Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
68	0.003533	0.1645	b3650	spoT	-9.27	0.026581	116 -- 140	36 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase	_____________115________________________141\n_____________\|__________________________\|\n5'-UAG...CGCCA_____A___AA___________C___GAAUU...CUC-3'\n______________GGAAC__GC__GAGCAGGAAGC_GCU\n______________\|:\|\|\|__\|\|__:\|\|\|\|:\|\|\|\|\|_:\|\|\n______________CUUUG__CG__UUCGUUCUUCG_UGA\n3'-UUU...CCCUA_____AA__AA_______________AUUUU...CAA-5'\n_____________\|__________________________\|\n_____________61_________________________35\n	130 -- 136	39 -- 45	-24.6059 kcal/mol	9.08429 kcal/mol	6.24973 kcal/mol	115 141@LB@ \| \|@LB@5'-UAG...CGCCA A AA C GAAUU...CUC-3'@LB@ GGAAC GC GAGCAGGAAGC GCU@LB@ \|:\|\|\| \|\| :\|\|\|\|:\|\|\|\|\| :\|\|@LB@ CUUUG CG UUCGUUCUUCG UGA@LB@3'-UUU...CCCUA AA AA AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -24.6059 kcal/mol@LB@Unfolding Energy - mRNA 9.08429 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 116 -- 140@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 39 -- 45@LB@
17	0.0004446	0.08107	b1976	mtfA	-9.25	0.026966	241 -- 268	36 -- 59	anti-repressor for DgsA(Mlc)	_____________240___________________________269\n_____________\|_____________________________\|\n5'-AUA...ACAUC________CCUUCCCU_____________AUCGA...AAC-3'\n______________AAAC_UGC________GGCAGGAAGCACU\n______________\|\|\|\|_\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|\n______________UUUG_ACG________UCGUUCUUCGUGA\n3'-UUU...CCUAC____A___AAU__________________AUUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________35\n	262 -- 268	36 -- 42	-23.9855 kcal/mol	8.48573 kcal/mol	6.24948 kcal/mol	240 269@LB@ \| \|@LB@5'-AUA...ACAUC CCUUCCCU AUCGA...AAC-3'@LB@ AAAC UGC GGCAGGAAGCACU@LB@ \|\|\|\| \|\|\| :\|\|\|:\|\|\|\|\|\|\|\|@LB@ UUUG ACG UCGUUCUUCGUGA@LB@3'-UUU...CCUAC A AAU AUUUU...CAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.9855 kcal/mol@LB@Unfolding Energy - mRNA 8.48573 kcal/mol@LB@Unfolding Energy - sRNA 6.24948 kcal/mol@LB@@LB@Position - mRNA 241 -- 268@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 36 -- 42@LB@
194	0.02335	0.3864	b4182	yjfJ	-9.08	0.030148	209 -- 238	10 -- 37	PspA/IM30 family protein	_____________208____________________________239\n_____________\|______________________________\|\n5'-GAA...GGAAU____________AU______UG________GUUUA...AGC-3'\n______________UUUAAAAAGUUU__UUACGC__GGGAAAUC\n______________:\|\|\|\|\|\|\|:\|\|:__\|\|\|\|:\|__:\|\|\|\|\|\|\|\n______________GAAUUUUUUAAG__AAUGUG__UCCUUUAG\n3'-UUU...UUCGU____________C_______G_________ACUAC...CAA-5'\n_____________\|______________________________\|\n_____________38_____________________________9\n	232 -- 238	10 -- 16	-23.4786 kcal/mol	5.49388 kcal/mol	8.90309 kcal/mol	208 239@LB@ \| \|@LB@5'-GAA...GGAAU AU UG GUUUA...AGC-3'@LB@ UUUAAAAAGUUU UUACGC GGGAAAUC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ GAAUUUUUUAAG AAUGUG UCCUUUAG@LB@3'-UUU...UUCGU C G ACUAC...CAA-5'@LB@ \| \|@LB@ 38 9@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -23.4786 kcal/mol@LB@Unfolding Energy - mRNA 5.49388 kcal/mol@LB@Unfolding Energy - sRNA 8.90309 kcal/mol@LB@@LB@Position - mRNA 209 -- 238@LB@Position - sRNA 10 -- 37@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 10 -- 16@LB@
132	0.01257	0.3067	b2516	rodZ	-8.98	0.032240	231 -- 240	34 -- 43	MreB assembly cytoskeletal protein	_____________230________241\n_____________\|__________\|\n5'-UAA...AAAAU__________CUACC...UUG-3'\n______________GAAGCACUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CUUCGUGAAU\n3'-UUU...UCGUU__________UUUUU...CAA-5'\n_____________\|__________\|\n_____________44_________33\n	234 -- 240	34 -- 40	-13.7965 kcal/mol	1.10051 kcal/mol	3.71643 kcal/mol	230 241@LB@ \| \|@LB@5'-UAA...AAAAU CUACC...UUG-3'@LB@ GAAGCACUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CUUCGUGAAU@LB@3'-UUU...UCGUU UUUUU...CAA-5'@LB@ \| \|@LB@ 44 33@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.7965 kcal/mol@LB@Unfolding Energy - mRNA 1.10051 kcal/mol@LB@Unfolding Energy - sRNA 3.71643 kcal/mol@LB@@LB@Position - mRNA 231 -- 240@LB@Position - sRNA 34 -- 43@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 34 -- 40@LB@
167	0.01879	0.3614	b4383	deoB	-8.94	0.033088	90 -- 118	37 -- 59	phosphopentomutase	_____________89____________________________119\n_____________\|_____________________________\|\n5'-AGG...CAAUU________CGAUA_____CC__A______ACCAA...AUA-3'\n______________AAACUUGC_____AAGCA__GG_AAGCAC\n______________\|\|\|\|\|\|\|\|_____\|\|\|\|\|__:\|_\|\|\|\|\|\|\n______________UUUGAACG_____UUCGU__UC_UUCGUG\n3'-UUU...CCUAC________AA___________________AAUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________36\n	91 -- 97	52 -- 58	-21.3309 kcal/mol	6.14475 kcal/mol	6.24627 kcal/mol	89 119@LB@ \| \|@LB@5'-AGG...CAAUU CGAUA CC A ACCAA...AUA-3'@LB@ AAACUUGC AAGCA GG AAGCAC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\| :\| \|\|\|\|\|\|@LB@ UUUGAACG UUCGU UC UUCGUG@LB@3'-UUU...CCUAC AA AAUUU...CAA-5'@LB@ \| \|@LB@ 60 36@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -21.3309 kcal/mol@LB@Unfolding Energy - mRNA 6.14475 kcal/mol@LB@Unfolding Energy - sRNA 6.24627 kcal/mol@LB@@LB@Position - mRNA 90 -- 118@LB@Position - sRNA 37 -- 59@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
139	0.01338	0.3093	b3765	yifB	-8.91	0.033732	103 -- 139	26 -- 57	magnesium chelatase family protein and putative transcriptional regulator	_____________102______________________________________140\n_____________\|________________________________________\|\n5'-AAA...ACUUC______ACAAA___A_____AUC__C______________ACGAA...CGA-3'\n______________ACUUGC_____UAA_CAGGA___AG_CACU___AAAAUUC\n______________\|\|\|\|\|\|_____\|\|\|_\|\|:\|\|___\|\|_\|\|\|\|___\|\|\|\|\|\|\|\n______________UGAACG_____AUU_GUUCU___UC_GUGA___UUUUAAG\n3'-UUU...UACUU______A_______C_______________AUU_______CAAUG...CAA-5'\n_____________\|________________________________________\|\n_____________58_______________________________________25\n	133 -- 139	26 -- 32	-18.0428 kcal/mol	2.85625 kcal/mol	6.27605 kcal/mol	102 140@LB@ \| \|@LB@5'-AAA...ACUUC ACAAA A AUC C ACGAA...CGA-3'@LB@ ACUUGC UAA CAGGA AG CACU AAAAUUC@LB@ \|\|\|\|\|\| \|\|\| \|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UGAACG AUU GUUCU UC GUGA UUUUAAG@LB@3'-UUU...UACUU A C AUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -18.0428 kcal/mol@LB@Unfolding Energy - mRNA 2.85625 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 103 -- 139@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 26 -- 32@LB@
63	0.003338	0.1645	b2671	ygaC	-8.88	0.034356	231 -- 246	25 -- 40	uncharacterized protein	_____________230______________247\n_____________\|________________\|\n5'-UAU...CGCGC____________G___GUUUU...AAA-3'\n______________GUACUUGAAAAA_UCG\n______________\|:\|\|\|\|:\|\|\|\|\|_\|\|\|\n______________CGUGAAUUUUUU_AGC\n3'-UUU...UUCUU____________A___AAUGU...CAA-5'\n_____________\|________________\|\n_____________41_______________24\n	231 -- 237	34 -- 40	-15.9773 kcal/mol	5.44668 kcal/mol	1.64821 kcal/mol	230 247@LB@ \| \|@LB@5'-UAU...CGCGC G GUUUU...AAA-3'@LB@ GUACUUGAAAAA UCG@LB@ \|:\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ CGUGAAUUUUUU AGC@LB@3'-UUU...UUCUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -15.9773 kcal/mol@LB@Unfolding Energy - mRNA 5.44668 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 231 -- 246@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 34 -- 40@LB@
13	0.0002543	0.06302	b3583	sgbE	-8.82	0.035786	171 -- 191	39 -- 61	L-ribulose-5-phosphate 4-epimerase	_____________170_____________________192\n_____________\|_______________________\|\n5'-CAA...UGGAU__________GUAU_________UGGAU...ACG-3'\n______________UGAAGC__GC____GCAGGAGGC\n______________\|\|\|\|:\|__\|\|____\|\|\|:\|\|:\|\|\n______________ACUUUG__CG____CGUUCUUCG\n3'-UUU...GCCCU______AA__AAUU_________UGAAU...CAA-5'\n_____________\|_______________________\|\n_____________62______________________38\n	185 -- 191	39 -- 45	-21.2799 kcal/mol	5.20492 kcal/mol	7.25518 kcal/mol	170 192@LB@ \| \|@LB@5'-CAA...UGGAU GUAU UGGAU...ACG-3'@LB@ UGAAGC GC GCAGGAGGC@LB@ \|\|\|\|:\| \|\| \|\|\|:\|\|:\|\|@LB@ ACUUUG CG CGUUCUUCG@LB@3'-UUU...GCCCU AA AAUU UGAAU...CAA-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 5.20492 kcal/mol@LB@Unfolding Energy - sRNA 7.25518 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 39 -- 45@LB@
121	0.01057	0.2813	b0452	tesB	-8.75	0.037433	210 -- 223	26 -- 40	acyl-CoA thioesterase 2	_____________209_____________224\n_____________\|_______________\|\n5'-CAA...GUCAG_______________ACUGA...AGG-3'\n______________GCGC_UAAAAAAUUU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|:\n______________CGUG_AUUUUUUAAG\n3'-UUU...UUCUU____A__________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	217 -- 223	26 -- 32	-10.9054 kcal/mol	0.50684 kcal/mol	1.64811 kcal/mol	209 224@LB@ \| \|@LB@5'-CAA...GUCAG ACUGA...AGG-3'@LB@ GCGC UAAAAAAUUU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:@LB@ CGUG AUUUUUUAAG@LB@3'-UUU...UUCUU A CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -10.9054 kcal/mol@LB@Unfolding Energy - mRNA 0.50684 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 210 -- 223@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 26 -- 32@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit	_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@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