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
22	0.001004	0.1545	b0583	entD	-18.10	0.004183	41 -- 63	1 -- 22	phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex	_____________40______________________64\n_____________\|_______________________\|\n5'-AUA...CAGAU__U____A___________G___AUGCC...UGC-3'\n______________UG_UGAC_AAGUGCGCGUC_UUC\n______________\|\|_\|:\|\|_\|\|:\|\|\|\|\|\|\|\|_\|\|\|\n______________AC_AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU__U________________A___-5'\n_____________\|______________________\|\n_____________23_____________________1\n	53 -- 59	5 -- 11	-24.6004 kcal/mol	5.24265 kcal/mol	1.25963 kcal/mol	40 64@LB@ \| \|@LB@5'-AUA...CAGAU U A G AUGCC...UGC-3'@LB@ UG UGAC AAGUGCGCGUC UUC@LB@ \|\| \|:\|\| \|\|:\|\|\|\|\|\|\|\| \|\|\|@LB@ AC AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -24.6004 kcal/mol@LB@Unfolding Energy - mRNA 5.24265 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 41 -- 63@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
23	0.001384	0.1943	b0399	phoB	-10.33	0.106753	53 -- 63	8 -- 18	response regulator in two-component regulatory system with PhoR	_____________52__________64\n_____________\|___________\|\n5'-AGG...ACCCA___________CAUUU...AAG-3'\n______________AACAGAUGUGC\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	57 -- 63	8 -- 14	-14.9736 kcal/mol	3.44457 kcal/mol	1.20363 kcal/mol	52 64@LB@ \| \|@LB@5'-AGG...ACCCA CAUUU...AAG-3'@LB@ AACAGAUGUGC@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.9736 kcal/mol@LB@Unfolding Energy - mRNA 3.44457 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 53 -- 63@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 8 -- 14@LB@
24	0.001508	0.1943	b0150	fhuA	-11.07	0.079438	192 -- 210	5 -- 21	ferrichrome outer membrane transporter	_____________191_________________211\n_____________\|___________________\|\n5'-GGA...UCAGA____UAC___UG_______CCAAA...CAG-3'\n______________GAUA___CAA__GCGCGUU\n______________\|\|\|\|___\|\|\|__\|\|\|\|\|\|:\n______________CUAU___GUU__CGCGCAG\n3'-UUU...UACUA____U_____UA_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	204 -- 210	5 -- 11	-17.2518 kcal/mol	4.92886 kcal/mol	1.24955 kcal/mol	191 211@LB@ \| \|@LB@5'-GGA...UCAGA UAC UG CCAAA...CAG-3'@LB@ GAUA CAA GCGCGUU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:@LB@ CUAU GUU CGCGCAG@LB@3'-UUU...UACUA U UA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -17.2518 kcal/mol@LB@Unfolding Energy - mRNA 4.92886 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 192 -- 210@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
25	0.001519	0.1943	b2817	amiC	-17.97	0.004427	110 -- 131	1 -- 21	N-acetylmuramoyl-L-alanine amidase	_____________109____________________132\n_____________\|______________________\|\n5'-AGU...UAUUA__________UA__________GCUAA...UCA-3'\n______________GAUGACAGAU__UGCGUCUUUC\n______________\|\|\|:\|\|\|:\|\|__:\|\|\|\|\|\|\|\|\|\n______________CUAUUGUUUA__GCGCAGAAAG\n3'-UUU...UACUA__________C___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	125 -- 131	1 -- 7	-25.6931 kcal/mol	6.46841 kcal/mol	1.25763 kcal/mol	109 132@LB@ \| \|@LB@5'-AGU...UAUUA UA GCUAA...UCA-3'@LB@ GAUGACAGAU UGCGUCUUUC@LB@ \|\|\|:\|\|\|:\|\| :\|\|\|\|\|\|\|\|\|@LB@ CUAUUGUUUA GCGCAGAAAG@LB@3'-UUU...UACUA C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -17.97 kcal/mol@LB@Hybridization Energy -25.6931 kcal/mol@LB@Unfolding Energy - mRNA 6.46841 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 131@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 1 -- 7@LB@
26	0.001545	0.1943	b1678	ldtE	-10.42	0.102915	208 -- 217	2 -- 11	murein L D-transpeptidase	_____________207________218\n_____________\|__________\|\n5'-UCU...GAAAC__________GCUUA...GCC-3'\n______________GCGCGUCUUU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGCGCAGAAA\n3'-UUU...GUUUA__________G-5'\n_____________\|__________\|\n_____________12_________1\n	211 -- 217	2 -- 8	-16.5846 kcal/mol	4.99595 kcal/mol	1.16977 kcal/mol	207 218@LB@ \| \|@LB@5'-UCU...GAAAC GCUUA...GCC-3'@LB@ GCGCGUCUUU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCAGAAA@LB@3'-UUU...GUUUA G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -16.5846 kcal/mol@LB@Unfolding Energy - mRNA 4.99595 kcal/mol@LB@Unfolding Energy - sRNA 1.16977 kcal/mol@LB@@LB@Position - mRNA 208 -- 217@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@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@
28	0.001743	0.2094	b2308	hisQ	-15.00	0.015715	1 -- 16	7 -- 21	histidine ABC transporter permease	______________1_______________17\n______________\|_______________\|\n___________5'-_________C______AAGCA...UUG-3'\n______________GAUAACGAA_UGCGCG\n______________\|\|\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________CUAUUGUUU_ACGCGC\n3'-UUU...UACUA________________AGAAAG-5'\n_____________\|________________\|\n_____________22_______________6\n	3 -- 9	13 -- 19	-21.0778 kcal/mol	4.83206 kcal/mol	1.24179 kcal/mol	1 17@LB@ \| \|@LB@ 5'- C AAGCA...UUG-3'@LB@ GAUAACGAA UGCGCG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|\|@LB@ CUAUUGUUU ACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.0778 kcal/mol@LB@Unfolding Energy - mRNA 4.83206 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 1 -- 16@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 13 -- 19@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
30	0.001906	0.2094	b0616	citE	-12.56	0.043465	103 -- 116	8 -- 21	citrate lyase citryl-ACP lyase (beta) subunit	_____________102____________117\n_____________\|______________\|\n5'-CAA...AUGUC_________G____ACUGG...UCU-3'\n______________GAUGACAAA_GCGC\n______________\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CUAUUGUUU_CGCG\n3'-UUU...UACUA_________A____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	105 -- 111	13 -- 19	-17.9482 kcal/mol	4.14919 kcal/mol	1.23638 kcal/mol	102 117@LB@ \| \|@LB@5'-CAA...AUGUC G ACUGG...UCU-3'@LB@ GAUGACAAA GCGC@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -17.9482 kcal/mol@LB@Unfolding Energy - mRNA 4.14919 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 103 -- 116@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 13 -- 19@LB@
31	0.001974	0.2094	b1080	flgI	-10.59	0.096403	87 -- 101	7 -- 21	putative flagellar basal body protein	_____________86______________102\n_____________\|_______________\|\n5'-AUU...ACUCA_______________CAUUG...AAA-3'\n______________GGUGGCGGAUGCGCG\n______________\|:\|::\|::\|\|\|\|\|\|\|\n______________CUAUUGUUUACGCGC\n3'-UUU...UACUA_______________AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	95 -- 101	7 -- 13	-22.6939 kcal/mol	10.8668 kcal/mol	1.24179 kcal/mol	86 102@LB@ \| \|@LB@5'-AUU...ACUCA CAUUG...AAA-3'@LB@ GGUGGCGGAUGCGCG@LB@ \|:\|::\|::\|\|\|\|\|\|\|@LB@ CUAUUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -22.6939 kcal/mol@LB@Unfolding Energy - mRNA 10.8668 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 87 -- 101@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 7 -- 13@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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