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
163	0.01533	0.3122	bsu19639	yoyE	-15.95	0.019304	185 -- 198	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________184_____________199\n_____________\|_______________\|\n5'-UCA...CGCAG__A____________ACAUG...AAU-3'\n______________GA_GGAGGGGU_GGG\n______________\|\|_:\|\|\|\|\|\|\|_\|\|\|\n______________CU_UCUCCCCA_CCC\n3'-UUU...CUAGA__A________A___CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	189 -- 195	29 -- 35	-22.4813 kcal/mol	5.74668 kcal/mol	0.783603 kcal/mol	184 199@LB@ \| \|@LB@5'-UCA...CGCAG A ACAUG...AAU-3'@LB@ GA GGAGGGGU GGG@LB@ \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CU UCUCCCCA CCC@LB@3'-UUU...CUAGA A A CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -22.4813 kcal/mol@LB@Unfolding Energy - mRNA 5.74668 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 185 -- 198@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 29 -- 35@LB@
75	0.005596	0.2441	bsu19669	yoyF	-14.84	0.032440	230 -- 255	26 -- 52	Evidence 5: No homology to any previously reported sequences	_____________229_________________________256\n_____________\|___________________________\|\n5'-GUA...CUGGA____GAAA_________UCAUAA____AAAAA...GUC-3'\n______________CGGA____GAUUUGAUA_______UGG\n______________\|\|\|\|____\|\|\|:\|\|\|\|\|_______\|\|\|\n______________GCCU____CUAGACUAU_______ACC\n3'-UUU...AAAAA____AGAA_________CUCCCCA___CCUUG...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________25\n	240 -- 246	36 -- 42	-17.4265 kcal/mol	1.6069 kcal/mol	0.980817 kcal/mol	229 256@LB@ \| \|@LB@5'-GUA...CUGGA GAAA UCAUAA AAAAA...GUC-3'@LB@ CGGA GAUUUGAUA UGG@LB@ \|\|\|\| \|\|\|:\|\|\|\|\| \|\|\|@LB@ GCCU CUAGACUAU ACC@LB@3'-UUU...AAAAA AGAA CUCCCCA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -17.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.6069 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 36 -- 42@LB@
57	0.003091	0.1809	bsu19720	yodR	-13.42	0.059995	155 -- 217	11 -- 51	coenzyme A transferase subunit beta	_____________154_________________________________________________________________218\n_____________\|___________________________________________________________________\|\n5'-GCU...ACCGG_______UG________________UACGAAGCGA____GUGAAGUGGAAAUGG__UU_________AGAAA...CCU-3'\n______________GGGUUUU___UUGA___GGGGGUUG__________GGGA_______________GC__GGGAGUAGC\n______________\|\|:\|:\|\|___:\|\|\|___:\|\|\|\|\|\|\|__________\|\|\|\|_______________:\|__\|:\|\|\|\|\|\|\|\n______________CCUAGAA___GACU___UCCCCAAC__________CCCU_______________UG__CUCUCAUCG\n3'-UUU...AAAAG_______CUA____AUC_______________________________________U__________AAGAG...AUA-5'\n_____________\|___________________________________________________________________\|\n_____________52__________________________________________________________________10\n	211 -- 217	11 -- 17	-37.5623 kcal/mol	14.1868 kcal/mol	9.95641 kcal/mol	154 218@LB@ \| \|@LB@5'-GCU...ACCGG UG UACGAAGCGA GUGAAGUGGAAAUGG UU AGAAA...CCU-3'@LB@ GGGUUUU UUGA GGGGGUUG GGGA GC GGGAGUAGC@LB@ \|\|:\|:\|\| :\|\|\| :\|\|\|\|\|\|\| \|\|\|\| :\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA GACU UCCCCAAC CCCU UG CUCUCAUCG@LB@3'-UUU...AAAAG CUA AUC U AAGAG...AUA-5'@LB@ \| \|@LB@ 52 10@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -37.5623 kcal/mol@LB@Unfolding Energy - mRNA 14.1868 kcal/mol@LB@Unfolding Energy - sRNA 9.95641 kcal/mol@LB@@LB@Position - mRNA 155 -- 217@LB@Position - sRNA 11 -- 51@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
73	0.005255	0.2402	bsu21750	scuA	-12.63	0.082513	190 -- 220	28 -- 51	SCO1 protein	_____________189_____________________________221\n_____________\|_______________________________\|\n5'-GGG...GGAAA____GGAU___A___A__UUAUCA_______AACGG...AGC-3'\n______________GGAU____GUC_UGA_GG______AGGGGUU\n______________\|\|\|\|____:\|\|_\|\|\|_:\|______\|\|\|\|\|\|\|\n______________CCUA____UAG_ACU_UC______UCCCCAA\n3'-UUU...AAAAG____GAAC_______A_______________CCCCU...AUA-5'\n_____________\|_______________________________\|\n_____________52______________________________27\n	214 -- 220	28 -- 34	-18.667 kcal/mol	5.06013 kcal/mol	0.974859 kcal/mol	189 221@LB@ \| \|@LB@5'-GGG...GGAAA GGAU A A UUAUCA AACGG...AGC-3'@LB@ GGAU GUC UGA GG AGGGGUU@LB@ \|\|\|\| :\|\| \|\|\| :\| \|\|\|\|\|\|\|@LB@ CCUA UAG ACU UC UCCCCAA@LB@3'-UUU...AAAAG GAAC A CCCCU...AUA-5'@LB@ \| \|@LB@ 52 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -18.667 kcal/mol@LB@Unfolding Energy - mRNA 5.06013 kcal/mol@LB@Unfolding Energy - sRNA 0.974859 kcal/mol@LB@@LB@Position - mRNA 190 -- 220@LB@Position - sRNA 28 -- 51@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 28 -- 34@LB@
13	0.0002088	0.05257	bsu22150	ypvA	-19.04	0.003759	161 -- 194	26 -- 53	ATP-dependent helicase YpvA	_____________160____________________________________195\n_____________\|______________________________________\|\n5'-GUG...UAUUA________________AUGUCGAA___UU_________AACUA...CCG-3'\n______________UUGG____UGGUCUGA________UAG__GGGGGUUGG\n______________\|:\|\|____\|\|:\|\|\|\|\|________\|\|\|__:\|\|\|\|\|\|\|\|\n______________AGCC____ACUAGACU________AUC__UCCCCAACC\n3'-UUU...AAAAA____UAGA______________________________CCUUG...AUA-5'\n_____________\|______________________________________\|\n_____________54_____________________________________25\n	188 -- 194	26 -- 32	-27.605 kcal/mol	7.58324 kcal/mol	0.986187 kcal/mol	160 195@LB@ \| \|@LB@5'-GUG...UAUUA AUGUCGAA UU AACUA...CCG-3'@LB@ UUGG UGGUCUGA UAG GGGGGUUGG@LB@ \|:\|\| \|\|:\|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|@LB@ AGCC ACUAGACU AUC UCCCCAACC@LB@3'-UUU...AAAAA UAGA CCUUG...AUA-5'@LB@ \| \|@LB@ 54 25@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -27.605 kcal/mol@LB@Unfolding Energy - mRNA 7.58324 kcal/mol@LB@Unfolding Energy - sRNA 0.986187 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 26 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 26 -- 32@LB@
174	0.01668	0.3152	bsu22210	yprB	-13.05	0.069799	168 -- 191	31 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'	_____________167______________________192\n_____________\|________________________\|\n5'-AUU...AGCUG_______AAAU___GUAA______AGGCC...AUG-3'\n______________UUGGAUC____GUC____GGAGGG\n______________\|:\|\|\|\|\|____:\|\|____:\|\|\|\|\|\n______________AGCCUAG____UAG____UCUCCC\n3'-UUU...AAAAA_______AAC____ACUA______CAACC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________30\n	168 -- 174	47 -- 53	-20.3327 kcal/mol	6.30079 kcal/mol	0.981784 kcal/mol	167 192@LB@ \| \|@LB@5'-AUU...AGCUG AAAU GUAA AGGCC...AUG-3'@LB@ UUGGAUC GUC GGAGGG@LB@ \|:\|\|\|\|\| :\|\| :\|\|\|\|\|@LB@ AGCCUAG UAG UCUCCC@LB@3'-UUU...AAAAA AAC ACUA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -20.3327 kcal/mol@LB@Unfolding Energy - mRNA 6.30079 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 47 -- 53@LB@
182	0.01724	0.3161	bsu22340	nth	-14.82	0.032761	30 -- 59	25 -- 52	endonuclease III	_____________29______________________________60\n_____________\|_______________________________\|\n5'-CAG...UUGAC______________A_____AGAAAAA____CUUAA...UAG-3'\n______________CGGAUUUUG_UUUG_AUGGA_______UGGG\n______________\|\|\|\|\|:\|\|\|_\|:\|\|_\|\|:\|\|_______\|\|\|\|\n______________GCCUAGAAC_AGAC_UAUCU_______ACCC\n3'-UUU...AAAAA_________U__________CCCCA______CUUGU...AUA-5'\n_____________\|_______________________________\|\n_____________53______________________________24\n	32 -- 38	44 -- 50	-22.2299 kcal/mol	6.43208 kcal/mol	0.980838 kcal/mol	29 60@LB@ \| \|@LB@5'-CAG...UUGAC A AGAAAAA CUUAA...UAG-3'@LB@ CGGAUUUUG UUUG AUGGA UGGG@LB@ \|\|\|\|\|:\|\|\| \|:\|\| \|\|:\|\| \|\|\|\|@LB@ GCCUAGAAC AGAC UAUCU ACCC@LB@3'-UUU...AAAAA U CCCCA CUUGU...AUA-5'@LB@ \| \|@LB@ 53 24@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -22.2299 kcal/mol@LB@Unfolding Energy - mRNA 6.43208 kcal/mol@LB@Unfolding Energy - sRNA 0.980838 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 25 -- 52@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 44 -- 50@LB@
50	0.002285	0.1525	bsu22460	ypjH	-13.49	0.058216	160 -- 194	23 -- 52	glycosyltransferase YpjH	_____________159____________________________________195\n_____________\|______________________________________\|\n5'-AAG...CCAAA_____GCUGAUG_______A_____U__C_________CGAAC...AUG-3'\n______________CGGAU_______CUUGAUC_UGAUG__G___UUGGGGG\n______________\|\|\|\|\|_______\|\|\|\|\|\|\|_\|\|\|\|:__\|___\|\|\|\|\|\|:\n______________GCCUA_______GAACUAG_ACUAU__C___AACCCCU\n3'-UUU...AAAAA_________________________CU_CCC_______UGUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________22\n	188 -- 194	23 -- 29	-25.8094 kcal/mol	11.3359 kcal/mol	0.981961 kcal/mol	159 195@LB@ \| \|@LB@5'-AAG...CCAAA GCUGAUG A U C CGAAC...AUG-3'@LB@ CGGAU CUUGAUC UGAUG G UUGGGGG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|: \| \|\|\|\|\|\|:@LB@ GCCUA GAACUAG ACUAU C AACCCCU@LB@3'-UUU...AAAAA CU CCC UGUCU...AUA-5'@LB@ \| \|@LB@ 53 22@LB@@LB@@LB@Energy -13.49 kcal/mol@LB@Hybridization Energy -25.8094 kcal/mol@LB@Unfolding Energy - mRNA 11.3359 kcal/mol@LB@Unfolding Energy - sRNA 0.981961 kcal/mol@LB@@LB@Position - mRNA 160 -- 194@LB@Position - sRNA 23 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 23 -- 29@LB@
5	2.545e-05	0.01698	bsu22540	qcrC	-19.98	0.002129	169 -- 196	23 -- 48	menaquinol-cytochrome c reductase cytochrome b/c subunit	_____________168____________________________197\n_____________\|______________________________\|\n5'-AAC...UAAAC__________CGA___AA____A_______UGACA...AAA-3'\n______________UCUUGAUCUG___AUA__AGGG___GGGGA\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|___\|\|\|\|\|\n______________AGAACUAGAC___UAU__UCCC___CCCCU\n3'-UUU...AGCCU________________C_____CAA_____UGUCU...AUA-5'\n_____________\|______________________________\|\n_____________49_____________________________22\n	172 -- 178	39 -- 45	-27.164 kcal/mol	6.20558 kcal/mol	0.979889 kcal/mol	168 197@LB@ \| \|@LB@5'-AAC...UAAAC CGA AA A UGACA...AAA-3'@LB@ UCUUGAUCUG AUA AGGG GGGGA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|@LB@ AGAACUAGAC UAU UCCC CCCCU@LB@3'-UUU...AGCCU C CAA UGUCU...AUA-5'@LB@ \| \|@LB@ 49 22@LB@@LB@@LB@Energy -19.98 kcal/mol@LB@Hybridization Energy -27.164 kcal/mol@LB@Unfolding Energy - mRNA 6.20558 kcal/mol@LB@Unfolding Energy - sRNA 0.979889 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 23 -- 48@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 39 -- 45@LB@
68	0.004453	0.2184	bsu22580	ypiB	-13.80	0.051176	183 -- 197	21 -- 39	Evidence 4: Homologs of previously reported genes of unknown function; PubMedId: 16847875	_____________182_________________198\n_____________\|___________________\|\n5'-AGC...CGAAC________A__________UACAU...ACU-3'\n______________GAUAGAGG_____GGGAAU\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|:\n______________CUAUCUCC_____CCCUUG\n3'-UUU...CUAGA________CCAAC______UCUCU...AUA-5'\n_____________\|___________________\|\n_____________40__________________20\n	184 -- 190	32 -- 38	-18.5124 kcal/mol	2.13446 kcal/mol	2.58006 kcal/mol	182 198@LB@ \| \|@LB@5'-AGC...CGAAC A UACAU...ACU-3'@LB@ GAUAGAGG GGGAAU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ CUAUCUCC CCCUUG@LB@3'-UUU...CUAGA CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 40 20@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.5124 kcal/mol@LB@Unfolding Energy - mRNA 2.13446 kcal/mol@LB@Unfolding Energy - sRNA 2.58006 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 21 -- 39@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 32 -- 38@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching