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
200	0.01989	0.3269	bsu30150	ytdP	-13.03	0.070310	188 -- 210	28 -- 52	AraC family transcriptional regulator	_____________187________________________211\n_____________\|__________________________\|\n5'-UUU...UGAAG_____G_UA______AAU________UUAUG...UAU-3'\n______________UGGAU_U_____UGA___GGGGGGUU\n______________:\|\|\|\|_\|_____\|\|\|___\|:\|\|\|\|\|\|\n______________GCCUA_A_____ACU___CUCCCCAA\n3'-UUU...AAAAA_____G_ACUAG___AU_________CCCCU...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________27\n	204 -- 210	28 -- 34	-18.7355 kcal/mol	4.72292 kcal/mol	0.980555 kcal/mol	187 211@LB@ \| \|@LB@5'-UUU...UGAAG G UA AAU UUAUG...UAU-3'@LB@ UGGAU U UGA GGGGGGUU@LB@ :\|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|@LB@ GCCUA A ACU CUCCCCAA@LB@3'-UUU...AAAAA G ACUAG AU CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -18.7355 kcal/mol@LB@Unfolding Energy - mRNA 4.72292 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
14	0.0002247	0.05257	bsu30160	ytcQ	-17.33	0.009670	159 -- 223	10 -- 51	peptide ABC transporter substrate-binding protein	_____________158__________________________________________________________________224\n_____________\|____________________________________________________________________\|\n5'-UUG...UGCUG___________AAAGGAUAAAGAAAUA___AAC________ACGA____A___AAAU___________UUUGA...GCA-3'\n______________GGAUCU__GUC________________UGA___GGAGGGGU____UGGG_AAC____GGAGGGU_GCU\n______________\|\|\|\|\|\|__:\|\|________________\|\|\|___:\|\|\|\|\|\|\|____\|\|\|\|_\|\|\|____:\|\|\|:\|\|_\|\|\|\n______________CCUAGA__UAG________________ACU___UCUCCCCA____ACCC_UUG____UCUCUCA_CGA\n3'-UUU...AAAAG______AC______________________A__________________C______________U___AGAGA...AUA-5'\n_____________\|____________________________________________________________________\|\n_____________52___________________________________________________________________9\n	214 -- 220	14 -- 20	-40.5 kcal/mol	13.2168 kcal/mol	9.95655 kcal/mol	158 224@LB@ \| \|@LB@5'-UUG...UGCUG AAAGGAUAAAGAAAUA AAC ACGA A AAAU UUUGA...GCA-3'@LB@ GGAUCU GUC UGA GGAGGGGU UGGG AAC GGAGGGU GCU@LB@ \|\|\|\|\|\| :\|\| \|\|\| :\|\|\|\|\|\|\| \|\|\|\| \|\|\| :\|\|\|:\|\| \|\|\|@LB@ CCUAGA UAG ACU UCUCCCCA ACCC UUG UCUCUCA CGA@LB@3'-UUU...AAAAG AC A C U AGAGA...AUA-5'@LB@ \| \|@LB@ 52 9@LB@@LB@@LB@Energy -17.33 kcal/mol@LB@Hybridization Energy -40.5 kcal/mol@LB@Unfolding Energy - mRNA 13.2168 kcal/mol@LB@Unfolding Energy - sRNA 9.95655 kcal/mol@LB@@LB@Position - mRNA 159 -- 223@LB@Position - sRNA 10 -- 51@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@LB@
25	0.0005172	0.06638	bsu30210	bioD	-10.94	0.155183	179 -- 210	28 -- 53	ATP-dependent dethiobiotin synthetase BioD	_____________178_______________________________211\n_____________\|_________________________________\|\n5'-GUC...UUCAA_____AAG___G___CACAUCAUUU________UUUUU...UCG-3'\n______________UCGGA____GA_CUG__________GAGGGGUU\n______________\|\|\|\|\|____\|\|_\|\|\|__________\|\|\|\|\|\|\|\|\n______________AGCCU____CU_GAC__________CUCCCCAA\n3'-UUU...AAAAA_____AGAA__A___UAU_______________CCCCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________27\n	204 -- 210	28 -- 34	-21.1469 kcal/mol	9.22099 kcal/mol	0.985925 kcal/mol	178 211@LB@ \| \|@LB@5'-GUC...UUCAA AAG G CACAUCAUUU UUUUU...UCG-3'@LB@ UCGGA GA CUG GAGGGGUU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU CU GAC CUCCCCAA@LB@3'-UUU...AAAAA AGAA A UAU CCCCU...AUA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -10.94 kcal/mol@LB@Hybridization Energy -21.1469 kcal/mol@LB@Unfolding Energy - mRNA 9.22099 kcal/mol@LB@Unfolding Energy - sRNA 0.985925 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
184	0.01795	0.3254	bsu30470	ytzC	-13.40	0.060457	189 -- 197	28 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________188_______198\n_____________\|_________\|\n5'-UUC...CAAGA_________ACUGU...AUU-3'\n______________GGAGGGGUU\n______________:\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-16.1349 kcal/mol	2.59994 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UUC...CAAGA ACUGU...AUU-3'@LB@ GGAGGGGUU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -13.40 kcal/mol@LB@Hybridization Energy -16.1349 kcal/mol@LB@Unfolding Energy - mRNA 2.59994 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
114	0.009837	0.2871	bsu30580	ytmA	-11.73	0.116519	193 -- 212	33 -- 52	peptidase YtmA	_____________192____________________213\n_____________\|______________________\|\n5'-AGA...GGAGG___CU_________________AAAAG...UGG-3'\n______________CGG__GUUUUGAUU__GUAGAG\n______________\|\|\|__:\|:\|\|\|\|\|:__:\|\|\|\|\|\n______________GCC__UAGAACUAG__UAUCUC\n3'-UUU...AAAAA______________AC______CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	200 -- 206	41 -- 47	-17.5653 kcal/mol	4.85678 kcal/mol	0.976367 kcal/mol	192 213@LB@ \| \|@LB@5'-AGA...GGAGG CU AAAAG...UGG-3'@LB@ CGG GUUUUGAUU GUAGAG@LB@ \|\|\| :\|:\|\|\|\|\|: :\|\|\|\|\|@LB@ GCC UAGAACUAG UAUCUC@LB@3'-UUU...AAAAA AC CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -17.5653 kcal/mol@LB@Unfolding Energy - mRNA 4.85678 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 41 -- 47@LB@
139	0.01217	0.2883	bsu30960	glgD	-11.28	0.137516	171 -- 191	30 -- 50	glycogen biosynthesis protein GlgD	_____________170____________________192\n_____________\|______________________\|\n5'-ACU...GAAUU_____AAUUA____________GCAGA...UUG-3'\n______________GAUUU_____CUGA_AGAGGGG\n______________\|\|\|:\|_____\|\|\|\|_\|\|\|\|\|\|\|\n______________CUAGA_____GACU_UCUCCCC\n3'-UUU...AAAGC_____ACUA_____A_______AACCC...AUA-5'\n_____________\|______________________\|\n_____________51_____________________29\n	185 -- 191	30 -- 36	-19.1028 kcal/mol	6.84884 kcal/mol	0.974272 kcal/mol	170 192@LB@ \| \|@LB@5'-ACU...GAAUU AAUUA GCAGA...UUG-3'@LB@ GAUUU CUGA AGAGGGG@LB@ \|\|\|:\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CUAGA GACU UCUCCCC@LB@3'-UUU...AAAGC ACUA A AACCC...AUA-5'@LB@ \| \|@LB@ 51 29@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -19.1028 kcal/mol@LB@Unfolding Energy - mRNA 6.84884 kcal/mol@LB@Unfolding Energy - sRNA 0.974272 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 30 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 30 -- 36@LB@
72	0.005249	0.2402	bsu31470	kapD	-7.49	0.439018	141 -- 147	21 -- 27	3'-5' exonuclease KapD	_____________140_____148\n_____________\|_______\|\n5'-UUU...GAGAA_______UGAUA...GAA-3'\n______________GGGGAAU\n______________\|\|\|\|\|\|:\n______________CCCCUUG\n3'-UUU...CCCAA_______UCUCU...AUA-5'\n_____________\|_______\|\n_____________28______20\n	141 -- 147	21 -- 27	-11.5159 kcal/mol	2.2254 kcal/mol	1.80207 kcal/mol	140 148@LB@ \| \|@LB@5'-UUU...GAGAA UGAUA...GAA-3'@LB@ GGGGAAU@LB@ \|\|\|\|\|\|:@LB@ CCCCUUG@LB@3'-UUU...CCCAA UCUCU...AUA-5'@LB@ \| \|@LB@ 28 20@LB@@LB@@LB@Energy -7.49 kcal/mol@LB@Hybridization Energy -11.5159 kcal/mol@LB@Unfolding Energy - mRNA 2.2254 kcal/mol@LB@Unfolding Energy - sRNA 1.80207 kcal/mol@LB@@LB@Position - mRNA 141 -- 147@LB@Position - sRNA 21 -- 27@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 21 -- 27@LB@
167	0.01619	0.3152	bsu31500	yuxK	-13.98	0.047449	182 -- 199	26 -- 51	Evidence 4: Homologs of previously reported genes of unknown function	_____________181__________________________200\n_____________\|____________________________\|\n5'-UAC...UUAAA______________________AUA___AGUGA...ACG-3'\n______________GGAUC__________GGAGGGG___UGG\n______________\|\|\|\|\|__________:\|\|\|\|\|\|___\|\|\|\n______________CCUAG__________UCUCCCC___ACC\n3'-UUU...AAAAG_____AACUAGACUA_______A_____CCUUG...AUA-5'\n_____________\|____________________________\|\n_____________52___________________________25\n	187 -- 193	30 -- 36	-20.9361 kcal/mol	5.98517 kcal/mol	0.975822 kcal/mol	181 200@LB@ \| \|@LB@5'-UAC...UUAAA AUA AGUGA...ACG-3'@LB@ GGAUC GGAGGGG UGG@LB@ \|\|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ CCUAG UCUCCCC ACC@LB@3'-UUU...AAAAG AACUAGACUA A CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -13.98 kcal/mol@LB@Hybridization Energy -20.9361 kcal/mol@LB@Unfolding Energy - mRNA 5.98517 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
67	0.004159	0.2071	bsu31830	yueE	-13.48	0.058566	169 -- 197	28 -- 51	phosphohydrolase YueE	_____________168___________________________198\n_____________\|_____________________________\|\n5'-UAG...UGUUA___U___AAAAAU____AAA_________UCCAU...AUG-3'\n______________GGA_UCU______AUCU___GGAGGGGUU\n______________\|\|\|_\|\|\|______\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CCU_AGA______UAGA___UCUCCCCAA\n3'-UUU...AAAAG_______AC________CUA_________CCCCU...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________27\n	191 -- 197	28 -- 34	-19.6632 kcal/mol	5.21125 kcal/mol	0.974859 kcal/mol	168 198@LB@ \| \|@LB@5'-UAG...UGUUA U AAAAAU AAA UCCAU...AUG-3'@LB@ GGA UCU AUCU GGAGGGGUU@LB@ \|\|\| \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CCU AGA UAGA UCUCCCCAA@LB@3'-UUU...AAAAG AC CUA CCCCU...AUA-5'@LB@ \| \|@LB@ 52 27@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.6632 kcal/mol@LB@Unfolding Energy - mRNA 5.21125 kcal/mol@LB@Unfolding Energy - sRNA 0.974859 kcal/mol@LB@@LB@Position - mRNA 169 -- 197@LB@Position - sRNA 28 -- 51@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
113	0.00948	0.2799	bsu31960	dhbF	-9.87	0.222399	16 -- 37	32 -- 53	dimodular nonribosomal peptide synthase	_____________15______________________38\n_____________\|_______________________\|\n5'-AGA...CUCGA___U__________C________AUCAU...CAG-3'\n______________UCG_GGUCUUGAUU_GGUA_AGG\n______________\|\|\|_\|:\|\|\|\|\|\|\|:_\|:\|\|_\|\|\|\n______________AGC_CUAGAACUAG_CUAU_UCC\n3'-UUU...AAAAA______________A____C___CCAAC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________31\n	22 -- 28	42 -- 48	-21.9493 kcal/mol	11.0963 kcal/mol	0.981755 kcal/mol	15 38@LB@ \| \|@LB@5'-AGA...CUCGA U C AUCAU...CAG-3'@LB@ UCG GGUCUUGAUU GGUA AGG@LB@ \|\|\| \|:\|\|\|\|\|\|\|: \|:\|\| \|\|\|@LB@ AGC CUAGAACUAG CUAU UCC@LB@3'-UUU...AAAAA A C CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -21.9493 kcal/mol@LB@Unfolding Energy - mRNA 11.0963 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 16 -- 37@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 42 -- 48@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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