Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
180	0.01774	0.3104	b0593	entC	-14.03	0.023631	112 -- 128	4 -- 19	isochorismate synthase 1	_____________111_______________129\n_____________\|_________________\|\n5'-GGC...AGAGU_____U___________GCUUU...CAG-3'\n______________UGACA_AGUGCGCGUUU\n______________\|:\|\|\|_\|:\|\|\|\|\|\|\|:\|\n______________AUUGU_UUACGCGCAGA\n3'-UUU...CUACU_________________AAG-5'\n_____________\|_________________\|\n_____________20________________3\n	122 -- 128	4 -- 10	-18.4725 kcal/mol	3.19872 kcal/mol	1.2406 kcal/mol	111 129@LB@ \| \|@LB@5'-GGC...AGAGU U GCUUU...CAG-3'@LB@ UGACA AGUGCGCGUUU@LB@ \|:\|\|\| \|:\|\|\|\|\|\|\|:\|@LB@ AUUGU UUACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -18.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.19872 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 112 -- 128@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 4 -- 10@LB@
100	0.01004	0.3104	b3166	truB	-9.42	0.151044	113 -- 128	5 -- 18	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________112______________129\n_____________\|________________\|\n5'-GGC...GGUUG__G________AU___AAACC...AAC-3'\n______________AA_GGAUGCGC__GUC\n______________\|\|_::\|\|\|\|\|\|__\|\|\|\n______________UU_UUUACGCG__CAG\n3'-UUU...UACUA__G_____________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	117 -- 123	8 -- 14	-15.4757 kcal/mol	4.82661 kcal/mol	1.2243 kcal/mol	112 129@LB@ \| \|@LB@5'-GGC...GGUUG G AU AAACC...AAC-3'@LB@ AA GGAUGCGC GUC@LB@ \|\| ::\|\|\|\|\|\| \|\|\|@LB@ UU UUUACGCG CAG@LB@3'-UUU...UACUA G AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -15.4757 kcal/mol@LB@Unfolding Energy - mRNA 4.82661 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 8 -- 14@LB@
53	0.004896	0.3024	b3790	wecD	-9.15	0.167607	125 -- 139	7 -- 21	TDP-fucosamine acetyltransferase	_____________124_____________140\n_____________\|_______________\|\n5'-CUG...GGCUC_________G_____AAGCG...UGA-3'\n______________GAUGACGAG_GUGUG\n______________\|\|\|:\|\|:\|:_\|:\|:\|\n______________CUAUUGUUU_CGCGC\n3'-UUU...UACUA_________A_____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	126 -- 132	14 -- 20	-15.9636 kcal/mol	5.57309 kcal/mol	1.24179 kcal/mol	124 140@LB@ \| \|@LB@5'-CUG...GGCUC G AAGCG...UGA-3'@LB@ GAUGACGAG GUGUG@LB@ \|\|\|:\|\|:\|: \|:\|:\|@LB@ CUAUUGUUU CGCGC@LB@3'-UUU...UACUA A AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.9636 kcal/mol@LB@Unfolding Energy - mRNA 5.57309 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 125 -- 139@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 14 -- 20@LB@
97	0.009805	0.3104	b1306	pspC	-10.74	0.090670	128 -- 139	7 -- 18	psp operon transcription co-activator	_____________127__________140\n_____________\|____________\|\n5'-CCG...AGCAA____________AACGU...CGG-3'\n______________AACGGAUGCGCG\n______________\|\|\|::\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	133 -- 139	7 -- 13	-18.5075 kcal/mol	6.55818 kcal/mol	1.20891 kcal/mol	127 140@LB@ \| \|@LB@5'-CCG...AGCAA AACGU...CGG-3'@LB@ AACGGAUGCGCG@LB@ \|\|\|::\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.5075 kcal/mol@LB@Unfolding Energy - mRNA 6.55818 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@LB@
161	0.01501	0.3104	b1709	btuD	-8.32	0.227073	129 -- 137	1 -- 9	vitamin B12 ABC transporter ATPase	_____________128_______138\n_____________\|_________\|\n5'-GCA...AUCCA_________CCCGG...GGC-3'\n______________GCGUUUUUC\n______________\|\|\|\|:\|\|\|\|\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	131 -- 137	1 -- 7	-11.771 kcal/mol	2.3321 kcal/mol	1.11751 kcal/mol	128 138@LB@ \| \|@LB@5'-GCA...AUCCA CCCGG...GGC-3'@LB@ GCGUUUUUC@LB@ \|\|\|\|:\|\|\|\|@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -11.771 kcal/mol@LB@Unfolding Energy - mRNA 2.3321 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 129 -- 137@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 1 -- 7@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
9	0.000195	0.07335	b1830	prc	-15.09	0.015143	131 -- 161	7 -- 38	carboxy-terminal protease for penicillin-binding protein 3	_____________130______________________________162\n_____________\|________________________________\|\n5'-CGA...UCCAG___________U___UCUU____U________CAGAA...CGG-3'\n______________CUGAAUUCGGG_AUG____UGAU__GUGCGCG\n______________\|\|\|\|\|\|\|\|:\|\|_\|\|\|____\|:\|:__:\|\|\|\|\|\|\n______________GACUUAAGUCC_UAC____AUUG__UACGCGC\n3'-UUU...GUAGA___________C___UACU____UU_______AGAAAG-5'\n_____________\|________________________________\|\n_____________39_______________________________6\n	155 -- 161	7 -- 13	-31.7028 kcal/mol	7.25259 kcal/mol	9.35859 kcal/mol	130 162@LB@ \| \|@LB@5'-CGA...UCCAG U UCUU U CAGAA...CGG-3'@LB@ CUGAAUUCGGG AUG UGAU GUGCGCG@LB@ \|\|\|\|\|\|\|\|:\|\| \|\|\| \|:\|: :\|\|\|\|\|\|@LB@ GACUUAAGUCC UAC AUUG UACGCGC@LB@3'-UUU...GUAGA C UACU UU AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -31.7028 kcal/mol@LB@Unfolding Energy - mRNA 7.25259 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 7 -- 13@LB@
185	0.01831	0.3104	b3164	pnp	-7.42	0.310961	131 -- 137	8 -- 14	polynucleotide phosphorylase/polyadenylase	_____________130_____138\n_____________\|_______\|\n5'-AGC...GCGAG_______AGAAG...UUA-3'\n______________GAUGCGC\n______________:\|\|\|\|\|\|\n______________UUACGCG\n3'-UUU...AUUGU_______CAGAAAG-5'\n_____________\|_______\|\n_____________15______7\n	131 -- 137	8 -- 14	-10.1419 kcal/mol	2.24272 kcal/mol	0.481462 kcal/mol	130 138@LB@ \| \|@LB@5'-AGC...GCGAG AGAAG...UUA-3'@LB@ GAUGCGC@LB@ :\|\|\|\|\|\|@LB@ UUACGCG@LB@3'-UUU...AUUGU CAGAAAG-5'@LB@ \| \|@LB@ 15 7@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -10.1419 kcal/mol@LB@Unfolding Energy - mRNA 2.24272 kcal/mol@LB@Unfolding Energy - sRNA 0.481462 kcal/mol@LB@@LB@Position - mRNA 131 -- 137@LB@Position - sRNA 8 -- 14@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 8 -- 14@LB@
112	0.01125	0.3104	b2515	ispG	-10.24	0.110168	132 -- 140	4 -- 12	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase	_____________131_______141\n_____________\|_________\|\n5'-CGU...CAGGU_________GACCC...UGA-3'\n______________UGCGCGUCU\n______________\|\|\|\|\|\|\|\|\|\n______________ACGCGCAGA\n3'-UUU...UGUUU_________AAG-5'\n_____________\|_________\|\n_____________13________3\n	134 -- 140	4 -- 10	-16.4542 kcal/mol	5.04928 kcal/mol	1.16019 kcal/mol	131 141@LB@ \| \|@LB@5'-CGU...CAGGU GACCC...UGA-3'@LB@ UGCGCGUCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGCGCAGA@LB@3'-UUU...UGUUU AAG-5'@LB@ \| \|@LB@ 13 3@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -16.4542 kcal/mol@LB@Unfolding Energy - mRNA 5.04928 kcal/mol@LB@Unfolding Energy - sRNA 1.16019 kcal/mol@LB@@LB@Position - mRNA 132 -- 140@LB@Position - sRNA 4 -- 12@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 4 -- 10@LB@
27	0.001549	0.1943	b0440	hupB	-11.81	0.059023	134 -- 149	5 -- 20	HU DNA-binding transcriptional regulator beta subunit	_____________133______________150\n_____________\|________________\|\n5'-CGC...CUGAU_____UGC________CGUAC...CUG-3'\n______________AUAAC___UGCGCGUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|:\n______________UAUUG___ACGCGCAG\n3'-UUU...ACUAC_____UUU________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	143 -- 149	5 -- 11	-15.9939 kcal/mol	2.93365 kcal/mol	1.24804 kcal/mol	133 150@LB@ \| \|@LB@5'-CGC...CUGAU UGC CGUAC...CUG-3'@LB@ AUAAC UGCGCGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ UAUUG ACGCGCAG@LB@3'-UUU...ACUAC UUU AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -15.9939 kcal/mol@LB@Unfolding Energy - mRNA 2.93365 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 134 -- 149@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 5 -- 11@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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