Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	Additional homologs
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase		_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 49 -- 55@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase		_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@LB@
136	0.004892	0.1265	b2349	intS	-8.19	0.139381	273 -- 281	3 -- 11	CPS-53 (KpLE1) prophage; putative prophage CPS-53 integrase		_____________272_______282\n_____________\|_________\|\n5'-AAG...AUGGC_________UAUGU...GGA-3'\n______________CUGUACCUU\n______________\|\|\|\|\|\|\|:\|\n______________GACAUGGGA\n3'-AUU...AUGGA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	275 -- 281	3 -- 9	-13.0022 kcal/mol	1.37836 kcal/mol	3.45478 kcal/mol	272 282@LB@ \| \|@LB@5'-AAG...AUGGC UAUGU...GGA-3'@LB@ CUGUACCUU@LB@ \|\|\|\|\|\|\|:\|@LB@ GACAUGGGA@LB@3'-AUU...AUGGA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -13.0022 kcal/mol@LB@Unfolding Energy - mRNA 1.37836 kcal/mol@LB@Unfolding Energy - sRNA 3.45478 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
180	0.007734	0.1511	b3617	kbl	-7.53	0.200168	193 -- 210	43 -- 60	glycine C-acetyltransferase		_____________192________________211\n_____________\|__________________\|\n5'-UUU...CUGGA_____GCAA_________AAUUU...AAG-3'\n______________GAAUC____UGCGUGGAG\n______________:\|\|\|\|____\|:\|\|\|\|:\|\|\n______________UUUAG____AUGCACUUC\n3'-AUU...GUCGG_____GCUA_________AUUUU...AUG-5'\n_____________\|__________________\|\n_____________61_________________42\n	204 -- 210	43 -- 49	-15.3085 kcal/mol	4.51554 kcal/mol	3.27548 kcal/mol	192 211@LB@ \| \|@LB@5'-UUU...CUGGA GCAA AAUUU...AAG-3'@LB@ GAAUC UGCGUGGAG@LB@ :\|\|\|\| \|:\|\|\|\|:\|\|@LB@ UUUAG AUGCACUUC@LB@3'-AUU...GUCGG GCUA AUUUU...AUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -15.3085 kcal/mol@LB@Unfolding Energy - mRNA 4.51554 kcal/mol@LB@Unfolding Energy - sRNA 3.27548 kcal/mol@LB@@LB@Position - mRNA 193 -- 210@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 43 -- 49@LB@
16	5.617e-05	0.01183	b0116	lpd	-12.59	0.006546	264 -- 293	29 -- 63	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase		_____________263__________________________________294\n_____________\|____________________________________\|\n5'-CCG...CCGCU___U____________C___UUU_____________ACCGUAA-3'\n______________GCC___UCCG_UUGCG_UGA______AGGUCUGGAA\n______________\|\|\|___\|\|\|\|_\|\|:\|\|_\|\|\|______\|\|\|\|\|\|\|:\|\|\n______________CGG___AGGC_AAUGC_ACU______UCCAGACUUU\n3'-AUU...UAAGU___UUU____U_________UCAUUU__________CUAUC...AUG-5'\n_____________\|____________________________________\|\n_____________64___________________________________28\n	286 -- 292	30 -- 36	-30.8342 kcal/mol	7.36676 kcal/mol	10.8887 kcal/mol	263 294@LB@ \| \|@LB@5'-CCG...CCGCU U C UUU ACCGUAA-3'@LB@ GCC UCCG UUGCG UGA AGGUCUGGAA@LB@ \|\|\| \|\|\|\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|:\|\|@LB@ CGG AGGC AAUGC ACU UCCAGACUUU@LB@3'-AUU...UAAGU UUU U UCAUUU CUAUC...AUG-5'@LB@ \| \|@LB@ 64 28@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -30.8342 kcal/mol@LB@Unfolding Energy - mRNA 7.36676 kcal/mol@LB@Unfolding Energy - sRNA 10.8887 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 29 -- 63@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 30 -- 36@LB@
193	0.008653	0.1558	b1677	lpp	-9.16	0.078007	273 -- 298	53 -- 76	murein lipoprotein		_____________272________________________299\n_____________\|__________________________\|\n5'-UCA...GCAAC________CGA______GUCU_____CG-3'\n______________GCUAAAAU___UCAGCU____UCUGA\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:____\|\|:\|\|\n______________CGAUUUUA___AGUCGG____AGGCU\n3'-AUU...CCCGC________UA_______UUU______AAUGC...AUG-5'\n_____________\|__________________________\|\n_____________77_________________________52\n	273 -- 279	70 -- 76	-19.09 kcal/mol	3.58418 kcal/mol	6.36489 kcal/mol	272 299@LB@ \| \|@LB@5'-UCA...GCAAC CGA GUCU CG-3'@LB@ GCUAAAAU UCAGCU UCUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|:\|\|@LB@ CGAUUUUA AGUCGG AGGCU@LB@3'-AUU...CCCGC UA UUU AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -19.09 kcal/mol@LB@Unfolding Energy - mRNA 3.58418 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 70 -- 76@LB@
82	0.001877	0.08053	b3199	lptC	-13.73	0.002422	95 -- 106	45 -- 56	periplasmic membrane-anchored LPS-binding protein; LPS export protein		_____________94___________107\n_____________\|____________\|\n5'-UAU...GCGCG____________CGCGC...UGG-3'\n______________CCGAUUACGUGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACU\n3'-AUU...GUUUA____________UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	100 -- 106	45 -- 51	-18.6784 kcal/mol	2.68909 kcal/mol	2.27945 kcal/mol	94 107@LB@ \| \|@LB@5'-UAU...GCGCG CGCGC...UGG-3'@LB@ CCGAUUACGUGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACU@LB@3'-AUU...GUUUA UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -18.6784 kcal/mol@LB@Unfolding Energy - mRNA 2.68909 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 95 -- 106@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 45 -- 51@LB@
127	0.004255	0.1179	b2838	lysA	-9.87	0.049362	214 -- 233	52 -- 69	diaminopimelate decarboxylase PLP-binding		_____________213__________________234\n_____________\|____________________\|\n5'-GGU...UUCAC________A_C___A_____CUCAC...CGC-3'\n______________UGUUCAGC_C_GAU_CCGAU\n______________\|:\|\|\|\|\|\|_\|_:\|\|_\|\|\|\|\|\n______________AUAAGUCG_G_UUA_GGCUA\n3'-AUU...AUUUU__________U_________AUGCA...AUG-5'\n_____________\|____________________\|\n_____________70___________________51\n	215 -- 221	62 -- 68	-18.1264 kcal/mol	2.0842 kcal/mol	6.19243 kcal/mol	213 234@LB@ \| \|@LB@5'-GGU...UUCAC A C A CUCAC...CGC-3'@LB@ UGUUCAGC C GAU CCGAU@LB@ \|:\|\|\|\|\|\| \| :\|\| \|\|\|\|\|@LB@ AUAAGUCG G UUA GGCUA@LB@3'-AUU...AUUUU U AUGCA...AUG-5'@LB@ \| \|@LB@ 70 51@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -18.1264 kcal/mol@LB@Unfolding Energy - mRNA 2.0842 kcal/mol@LB@Unfolding Energy - sRNA 6.19243 kcal/mol@LB@@LB@Position - mRNA 214 -- 233@LB@Position - sRNA 52 -- 69@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 62 -- 68@LB@
79	0.001698	0.07533	b2890	lysS	-8.16	0.142186	53 -- 64	54 -- 65	lysine tRNA synthetase constitutive	b4129	_____________52___________65\n_____________\|____________\|\n5'-AAA...UGGGG____________UUCUU...GGA-3'\n______________CAGCCAGAUUCG\n______________\|\|\|\|\|\|:\|\|:\|\|\n______________GUCGGUUUAGGC\n3'-AUU...UAUAA____________UAAUG...AUG-5'\n_____________\|____________\|\n_____________66___________53\n	58 -- 64	54 -- 60	-18.439 kcal/mol	4.14677 kcal/mol	6.15795 kcal/mol	52 65@LB@ \| \|@LB@5'-AAA...UGGGG UUCUU...GGA-3'@LB@ CAGCCAGAUUCG@LB@ \|\|\|\|\|\|:\|\|:\|\|@LB@ GUCGGUUUAGGC@LB@3'-AUU...UAUAA UAAUG...AUG-5'@LB@ \| \|@LB@ 66 53@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -18.439 kcal/mol@LB@Unfolding Energy - mRNA 4.14677 kcal/mol@LB@Unfolding Energy - sRNA 6.15795 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 54 -- 65@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 54 -- 60@LB@
126	0.00422	0.1178	b1621	malX	-14.96	0.000732	43 -- 87	1 -- 56	maltose and glucose-specific PTS enzyme IIB component and IIC component		_____________42__________________________________________________________88\n_____________\|___________________________________________________________\|\n5'-AUG...ACUCC____________C___________________A______________UAUU________ACCCG...GCA-3'\n______________CUGAUUAUGUGA_______________AGAUA_AACGUUUUACCUUU____UAUCUUAU\n______________\|:\|\|\|\|\|:\|\|\|\|_______________\|\|\|\|\|_\|\|\|:\|:\|\|\|\|\|\|:\|____\|\|:\|:\|\|:\n______________GGCUAAUGCACU_______________UCUAU_UUGUAGAAUGGAGA____AUGGGAUG\n3'-AUU...GUUUA____________UCAUUUUCCAGACUU_____C______________C___________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	81 -- 87	1 -- 7	-37.7188 kcal/mol	10.08 kcal/mol	12.7022 kcal/mol	42 88@LB@ \| \|@LB@5'-AUG...ACUCC C A UAUU ACCCG...GCA-3'@LB@ CUGAUUAUGUGA AGAUA AACGUUUUACCUUU UAUCUUAU@LB@ \|:\|\|\|\|\|:\|\|\|\| \|\|\|\|\| \|\|\|:\|:\|\|\|\|\|\|:\| \|\|:\|:\|\|:@LB@ GGCUAAUGCACU UCUAU UUGUAGAAUGGAGA AUGGGAUG@LB@3'-AUU...GUUUA UCAUUUUCCAGACUU C C -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -14.96 kcal/mol@LB@Hybridization Energy -37.7188 kcal/mol@LB@Unfolding Energy - mRNA 10.08 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 43 -- 87@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 1 -- 7@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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