Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
81	0.006985	0.2822	b0333	prpC	-14.20	0.012743	251 -- 274	6 -- 28	2-methylcitrate synthase	_____________250______________________275\n_____________\|________________________\|\n5'-ACU...CCGAA_____________CUUUCU_____UCCGG...GCA-3'\n______________AAAAUCUGUGGCA______GGCGU\n______________\|\|\|\|\|\|\|\|\|\|:\|\|______\|\|\|:\|\n______________UUUUAGACACUGU______CCGUA\n3'-UUU...UUUUA_____________UAUUU______UAUUG-5'\n_____________\|________________________\|\n_____________29_______________________5\n	257 -- 263	16 -- 22	-23.1913 kcal/mol	4.0983 kcal/mol	4.89176 kcal/mol	250 275@LB@ \| \|@LB@5'-ACU...CCGAA CUUUCU UCCGG...GCA-3'@LB@ AAAAUCUGUGGCA GGCGU@LB@ \|\|\|\|\|\|\|\|\|\|:\|\| \|\|\|:\|@LB@ UUUUAGACACUGU CCGUA@LB@3'-UUU...UUUUA UAUUU UAUUG-5'@LB@ \| \|@LB@ 29 5@LB@@LB@@LB@Energy -14.20 kcal/mol@LB@Hybridization Energy -23.1913 kcal/mol@LB@Unfolding Energy - mRNA 4.0983 kcal/mol@LB@Unfolding Energy - sRNA 4.89176 kcal/mol@LB@@LB@Position - mRNA 251 -- 274@LB@Position - sRNA 6 -- 28@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 16 -- 22@LB@
82	0.006986	0.2822	b3128	garD	-14.80	0.008847	185 -- 224	15 -- 66	D-galactarate dehydrogenase	_____________184__________________________________________________225\n_____________\|____________________________________________________\|\n5'-AUA...CUGGC________AUU_____________________UC__________A_______GAAAC...UGA-3'\n______________UGGAGAAU_____GCA___CAAUGGCC_AACA______GAAAUC___GACAA\n______________\|\|\|\|:\|\|\|_____\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|___\|\|\|\|\|\n______________ACCUUUUA_____CGU___GUUACCGG_UUGU______UUUUAG___CUGUU\n3'-UUU...AUACA________GUCAC___UAC________G____CUUUUA______ACA_____AUUUC...UUG-5'\n_____________\|____________________________________________________\|\n_____________67___________________________________________________14\n	200 -- 206	40 -- 46	-31.4715 kcal/mol	5.54782 kcal/mol	11.1209 kcal/mol	184 225@LB@ \| \|@LB@5'-AUA...CUGGC AUU UC A GAAAC...UGA-3'@LB@ UGGAGAAU GCA CAAUGGCC AACA GAAAUC GACAA@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|@LB@ ACCUUUUA CGU GUUACCGG UUGU UUUUAG CUGUU@LB@3'-UUU...AUACA GUCAC UAC G CUUUUA ACA AUUUC...UUG-5'@LB@ \| \|@LB@ 67 14@LB@@LB@@LB@Energy -14.80 kcal/mol@LB@Hybridization Energy -31.4715 kcal/mol@LB@Unfolding Energy - mRNA 5.54782 kcal/mol@LB@Unfolding Energy - sRNA 11.1209 kcal/mol@LB@@LB@Position - mRNA 185 -- 224@LB@Position - sRNA 15 -- 66@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
83	0.007014	0.2822	b0815	opgE	-11.11	0.070482	164 -- 204	2 -- 58	OPG biosynthetic transmembrane phosphoethanolamine transferase	_____________163________________________________________________________205\n_____________\|__________________________________________________________\|\n5'-UUU...GACGC_____________C__________________________U_______U_________AUUUA...GCU-3'\n______________CAG_GGUAA_GCA_AUGGC_______________GUUUGU_ACGAUAG_GGCAUAUGA\n______________\|\|\|_\|\|:\|\|_\|\|\|_\|\|\|\|\|_______________:\|:\|\|\|_\|\|:\|\|\|:_\|\|\|\|\|\|\|:\|\n______________GUC_CCGUU_CGU_UACCG_______________UAGACA_UGUUAUU_CCGUAUAUU\n3'-UUU...UUUUA___A_____A_________GGUUGUCUUUUAUUU______C_______U_________G-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	197 -- 203	3 -- 9	-40.5172 kcal/mol	17.2586 kcal/mol	12.1475 kcal/mol	163 205@LB@ \| \|@LB@5'-UUU...GACGC C U U AUUUA...GCU-3'@LB@ CAG GGUAA GCA AUGGC GUUUGU ACGAUAG GGCAUAUGA@LB@ \|\|\| \|\|:\|\| \|\|\| \|\|\|\|\| :\|:\|\|\| \|\|:\|\|\|: \|\|\|\|\|\|\|:\|@LB@ GUC CCGUU CGU UACCG UAGACA UGUUAUU CCGUAUAUU@LB@3'-UUU...UUUUA A A GGUUGUCUUUUAUUU C U G-5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -40.5172 kcal/mol@LB@Unfolding Energy - mRNA 17.2586 kcal/mol@LB@Unfolding Energy - sRNA 12.1475 kcal/mol@LB@@LB@Position - mRNA 164 -- 204@LB@Position - sRNA 2 -- 58@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
84	0.00705	0.2822	b2341	fadJ	-9.52	0.152421	171 -- 187	39 -- 55	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase	_____________170_______________188\n_____________\|_________________\|\n5'-CAU...GGGCU_____CG__________UGGAG...CGG-3'\n______________UGGCG__GCAAUGGUUC\n______________\|\|\|\|:__\|\|\|\|\|\|\|::\|\n______________ACCGU__CGUUACCGGG\n3'-UUU...UAGUC_____UA__________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	181 -- 187	39 -- 45	-22.4983 kcal/mol	8.21876 kcal/mol	4.76312 kcal/mol	170 188@LB@ \| \|@LB@5'-CAU...GGGCU CG UGGAG...CGG-3'@LB@ UGGCG GCAAUGGUUC@LB@ \|\|\|\|: \|\|\|\|\|\|\|::\|@LB@ ACCGU CGUUACCGGG@LB@3'-UUU...UAGUC UA UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -22.4983 kcal/mol@LB@Unfolding Energy - mRNA 8.21876 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 171 -- 187@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 39 -- 45@LB@
85	0.007532	0.2889	b4252	tabA	-7.64	0.334848	14 -- 22	41 -- 49	biofilm modulator regulated by toxins; DUF386 family protein cupin superfamily protein	_____________13________23\n_____________\|_________\|\n5'-UCU...ACAGC_________GGGGG...CAA-3'\n______________UGCAAUGGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGUUACCG\n3'-UUU...CCGUU_________GGUUG...UUG-5'\n_____________\|_________\|\n_____________50________40\n	16 -- 22	41 -- 47	-14.0816 kcal/mol	4.16801 kcal/mol	2.27678 kcal/mol	13 23@LB@ \| \|@LB@5'-UCU...ACAGC GGGGG...CAA-3'@LB@ UGCAAUGGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGUUACCG@LB@3'-UUU...CCGUU GGUUG...UUG-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -14.0816 kcal/mol@LB@Unfolding Energy - mRNA 4.16801 kcal/mol@LB@Unfolding Energy - sRNA 2.27678 kcal/mol@LB@@LB@Position - mRNA 14 -- 22@LB@Position - sRNA 41 -- 49@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 41 -- 47@LB@
86	0.007534	0.2889	b0189	rof	-5.95	0.582576	103 -- 121	40 -- 57	modulator of Rho-dependent transcription termination	_____________102_________________122\n_____________\|___________________\|\n5'-AGG...UUGAA____CUG____A_______GCCGA...GCG-3'\n______________AGUG___AAUG_AAUGGCU\n______________\|\|\|\|___\|\|\|\|_\|\|\|\|\|\|:\n______________UCAC___UUAC_UUACCGG\n3'-UUU...UUUAG____CG_____G_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________58__________________39\n	115 -- 121	40 -- 46	-14.9441 kcal/mol	3.94739 kcal/mol	5.04912 kcal/mol	102 122@LB@ \| \|@LB@5'-AGG...UUGAA CUG A GCCGA...GCG-3'@LB@ AGUG AAUG AAUGGCU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:@LB@ UCAC UUAC UUACCGG@LB@3'-UUU...UUUAG CG G GUUGU...UUG-5'@LB@ \| \|@LB@ 58 39@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -14.9441 kcal/mol@LB@Unfolding Energy - mRNA 3.94739 kcal/mol@LB@Unfolding Energy - sRNA 5.04912 kcal/mol@LB@@LB@Position - mRNA 103 -- 121@LB@Position - sRNA 40 -- 57@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.007653	0.2889	b1881	cheZ	-13.56	0.018568	164 -- 190	2 -- 28	chemotaxis regulator protein phosphatase for CheY	_____________163_________________________191\n_____________\|___________________________\|\n5'-AUU...UCAAC_______U___G__ACU__________GGAUG...GGG-3'\n______________AAAAUCU_UGA_AA___GGGCAUGUGA\n______________\|\|\|\|\|\|\|_\|\|\|_\|\|___:\|\|\|\|\|:\|:\|\n______________UUUUAGA_ACU_UU___UCCGUAUAUU\n3'-UUU...UUUUA_______C___G__AUU__________G-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	183 -- 189	3 -- 9	-22.696 kcal/mol	4.24203 kcal/mol	4.89261 kcal/mol	163 191@LB@ \| \|@LB@5'-AUU...UCAAC U G ACU GGAUG...GGG-3'@LB@ AAAAUCU UGA AA GGGCAUGUGA@LB@ \|\|\|\|\|\|\| \|\|\| \|\| :\|\|\|\|\|:\|:\|@LB@ UUUUAGA ACU UU UCCGUAUAUU@LB@3'-UUU...UUUUA C G AUU G-5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -13.56 kcal/mol@LB@Hybridization Energy -22.696 kcal/mol@LB@Unfolding Energy - mRNA 4.24203 kcal/mol@LB@Unfolding Energy - sRNA 4.89261 kcal/mol@LB@@LB@Position - mRNA 164 -- 190@LB@Position - sRNA 2 -- 28@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 3 -- 9@LB@
88	0.007723	0.2889	b4403	yjtD	-13.82	0.016006	193 -- 211	1 -- 21	putative methyltransferase	_____________192___________________212\n_____________\|_____________________\|\n5'-AUU...GAAGA_________U___________GAUUA...UUG-3'\n______________GUGGCAAUA___GCGUAUAAC\n______________\|\|\|:\|\|\|\|\|___\|\|:\|\|\|\|\|\|\n______________CACUGUUAU___CGUAUAUUG\n3'-UUU...UUAGA_________UUC_________-5'\n_____________\|____________________\|\n_____________22___________________1\n	205 -- 211	1 -- 7	-21.8234 kcal/mol	3.59402 kcal/mol	4.41334 kcal/mol	192 212@LB@ \| \|@LB@5'-AUU...GAAGA U GAUUA...UUG-3'@LB@ GUGGCAAUA GCGUAUAAC@LB@ \|\|\|:\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ CACUGUUAU CGUAUAUUG@LB@3'-UUU...UUAGA UUC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -21.8234 kcal/mol@LB@Unfolding Energy - mRNA 3.59402 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 193 -- 211@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 1 -- 7@LB@
89	0.007733	0.2889	b3426	glpD	-8.48	0.239884	186 -- 234	7 -- 64	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________185__________________________________________________________235\n_____________\|____________________________________________________________\|\n5'-AAC...CGAAA_U____G________________AAA________UCU_______________________GCAUC...AGG-3'\n______________G_GAAU_AG_GGCA__GC_AUGG___CCAA_AGA______GA_UUGUGAUAG__GGGGCG\n______________\|_:\|\|\|_\|\|_\|\|\|\|__\|\|_\|\|\|\|___\|\|\|\|_\|\|\|______:\|_:\|\|\|\|\|:\|:__::\|\|\|:\n______________C_UUUA_UC_CCGU__CG_UACC___GGUU_UCU______UU_GACACUGUU__UUCCGU\n3'-UUU...ACAAC_U____G__A____UA__U____G______G___UUUAUU__A_________AU______AUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________65___________________________________________________________6\n	222 -- 228	15 -- 21	-34.508 kcal/mol	13.8761 kcal/mol	12.1536 kcal/mol	185 235@LB@ \| \|@LB@5'-AAC...CGAAA U G AAA UCU GCAUC...AGG-3'@LB@ G GAAU AG GGCA GC AUGG CCAA AGA GA UUGUGAUAG GGGGCG@LB@ \| :\|\|\| \|\| \|\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\| :\| :\|\|\|\|\|:\|: ::\|\|\|:@LB@ C UUUA UC CCGU CG UACC GGUU UCU UU GACACUGUU UUCCGU@LB@3'-UUU...ACAAC U G A UA U G G UUUAUU A AU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -34.508 kcal/mol@LB@Unfolding Energy - mRNA 13.8761 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 186 -- 234@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 15 -- 21@LB@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase	_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@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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service.

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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