Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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
96	0.00803	0.2778	bsu39710	iolF	-10.11	0.206009	172 -- 191	30 -- 53	minor myo-inositol transporter IolF	_____________171______________________192\n_____________\|________________________\|\n5'-GGC...AGUUG__________________AU____AAUGA...CCG-3'\n______________UUGGAUCU_GG_CU__UA__GGGG\n______________\|:\|\|\|\|\|\|_\|:_\|\|__\|\|__\|\|\|\|\n______________AGCCUAGA_CU_GA__AU__CCCC\n3'-UUU...AAAAA________A__A__CU__CU____AACCC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________29\n	173 -- 179	46 -- 52	-17.6548 kcal/mol	6.56277 kcal/mol	0.985344 kcal/mol	171 192@LB@ \| \|@LB@5'-GGC...AGUUG AU AAUGA...CCG-3'@LB@ UUGGAUCU GG CU UA GGGG@LB@ \|:\|\|\|\|\|\| \|: \|\| \|\| \|\|\|\|@LB@ AGCCUAGA CU GA AU CCCC@LB@3'-UUU...AAAAA A A CU CU AACCC...AUA-5'@LB@ \| \|@LB@ 54 29@LB@@LB@@LB@Energy -10.11 kcal/mol@LB@Hybridization Energy -17.6548 kcal/mol@LB@Unfolding Energy - mRNA 6.56277 kcal/mol@LB@Unfolding Energy - sRNA 0.985344 kcal/mol@LB@@LB@Position - mRNA 172 -- 191@LB@Position - sRNA 30 -- 53@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 46 -- 52@LB@
99	0.00842	0.2778	bsu19470	yojF	-13.80	0.051174	184 -- 193	30 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183________194\n_____________\|__________\|\n5'-GAA...AAGAA__A_______AGCAA...CAG-3'\n______________GA_AGAGGGG\n______________\|\|_\|\|\|\|\|\|\|\n______________CU_UCUCCCC\n3'-UUU...CUAGA__A_______AACCC...AUA-5'\n_____________\|__________\|\n_____________40_________29\n	187 -- 193	30 -- 36	-15.454 kcal/mol	0.87683 kcal/mol	0.779184 kcal/mol	183 194@LB@ \| \|@LB@5'-GAA...AAGAA A AGCAA...CAG-3'@LB@ GA AGAGGGG@LB@ \|\| \|\|\|\|\|\|\|@LB@ CU UCUCCCC@LB@3'-UUU...CUAGA A AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -15.454 kcal/mol@LB@Unfolding Energy - mRNA 0.87683 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
100	0.008436	0.2778	bsu35250	ftsX	-12.75	0.078592	182 -- 188	30 -- 36	cell division protein FtsX	_____________181_____189\n_____________\|_______\|\n5'-UGC...AGUCA_______AGUAU...CGC-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	182 -- 188	30 -- 36	-13.7147 kcal/mol	0.82624 kcal/mol	0.133643 kcal/mol	181 189@LB@ \| \|@LB@5'-UGC...AGUCA AGUAU...CGC-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.75 kcal/mol@LB@Hybridization Energy -13.7147 kcal/mol@LB@Unfolding Energy - mRNA 0.82624 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 182 -- 188@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 30 -- 36@LB@
102	0.008773	0.2778	bsu06170	ydjE	-10.58	0.175640	264 -- 284	30 -- 50	sugar kinase YdjE	_____________263___________________285\n_____________\|_____________________\|\n5'-GGG...AUGUU__CG_______A_____A___CGCCA...AAA-3'\n______________GA__UUGAUUU_AUGGA_GGG\n______________\|\|__\|\|\|\|\|:\|_\|\|:\|\|_\|\|\|\n______________CU__AACUAGA_UAUCU_CCC\n3'-UUU...AAAGC__AG_______C_____C___AACCC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________29\n	268 -- 274	40 -- 46	-17.5575 kcal/mol	6.00068 kcal/mol	0.974272 kcal/mol	263 285@LB@ \| \|@LB@5'-GGG...AUGUU CG A A CGCCA...AAA-3'@LB@ GA UUGAUUU AUGGA GGG@LB@ \|\| \|\|\|\|\|:\| \|\|:\|\| \|\|\|@LB@ CU AACUAGA UAUCU CCC@LB@3'-UUU...AAAGC AG C C AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -17.5575 kcal/mol@LB@Unfolding Energy - mRNA 6.00068 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 264 -- 284@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 40 -- 46@LB@
104	0.009018	0.2778	bsu08080	acoC	-12.10	0.101314	188 -- 194	30 -- 36	dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system	_____________187_____195\n_____________\|_______\|\n5'-UGC...AUUAA_______ACACA...GAG-3'\n______________AGGGGGG\n______________\|\|:\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.004 kcal/mol	0.767034 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGC...AUUAA ACACA...GAG-3'@LB@ AGGGGGG@LB@ \|\|:\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -13.004 kcal/mol@LB@Unfolding Energy - mRNA 0.767034 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
106	0.009109	0.2778	bsu01390	infA	-12.86	0.075307	175 -- 189	30 -- 45	translation initiation factor IF-1	_____________174______________190\n_____________\|________________\|\n5'-CCA...GUUAC____________A___AGAAC...UGG-3'\n______________UGAUUUGA_AGA_GGG\n______________\|\|\|\|:\|\|\|_\|\|\|_\|\|\|\n______________ACUAGACU_UCU_CCC\n3'-UUU...CUAGA________A___C___AACCC...AUA-5'\n_____________\|________________\|\n_____________46_______________29\n	176 -- 182	38 -- 44	-16.3452 kcal/mol	2.51395 kcal/mol	0.969561 kcal/mol	174 190@LB@ \| \|@LB@5'-CCA...GUUAC A AGAAC...UGG-3'@LB@ UGAUUUGA AGA GGG@LB@ \|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ ACUAGACU UCU CCC@LB@3'-UUU...CUAGA A C AACCC...AUA-5'@LB@ \| \|@LB@ 46 29@LB@@LB@@LB@Energy -12.86 kcal/mol@LB@Hybridization Energy -16.3452 kcal/mol@LB@Unfolding Energy - mRNA 2.51395 kcal/mol@LB@Unfolding Energy - sRNA 0.969561 kcal/mol@LB@@LB@Position - mRNA 175 -- 189@LB@Position - sRNA 30 -- 45@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
109	0.009307	0.2778	bsu07880	yfkJ	-15.70	0.021808	288 -- 299	30 -- 51	low molecular weight protein-tyrosine-phosphatase YfkJ	_____________287____________________300\n_____________\|______________________\|\n5'-GGU...AAAAA______________________A-3'\n______________GGAU__________UAGAGGGG\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CCUA__________AUCUCCCC\n3'-UUU...AAAAG____GAACUAGACU________AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	293 -- 299	30 -- 36	-17.0834 kcal/mol	0.412933 kcal/mol	0.974282 kcal/mol	287 300@LB@ \| \|@LB@5'-GGU...AAAAA A-3'@LB@ GGAU UAGAGGGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUA AUCUCCCC@LB@3'-UUU...AAAAG GAACUAGACU AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -17.0834 kcal/mol@LB@Unfolding Energy - mRNA 0.412933 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 288 -- 299@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 30 -- 36@LB@
124	0.01102	0.2883	bsu36860	atpE	-15.23	0.027175	263 -- 293	30 -- 52	ATP synthase subunit c	_____________262_______________________________294\n_____________\|_________________________________\|\n5'-AAA...GGUAA____________GUUUCACGUAC__________AUUGCCC-3'\n______________CGG__UUUGAUU___________GGUAGAGGGG\n______________\|\|\|__:\|\|\|\|\|:___________\|:\|\|\|\|\|\|\|\|\n______________GCC__GAACUAG___________CUAUCUCCCC\n3'-UUU...AAAAA___UA_______A____________________AACCC...AUA-5'\n_____________\|_________________________________\|\n_____________53________________________________29\n	287 -- 293	30 -- 36	-22.7251 kcal/mol	6.51858 kcal/mol	0.979974 kcal/mol	262 294@LB@ \| \|@LB@5'-AAA...GGUAA GUUUCACGUAC AUUGCCC-3'@LB@ CGG UUUGAUU GGUAGAGGGG@LB@ \|\|\| :\|\|\|\|\|: \|:\|\|\|\|\|\|\|\|@LB@ GCC GAACUAG CUAUCUCCCC@LB@3'-UUU...AAAAA UA A AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.23 kcal/mol@LB@Hybridization Energy -22.7251 kcal/mol@LB@Unfolding Energy - mRNA 6.51858 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 30 -- 36@LB@
128	0.01143	0.2883	bsu29690	acuA	-15.81	0.020690	248 -- 269	30 -- 52	acetoin utilization protein AcuA	_____________247_____________________270\n_____________\|_______________________\|\n5'-UAU...GCAAC___C____UA_________A___CCUGU...AUG-3'\n______________CGG_UCUU___CUGAUAGA_GGG\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC_AGAA___GACUAUCU_CCC\n3'-UUU...AAAAA___U____CUA________C___AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	259 -- 265	34 -- 40	-22.8929 kcal/mol	6.10629 kcal/mol	0.979974 kcal/mol	247 270@LB@ \| \|@LB@5'-UAU...GCAAC C UA A CCUGU...AUG-3'@LB@ CGG UCUU CUGAUAGA GGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC AGAA GACUAUCU CCC@LB@3'-UUU...AAAAA U CUA C AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.81 kcal/mol@LB@Hybridization Energy -22.8929 kcal/mol@LB@Unfolding Energy - mRNA 6.10629 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@LB@
130	0.01149	0.2883	bsu02620	phoD	-13.55	0.056825	174 -- 193	30 -- 50	alkaline phosphatase D	_____________173____________________194\n_____________\|______________________\|\n5'-GCC...GAGAC____AA___G____G_______AUCUU...CGG-3'\n______________GAUC__UGA___GA_AGAGGGG\n______________\|\|\|\|__\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________CUAG__ACU___CU_UCUCCCC\n3'-UUU...AAAGC____A____AGA__A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	187 -- 193	30 -- 36	-18.9864 kcal/mol	4.46268 kcal/mol	0.974272 kcal/mol	173 194@LB@ \| \|@LB@5'-GCC...GAGAC AA G G AUCUU...CGG-3'@LB@ GAUC UGA GA AGAGGGG@LB@ \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\|@LB@ CUAG ACU CU UCUCCCC@LB@3'-UUU...AAAGC A AGA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -18.9864 kcal/mol@LB@Unfolding Energy - mRNA 4.46268 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@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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