Input and runtime details for job 4894743 (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 4894743 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:26 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:36:09 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 05:38:38 CET 2018
	Post-Processing Finished		@ Sat Feb 17 05:38:45 CET 2018
	Job Completed		@ Sat Feb 17 05:39:16 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4894743&toolName=CopraRNA ( 30 days expiry )

Description of the job

SR1

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
162	0.007531	0.1751	bsu14350	yknX	-8.74	0.495402	179 -- 195	123 -- 140	efflux system component YknX	_____________178________________196\n_____________\|__________________\|\n5'-UGA...UCAAU____________G_____AGCUC...CCG-3'\n______________UCUGUGGCGGGU__CAUA\n______________\|\|:\|::\|\|::\|\|__\|\|\|\|\n______________AGGCGUCGUUCA__GUAU\n3'-AUU...GUAAC____________AG____AUUAC...CAA-5'\n_____________\|__________________\|\n_____________141________________122\n	184 -- 190	129 -- 135	-18.5785 kcal/mol	5.82762 kcal/mol	6.13212 kcal/mol	178 196@LB@ \| \|@LB@5'-UGA...UCAAU G AGCUC...CCG-3'@LB@ UCUGUGGCGGGU CAUA@LB@ \|\|:\|::\|\|::\|\| \|\|\|\|@LB@ AGGCGUCGUUCA GUAU@LB@3'-AUU...GUAAC AG AUUAC...CAA-5'@LB@ \| \|@LB@ 141 122@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -18.5785 kcal/mol@LB@Unfolding Energy - mRNA 5.82762 kcal/mol@LB@Unfolding Energy - sRNA 6.13212 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 123 -- 140@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 129 -- 135@LB@
134	0.00626	0.1741	bsu03360	yciC	-8.59	0.518951	99 -- 108	130 -- 139	metal chaperone YciC	_____________98_______109\n_____________\|________\|\n5'-AGG...GGGCG________AAAUG...UAG-3'\n______________GCAGCGAG\n______________\|\|\|\|\|:\|\|\n______________CGUCGUUC\n3'-AUU...ACAGG________AAGGU...CAA-5'\n_____________\|________\|\n_____________140______129\n	102 -- 108	130 -- 136	-12.856 kcal/mol	2.76877 kcal/mol	2.9981 kcal/mol	98 109@LB@ \| \|@LB@5'-AGG...GGGCG AAAUG...UAG-3'@LB@ GCAGCGAG@LB@ \|\|\|\|\|:\|\|@LB@ CGUCGUUC@LB@3'-AUU...ACAGG AAGGU...CAA-5'@LB@ \| \|@LB@ 140 129@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -12.856 kcal/mol@LB@Unfolding Energy - mRNA 2.76877 kcal/mol@LB@Unfolding Energy - sRNA 2.9981 kcal/mol@LB@@LB@Position - mRNA 99 -- 108@LB@Position - sRNA 130 -- 139@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 130 -- 136@LB@
36	0.001118	0.1204	bsu17650	yncE	-8.56	0.524973	291 -- 300	61 -- 70	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type h: extrachromosomal origin'	_____________290_______300\n_____________\|_________\|\n5'-GUA...AUAGG__________-3'\n______________UGGCAAACGA\n______________\|\|\|\|\|\|\|\|:\|\n______________ACCGUUUGUU\n3'-AUU...UUAGA__________AGCAU...CAA-5'\n_____________\|__________\|\n_____________71_________60\n	294 -- 300	61 -- 67	-13.5985 kcal/mol	0.387687 kcal/mol	4.67716 kcal/mol	290 300@LB@ \| \|@LB@5'-GUA...AUAGG -3'@LB@ UGGCAAACGA@LB@ \|\|\|\|\|\|\|\|:\|@LB@ ACCGUUUGUU@LB@3'-AUU...UUAGA AGCAU...CAA-5'@LB@ \| \|@LB@ 71 60@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -13.5985 kcal/mol@LB@Unfolding Energy - mRNA 0.387687 kcal/mol@LB@Unfolding Energy - sRNA 4.67716 kcal/mol@LB@@LB@Position - mRNA 291 -- 300@LB@Position - sRNA 61 -- 70@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 61 -- 67@LB@
119	0.005369	0.1741	bsu33250	yvrL	-8.38	0.555183	10 -- 36	76 -- 105	membrane-bound negative regulator YvrL	_____________9__________37\n_____________\|__________\|\n5'-AUG...CCUUC__________UUGCG...AUA-3'\n______________AAAACGCUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUUUGCGAAU\n3'-AUU...UAAAC__________UAAAG...CAA-5'\n_____________\|__________\|\n_____________106________75\n	224 -- 230	13 -- 19	-10.8458 kcal/mol	2.09283 kcal/mol	3.31287 kcal/mol	9 37@LB@ \| \|@LB@5'-AUG...CCUUC UUGCG...AUA-3'@LB@ AAAACGCUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUUUGCGAAU@LB@3'-AUU...UAAAC UAAAG...CAA-5'@LB@ \| \|@LB@ 106 75@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -10.8458 kcal/mol@LB@Unfolding Energy - mRNA 2.09283 kcal/mol@LB@Unfolding Energy - sRNA 3.31287 kcal/mol@LB@@LB@Position - mRNA 10 -- 36@LB@Position - sRNA 76 -- 105@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 13 -- 19@LB@
107	0.004539	0.1633	bsu11020	yitK	-8.14	0.595243	151 -- 171	155 -- 171	nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription	_____________150___________________172\n_____________\|_____________________\|\n5'-ACC...UUCUC________ACUAUA_______CAUAA...AUG-3'\n______________UUUAUUCU______AUCAACA\n______________\|\|\|\|:\|\|\|______\|\|\|\|\|\|\|\n______________AAAUGAGA______UAGUUGU\n3'-AUU...AAAAA________AG___________CCUGU...CAA-5'\n_____________\|_____________________\|\n_____________172___________________154\n	165 -- 171	155 -- 161	-10.3591 kcal/mol	1.70839 kcal/mol	1.4241 kcal/mol	150 172@LB@ \| \|@LB@5'-ACC...UUCUC ACUAUA CAUAA...AUG-3'@LB@ UUUAUUCU AUCAACA@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ AAAUGAGA UAGUUGU@LB@3'-AUU...AAAAA AG CCUGU...CAA-5'@LB@ \| \|@LB@ 172 154@LB@@LB@@LB@Energy -8.14 kcal/mol@LB@Hybridization Energy -10.3591 kcal/mol@LB@Unfolding Energy - mRNA 1.70839 kcal/mol@LB@Unfolding Energy - sRNA 1.4241 kcal/mol@LB@@LB@Position - mRNA 151 -- 171@LB@Position - sRNA 155 -- 171@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 155 -- 161@LB@
87	0.003215	0.1423	bsu04140	pbpC	-8.12	0.599206	128 -- 139	96 -- 107	penicillin-binding protein 3	______________128_____140\n______________\|_______\|\n___________5'-________AAGGC...CAU-3'\n______________UCUUGUUC\n______________\|\|\|\|:\|\|\|\n______________AGAAUAAG\n3'-AUU...GGUAG________GGGUA...CAA-5'\n_____________\|________\|\n_____________108______95\n	2 -- 8	42 -- 48	-8.08477 kcal/mol	0.903572 kcal/mol	0.0615861 kcal/mol	128 140@LB@ \| \|@LB@ 5'- AAGGC...CAU-3'@LB@ UCUUGUUC@LB@ \|\|\|\|:\|\|\|@LB@ AGAAUAAG@LB@3'-AUU...GGUAG GGGUA...CAA-5'@LB@ \| \|@LB@ 108 95@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -8.08477 kcal/mol@LB@Unfolding Energy - mRNA 0.903572 kcal/mol@LB@Unfolding Energy - sRNA 0.0615861 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 96 -- 107@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 42 -- 48@LB@
61	0.001915	0.1214	bsu19720	yodR	-8.11	0.600668	13 -- 29	71 -- 89	coenzyme A transferase subunit beta	_____________12___________30\n_____________\|____________\|\n5'-GCU...GAAGA____A_______ACCGG...CCU-3'\n______________AAUG_UUGUCAC\n______________\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAC_AACAGUG\n3'-AUU...GUAUA____________AAAGA...CAA-5'\n_____________\|____________\|\n_____________90___________70\n	143 -- 149	111 -- 117	-12.213 kcal/mol	1.50216 kcal/mol	3.63424 kcal/mol	12 30@LB@ \| \|@LB@5'-GCU...GAAGA A ACCGG...CCU-3'@LB@ AAUG UUGUCAC@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ UUAC AACAGUG@LB@3'-AUU...GUAUA AAAGA...CAA-5'@LB@ \| \|@LB@ 90 70@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -12.213 kcal/mol@LB@Unfolding Energy - mRNA 1.50216 kcal/mol@LB@Unfolding Energy - sRNA 3.63424 kcal/mol@LB@@LB@Position - mRNA 13 -- 29@LB@Position - sRNA 71 -- 89@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 111 -- 117@LB@
101	0.004166	0.1594	bsu11270	yjzD	-8.07	0.607351	275 -- 290	119 -- 136	Evidence 4: Homologs of previously reported genes of unknown function	_____________274________________291\n_____________\|__________________\|\n5'-UAG...AUGAA________UA________UUCAA...CAU-3'\n______________CAGC__GU__CGUAUAAU\n______________\|\|\|\|__\|\|__\|:\|\|\|\|\|\|\n______________GUCG__CA__GUAUAUUA\n3'-AUU...CAGGC____UU__AG________CAACA...CAA-5'\n_____________\|__________________\|\n_____________137________________118\n	284 -- 290	119 -- 125	-12.692 kcal/mol	1.37877 kcal/mol	3.96273 kcal/mol	274 291@LB@ \| \|@LB@5'-UAG...AUGAA UA UUCAA...CAU-3'@LB@ CAGC GU CGUAUAAU@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ GUCG CA GUAUAUUA@LB@3'-AUU...CAGGC UU AG CAACA...CAA-5'@LB@ \| \|@LB@ 137 118@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -12.692 kcal/mol@LB@Unfolding Energy - mRNA 1.37877 kcal/mol@LB@Unfolding Energy - sRNA 3.96273 kcal/mol@LB@@LB@Position - mRNA 275 -- 290@LB@Position - sRNA 119 -- 136@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 119 -- 125@LB@
155	0.00708	0.1751	bsu17280	ymaD	-7.93	0.631070	192 -- 223	42 -- 69	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 16267290; Product type pe : enzyme'	_____________191______________________________224\n_____________\|________________________________\|\n5'-AAA...AAGGA___A_______G_CAGA_____AU________AAAAG...UUC-3'\n______________GGC_AAACAAU_G____UCAUC__UUUUAUUU\n______________\|\|\|_\|\|\|\|\|\|\|_\|____:\|\|\|\|__\|:\|\|\|\|\|:\n______________CCG_UUUGUUA_C____GGUAG__AGAAUAAG\n3'-AUU...UAGAA___________G_AUG________________GGGUA...CAA-5'\n_____________\|________________________________\|\n_____________70_______________________________41\n	217 -- 223	42 -- 48	-20.5024 kcal/mol	4.54925 kcal/mol	8.89481 kcal/mol	191 224@LB@ \| \|@LB@5'-AAA...AAGGA A G CAGA AU AAAAG...UUC-3'@LB@ GGC AAACAAU G UCAUC UUUUAUUU@LB@ \|\|\| \|\|\|\|\|\|\| \| :\|\|\|\| \|:\|\|\|\|\|:@LB@ CCG UUUGUUA C GGUAG AGAAUAAG@LB@3'-AUU...UAGAA G AUG GGGUA...CAA-5'@LB@ \| \|@LB@ 70 41@LB@@LB@@LB@Energy -7.93 kcal/mol@LB@Hybridization Energy -20.5024 kcal/mol@LB@Unfolding Energy - mRNA 4.54925 kcal/mol@LB@Unfolding Energy - sRNA 8.89481 kcal/mol@LB@@LB@Position - mRNA 192 -- 223@LB@Position - sRNA 42 -- 69@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 42 -- 48@LB@
169	0.007812	0.1751	bsu04680	rsbS	-7.92	0.633185	77 -- 93	53 -- 67	RsbT antagonist protein RsbS	_____________76___________________94\n_____________\|____________________\|\n5'-UAU...GGAAA______AAACAA________CUGGG...AAG-3'\n______________UUGCUC______UCGUCAAC\n______________\|\|:\|\|\|______\|\|:\|\|\|\|\|\n______________AAUGAG______AGUAGUUG\n3'-AUU...AAAAA______A_____________UCCUG...CAA-5'\n_____________\|____________________\|\n_____________68___________________52\n	85 -- 91	156 -- 162	-12.3218 kcal/mol	3.62054 kcal/mol	1.40896 kcal/mol	76 94@LB@ \| \|@LB@5'-UAU...GGAAA AAACAA CUGGG...AAG-3'@LB@ UUGCUC UCGUCAAC@LB@ \|\|:\|\|\| \|\|:\|\|\|\|\|@LB@ AAUGAG AGUAGUUG@LB@3'-AUU...AAAAA A UCCUG...CAA-5'@LB@ \| \|@LB@ 68 52@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -12.3218 kcal/mol@LB@Unfolding Energy - mRNA 3.62054 kcal/mol@LB@Unfolding Energy - sRNA 1.40896 kcal/mol@LB@@LB@Position - mRNA 77 -- 93@LB@Position - sRNA 53 -- 67@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 156 -- 162@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)

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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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