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	Additional homologs
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@
35	0.00713	0.6129	b2025	hisF	-8.66	0.076851	182 -- 193	46 -- 57	imidazole glycerol phosphate synthase catalytic subunit with HisH		_____________181__________194\n_____________\|____________\|\n5'-UCG...AUUCA____G_______CCAUC...UGC-3'\n______________CCGU_AAGGAGG\n______________\|\|\|\|_\|\|:\|\|\|\|\n______________GGCA_UUUCUCC\n3'-UUU...AACCG____G_______UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	187 -- 193	46 -- 52	-16.1254 kcal/mol	4.72855 kcal/mol	2.7365 kcal/mol	181 194@LB@ \| \|@LB@5'-UCG...AUUCA G CCAUC...UGC-3'@LB@ CCGU AAGGAGG@LB@ \|\|\|\| \|\|:\|\|\|\|@LB@ GGCA UUUCUCC@LB@3'-UUU...AACCG G UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -16.1254 kcal/mol@LB@Unfolding Energy - mRNA 4.72855 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 46 -- 52@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@
127	0.0247	0.6177	b3306	rpsH	-8.61	0.078593	53 -- 64	46 -- 57	30S ribosomal subunit protein S8		_____________52___________65\n_____________\|____________\|\n5'-AGC...CGCUG________C___UCGUC...AAG-3'\n______________CCGUCAAA_AGG\n______________\|\|\|\|\|\|\|\|_\|\|\|\n______________GGCAGUUU_UCC\n3'-UUU...AACCG________C___UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	54 -- 60	50 -- 56	-14.2597 kcal/mol	2.91134 kcal/mol	2.7365 kcal/mol	52 65@LB@ \| \|@LB@5'-AGC...CGCUG C UCGUC...AAG-3'@LB@ CCGUCAAA AGG@LB@ \|\|\|\|\|\|\|\| \|\|\|@LB@ GGCAGUUU UCC@LB@3'-UUU...AACCG C UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -14.2597 kcal/mol@LB@Unfolding Energy - mRNA 2.91134 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 50 -- 56@LB@
162	0.03332	0.6177	b3304	rplR	-8.58	0.079933	170 -- 177	46 -- 53	50S ribosomal subunit protein L18		_____________169______178\n_____________\|________\|\n5'-AUC...CGUAC________CUAAG...GUC-3'\n______________CAAAGAGG\n______________\|\|\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	171 -- 177	46 -- 52	-11.2869 kcal/mol	1.80103 kcal/mol	0.910679 kcal/mol	169 178@LB@ \| \|@LB@5'-AUC...CGUAC CUAAG...GUC-3'@LB@ CAAAGAGG@LB@ \|\|\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.2869 kcal/mol@LB@Unfolding Energy - mRNA 1.80103 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 170 -- 177@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 46 -- 52@LB@
89	0.01853	0.6177	b1448	mnaT	-8.57	0.080000	123 -- 134	43 -- 54	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________122__________135\n_____________\|____________\|\n5'-CGC...UAAUU___UC_______CCGUU...CGG-3'\n______________UCA__GAGGAAU\n______________\|\|\|__\|\|\|\|\|\|\|\n______________AGU__CUCCUUA\n3'-UUU...CGGGC___UU_______AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	128 -- 134	43 -- 49	-11.9422 kcal/mol	2.42412 kcal/mol	0.944705 kcal/mol	122 135@LB@ \| \|@LB@5'-CGC...UAAUU UC CCGUU...CGG-3'@LB@ UCA GAGGAAU@LB@ \|\|\| \|\|\|\|\|\|\|@LB@ AGU CUCCUUA@LB@3'-UUU...CGGGC UU AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -11.9422 kcal/mol@LB@Unfolding Energy - mRNA 2.42412 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 123 -- 134@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 43 -- 49@LB@
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
168	0.03398	0.6177	b0321	yahG	-8.56	0.080369	183 -- 192	44 -- 53	DUF1116 family protein	b4572	_____________182________193\n_____________\|__________\|\n5'-AUC...AUCUG__________GAAGC...AAC-3'\n______________CAAAGGGGAG\n______________\|\|\|\|\|:\|\|\|:\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	186 -- 192	44 -- 50	-12.9704 kcal/mol	3.47901 kcal/mol	0.927997 kcal/mol	182 193@LB@ \| \|@LB@5'-AUC...AUCUG GAAGC...AAC-3'@LB@ CAAAGGGGAG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.9704 kcal/mol@LB@Unfolding Energy - mRNA 3.47901 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 183 -- 192@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 44 -- 50@LB@
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator		_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system		_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@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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