Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@LB@
117	0.006292	0.1893	b1769	ydjE	-12.05	0.056060	116 -- 139	36 -- 59	putative MFS sugar transporter membrane protein	b1775	_____________115______________________140\n_____________\|________________________\|\n5'-AUU...UGUUC_______U____A__AA_______UAAAG...UAA-3'\n______________CUGCGCC_UGAA_UA__AUGAUGA\n______________\|\|\|\|\|\|\|_\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________GACGCGG_AUUU_AU__UACUACU\n3'-UUU...GAACC_______C____A__AA_______CAAUG...GUG-5'\n_____________\|________________________\|\n_____________60_______________________35\n	133 -- 139	36 -- 42	-22.8542 kcal/mol	3.06151 kcal/mol	7.74108 kcal/mol	115 140@LB@ \| \|@LB@5'-AUU...UGUUC U A AA UAAAG...UAA-3'@LB@ CUGCGCC UGAA UA AUGAUGA@LB@ \|\|\|\|\|\|\| \|:\|\| \|\| \|\|\|\|\|\|\|@LB@ GACGCGG AUUU AU UACUACU@LB@3'-UUU...GAACC C A AA CAAUG...GUG-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -22.8542 kcal/mol@LB@Unfolding Energy - mRNA 3.06151 kcal/mol@LB@Unfolding Energy - sRNA 7.74108 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 36 -- 42@LB@
61	0.003042	0.1727	b0104	guaC	-6.79	0.490983	117 -- 124	52 -- 59	GMP reductase		_____________116______125\n_____________\|________\|\n5'-AUG...CAGUC________CAUUG...GUC-3'\n______________UUGCGCCG\n______________:\|\|\|\|\|\|\|\n______________GACGCGGC\n3'-UUU...GAACC________AUUUA...GUG-5'\n_____________\|________\|\n_____________60_______51\n	118 -- 124	52 -- 58	-14.4979 kcal/mol	2.89251 kcal/mol	4.81798 kcal/mol	116 125@LB@ \| \|@LB@5'-AUG...CAGUC CAUUG...GUC-3'@LB@ UUGCGCCG@LB@ :\|\|\|\|\|\|\|@LB@ GACGCGGC@LB@3'-UUU...GAACC AUUUA...GUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -14.4979 kcal/mol@LB@Unfolding Energy - mRNA 2.89251 kcal/mol@LB@Unfolding Energy - sRNA 4.81798 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 52 -- 58@LB@
92	0.004911	0.1855	b3732	atpD	-9.01	0.211333	117 -- 128	1 -- 11	F1 sector of membrane-bound ATP synthase beta subunit		_____________116__________129\n_____________\|____________\|\n5'-GGC...GCUCG_______A____UACUC...AAA-3'\n______________UCAGGCC_GCAU\n______________\|\|\|\|\|\|\|_\|\|\|:\n______________AGUCCGG_CGUG\n3'-UUU...CAAAA____________-5'\n_____________\|___________\|\n_____________12__________1\n	117 -- 123	5 -- 11	-17.8068 kcal/mol	3.15312 kcal/mol	5.60325 kcal/mol	116 129@LB@ \| \|@LB@5'-GGC...GCUCG A UACUC...AAA-3'@LB@ UCAGGCC GCAU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ AGUCCGG CGUG@LB@3'-UUU...CAAAA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -17.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.15312 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 117 -- 128@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 5 -- 11@LB@
113	0.005997	0.1855	b1765	ydjA	-10.36	0.119141	118 -- 144	49 -- 76	putative oxidoreductase		_____________117___________________________145\n_____________\|_____________________________\|\n5'-AUU...CUUGU__G__________GC__A___________CAAAA...GUA-3'\n______________CA_CAGG__AAUU__GG_CUGUGCUGUAA\n______________\|\|_\|\|\|\|__\|\|\|:__\|\|_\|\|\|:\|\|:\|\|\|\|\n______________GU_GUCC__UUAG__CC_GACGCGGCAUU\n3'-UUU...CGGUU__G____CU____AA______________UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________77____________________________48\n	138 -- 144	49 -- 55	-28.7704 kcal/mol	9.07167 kcal/mol	9.34253 kcal/mol	117 145@LB@ \| \|@LB@5'-AUU...CUUGU G GC A CAAAA...GUA-3'@LB@ CA CAGG AAUU GG CUGUGCUGUAA@LB@ \|\| \|\|\|\| \|\|\|: \|\| \|\|\|:\|\|:\|\|\|\|@LB@ GU GUCC UUAG CC GACGCGGCAUU@LB@3'-UUU...CGGUU G CU AA UAAUA...GUG-5'@LB@ \| \|@LB@ 77 48@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -28.7704 kcal/mol@LB@Unfolding Energy - mRNA 9.07167 kcal/mol@LB@Unfolding Energy - sRNA 9.34253 kcal/mol@LB@@LB@Position - mRNA 118 -- 144@LB@Position - sRNA 49 -- 76@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 49 -- 55@LB@
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein		_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@LB@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
68	0.00345	0.1727	b3168	infB	-10.64	0.105292	126 -- 148	49 -- 77	translation initiation factor IF-2		_____________125___________________________149\n_____________\|_____________________________\|\n5'-AAG...CCGGA______________A______________UAUUU...CUG-3'\n______________GCACU_____GAUU_UGGCUGC_CCGUAA\n______________:\|\|\|:_____:\|\|:_\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UGUGG_____UUAG_ACCGACG_GGCAUU\n3'-UUU...GCGGU_____UCCCU____A_______C______UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	136 -- 142	56 -- 62	-27.6009 kcal/mol	7.61735 kcal/mol	9.34562 kcal/mol	125 149@LB@ \| \|@LB@5'-AAG...CCGGA A UAUUU...CUG-3'@LB@ GCACU GAUU UGGCUGC CCGUAA@LB@ :\|\|\|: :\|\|: \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUGG UUAG ACCGACG GGCAUU@LB@3'-UUU...GCGGU UCCCU A C UAAUA...GUG-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -27.6009 kcal/mol@LB@Unfolding Energy - mRNA 7.61735 kcal/mol@LB@Unfolding Energy - sRNA 9.34562 kcal/mol@LB@@LB@Position - mRNA 126 -- 148@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 56 -- 62@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3		_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase		_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@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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