol@LB@Unfolding Energy - sRNA 11.2154 kcal/mol@LB@@LB@Position - mRNA 208 -- 236@LB@Position - sRNA 47 -- 69@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 47 -- 53@LB@
194	0.04051	0.6177	b0814	ompX	-6.96	0.165642	107 -- 118	50 -- 61	outer membrane protein X	_____________106__________119\n_____________\|____________\|\n5'-CUG...UGAAA____________CAUCA...CAC-3'\n______________UGGCCCGUUAGA\n______________\|\|\|\|\|\|\|\|:\|:\|\n______________ACCGGGCAGUUU\n3'-UUU...CGAUA____________CUCCU...ACA-5'\n_____________\|____________\|\n_____________62___________49\n	111 -- 117	51 -- 57	-20.1081 kcal/mol	2.98628 kcal/mol	10.1573 kcal/mol	106 119@LB@ \| \|@LB@5'-CUG...UGAAA CAUCA...CAC-3'@LB@ UGGCCCGUUAGA@LB@ \|\|\|\|\|\|\|\|:\|:\|@LB@ ACCGGGCAGUUU@LB@3'-UUU...CGAUA CUCCU...ACA-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -20.1081 kcal/mol@LB@Unfolding Energy - mRNA 2.98628 kcal/mol@LB@Unfolding Energy - sRNA 10.1573 kcal/mol@LB@@LB@Position - mRNA 107 -- 118@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 51 -- 57@LB@
7	0.001184	0.5444	b0817	mntR	-11.99	0.016054	285 -- 294	46 -- 55	Mn(2+)-responsive manganese regulon transcriptional regulator	_____________284________295\n_____________\|__________\|\n5'-CUU...GCCAG__________CGCAUC-3'\n______________GUCAGAGAGG\n______________\|\|\|\|:\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	288 -- 294	46 -- 52	-16.1275 kcal/mol	3.21103 kcal/mol	0.924411 kcal/mol	284 295@LB@ \| \|@LB@5'-CUU...GCCAG CGCAUC-3'@LB@ GUCAGAGAGG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -16.1275 kcal/mol@LB@Unfolding Energy - mRNA 3.21103 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 285 -- 294@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@LB@
56	0.01199	0.6177	b0836	bssR	-10.68	0.029916	18 -- 32	42 -- 55	repressor of biofilm formation by indole transport regulation	_____________17______________33\n_____________\|_______________\|\n5'-AUU...GAAAG_______C_______CUACA...ACA-3'\n______________GUCAGGG_AGGGAUU\n______________\|\|\|\|::\|_\|\|\|:\|\|\|\n______________CAGUUUC_UCCUUAA\n3'-UUU...CCGGG_______________AGUAA...ACA-5'\n_____________\|_______________\|\n_____________56______________41\n	26 -- 32	42 -- 48	-16.3055 kcal/mol	4.68166 kcal/mol	0.947316 kcal/mol	17 33@LB@ \| \|@LB@5'-AUU...GAAAG C CUACA...ACA-3'@LB@ GUCAGGG AGGGAUU@LB@ \|\|\|\|::\| \|\|\|:\|\|\|@LB@ CAGUUUC UCCUUAA@LB@3'-UUU...CCGGG AGUAA...ACA-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -16.3055 kcal/mol@LB@Unfolding Energy - mRNA 4.68166 kcal/mol@LB@Unfolding Energy - sRNA 0.947316 kcal/mol@LB@@LB@Position - mRNA 18 -- 32@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 42 -- 48@LB@
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator	_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
5	0.0004437	0.2856	b0847	ybjL	-12.50	0.012601	224 -- 253	26 -- 55	putative transporter	_____________223____________________________254\n_____________\|______________________________\|\n5'-CUU...GAAUU______U_______A____CUG________UGUGG...GUU-3'\n______________GUUAAA_GGGAAUU_CAUU___UUAUUAUU\n______________\|\|:\|\|\|_:\|\|\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAGUUU_UCCUUAA_GUAA___AAUAAUAA\n3'-UUU...CCGGG______C_______A____AAA________UACGG...ACA-5'\n_____________\|______________________________\|\n_____________56_____________________________25\n	247 -- 253	26 -- 32	-19.6848 kcal/mol	5.99374 kcal/mol	1.18815 kcal/mol	223 254@LB@ \| \|@LB@5'-CUU...GAAUU U A CUG UGUGG...GUU-3'@LB@ GUUAAA GGGAAUU CAUU UUAUUAUU@LB@ \|\|:\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAGUUU UCCUUAA GUAA AAUAAUAA@LB@3'-UUU...CCGGG C A AAA UACGG...ACA-5'@LB@ \| \|@LB@ 56 25@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -19.6848 kcal/mol@LB@Unfolding Energy - mRNA 5.99374 kcal/mol@LB@Unfolding Energy - sRNA 1.18815 kcal/mol@LB@@LB@Position - mRNA 224 -- 253@LB@Position - sRNA 26 -- 55@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 26 -- 32@LB@
131	0.02569	0.6177	b0848	ybjM	-8.44	0.085177	187 -- 197	44 -- 55	inner membrane protein	_____________186__________198\n_____________\|____________\|\n5'-GAA...GCAGU____________CGAGU...GGG-3'\n______________GUC_AGGAGGAA\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________CAG_UUCUCCUU\n3'-UUU...CCGGG___U________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	191 -- 197	44 -- 50	-13.6185 kcal/mol	4.23971 kcal/mol	0.941432 kcal/mol	186 198@LB@ \| \|@LB@5'-GAA...GCAGU CGAGU...GGG-3'@LB@ GUC AGGAGGAA@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CAG UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -13.6185 kcal/mol@LB@Unfolding Energy - mRNA 4.23971 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 187 -- 197@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
18	0.003456	0.593	b0867	amiD	-11.23	0.023022	276 -- 289	39 -- 52	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________275____________290\n_____________\|______________\|\n5'-GAU...UCGAG__________A___GCUUG...CCC-3'\n______________AAAGAGGGAU_UCA\n______________\|\|\|\|\|\|\|:\|\|_\|\|\|\n______________UUUCUCCUUA_AGU\n3'-UUU...GGCAG__________A___AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	279 -- 285	43 -- 49	-14.4178 kcal/mol	2.13665 kcal/mol	1.05043 kcal/mol	275 290@LB@ \| \|@LB@5'-GAU...UCGAG A GCUUG...CCC-3'@LB@ AAAGAGGGAU UCA@LB@ \|\|\|\|\|\|\|:\|\| \|\|\|@LB@ UUUCUCCUUA AGU@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.4178 kcal/mol@LB@Unfolding Energy - mRNA 2.13665 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 276 -- 289@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 43 -- 49@LB@
133	0.02604	0.6177	b0876	ybjD	-5.23	0.342712	179 -- 199	45 -- 55	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________178___________________200\n_____________\|_____________________\|\n5'-CGU...GAUAA____CAUAUUUCUG_______UAUGA...GGG-3'\n______________GUCA__________GAGGGGA\n______________\|\|\|\|__________:\|\|:\|\|\|\n______________CAGU__________UUCUCCU\n3'-UUU...CCGGG_____________________UAAAG...ACA-5'\n_____________\|_____________________\|\n_____________56____________________44\n	193 -- 199	45 -- 51	-10.7419 kcal/mol	4.58374 kcal/mol	0.930875 kcal/mol	178 200@LB@ \| \|@LB@5'-CGU...GAUAA CAUAUUUCUG UAUGA...GGG-3'@LB@ GUCA GAGGGGA@LB@ \|\|\|\| :\|\|:\|\|\|@LB@ CAGU UUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -10.7419 kcal/mol@LB@Unfolding Energy - mRNA 4.58374 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 199@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 45 -- 51@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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