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
84	0.006671	0.2588	bsu14270	moeB	-18.74	0.004465	187 -- 207	32 -- 51	molybdopterin-synthase adenylyltransferase	_____________186___________________208\n_____________\|_____________________\|\n5'-UUG...GAUAA___GAACA_____________AACGU...GAG-3'\n______________GGA_____GGUUUGAUGGAGG\n______________\|\|\|_____\|:\|:\|\|\|\|:\|\|\|\|\n______________CCU_____CUAGACUAUCUCC\n3'-UUU...AAAAG___AGAA______________CCAAC...AUA-5'\n_____________\|_____________________\|\n_____________52____________________31\n	201 -- 207	32 -- 38	-23.059 kcal/mol	3.35069 kcal/mol	0.97021 kcal/mol	186 208@LB@ \| \|@LB@5'-UUG...GAUAA GAACA AACGU...GAG-3'@LB@ GGA GGUUUGAUGGAGG@LB@ \|\|\| \|:\|:\|\|\|\|:\|\|\|\|@LB@ CCU CUAGACUAUCUCC@LB@3'-UUU...AAAAG AGAA CCAAC...AUA-5'@LB@ \| \|@LB@ 52 31@LB@@LB@@LB@Energy -18.74 kcal/mol@LB@Hybridization Energy -23.059 kcal/mol@LB@Unfolding Energy - mRNA 3.35069 kcal/mol@LB@Unfolding Energy - sRNA 0.97021 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 32 -- 51@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 32 -- 38@LB@
116	0.01008	0.2881	bsu32800	yusH	-9.74	0.231897	187 -- 194	31 -- 38	glycine cleavage system H protein	_____________186______195\n_____________\|________\|\n5'-AUC...AAAAA________AUUCA...CCG-3'\n______________AUGGAGGG\n______________\|\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	188 -- 194	31 -- 37	-12.574 kcal/mol	2.17853 kcal/mol	0.65488 kcal/mol	186 195@LB@ \| \|@LB@5'-AUC...AAAAA AUUCA...CCG-3'@LB@ AUGGAGGG@LB@ \|\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.574 kcal/mol@LB@Unfolding Energy - mRNA 2.17853 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
189	0.01911	0.3269	bsu24290	xseB	-12.91	0.073825	187 -- 193	30 -- 36	exodeoxyribonuclease 7 small subunit	_____________186_____194\n_____________\|_______\|\n5'-CAU...AAAAG_______AAGAA...UAG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	187 -- 193	30 -- 36	-14.0184 kcal/mol	0.973532 kcal/mol	0.133643 kcal/mol	186 194@LB@ \| \|@LB@5'-CAU...AAAAG AAGAA...UAG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.91 kcal/mol@LB@Hybridization Energy -14.0184 kcal/mol@LB@Unfolding Energy - mRNA 0.973532 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
10	0.0001049	0.035	bsu34190	yvfH	-16.62	0.013859	188 -- 201	23 -- 36	L-lactate permease	_____________187____________202\n_____________\|______________\|\n5'-UGG...UUCAA_________U____UGCAA...CGA-3'\n______________GGAGGGGUU_GGGA\n______________:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UCUCCCCAA_CCCU\n3'-UUU...GACUA_________C____UGUCU...AUA-5'\n_____________\|______________\|\n_____________37_____________22\n	190 -- 196	28 -- 34	-23.4111 kcal/mol	6.64684 kcal/mol	0.139628 kcal/mol	187 202@LB@ \| \|@LB@5'-UGG...UUCAA U UGCAA...CGA-3'@LB@ GGAGGGGUU GGGA@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCCCAA CCCU@LB@3'-UUU...GACUA C UGUCU...AUA-5'@LB@ \| \|@LB@ 37 22@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -23.4111 kcal/mol@LB@Unfolding Energy - mRNA 6.64684 kcal/mol@LB@Unfolding Energy - sRNA 0.139628 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 23 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@LB@
52	0.002415	0.1549	bsu03320	nasB	-8.41	0.344801	188 -- 199	36 -- 51	assimilatory nitrate reductase electron transfer subunit	_____________187______________200\n_____________\|________________\|\n5'-UUU...CCAAA________________CAUGA...UCA-3'\n______________GGA____GGUCUGAUA\n______________\|\|\|____\|:\|\|\|\|\|\|\|\n______________CCU____CUAGACUAU\n3'-UUU...AAAAG___AGAA_________CUCCC...AUA-5'\n_____________\|________________\|\n_____________52_______________35\n	193 -- 199	36 -- 42	-13.3061 kcal/mol	3.93547 kcal/mol	0.960469 kcal/mol	187 200@LB@ \| \|@LB@5'-UUU...CCAAA CAUGA...UCA-3'@LB@ GGA GGUCUGAUA@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ CCU CUAGACUAU@LB@3'-UUU...AAAAG AGAA CUCCC...AUA-5'@LB@ \| \|@LB@ 52 35@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3061 kcal/mol@LB@Unfolding Energy - mRNA 3.93547 kcal/mol@LB@Unfolding Energy - sRNA 0.960469 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 36 -- 51@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 36 -- 42@LB@
53	0.002724	0.1697	bsu06970	yesO	-13.13	0.067695	188 -- 199	26 -- 36	ABC transporter substrate-binding protein	_____________187__________200\n_____________\|____________\|\n5'-CGA...AUUAA_______A____UUUGA...UUA-3'\n______________AGGGGGG_UUGG\n______________\|\|:\|\|\|\|_\|\|\|\|\n______________UCUCCCC_AACC\n3'-UUU...GACUA____________CCUUG...AUA-5'\n_____________\|____________\|\n_____________37___________25\n	188 -- 194	30 -- 36	-17.5942 kcal/mol	4.33325 kcal/mol	0.135623 kcal/mol	187 200@LB@ \| \|@LB@5'-CGA...AUUAA A UUUGA...UUA-3'@LB@ AGGGGGG UUGG@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UCUCCCC AACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -17.5942 kcal/mol@LB@Unfolding Energy - mRNA 4.33325 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@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@
145	0.01267	0.2913	bsu36760	murAA	-10.92	0.156018	188 -- 194	30 -- 36	UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	_____________187_____195\n_____________\|_______\|\n5'-UAG...GACGC_______AAUAC...UAU-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.3986 kcal/mol	2.34028 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UAG...GACGC AAUAC...UAU-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -13.3986 kcal/mol@LB@Unfolding Energy - mRNA 2.34028 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@
155	0.01391	0.2994	bsu24780	yqgY	-10.29	0.193646	188 -- 194	30 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________187_____195\n_____________\|_______\|\n5'-UGU...UCUCG_______AUAAA...GAC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.7207 kcal/mol	3.29345 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-UGU...UCUCG AUAAA...GAC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -13.7207 kcal/mol@LB@Unfolding Energy - mRNA 3.29345 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@
196	0.01947	0.3269	bsu15810	spoVM	-12.63	0.082660	188 -- 194	30 -- 36	stage V sporulation protein M	_____________187_____195\n_____________\|_______\|\n5'-AAA...UUAUA_______ACAAA...GCC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.8815 kcal/mol	1.12038 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-AAA...UUAUA ACAAA...GCC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8815 kcal/mol@LB@Unfolding Energy - mRNA 1.12038 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@

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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