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
128	0.004347	0.1195	b3690	cbrA	-9.56	0.060736	197 -- 211	17 -- 31	colicin M resistance protein; FAD-binding protein putative oxidoreductase		_____________196_____________212\n_____________\|_______________\|\n5'-CAG...AGUGA_______________CGACG...AAA-3'\n______________AAAGAUGGAACAUUU\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\n______________UUUCUAUCUUGUAGA\n3'-AUU...CAGAC_______________AUGGA...AUG-5'\n_____________\|_______________\|\n_____________32______________16\n	204 -- 210	18 -- 24	-17.0326 kcal/mol	3.22818 kcal/mol	4.26586 kcal/mol	196 212@LB@ \| \|@LB@5'-CAG...AGUGA CGACG...AAA-3'@LB@ AAAGAUGGAACAUUU@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|@LB@ UUUCUAUCUUGUAGA@LB@3'-AUU...CAGAC AUGGA...AUG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -17.0326 kcal/mol@LB@Unfolding Energy - mRNA 3.22818 kcal/mol@LB@Unfolding Energy - sRNA 4.26586 kcal/mol@LB@@LB@Position - mRNA 197 -- 211@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
167	0.00683	0.1439	b0387	yaiI	-9.54	0.061403	53 -- 70	51 -- 65	UPF0178 family protein		_____________52_________________71\n_____________\|__________________\|\n5'-CAC...UGCCG_______UAAAA______UUCUU...CAA-3'\n______________CAGCCAA_____CCGAUU\n______________\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________GUCGGUU_____GGCUAA\n3'-AUU...UAUAA_______UA_________UGCAC...AUG-5'\n_____________\|__________________\|\n_____________66_________________50\n	53 -- 59	59 -- 65	-16.8495 kcal/mol	1.14267 kcal/mol	6.18987 kcal/mol	52 71@LB@ \| \|@LB@5'-CAC...UGCCG UAAAA UUCUU...CAA-3'@LB@ CAGCCAA CCGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCGGUU GGCUAA@LB@3'-AUU...UAUAA UA UGCAC...AUG-5'@LB@ \| \|@LB@ 66 50@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -16.8495 kcal/mol@LB@Unfolding Energy - mRNA 1.14267 kcal/mol@LB@Unfolding Energy - sRNA 6.18987 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 51 -- 65@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 59 -- 65@LB@
191	0.008587	0.1558	b0823	ybiW	-9.49	0.063221	47 -- 54	1 -- 8	putative pyruvate formate lyase	b3951	_____________46_______55\n_____________\|________\|\n5'-ACC...UUUUC________CACAC...CGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	48 -- 54	1 -- 7	-12.4662 kcal/mol	0.878635 kcal/mol	2.11603 kcal/mol	46 55@LB@ \| \|@LB@5'-ACC...UUUUC CACAC...CGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -12.4662 kcal/mol@LB@Unfolding Energy - mRNA 0.878635 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 47 -- 54@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 1 -- 7@LB@
171	0.00718	0.1466	b1708	nlpC	-9.44	0.065343	288 -- 298	49 -- 59	putative C40 clan peptidase lipoprotein		_____________287_________299\n_____________\|___________\|\n5'-AAA...UUUCU___________CG-3'\n______________GAUUCGAUUAC\n______________:\|\|:\|\|\|\|\|\|\|\n______________UUAGGCUAAUG\n3'-AUU...UCGGU___________CACUU...AUG-5'\n_____________\|___________\|\n_____________60__________48\n	292 -- 298	49 -- 55	-11.5278 kcal/mol	1.77565 kcal/mol	0.318405 kcal/mol	287 299@LB@ \| \|@LB@5'-AAA...UUUCU CG-3'@LB@ GAUUCGAUUAC@LB@ :\|\|:\|\|\|\|\|\|\|@LB@ UUAGGCUAAUG@LB@3'-AUU...UCGGU CACUU...AUG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -11.5278 kcal/mol@LB@Unfolding Energy - mRNA 1.77565 kcal/mol@LB@Unfolding Energy - sRNA 0.318405 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
24	0.0002009	0.02687	b1487	ddpA	-9.43	0.065911	261 -- 269	48 -- 56	D D-dipeptide ABC transporter periplasmic binding protein		_____________260_______270\n_____________\|_________\|\n5'-UCA...AUUUC_________CACGC...UGA-3'\n______________CCGGUUGCG\n______________\|\|\|:\|\|:\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	263 -- 269	48 -- 54	-13.2683 kcal/mol	2.26031 kcal/mol	1.55919 kcal/mol	260 270@LB@ \| \|@LB@5'-UCA...AUUUC CACGC...UGA-3'@LB@ CCGGUUGCG@LB@ \|\|\|:\|\|:\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2683 kcal/mol@LB@Unfolding Energy - mRNA 2.26031 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 261 -- 269@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 48 -- 54@LB@
85	0.002234	0.09158	b0118	acnB	-9.43	0.065848	121 -- 128	1 -- 8	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase		_____________120______129\n_____________\|________\|\n5'-GAG...GCAUU________AAACU...UGC-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	122 -- 128	1 -- 7	-13.4001 kcal/mol	1.87598 kcal/mol	2.11603 kcal/mol	120 129@LB@ \| \|@LB@5'-GAG...GCAUU AAACU...UGC-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.4001 kcal/mol@LB@Unfolding Energy - mRNA 1.87598 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 121 -- 128@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 1 -- 7@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase		_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@LB@
138	0.004994	0.127	b3633	waaA	-9.37	0.068643	230 -- 259	48 -- 75	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)		_____________229____________________________260\n_____________\|______________________________\|\n5'-UCG...CUUCU___CCU__________CU_______A____GCUCU...AAC-3'\n______________CUA___UAUUCAGCCG__GAUCUGG_UACG\n______________\|\|\|___\|\|\|\|\|\|\|\|\|:__:\|\|\|:\|:_\|\|\|\|\n______________GAU___AUAAGUCGGU__UUAGGCU_AUGC\n3'-AUU...CCGCC___UUU___________________A____ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	248 -- 254	53 -- 59	-25.3567 kcal/mol	8.33931 kcal/mol	7.67232 kcal/mol	229 260@LB@ \| \|@LB@5'-UCG...CUUCU CCU CU A GCUCU...AAC-3'@LB@ CUA UAUUCAGCCG GAUCUGG UACG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: :\|\|\|:\|: \|\|\|\|@LB@ GAU AUAAGUCGGU UUAGGCU AUGC@LB@3'-AUU...CCGCC UUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -25.3567 kcal/mol@LB@Unfolding Energy - mRNA 8.33931 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 53 -- 59@LB@
120	0.003999	0.1172	b2582	trxC	-9.28	0.072721	206 -- 219	4 -- 16	thioredoxin 2		_____________205____________220\n_____________\|______________\|\n5'-CUC...AUGAA____G_________AUUGU...UUG-3'\n______________UACC_UUUGUACCC\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|\n______________AUGG_AGACAUGGG\n3'-AUU...GUAGA______________AUG-5'\n_____________\|______________\|\n_____________17_____________3\n	213 -- 219	4 -- 10	-18.1109 kcal/mol	2.27225 kcal/mol	6.59015 kcal/mol	205 220@LB@ \| \|@LB@5'-CUC...AUGAA G AUUGU...UUG-3'@LB@ UACC UUUGUACCC@LB@ \|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGG AGACAUGGG@LB@3'-AUU...GUAGA AUG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -18.1109 kcal/mol@LB@Unfolding Energy - mRNA 2.27225 kcal/mol@LB@Unfolding Energy - sRNA 6.59015 kcal/mol@LB@@LB@Position - mRNA 206 -- 219@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 4 -- 10@LB@
45	0.0004826	0.03773	b4133	cadC	-9.27	0.072737	38 -- 110	5 -- 66	cadBA operon transcriptional activator		_____________37______________________________________________________________________________111\n_____________\|_______________________________________________________________________________\|\n5'-GAU...GGUUC_____A______U_______AAUACUAUGUAAUCAA_____UUAU_______UAAAAAU__________A_________AAUAA...UAA-3'\n______________UCAGU_AAAUCC__UU_CGU________________GAAGU____GG_CUGG_______AACGUCUUGC_UUC___ACC\n______________\|\|\|\|:_\|\|\|\|\|\|__\|\|_\|\|\|________________\|\|\|\|\|____\|\|_\|\|\|:_______\|\|\|:\|\|\|\|:\|_:\|\|___\|\|\|\n______________AGUCG_UUUAGG__AA_GCA________________CUUCA____CC_GACU_______UUGUAGAAUG_GAG___UGG\n3'-AUU...UUAUA_____G______CU__U________________________UUUU__A____UUCUAUC______________ACA___GAUG-5'\n_____________\|_______________________________________________________________________________\|\n_____________67______________________________________________________________________________4\n	97 -- 103	14 -- 20	-38.0459 kcal/mol	10.2122 kcal/mol	18.5819 kcal/mol	37 111@LB@ \| \|@LB@5'-GAU...GGUUC A U AAUACUAUGUAAUCAA UUAU UAAAAAU A AAUAA...UAA-3'@LB@ UCAGU AAAUCC UU CGU GAAGU GG CUGG AACGUCUUGC UUC ACC@LB@ \|\|\|\|: \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\| \|\|\|: \|\|\|:\|\|\|\|:\| :\|\| \|\|\|@LB@ AGUCG UUUAGG AA GCA CUUCA CC GACU UUGUAGAAUG GAG UGG@LB@3'-AUU...UUAUA G CU U UUUU A UUCUAUC ACA GAUG-5'@LB@ \| \|@LB@ 67 4@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -38.0459 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 18.5819 kcal/mol@LB@@LB@Position - mRNA 38 -- 110@LB@Position - sRNA 5 -- 66@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 14 -- 20@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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