Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
58	0.01138	0.5385	b2595	bamD	-7.85	0.240744	21 -- 29	72 -- 80	BamABCDE complex OM biogenesis lipoprotein	_____________20________30\n_____________\|_________\|\n5'-CUG...ACCGA_________CGGAC...AUG-3'\n______________GUUGGUUUU\n______________\|\|\|\|\|:\|\|\|\n______________CAACCGAAA\n3'-CGC...AAGUG_________UCAAU...AAG-5'\n_____________\|_________\|\n_____________81________71\n	23 -- 29	72 -- 78	-10.2023 kcal/mol	2.1418 kcal/mol	0.205868 kcal/mol	20 30@LB@ \| \|@LB@5'-CUG...ACCGA CGGAC...AUG-3'@LB@ GUUGGUUUU@LB@ \|\|\|\|\|:\|\|\|@LB@ CAACCGAAA@LB@3'-CGC...AAGUG UCAAU...AAG-5'@LB@ \| \|@LB@ 81 71@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -10.2023 kcal/mol@LB@Unfolding Energy - mRNA 2.1418 kcal/mol@LB@Unfolding Energy - sRNA 0.205868 kcal/mol@LB@@LB@Position - mRNA 21 -- 29@LB@Position - sRNA 72 -- 80@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 72 -- 78@LB@
133	0.02275	0.5385	b0177	bamA	-6.79	0.350358	265 -- 271	23 -- 29	BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor	_____________264_____272\n_____________\|_______\|\n5'-CUG...UGCUG_______CGUAG...GCC-3'\n______________AAGGGUU\n______________\|\|\|\|\|\|\|\n______________UUCCCAA\n3'-CGC...UGAAG_______UUUUC...AAG-5'\n_____________\|_______\|\n_____________30______22\n	265 -- 271	23 -- 29	-7.93739 kcal/mol	1.09969 kcal/mol	0.0462613 kcal/mol	264 272@LB@ \| \|@LB@5'-CUG...UGCUG CGUAG...GCC-3'@LB@ AAGGGUU@LB@ \|\|\|\|\|\|\|@LB@ UUCCCAA@LB@3'-CGC...UGAAG UUUUC...AAG-5'@LB@ \| \|@LB@ 30 22@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -7.93739 kcal/mol@LB@Unfolding Energy - mRNA 1.09969 kcal/mol@LB@Unfolding Energy - sRNA 0.0462613 kcal/mol@LB@@LB@Position - mRNA 265 -- 271@LB@Position - sRNA 23 -- 29@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
196	0.0344	0.5559	b0954	fabA	-7.50	0.274211	100 -- 110	74 -- 84	beta-hydroxydecanoyl thioester dehydrase	_____________99__________111\n_____________\|___________\|\n5'-GUG...GGCCA___________GAACU...ACA-3'\n______________UUACGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGA\n3'-CGC...UUUCA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	104 -- 110	74 -- 80	-16.8122 kcal/mol	8.80896 kcal/mol	0.508159 kcal/mol	99 111@LB@ \| \|@LB@5'-GUG...GGCCA GAACU...ACA-3'@LB@ UUACGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGA@LB@3'-CGC...UUUCA AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -16.8122 kcal/mol@LB@Unfolding Energy - mRNA 8.80896 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 100 -- 110@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 74 -- 80@LB@
198	0.03475	0.5559	b1249	clsA	-8.08	0.221640	216 -- 230	57 -- 82	cardiolipin synthase 1	_____________215________________________231\n_____________\|__________________________\|\n5'-GUC...UUUAU__________________________UUGGC...CAG-3'\n______________ACGUUGGU___________GAGUUGG\n______________\|\|\|\|\|\|\|:___________\|\|\|\|\|\|:\n______________UGCAACCG___________CUCAACU\n3'-CGC...UCAAG________AAAUCAAUAAG_______CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________83_________________________56\n	224 -- 230	57 -- 63	-16.5635 kcal/mol	7.18735 kcal/mol	1.29708 kcal/mol	215 231@LB@ \| \|@LB@5'-GUC...UUUAU UUGGC...CAG-3'@LB@ ACGUUGGU GAGUUGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|\|\|:@LB@ UGCAACCG CUCAACU@LB@3'-CGC...UCAAG AAAUCAAUAAG CUUUG...AAG-5'@LB@ \| \|@LB@ 83 56@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -16.5635 kcal/mol@LB@Unfolding Energy - mRNA 7.18735 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 216 -- 230@LB@Position - sRNA 57 -- 82@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 57 -- 63@LB@
117	0.01966	0.5385	b1203	ychF	-10.24	0.095997	26 -- 41	73 -- 87	catalase inhibitor protein; ATPase K+-dependent ribosome-associated	_____________25_______________42\n_____________\|________________\|\n5'-GAA...AAUGU_______A_A______GACCA...CAU-3'\n______________GGUUUAC_G_UGGCUU\n______________:\|\|\|:\|\|_\|_\|\|\|\|\|\|\n______________UCAAGUG_C_ACCGAA\n3'-CGC...CGUUU_________A______AUCAA...AAG-5'\n_____________\|________________\|\n_____________88_______________72\n	26 -- 32	81 -- 87	-15.1856 kcal/mol	4.42747 kcal/mol	0.51474 kcal/mol	25 42@LB@ \| \|@LB@5'-GAA...AAUGU A A GACCA...CAU-3'@LB@ GGUUUAC G UGGCUU@LB@ :\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ UCAAGUG C ACCGAA@LB@3'-CGC...CGUUU A AUCAA...AAG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.1856 kcal/mol@LB@Unfolding Energy - mRNA 4.42747 kcal/mol@LB@Unfolding Energy - sRNA 0.51474 kcal/mol@LB@@LB@Position - mRNA 26 -- 41@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 81 -- 87@LB@
33	0.006009	0.5385	b1264	trpE	-12.63	0.036478	39 -- 48	79 -- 88	component I of anthranilate synthase	_____________38_________49\n_____________\|__________\|\n5'-UGU...UACGC__________AAAAA...CGG-3'\n______________AAGUUCACGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUCAAGUGCA\n3'-CGC...GCGUU__________ACCGA...AAG-5'\n_____________\|__________\|\n_____________89_________78\n	42 -- 48	79 -- 85	-13.8612 kcal/mol	0.721964 kcal/mol	0.505265 kcal/mol	38 49@LB@ \| \|@LB@5'-UGU...UACGC AAAAA...CGG-3'@LB@ AAGUUCACGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUCAAGUGCA@LB@3'-CGC...GCGUU ACCGA...AAG-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8612 kcal/mol@LB@Unfolding Energy - mRNA 0.721964 kcal/mol@LB@Unfolding Energy - sRNA 0.505265 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 79 -- 85@LB@
35	0.006586	0.5385	b2351	gtrB	-12.36	0.040837	174 -- 213	48 -- 89	CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase	_____________173________________________________________214\n_____________\|__________________________________________\|\n5'-GCA...UAUUC_____________U______GG__G___AA___A__UA____UUGUA...AAG-3'\n______________AAAGUUCAU__UG_CUUUAG__AU_CGA__UGA_GA__UCUC\n______________\|\|\|\|\|\|\|\|:__\|\|_\|\|\|\|\|\|__\|\|_\|\|\|__\|\|\|_:\|__\|\|\|\|\n______________UUUCAAGUG__AC_GAAAUC__UA_GCU__ACU_UU__AGAG\n3'-CGC...GGCGU_________CA__C______AA__A___CA___C__UG____CUUUG...AAG-5'\n_____________\|__________________________________________\|\n_____________90_________________________________________47\n	176 -- 182	81 -- 87	-27.281 kcal/mol	10.5075 kcal/mol	4.41572 kcal/mol	173 214@LB@ \| \|@LB@5'-GCA...UAUUC U GG G AA A UA UUGUA...AAG-3'@LB@ AAAGUUCAU UG CUUUAG AU CGA UGA GA UCUC@LB@ \|\|\|\|\|\|\|\|: \|\| \|\|\|\|\|\| \|\| \|\|\| \|\|\| :\| \|\|\|\|@LB@ UUUCAAGUG AC GAAAUC UA GCU ACU UU AGAG@LB@3'-CGC...GGCGU CA C AA A CA C UG CUUUG...AAG-5'@LB@ \| \|@LB@ 90 47@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -27.281 kcal/mol@LB@Unfolding Energy - mRNA 10.5075 kcal/mol@LB@Unfolding Energy - sRNA 4.41572 kcal/mol@LB@@LB@Position - mRNA 174 -- 213@LB@Position - sRNA 48 -- 89@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 81 -- 87@LB@
106	0.01861	0.5385	b2754	ygbF	-9.88	0.110684	283 -- 300	13 -- 30	CRISPR adaptation ssRNA endonuclease	_____________282_______________300\n_____________\|_________________\|\n5'-UGG...ACGUG_______AUAUGU_____-3'\n______________CAGGGGU______AGGUG\n______________\|\|:\|\|\|\|______\|\|\|\|\|\n______________GUUCCCA______UCCAC\n3'-CGC...CUGAA_______AUUUUC_____GGCGA...AAG-5'\n_____________\|__________________\|\n_____________31_________________12\n	283 -- 289	24 -- 30	-16.4011 kcal/mol	3.18452 kcal/mol	3.3319 kcal/mol	282 300@LB@ \| \|@LB@5'-UGG...ACGUG AUAUGU -3'@LB@ CAGGGGU AGGUG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ GUUCCCA UCCAC@LB@3'-CGC...CUGAA AUUUUC GGCGA...AAG-5'@LB@ \| \|@LB@ 31 12@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.4011 kcal/mol@LB@Unfolding Energy - mRNA 3.18452 kcal/mol@LB@Unfolding Energy - sRNA 3.3319 kcal/mol@LB@@LB@Position - mRNA 283 -- 300@LB@Position - sRNA 13 -- 30@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@LB@
15	0.002894	0.5385	b2780	pyrG	-11.46	0.058961	111 -- 140	60 -- 90	CTP synthetase	_____________110_______________________________141\n_____________\|_________________________________\|\n5'-UGU...AUAAU________________ACA___CA_________AUACU...GCC-3'\n______________GAAAGUUUG___UGGC___GGU__UGUUCGGGU\n______________:\|\|\|\|\|\|::___\|\|\|\|___:\|\|__\|:\|\|\|\|:\|\|\n______________UUUUCAAGU___ACCG___UCA__AUAAGCUCA\n3'-CGC...AGGCG_________GCA____AAA______________ACUCU...AAG-5'\n_____________\|_________________________________\|\n_____________91________________________________59\n	134 -- 140	60 -- 66	-21.5125 kcal/mol	8.34782 kcal/mol	1.70935 kcal/mol	110 141@LB@ \| \|@LB@5'-UGU...AUAAU ACA CA AUACU...GCC-3'@LB@ GAAAGUUUG UGGC GGU UGUUCGGGU@LB@ :\|\|\|\|\|\|:: \|\|\|\| :\|\| \|:\|\|\|\|:\|\|@LB@ UUUUCAAGU ACCG UCA AUAAGCUCA@LB@3'-CGC...AGGCG GCA AAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -21.5125 kcal/mol@LB@Unfolding Energy - mRNA 8.34782 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 111 -- 140@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 60 -- 66@LB@
90	0.01553	0.5385	b1043	csgC	-15.92	0.009464	100 -- 115	69 -- 84	curli assembly protein	_____________99_______________116\n_____________\|________________\|\n5'-GUG...GUGAC___G____________AACAA...UUA-3'\n______________UCA_GUUGGCUUUGGU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:\|\|\n______________AGU_CAACCGAAAUCA\n3'-CGC...UUUCA___G____________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	109 -- 115	69 -- 75	-23.6243 kcal/mol	7.14442 kcal/mol	0.563592 kcal/mol	99 116@LB@ \| \|@LB@5'-GUG...GUGAC G AACAA...UUA-3'@LB@ UCA GUUGGCUUUGGU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|:\|\|@LB@ AGU CAACCGAAAUCA@LB@3'-CGC...UUUCA G AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -23.6243 kcal/mol@LB@Unfolding Energy - mRNA 7.14442 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 100 -- 115@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 69 -- 75@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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