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
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA	_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@LB@
102	0.02032	0.6177	b1267	yciO	-10.56	0.031637	188 -- 197	44 -- 53	putative RNA binding protein	_____________187________198\n_____________\|__________\|\n5'-GCG...CACCA__________AUUAU...CAA-3'\n______________CAGAGAGGGA\n______________\|\|:\|\|\|\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	46 -- 52	-13.8947 kcal/mol	2.40877 kcal/mol	0.927997 kcal/mol	187 198@LB@ \| \|@LB@5'-GCG...CACCA AUUAU...CAA-3'@LB@ CAGAGAGGGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.8947 kcal/mol@LB@Unfolding Energy - mRNA 2.40877 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 188 -- 197@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
97	0.01904	0.6177	b3102	yqjG	-9.04	0.064335	159 -- 168	44 -- 53	putative S-transferase	_____________158________169\n_____________\|__________\|\n5'-GCA...AAAAA__________GCUCC...GGC-3'\n______________CGAGGAGGAA\n______________\|:\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-13.5343 kcal/mol	3.56251 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-GCA...AAAAA GCUCC...GGC-3'@LB@ CGAGGAGGAA@LB@ \|:\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.5343 kcal/mol@LB@Unfolding Energy - mRNA 3.56251 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
112	0.02248	0.6177	b2796	sdaC	-8.62	0.078257	115 -- 131	34 -- 50	putative serine transporter	_____________114_______________132\n_____________\|_________________\|\n5'-AUC...CCGAU___CA____________ACGGU...CAA-3'\n______________AGA__GAUUUCAUUUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|\|\|\n______________UCU__UUAAAGUAAAAA\n3'-UUU...CAGUU___CC____________AAUAA...ACA-5'\n_____________\|_________________\|\n_____________51________________33\n	125 -- 131	34 -- 40	-11.667 kcal/mol	1.97198 kcal/mol	1.0739 kcal/mol	114 132@LB@ \| \|@LB@5'-AUC...CCGAU CA ACGGU...CAA-3'@LB@ AGA GAUUUCAUUUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\|\|\|@LB@ UCU UUAAAGUAAAAA@LB@3'-UUU...CAGUU CC AAUAA...ACA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.667 kcal/mol@LB@Unfolding Energy - mRNA 1.97198 kcal/mol@LB@Unfolding Energy - sRNA 1.0739 kcal/mol@LB@@LB@Position - mRNA 115 -- 131@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 34 -- 40@LB@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase	_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@LB@
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator	_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@LB@
5	0.0004437	0.2856	b0847	ybjL	-12.50	0.012601	224 -- 253	26 -- 55	putative transporter	_____________223____________________________254\n_____________\|______________________________\|\n5'-CUU...GAAUU______U_______A____CUG________UGUGG...GUU-3'\n______________GUUAAA_GGGAAUU_CAUU___UUAUUAUU\n______________\|\|:\|\|\|_:\|\|\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAGUUU_UCCUUAA_GUAA___AAUAAUAA\n3'-UUU...CCGGG______C_______A____AAA________UACGG...ACA-5'\n_____________\|______________________________\|\n_____________56_____________________________25\n	247 -- 253	26 -- 32	-19.6848 kcal/mol	5.99374 kcal/mol	1.18815 kcal/mol	223 254@LB@ \| \|@LB@5'-CUU...GAAUU U A CUG UGUGG...GUU-3'@LB@ GUUAAA GGGAAUU CAUU UUAUUAUU@LB@ \|\|:\|\|\| :\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAGUUU UCCUUAA GUAA AAUAAUAA@LB@3'-UUU...CCGGG C A AAA UACGG...ACA-5'@LB@ \| \|@LB@ 56 25@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -19.6848 kcal/mol@LB@Unfolding Energy - mRNA 5.99374 kcal/mol@LB@Unfolding Energy - sRNA 1.18815 kcal/mol@LB@@LB@Position - mRNA 224 -- 253@LB@Position - sRNA 26 -- 55@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 26 -- 32@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
39	0.007917	0.6129	b3657	yicJ	-11.19	0.023423	220 -- 230	47 -- 57	putative transporter	_____________219_________231\n_____________\|___________\|\n5'-CAG...GUUGU___________AAAAU...UGU-3'\n______________CCGUUAAAGAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	224 -- 230	47 -- 53	-15.9196 kcal/mol	1.98973 kcal/mol	2.73556 kcal/mol	219 231@LB@ \| \|@LB@5'-CAG...GUUGU AAAAU...UGU-3'@LB@ CCGUUAAAGAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -15.9196 kcal/mol@LB@Unfolding Energy - mRNA 1.98973 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 220 -- 230@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 224 -- 230@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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