Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
28	0.005203	0.5385	b3308	rplE	-12.95	0.031988	121 -- 134	62 -- 77	50S ribosomal subunit protein L5	_____________120______________135\n_____________\|________________\|\n5'-AAA...GUGUA________________AGACG...AGA-3'\n______________GGCUUUAG__AUUCGA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________CCGAAAUC__UAAGCU\n3'-CGC...UGCAA________AA______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	122 -- 128	70 -- 76	-17.2589 kcal/mol	3.56808 kcal/mol	0.736118 kcal/mol	120 135@LB@ \| \|@LB@5'-AAA...GUGUA AGACG...AGA-3'@LB@ GGCUUUAG AUUCGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCGAAAUC UAAGCU@LB@3'-CGC...UGCAA AA CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -17.2589 kcal/mol@LB@Unfolding Energy - mRNA 3.56808 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 121 -- 134@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 70 -- 76@LB@
23	0.004272	0.5385	b3315	rplV	-10.64	0.081808	245 -- 278	60 -- 90	50S ribosomal subunit protein L22	_____________244________________________________279\n_____________\|__________________________________\|\n5'-CGC...GCUCA__________C___UU___GACCUG_____C___AAGAA...UGG-3'\n______________GAAGGUUCGC_UUG__GCU______AUUCG_GGU\n______________:\|\|:\|\|\|\|:\|_\|\|\|__\|\|\|______\|\|\|\|\|_:\|\|\n______________UUUUCAAGUG_AAC__CGA______UAAGC_UCA\n3'-CGC...AGGCG__________C________AAUCAA_________ACUCU...AAG-5'\n_____________\|__________________________________\|\n_____________91_________________________________59\n	248 -- 254	81 -- 87	-21.0379 kcal/mol	8.68511 kcal/mol	1.70935 kcal/mol	244 279@LB@ \| \|@LB@5'-CGC...GCUCA C UU GACCUG C AAGAA...UGG-3'@LB@ GAAGGUUCGC UUG GCU AUUCG GGU@LB@ :\|\|:\|\|\|\|:\| \|\|\| \|\|\| \|\|\|\|\| :\|\|@LB@ UUUUCAAGUG AAC CGA UAAGC UCA@LB@3'-CGC...AGGCG C AAUCAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -21.0379 kcal/mol@LB@Unfolding Energy - mRNA 8.68511 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 245 -- 278@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 81 -- 87@LB@
87	0.01529	0.5385	b3636	rpmG	-10.80	0.076825	199 -- 224	53 -- 84	50S ribosomal subunit protein L33	_____________198______________________________225\n_____________\|________________________________\|\n5'-CAC...AUAAA___________AA__G________________AUCAA...AAC-3'\n______________UCA___UGGCU__AG_UAUUCG___UGAGAAA\n______________\|\|\|___\|\|\|\|\|__\|\|_\|\|\|\|\|\|___\|\|\|\|\|\|\|\n______________AGU___ACCGA__UC_AUAAGC___ACUCUUU\n3'-CGC...UUUCA___GCA_____AA__A______UCA_______GAGAG...AAG-5'\n_____________\|________________________________\|\n_____________85_______________________________52\n	218 -- 224	53 -- 59	-20.7518 kcal/mol	5.65772 kcal/mol	4.29409 kcal/mol	198 225@LB@ \| \|@LB@5'-CAC...AUAAA AA G AUCAA...AAC-3'@LB@ UCA UGGCU AG UAUUCG UGAGAAA@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AGU ACCGA UC AUAAGC ACUCUUU@LB@3'-CGC...UUUCA GCA AA A UCA GAGAG...AAG-5'@LB@ \| \|@LB@ 85 52@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -20.7518 kcal/mol@LB@Unfolding Energy - mRNA 5.65772 kcal/mol@LB@Unfolding Energy - sRNA 4.29409 kcal/mol@LB@@LB@Position - mRNA 199 -- 224@LB@Position - sRNA 53 -- 84@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 53 -- 59@LB@
113	0.0192	0.5385	b2573	rpoE	-9.32	0.137991	165 -- 193	49 -- 83	RNA polymerase sigma E factor	_____________164___________________________________194\n_____________\|_____________________________________\|\n5'-ACA...GAUAG________AAA_______UG_________________ACCUC...UGG-3'\n______________CGCG_UGG___UUUGGUU_________GGGAGACUUU\n______________\|:\|\|_\|\|\|___\|\|\|:\|\|\|_________\|:\|\|:\|\|\|:\|\n______________GUGC_ACC___AAAUCAA_________CUCUUUGAGA\n3'-CGC...UUCAA____A___G_________UAAGCUCAA__________GCUUU...AAG-5'\n_____________\|_____________________________________\|\n_____________84____________________________________48\n	184 -- 190	52 -- 58	-21.709 kcal/mol	7.98 kcal/mol	4.40602 kcal/mol	164 194@LB@ \| \|@LB@5'-ACA...GAUAG AAA UG ACCUC...UGG-3'@LB@ CGCG UGG UUUGGUU GGGAGACUUU@LB@ \|:\|\| \|\|\| \|\|\|:\|\|\| \|:\|\|:\|\|\|:\|@LB@ GUGC ACC AAAUCAA CUCUUUGAGA@LB@3'-CGC...UUCAA A G UAAGCUCAA GCUUU...AAG-5'@LB@ \| \|@LB@ 84 48@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.709 kcal/mol@LB@Unfolding Energy - mRNA 7.98 kcal/mol@LB@Unfolding Energy - sRNA 4.40602 kcal/mol@LB@@LB@Position - mRNA 165 -- 193@LB@Position - sRNA 49 -- 83@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 52 -- 58@LB@
79	0.01412	0.5385	b2830	rppH	-5.99	0.454649	93 -- 100	64 -- 71	RNA pyrophosphohydrolase	_____________92_______101\n_____________\|________\|\n5'-UUC...CUGUG________AAUUG...GGC-3'\n______________AGUUAUUC\n______________\|\|\|\|\|\|\|\|\n______________UCAAUAAG\n3'-CGC...CGAAA________CUCAA...AAG-5'\n_____________\|________\|\n_____________72_______63\n	94 -- 100	64 -- 70	-7.84269 kcal/mol	1.74359 kcal/mol	0.11296 kcal/mol	92 101@LB@ \| \|@LB@5'-UUC...CUGUG AAUUG...GGC-3'@LB@ AGUUAUUC@LB@ \|\|\|\|\|\|\|\|@LB@ UCAAUAAG@LB@3'-CGC...CGAAA CUCAA...AAG-5'@LB@ \| \|@LB@ 72 63@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -7.84269 kcal/mol@LB@Unfolding Energy - mRNA 1.74359 kcal/mol@LB@Unfolding Energy - sRNA 0.11296 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 64 -- 71@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 64 -- 70@LB@
81	0.01462	0.5385	b3296	rpsD	-10.19	0.098165	202 -- 218	60 -- 78	30S ribosomal subunit protein S4	_____________201_________________219\n_____________\|___________________\|\n5'-AAG...GAAAA____A____A_________CCUAA...AAA-3'\n______________UGGC___AG_UAUUUGGGU\n______________\|\|\|\|___\|\|_\|\|\|\|:\|:\|\|\n______________ACCG___UC_AUAAGCUCA\n3'-CGC...GUGCA____AAA__A_________ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	212 -- 218	60 -- 66	-14.6837 kcal/mol	3.69927 kcal/mol	0.797083 kcal/mol	201 219@LB@ \| \|@LB@5'-AAG...GAAAA A A CCUAA...AAA-3'@LB@ UGGC AG UAUUUGGGU@LB@ \|\|\|\| \|\| \|\|\|\|:\|:\|\|@LB@ ACCG UC AUAAGCUCA@LB@3'-CGC...GUGCA AAA A ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -14.6837 kcal/mol@LB@Unfolding Energy - mRNA 3.69927 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 202 -- 218@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 60 -- 66@LB@
63	0.01271	0.5385	b3306	rpsH	-10.49	0.086924	89 -- 100	56 -- 67	30S ribosomal subunit protein S8	_____________88___________101\n_____________\|____________\|\n5'-AGC...CGGAA____________CCGUA...AAG-3'\n______________GUUCGGGUUGAG\n______________:\|\|\|\|:\|\|\|\|\|\|\n______________UAAGCUCAACUC\n3'-CGC...AUCAA____________UUUGA...AAG-5'\n_____________\|____________\|\n_____________68___________55\n	94 -- 100	56 -- 62	-16.8063 kcal/mol	4.74141 kcal/mol	1.57281 kcal/mol	88 101@LB@ \| \|@LB@5'-AGC...CGGAA CCGUA...AAG-3'@LB@ GUUCGGGUUGAG@LB@ :\|\|\|\|:\|\|\|\|\|\|@LB@ UAAGCUCAACUC@LB@3'-CGC...AUCAA UUUGA...AAG-5'@LB@ \| \|@LB@ 68 55@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -16.8063 kcal/mol@LB@Unfolding Energy - mRNA 4.74141 kcal/mol@LB@Unfolding Energy - sRNA 1.57281 kcal/mol@LB@@LB@Position - mRNA 89 -- 100@LB@Position - sRNA 56 -- 67@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 56 -- 62@LB@
17	0.003067	0.5385	b1628	rsxB	-11.62	0.055094	175 -- 198	58 -- 77	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________174______________________199\n_____________\|________________________\|\n5'-CAC...UUAUG_________G_____GUGA_____UAAUG...ACG-3'\n______________GGCUUUAGU_GUUUG____AGUUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|____\|\|\|\|\|\n______________CCGAAAUCA_UAAGC____UCAAC\n3'-CGC...UGCAA_________A______________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________78_______________________57\n	177 -- 183	69 -- 75	-20.3316 kcal/mol	7.50919 kcal/mol	1.19974 kcal/mol	174 199@LB@ \| \|@LB@5'-CAC...UUAUG G GUGA UAAUG...ACG-3'@LB@ GGCUUUAGU GUUUG AGUUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\| \|\|\|\|\|@LB@ CCGAAAUCA UAAGC UCAAC@LB@3'-CGC...UGCAA A UCUUU...AAG-5'@LB@ \| \|@LB@ 78 57@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -20.3316 kcal/mol@LB@Unfolding Energy - mRNA 7.50919 kcal/mol@LB@Unfolding Energy - sRNA 1.19974 kcal/mol@LB@@LB@Position - mRNA 175 -- 198@LB@Position - sRNA 58 -- 77@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 69 -- 75@LB@
67	0.01284	0.5385	b1294	sapA	-9.42	0.132690	25 -- 48	61 -- 86	antimicrobial peptide transport ABC transporter periplasmic binding protein	_____________24_________________________49\n_____________\|__________________________\|\n5'-UAC...AAGUU________GA___A_______A____AAAUC...ACA-3'\n______________GUUC_UGU__GUU_UAGUUAU__GAG\n______________\|\|\|\|_:\|\|__\|:\|_\|\|\|\|\|\|\|__\|\|\|\n______________CAAG_GCA__CGA_AUCAAUA__CUC\n3'-CGC...GUUUU____U___AC___A_______AG___AACUC...AAG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	38 -- 44	66 -- 72	-17.3513 kcal/mol	6.21881 kcal/mol	1.70915 kcal/mol	24 49@LB@ \| \|@LB@5'-UAC...AAGUU GA A A AAAUC...ACA-3'@LB@ GUUC UGU GUU UAGUUAU GAG@LB@ \|\|\|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ CAAG GCA CGA AUCAAUA CUC@LB@3'-CGC...GUUUU U AC A AG AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -17.3513 kcal/mol@LB@Unfolding Energy - mRNA 6.21881 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
110	0.0189	0.5385	b3175	secG	-9.72	0.118042	86 -- 106	67 -- 90	preprotein translocase membrane subunit	_____________85_______________________107\n_____________\|________________________\|\n5'-GCG...CUUGC__________UC____________GUAUU...CCU-3'\n______________GAAGG_UCAU____GCUUUGGUUA\n______________:\|\|:\|_\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________UUUUC_AGUG____CGAAAUCAAU\n3'-CGC...AGGCG_____A____CAAC__________AAGCU...AAG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	100 -- 106	67 -- 73	-15.607 kcal/mol	5.31183 kcal/mol	0.573552 kcal/mol	85 107@LB@ \| \|@LB@5'-GCG...CUUGC UC GUAUU...CCU-3'@LB@ GAAGG UCAU GCUUUGGUUA@LB@ :\|\|:\| \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ UUUUC AGUG CGAAAUCAAU@LB@3'-CGC...AGGCG A CAAC AAGCU...AAG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -9.72 kcal/mol@LB@Hybridization Energy -15.607 kcal/mol@LB@Unfolding Energy - mRNA 5.31183 kcal/mol@LB@Unfolding Energy - sRNA 0.573552 kcal/mol@LB@@LB@Position - mRNA 86 -- 106@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 67 -- 73@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