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
140	0.01224	0.2883	bsu36480	ywoD	-6.33	0.569704	31 -- 37	66 -- 72	MFS transporter	_____________30______38\n_____________\|_______\|\n5'-AUU...AUAUC_______AAAGC...AUA-3'\n______________GGGGUGG\n______________\|\|\|\|\|:\|\n______________CCCCAUC\n3'-UUU...ACCGC_______GCGGU...AUA-5'\n_____________\|_______\|\n_____________73______65\n	31 -- 37	66 -- 72	-11.1749 kcal/mol	4.83937 kcal/mol	0.00366414 kcal/mol	30 38@LB@ \| \|@LB@5'-AUU...AUAUC AAAGC...AUA-3'@LB@ GGGGUGG@LB@ \|\|\|\|\|:\|@LB@ CCCCAUC@LB@3'-UUU...ACCGC GCGGU...AUA-5'@LB@ \| \|@LB@ 73 65@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -11.1749 kcal/mol@LB@Unfolding Energy - mRNA 4.83937 kcal/mol@LB@Unfolding Energy - sRNA 0.00366414 kcal/mol@LB@@LB@Position - mRNA 31 -- 37@LB@Position - sRNA 66 -- 72@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 66 -- 72@LB@
91	0.007102	0.2604	bsu36520	glnK	-7.98	0.387566	247 -- 267	32 -- 49	nitrogen regulatory PII-like protein	_____________246____________________268\n_____________\|______________________\|\n5'-GGU...GGCAA_______AAAG_______C___AACUC...CUU-3'\n______________AUUUUGA____CUGA_AG_AGG\n______________\|\|:\|\|\|\|____\|\|\|\|_\|\|_\|\|\|\n______________UAGAACU____GACU_UC_UCC\n3'-UUU...AAGCC_______A_______A______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________50_____________________31\n	247 -- 253	43 -- 49	-11.0905 kcal/mol	2.14263 kcal/mol	0.970192 kcal/mol	246 268@LB@ \| \|@LB@5'-GGU...GGCAA AAAG C AACUC...CUU-3'@LB@ AUUUUGA CUGA AG AGG@LB@ \|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|@LB@ UAGAACU GACU UC UCC@LB@3'-UUU...AAGCC A A CCAAC...AUA-5'@LB@ \| \|@LB@ 50 31@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -11.0905 kcal/mol@LB@Unfolding Energy - mRNA 2.14263 kcal/mol@LB@Unfolding Energy - sRNA 0.970192 kcal/mol@LB@@LB@Position - mRNA 247 -- 267@LB@Position - sRNA 32 -- 49@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 43 -- 49@LB@
199	0.01988	0.3269	bsu36590	clsA	-10.32	0.192119	169 -- 195	28 -- 48	cardiolipin synthase	_____________168_________________________196\n_____________\|___________________________\|\n5'-UUA...AAUCU_______AAAUA___AUG__C______ACAAA...CUU-3'\n______________UCUUGAU_____UGA___AG_GGGGUU\n______________\|\|\|\|\|\|\|_____\|\|\|___\|\|_\|\|\|\|\|\|\n______________AGAACUA_____ACU___UC_CCCCAA\n3'-UUU...AGCCU_______G_______A____U______CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________49__________________________27\n	169 -- 175	42 -- 48	-17.4562 kcal/mol	6.16425 kcal/mol	0.974701 kcal/mol	168 196@LB@ \| \|@LB@5'-UUA...AAUCU AAAUA AUG C ACAAA...CUU-3'@LB@ UCUUGAU UGA AG GGGGUU@LB@ \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|@LB@ AGAACUA ACU UC CCCCAA@LB@3'-UUU...AGCCU G A U CCCCU...AUA-5'@LB@ \| \|@LB@ 49 27@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.4562 kcal/mol@LB@Unfolding Energy - mRNA 6.16425 kcal/mol@LB@Unfolding Energy - sRNA 0.974701 kcal/mol@LB@@LB@Position - mRNA 169 -- 195@LB@Position - sRNA 28 -- 48@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 42 -- 48@LB@
41	0.001775	0.1444	bsu36710	fdhD	-11.37	0.133163	186 -- 192	30 -- 36	protein FdhD	_____________185_____193\n_____________\|_______\|\n5'-UCG...AUUGC_______AAGAG...CAG-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-13.1021 kcal/mol	1.59974 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCG...AUUGC AAGAG...CAG-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -13.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.59974 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@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@
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@
8	5.206e-05	0.02171	bsu37180	fadF	-12.43	0.089383	154 -- 199	26 -- 74	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 17189250; Product type pe : enzyme'	_____________153____________________________________________________200\n_____________\|______________________________________________________\|\n5'-CAA...AGAUU_________G_GA___________C______U___A_UAAAA______AA____AAUGA...ACA-3'\n______________CGGGGGUAG_G__________UCG_GGUCUU_AUC_G_____AGGGGG__UUGG\n______________\|\|\|\|\|\|\|\|\|_\|__________\|\|\|_\|:\|\|\|\|_\|\|\|_\|_____\|\|:\|\|\|__\|\|\|\|\n______________GCCCCCAUC_C__________AGC_CUAGAA_UAG_C_____UCUCCC__AACC\n3'-UUU...GAACC_________G_GGUUCAAAAA__________C___A_UA_________C_____CCUUG...AUA-5'\n_____________\|______________________________________________________\|\n_____________75_____________________________________________________25\n	156 -- 162	66 -- 72	-40.4869 kcal/mol	12.2576 kcal/mol	15.8011 kcal/mol	153 200@LB@ \| \|@LB@5'-CAA...AGAUU G GA C U A UAAAA AA AAUGA...ACA-3'@LB@ CGGGGGUAG G UCG GGUCUU AUC G AGGGGG UUGG@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\| \|:\|\|\|\| \|\|\| \| \|\|:\|\|\| \|\|\|\|@LB@ GCCCCCAUC C AGC CUAGAA UAG C UCUCCC AACC@LB@3'-UUU...GAACC G GGUUCAAAAA C A UA C CCUUG...AUA-5'@LB@ \| \|@LB@ 75 25@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -40.4869 kcal/mol@LB@Unfolding Energy - mRNA 12.2576 kcal/mol@LB@Unfolding Energy - sRNA 15.8011 kcal/mol@LB@@LB@Position - mRNA 154 -- 199@LB@Position - sRNA 26 -- 74@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 66 -- 72@LB@
153	0.01377	0.2994	bsu37510	pbpG	-15.25	0.026855	95 -- 111	23 -- 38	penicillin-binding protein 2D	_____________94_________________112\n_____________\|__________________\|\n5'-UGU...AAAGU_______AU__C______AAAAG...UGU-3'\n______________AUAGAGG__GG__GGGGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|\|\|\|\n______________UAUCUCC__CC__CCCCU\n3'-UUU...UAGAC___________AA_____UGUCU...AUA-5'\n_____________\|__________________\|\n_____________39_________________22\n	95 -- 101	32 -- 38	-18.2895 kcal/mol	2.3676 kcal/mol	0.66977 kcal/mol	94 112@LB@ \| \|@LB@5'-UGU...AAAGU AU C AAAAG...UGU-3'@LB@ AUAGAGG GG GGGGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UAUCUCC CC CCCCU@LB@3'-UUU...UAGAC AA UGUCU...AUA-5'@LB@ \| \|@LB@ 39 22@LB@@LB@@LB@Energy -15.25 kcal/mol@LB@Hybridization Energy -18.2895 kcal/mol@LB@Unfolding Energy - mRNA 2.3676 kcal/mol@LB@Unfolding Energy - sRNA 0.66977 kcal/mol@LB@@LB@Position - mRNA 95 -- 111@LB@Position - sRNA 23 -- 38@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 32 -- 38@LB@
191	0.01913	0.3269	bsu37760	rocC	-14.43	0.038902	267 -- 280	26 -- 36	amino acid permease RocC	_____________266____________281\n_____________\|______________\|\n5'-CCG...CUUUG________GAU___CACUG...GCU-3'\n______________GGAGGGGU___UGG\n______________:\|\|\|\|\|\|\|___\|\|\|\n______________UCUCCCCA___ACC\n3'-UUU...GACUA______________CCUUG...AUA-5'\n_____________\|______________\|\n_____________37_____________25\n	268 -- 274	29 -- 35	-16.8756 kcal/mol	2.30826 kcal/mol	0.135623 kcal/mol	266 281@LB@ \| \|@LB@5'-CCG...CUUUG GAU CACUG...GCU-3'@LB@ GGAGGGGU UGG@LB@ :\|\|\|\|\|\|\| \|\|\|@LB@ UCUCCCCA ACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -16.8756 kcal/mol@LB@Unfolding Energy - mRNA 2.30826 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 267 -- 280@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 29 -- 35@LB@
142	0.01236	0.2883	bsu37940	ywdJ	-14.78	0.033255	157 -- 193	27 -- 52	purine permease YwdJ	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGA...GGAAA____GAG____U_______UUUUAAAG____A_____AGCUU...ACU-3'\n______________CGGA___UCUU_AUUUGAU________AGAG_GGUUG\n______________\|\|\|\|___\|\|\|\|_\|\|:\|\|\|\|________\|\|\|\|_\|\|\|\|\|\n______________GCCU___AGAA_UAGACUA________UCUC_CCAAC\n3'-UUU...AAAAA___________C___________________C_____CCCUU...AUA-5'\n_____________\|_____________________________________\|\n_____________53____________________________________26\n	169 -- 175	37 -- 43	-23.5373 kcal/mol	7.77274 kcal/mol	0.980744 kcal/mol	156 194@LB@ \| \|@LB@5'-GGA...GGAAA GAG U UUUUAAAG A AGCUU...ACU-3'@LB@ CGGA UCUU AUUUGAU AGAG GGUUG@LB@ \|\|\|\| \|\|\|\| \|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ GCCU AGAA UAGACUA UCUC CCAAC@LB@3'-UUU...AAAAA C C CCCUU...AUA-5'@LB@ \| \|@LB@ 53 26@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.5373 kcal/mol@LB@Unfolding Energy - mRNA 7.77274 kcal/mol@LB@Unfolding Energy - sRNA 0.980744 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 27 -- 52@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 37 -- 43@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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