Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
154	0.03071	0.6177	b0368	tauD	-7.18	0.150437	69 -- 85	40 -- 55	taurine dioxygenase 2-oxoglutarate-dependent	_____________68________________86\n_____________\|_________________\|\n5'-GUG...GUUCA_____C___U_______UCGCA...AAC-3'\n______________GUCAG_GGG_GAAUUUC\n______________\|\|\|\|:_\|:\|_\|\|\|\|\|\|\|\n______________CAGUU_CUC_CUUAAAG\n3'-UUU...CCGGG_____U___________UAAAA...ACA-5'\n_____________\|_________________\|\n_____________56________________39\n	79 -- 85	40 -- 46	-16.0696 kcal/mol	7.86965 kcal/mol	1.01784 kcal/mol	68 86@LB@ \| \|@LB@5'-GUG...GUUCA C U UCGCA...AAC-3'@LB@ GUCAG GGG GAAUUUC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|\|@LB@ CAGUU CUC CUUAAAG@LB@3'-UUU...CCGGG U UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.0696 kcal/mol@LB@Unfolding Energy - mRNA 7.86965 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 40 -- 46@LB@
182	0.03771	0.6177	b0397	sbcC	-11.00	0.025718	84 -- 100	39 -- 56	exonuclease dsDNA ATP-dependent	_____________83_________________101\n_____________\|__________________\|\n5'-GAA...CUCAG___________UG_____AUCGC...UUG-3'\n______________CGUCGAAGAGG___UUCA\n______________\|\|\|\|:\|\|\|\|\|\|___\|\|\|\|\n______________GCAGUUUCUCC___AAGU\n3'-UUU...ACCGG___________UUA____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	88 -- 94	46 -- 52	-19.0672 kcal/mol	6.9127 kcal/mol	1.15786 kcal/mol	83 101@LB@ \| \|@LB@5'-GAA...CUCAG UG AUCGC...UUG-3'@LB@ CGUCGAAGAGG UUCA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ GCAGUUUCUCC AAGU@LB@3'-UUU...ACCGG UUA AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0672 kcal/mol@LB@Unfolding Energy - mRNA 6.9127 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 84 -- 100@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 46 -- 52@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
95	0.01894	0.6177	b0407	yajC	-8.94	0.067585	73 -- 105	45 -- 79	SecYEG protein translocase auxillary subunit	_____________72___________________________________106\n_____________\|____________________________________\|\n5'-UCU...CGUUU______G___U_A___AA______A___________UAAAU...UUU-3'\n______________GAUGGC_GGU_U_CGC____GGCU__UUGAAGAGGG\n______________:\|\|\|\|\|_::\|_\|_\|\|\|____\|\|\|:__\|::\|\|\|\|\|\|:\n______________UUACCG_UUA_A_GCG____CCGG__AGUUUCUCCU\n______3'-UUUUU______G___U_____AUAA____GC__________UAAAG...ACA-5'\n_____________\|____________________________________\|\n_____________80___________________________________44\n	99 -- 105	45 -- 51	-30.8043 kcal/mol	8.31146 kcal/mol	13.5551 kcal/mol	72 106@LB@ \| \|@LB@5'-UCU...CGUUU G U A AA A UAAAU...UUU-3'@LB@ GAUGGC GGU U CGC GGCU UUGAAGAGGG@LB@ :\|\|\|\|\| ::\| \| \|\|\| \|\|\|: \|::\|\|\|\|\|\|:@LB@ UUACCG UUA A GCG CCGG AGUUUCUCCU@LB@ 3'-UUUUU G U AUAA GC UAAAG...ACA-5'@LB@ \| \|@LB@ 80 44@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -30.8043 kcal/mol@LB@Unfolding Energy - mRNA 8.31146 kcal/mol@LB@Unfolding Energy - sRNA 13.5551 kcal/mol@LB@@LB@Position - mRNA 73 -- 105@LB@Position - sRNA 45 -- 79@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 45 -- 51@LB@
143	0.02773	0.6177	b0409	secF	-7.84	0.111773	181 -- 195	43 -- 55	SecYEG protein translocase auxillary subunit	_____________180_____________196\n_____________\|_______________\|\n5'-CUU...AAGCU_____UCU_______GCGAU...UGU-3'\n______________GUCAA___GAGGAGU\n______________\|\|\|\|\|___\|\|\|\|\|:\|\n______________CAGUU___CUCCUUA\n3'-UUU...CCGGG_____U_________AAGUA...ACA-5'\n_____________\|_______________\|\n_____________56______________42\n	189 -- 195	43 -- 49	-13.7308 kcal/mol	4.94116 kcal/mol	0.946481 kcal/mol	180 196@LB@ \| \|@LB@5'-CUU...AAGCU UCU GCGAU...UGU-3'@LB@ GUCAA GAGGAGU@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ CAGUU CUCCUUA@LB@3'-UUU...CCGGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -13.7308 kcal/mol@LB@Unfolding Energy - mRNA 4.94116 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 43 -- 49@LB@
88	0.01799	0.6177	b0415	ribE	-8.66	0.076826	57 -- 64	47 -- 54	riboflavin synthase beta chain	_____________56_______65\n_____________\|________\|\n5'-CGG...UAAAU________AUACG...GUG-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	58 -- 64	47 -- 53	-10.4141 kcal/mol	0.855178 kcal/mol	0.897871 kcal/mol	56 65@LB@ \| \|@LB@5'-CGG...UAAAU AUACG...GUG-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -10.4141 kcal/mol@LB@Unfolding Energy - mRNA 0.855178 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 57 -- 64@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 47 -- 53@LB@
79	0.01695	0.6177	b0435	bolA	-9.02	0.064980	184 -- 202	38 -- 55	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________183_________________203\n_____________\|___________________\|\n5'-UGA...GCGUU___G______AU_______GAUGA...CCG-3'\n______________GUC_GAGGAG__AUUUCAU\n______________\|\|\|_:\|:\|\|\|__\|\|\|\|\|\|\|\n______________CAG_UUUCUC__UAAAGUA\n3'-UUU...CCGGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	196 -- 202	38 -- 44	-15.2358 kcal/mol	5.04311 kcal/mol	1.17036 kcal/mol	183 203@LB@ \| \|@LB@5'-UGA...GCGUU G AU GAUGA...CCG-3'@LB@ GUC GAGGAG AUUUCAU@LB@ \|\|\| :\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAG UUUCUC UAAAGUA@LB@3'-UUU...CCGGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.2358 kcal/mol@LB@Unfolding Energy - mRNA 5.04311 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
66	0.01414	0.6177	b0440	hupB	-10.30	0.035643	184 -- 193	44 -- 53	HU DNA-binding transcriptional regulator beta subunit	_____________183________194\n_____________\|__________\|\n5'-CGC...AAUUA__________GAGAA...CUG-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	187 -- 193	44 -- 50	-11.552 kcal/mol	0.319105 kcal/mol	0.927997 kcal/mol	183 194@LB@ \| \|@LB@5'-CGC...AAUUA GAGAA...CUG-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -11.552 kcal/mol@LB@Unfolding Energy - mRNA 0.319105 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
67	0.01414	0.6177	b0474	adk	-7.17	0.151538	186 -- 198	39 -- 51	adenylate kinase	_____________185___________199\n_____________\|_____________\|\n5'-ACC...AUUUU_______U_____CAAUG...AUA-3'\n______________AAGGGGA_UUUCG\n______________\|\|\|:\|\|\|_\|\|\|\|:\n______________UUCUCCU_AAAGU\n3'-UUU...GCAGU_______U_____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________52____________38\n	186 -- 192	45 -- 51	-12.5937 kcal/mol	4.3836 kcal/mol	1.04441 kcal/mol	185 199@LB@ \| \|@LB@5'-ACC...AUUUU U CAAUG...AUA-3'@LB@ AAGGGGA UUUCG@LB@ \|\|\|:\|\|\| \|\|\|\|:@LB@ UUCUCCU AAAGU@LB@3'-UUU...GCAGU U AAAAA...ACA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -12.5937 kcal/mol@LB@Unfolding Energy - mRNA 4.3836 kcal/mol@LB@Unfolding Energy - sRNA 1.04441 kcal/mol@LB@@LB@Position - mRNA 186 -- 198@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
38	0.007716	0.6129	b0480	ushA	-6.97	0.165152	186 -- 197	45 -- 55	bifunctional UDP-sugar hydrolase/5'-nucleotidase	_____________185__________198\n_____________\|____________\|\n5'-AGG...AUCAG_________A__AGUAU...AAA-3'\n______________GUCAGGGAG_GA\n______________\|\|\|\|::\|\|\|_\|\|\n______________CAGUUUCUC_CU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	188 -- 194	47 -- 53	-13.3467 kcal/mol	5.44454 kcal/mol	0.930875 kcal/mol	185 198@LB@ \| \|@LB@5'-AGG...AUCAG A AGUAU...AAA-3'@LB@ GUCAGGGAG GA@LB@ \|\|\|\|::\|\|\| \|\|@LB@ CAGUUUCUC CU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -13.3467 kcal/mol@LB@Unfolding Energy - mRNA 5.44454 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@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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