Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
187	0.008276	0.1556	b0827	moeA	-6.51	0.330510	82 -- 91	23 -- 32	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein		_____________81_________92\n_____________\|__________\|\n5'-AUU...AUAUA__________UAUGG...UAC-3'\n______________GAAAGAUGGA\n______________\|\|\|\|\|\|\|:\|\|\n______________CUUUCUAUCU\n3'-AUU...CCAGA__________UGUAG...AUG-5'\n_____________\|__________\|\n_____________33_________22\n	85 -- 91	23 -- 29	-12.1772 kcal/mol	2.37895 kcal/mol	3.23951 kcal/mol	81 92@LB@ \| \|@LB@5'-AUU...AUAUA UAUGG...UAC-3'@LB@ GAAAGAUGGA@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUUUCUAUCU@LB@3'-AUU...CCAGA UGUAG...AUG-5'@LB@ \| \|@LB@ 33 22@LB@@LB@@LB@Energy -6.51 kcal/mol@LB@Hybridization Energy -12.1772 kcal/mol@LB@Unfolding Energy - mRNA 2.37895 kcal/mol@LB@Unfolding Energy - sRNA 3.23951 kcal/mol@LB@@LB@Position - mRNA 82 -- 91@LB@Position - sRNA 23 -- 32@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 23 -- 29@LB@
40	0.0004513	0.03766	b3291	mscL	-6.99	0.263134	48 -- 58	55 -- 65	mechanosensitive channel protein high conductance		_____________47__________59\n_____________\|___________\|\n5'-UGU...UCUUC________C__UUUCU...UCU-3'\n______________CAGCCAAG_CC\n______________\|\|\|\|\|\|\|:_\|\|\n______________GUCGGUUU_GG\n3'-AUU...UAUAA________A__CUAAU...AUG-5'\n_____________\|___________\|\n_____________66__________54\n	49 -- 55	58 -- 64	-14.9389 kcal/mol	1.90813 kcal/mol	6.05961 kcal/mol	47 59@LB@ \| \|@LB@5'-UGU...UCUUC C UUUCU...UCU-3'@LB@ CAGCCAAG CC@LB@ \|\|\|\|\|\|\|: \|\|@LB@ GUCGGUUU GG@LB@3'-AUU...UAUAA A CUAAU...AUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -14.9389 kcal/mol@LB@Unfolding Energy - mRNA 1.90813 kcal/mol@LB@Unfolding Energy - sRNA 6.05961 kcal/mol@LB@@LB@Position - mRNA 48 -- 58@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 58 -- 64@LB@
10	2.605e-05	0.009165	b3599	mtlA	-16.58	0.000118	1 -- 31	4 -- 28	mannitol-specific PTS enzyme: IIA IIB and IIC components		______________1_______________________________32\n______________\|_______________________________\|\n___________5'-___________ACGUCAA________C_____CCUAU...UCA-3'\n______________GAU_GAACGUC_______UUACCUCU_UACCC\n______________\|\|\|_\|\|\|\|:\|\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUA_CUUGUAG_______AAUGGAGA_AUGGG\n3'-AUU...ACUUU___U______________________C_____AUG-5'\n_____________\|________________________________\|\n_____________29_______________________________3\n	19 -- 25	10 -- 16	-27.7982 kcal/mol	3.19385 kcal/mol	8.04825 kcal/mol	1 32@LB@ \| \|@LB@ 5'- ACGUCAA C CCUAU...UCA-3'@LB@ GAU GAACGUC UUACCUCU UACCC@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUA CUUGUAG AAUGGAGA AUGGG@LB@3'-AUU...ACUUU U C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -16.58 kcal/mol@LB@Hybridization Energy -27.7982 kcal/mol@LB@Unfolding Energy - mRNA 3.19385 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 10 -- 16@LB@
51	0.0006491	0.04477	b3224	nanT	-16.25	0.000177	140 -- 151	1 -- 12	sialic acid transporter	b4279	_____________139__________152\n_____________\|____________\|\n5'-CGC...ACGCA____________AAUUU...GUU-3'\n______________UCUGUACCCUAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACAUGGGAUG\n3'-AUU...AAUGG____________-5'\n_____________\|___________\|\n_____________13__________1\n	145 -- 151	1 -- 7	-21.6524 kcal/mol	1.93745 kcal/mol	3.49051 kcal/mol	139 152@LB@ \| \|@LB@5'-CGC...ACGCA AAUUU...GUU-3'@LB@ UCUGUACCCUAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACAUGGGAUG@LB@3'-AUU...AAUGG -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -21.6524 kcal/mol@LB@Unfolding Energy - mRNA 1.93745 kcal/mol@LB@Unfolding Energy - sRNA 3.49051 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
93	0.002634	0.09947	b2202	napC	-9.04	0.084220	177 -- 197	34 -- 54	quinol dehydrogenase electron source for NapAB		_____________176___________________198\n_____________\|_____________________\|\n5'-ACG...CAAAA_______G___A_________AUUAU...GUU-3'\n______________GGUUACG_GAA_UAAGAGGUU\n______________\|:\|\|\|\|\|_\|\|\|_\|\|\|:\|\|\|\|:\n______________CUAAUGC_CUU_AUUUUCCAG\n3'-AUU...UUAGG_______A___C_________ACUUU...AUG-5'\n_____________\|_____________________\|\n_____________55____________________33\n	177 -- 183	48 -- 54	-21.2793 kcal/mol	4.43682 kcal/mol	7.71857 kcal/mol	176 198@LB@ \| \|@LB@5'-ACG...CAAAA G A AUUAU...GUU-3'@LB@ GGUUACG GAA UAAGAGGUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|:@LB@ CUAAUGC CUU AUUUUCCAG@LB@3'-AUU...UUAGG A C ACUUU...AUG-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.2793 kcal/mol@LB@Unfolding Energy - mRNA 4.43682 kcal/mol@LB@Unfolding Energy - sRNA 7.71857 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
77	0.00159	0.07263	b2159	nfo	-11.23	0.018951	134 -- 154	4 -- 22	endonuclease IV with intrinsic 3'-5' exonuclease activity		_____________133___________________155\n_____________\|_____________________\|\n5'-GAC...CCACU__________C____UA____GCUAU...CCA-3'\n______________ACAUCUUGCU_CUGU__ACCC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|__\|\|\|\|\n______________UGUAGAAUGG_GACA__UGGG\n3'-AUU...UAUCU__________A__________AUG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	134 -- 140	16 -- 22	-23.2044 kcal/mol	4.007 kcal/mol	7.98841 kcal/mol	133 155@LB@ \| \|@LB@5'-GAC...CCACU C UA GCUAU...CCA-3'@LB@ ACAUCUUGCU CUGU ACCC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|\|\|\|@LB@ UGUAGAAUGG GACA UGGG@LB@3'-AUU...UAUCU A AUG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -23.2044 kcal/mol@LB@Unfolding Energy - mRNA 4.007 kcal/mol@LB@Unfolding Energy - sRNA 7.98841 kcal/mol@LB@@LB@Position - mRNA 134 -- 154@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 16 -- 22@LB@
171	0.00718	0.1466	b1708	nlpC	-9.44	0.065343	288 -- 298	49 -- 59	putative C40 clan peptidase lipoprotein		_____________287_________299\n_____________\|___________\|\n5'-AAA...UUUCU___________CG-3'\n______________GAUUCGAUUAC\n______________:\|\|:\|\|\|\|\|\|\|\n______________UUAGGCUAAUG\n3'-AUU...UCGGU___________CACUU...AUG-5'\n_____________\|___________\|\n_____________60__________48\n	292 -- 298	49 -- 55	-11.5278 kcal/mol	1.77565 kcal/mol	0.318405 kcal/mol	287 299@LB@ \| \|@LB@5'-AAA...UUUCU CG-3'@LB@ GAUUCGAUUAC@LB@ :\|\|:\|\|\|\|\|\|\|@LB@ UUAGGCUAAUG@LB@3'-AUU...UCGGU CACUU...AUG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -11.5278 kcal/mol@LB@Unfolding Energy - mRNA 1.77565 kcal/mol@LB@Unfolding Energy - sRNA 0.318405 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon		_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@LB@
152	0.006159	0.1406	b2467	nudK	-9.74	0.053801	255 -- 261	1 -- 7	GDP-mannose pyrophosphatase		_____________254_____262\n_____________\|_______\|\n5'-CAA...AUUUC_______ACAAC...AAG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	255 -- 261	1 -- 7	-11.9691 kcal/mol	0.21022 kcal/mol	2.03949 kcal/mol	254 262@LB@ \| \|@LB@5'-CAA...AUUUC ACAAC...AAG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.9691 kcal/mol@LB@Unfolding Energy - mRNA 0.21022 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 255 -- 261@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 1 -- 7@LB@
109	0.003426	0.1101	b2280	nuoJ	-6.41	0.346318	31 -- 43	48 -- 59	NADH:ubiquinone oxidoreductase membrane subunit J		_____________30____________44\n_____________\|_____________\|\n5'-GAU...GCCAG_________U___AGAAA...UUA-3'\n______________GAUCUGGUU_ACG\n______________:\|\|\|:\|:\|\|_\|\|\|\n______________UUAGGCUAA_UGC\n3'-AUU...UCGGU_____________ACUUC...AUG-5'\n_____________\|_____________\|\n_____________60____________47\n	33 -- 39	51 -- 57	-11.2654 kcal/mol	3.27917 kcal/mol	1.55995 kcal/mol	30 44@LB@ \| \|@LB@5'-GAU...GCCAG U AGAAA...UUA-3'@LB@ GAUCUGGUU ACG@LB@ :\|\|\|:\|:\|\| \|\|\|@LB@ UUAGGCUAA UGC@LB@3'-AUU...UCGGU ACUUC...AUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -11.2654 kcal/mol@LB@Unfolding Energy - mRNA 3.27917 kcal/mol@LB@Unfolding Energy - sRNA 1.55995 kcal/mol@LB@@LB@Position - mRNA 31 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 51 -- 57@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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