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
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@
9	0.001801	0.593	b1276	acnA	-10.22	0.037037	184 -- 198	44 -- 55	aconitate hydratase 1; aconitase A	_____________183_____________199\n_____________\|_______________\|\n5'-CUU...ACCCU____UUA________CUAUG...GCG-3'\n______________GUCA___AGGAGGAG\n______________\|\|\|\|___\|:\|\|\|\|\|:\n______________CAGU___UUCUCCUU\n3'-UUU...CCGGG_______________AAAGU...ACA-5'\n_____________\|_______________\|\n_____________56______________43\n	192 -- 198	44 -- 50	-13.3918 kcal/mol	2.22696 kcal/mol	0.941432 kcal/mol	183 199@LB@ \| \|@LB@5'-CUU...ACCCU UUA CUAUG...GCG-3'@LB@ GUCA AGGAGGAG@LB@ \|\|\|\| \|:\|\|\|\|\|:@LB@ CAGU UUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -13.3918 kcal/mol@LB@Unfolding Energy - mRNA 2.22696 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability	_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase	_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
103	0.02062	0.6177	b1332	ynaJ	-7.81	0.113347	36 -- 54	40 -- 55	DUF2534 family putative inner membrane protein	_____________35__________________55\n_____________\|___________________\|\n5'-AAA...ACUGA____GCC____A_______CCCGC...CCA-3'\n______________GUCA___GAGA_GAAUUUC\n______________\|\|\|\|___:\|\|\|_\|\|\|\|\|\|\|\n______________CAGU___UUCU_CUUAAAG\n3'-UUU...CCGGG___________C_______UAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________39\n	48 -- 54	40 -- 46	-13.2524 kcal/mol	4.4222 kcal/mol	1.01784 kcal/mol	35 55@LB@ \| \|@LB@5'-AAA...ACUGA GCC A CCCGC...CCA-3'@LB@ GUCA GAGA GAAUUUC@LB@ \|\|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CAGU UUCU CUUAAAG@LB@3'-UUU...CCGGG C UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -13.2524 kcal/mol@LB@Unfolding Energy - mRNA 4.4222 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 40 -- 46@LB@
75	0.01577	0.6177	b1345	intR	-9.71	0.047033	139 -- 151	42 -- 53	Rac prophage; integrase	_____________138___________152\n_____________\|_____________\|\n5'-UAA...GACAG____C________AUCUG...GGG-3'\n______________CAAA_GAGGGAUU\n______________\|\|\|\|_\|\|\|\|:\|\|\|\n______________GUUU_CUCCUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	145 -- 151	42 -- 48	-12.4741 kcal/mol	1.8255 kcal/mol	0.933904 kcal/mol	138 152@LB@ \| \|@LB@5'-UAA...GACAG C AUCUG...GGG-3'@LB@ CAAA GAGGGAUU@LB@ \|\|\|\| \|\|\|\|:\|\|\|@LB@ GUUU CUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -12.4741 kcal/mol@LB@Unfolding Energy - mRNA 1.8255 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 139 -- 151@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 42 -- 48@LB@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding	_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
85	0.01786	0.6177	b1427	rimL	-14.01	0.006161	123 -- 133	46 -- 56	ribosomal-protein-L7/L12-serine acetyltransferase	_____________122_________134\n_____________\|___________\|\n5'-GAU...GAGAG___________UGUAA...CCU-3'\n______________CGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCC\n3'-UUU...ACCGG___________UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	127 -- 133	46 -- 52	-17.3934 kcal/mol	2.45026 kcal/mol	0.93204 kcal/mol	122 134@LB@ \| \|@LB@5'-GAU...GAGAG UGUAA...CCU-3'@LB@ CGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -17.3934 kcal/mol@LB@Unfolding Energy - mRNA 2.45026 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 123 -- 133@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 46 -- 52@LB@
119	0.02381	0.6177	b1434	ydcN	-8.41	0.086264	87 -- 94	43 -- 50	putative DNA-binding transcriptional regulator	_____________86_______95\n_____________\|________\|\n5'-CGG...UGGGU________AGAAA...CUA-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	88 -- 94	43 -- 49	-10.2233 kcal/mol	0.967994 kcal/mol	0.845564 kcal/mol	86 95@LB@ \| \|@LB@5'-CGG...UGGGU AGAAA...CUA-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -10.2233 kcal/mol@LB@Unfolding Energy - mRNA 0.967994 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 87 -- 94@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 43 -- 49@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@

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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