Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
78	0.004296	0.1855	b3258	panF	-10.37	0.118507	142 -- 153	52 -- 62	pantothenate:sodium symporter	_____________141__________154\n_____________\|____________\|\n5'-GGC...UUUAU___A________GGCGA...UUA-3'\n______________UGG_CUGUGCUG\n______________\|\|\|_\|\|\|:\|\|:\|\n______________ACC_GACGCGGC\n3'-UUU...UUAGA____________AUUUA...GUG-5'\n_____________\|____________\|\n_____________63___________51\n	147 -- 153	52 -- 58	-17.1407 kcal/mol	1.89201 kcal/mol	4.8804 kcal/mol	141 154@LB@ \| \|@LB@5'-GGC...UUUAU A GGCGA...UUA-3'@LB@ UGG CUGUGCUG@LB@ \|\|\| \|\|\|:\|\|:\|@LB@ ACC GACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -17.1407 kcal/mol@LB@Unfolding Energy - mRNA 1.89201 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 52 -- 58@LB@
80	0.004451	0.1855	b3578	yiaN	-12.19	0.052777	198 -- 212	52 -- 66	2 3-diketo-L-gulonate TRAP transporter large permease protein	_____________197_____________213\n_____________\|_______________\|\n5'-GGC...GCUUA___A___________AUUUU...UCU-3'\n______________AUC_UGGCUGUGCUG\n______________\|\|\|_\|\|\|\|\|\|:\|\|:\|\n______________UAG_ACCGACGCGGC\n3'-UUU...CCCUU___A___________AUUUA...GUG-5'\n_____________\|_______________\|\n_____________67______________51\n	206 -- 212	52 -- 58	-22.6247 kcal/mol	3.67694 kcal/mol	6.76246 kcal/mol	197 213@LB@ \| \|@LB@5'-GGC...GCUUA A AUUUU...UCU-3'@LB@ AUC UGGCUGUGCUG@LB@ \|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ UAG ACCGACGCGGC@LB@3'-UUU...CCCUU A AUUUA...GUG-5'@LB@ \| \|@LB@ 67 51@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -22.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.67694 kcal/mol@LB@Unfolding Energy - sRNA 6.76246 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 52 -- 66@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 52 -- 58@LB@
107	0.005754	0.1855	b3447	ggt	-8.41	0.270031	252 -- 270	52 -- 70	gamma-glutamyltranspeptidase	_____________251_________________271\n_____________\|___________________\|\n5'-GUU...UCUCA_______GUUUUA______CCGCC...CGU-3'\n______________GGAAGUU______GCGCCG\n______________\|\|\|\|:\|:______\|\|\|\|\|\|\n______________CCUUUAG______CGCGGC\n3'-UUU...UGGUC_______AACCGA______AUUUA...GUG-5'\n_____________\|___________________\|\n_____________71__________________51\n	252 -- 258	64 -- 70	-19.4063 kcal/mol	4.14766 kcal/mol	6.84683 kcal/mol	251 271@LB@ \| \|@LB@5'-GUU...UCUCA GUUUUA CCGCC...CGU-3'@LB@ GGAAGUU GCGCCG@LB@ \|\|\|\|:\|: \|\|\|\|\|\|@LB@ CCUUUAG CGCGGC@LB@3'-UUU...UGGUC AACCGA AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.4063 kcal/mol@LB@Unfolding Energy - mRNA 4.14766 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 252 -- 270@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 64 -- 70@LB@
166	0.009748	0.2068	b1261	trpB	-12.89	0.038353	88 -- 97	52 -- 61	tryptophan synthase beta subunit	_____________87_________98\n_____________\|__________\|\n5'-UGG...AAACC__________GACUU...UCA-3'\n______________GGCUGCGCCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCGACGCGGC\n3'-UUU...UAGAA__________AUUUA...GUG-5'\n_____________\|__________\|\n_____________62_________51\n	91 -- 97	52 -- 58	-23.3299 kcal/mol	5.56351 kcal/mol	4.87533 kcal/mol	87 98@LB@ \| \|@LB@5'-UGG...AAACC GACUU...UCA-3'@LB@ GGCUGCGCCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCGACGCGGC@LB@3'-UUU...UAGAA AUUUA...GUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -23.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.56351 kcal/mol@LB@Unfolding Energy - sRNA 4.87533 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
170	0.01004	0.2071	b3887	dtd	-7.24	0.420466	57 -- 66	52 -- 62	D-tyr-tRNA(Tyr) deacylase	_____________56__________67\n_____________\|___________\|\n5'-GGA...AUUUA___________GCGGU...UCG-3'\n______________UGG_UGUGCUG\n______________\|\|\|_\|\|:\|\|:\|\n______________ACC_ACGCGGC\n3'-UUU...UUAGA___G_______AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	60 -- 66	52 -- 58	-13.8062 kcal/mol	1.68508 kcal/mol	4.8804 kcal/mol	56 67@LB@ \| \|@LB@5'-GGA...AUUUA GCGGU...UCG-3'@LB@ UGG UGUGCUG@LB@ \|\|\| \|\|:\|\|:\|@LB@ ACC ACGCGGC@LB@3'-UUU...UUAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.8062 kcal/mol@LB@Unfolding Energy - mRNA 1.68508 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 57 -- 66@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 52 -- 58@LB@
172	0.0102	0.2071	b1383	ydbL	-9.96	0.141752	21 -- 31	52 -- 62	DUF1318 family protein	_____________20__________32\n_____________\|___________\|\n5'-AAA...UUUAC___________ACGUC...UAG-3'\n______________UGGCUGCGUUG\n______________\|\|\|\|\|\|\|\|::\|\n______________ACCGACGCGGC\n3'-UUU...UUAGA___________AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	25 -- 31	52 -- 58	-19.6889 kcal/mol	4.85225 kcal/mol	4.8804 kcal/mol	20 32@LB@ \| \|@LB@5'-AAA...UUUAC ACGUC...UAG-3'@LB@ UGGCUGCGUUG@LB@ \|\|\|\|\|\|\|\|::\|@LB@ ACCGACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -19.6889 kcal/mol@LB@Unfolding Energy - mRNA 4.85225 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 21 -- 31@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 52 -- 58@LB@
181	0.0108	0.2089	b1683	sufB	-11.33	0.077347	153 -- 175	52 -- 74	component of SufBCD Fe-S cluster assembly scaffold	_____________152_______________________176\n_____________\|_________________________\|\n5'-GUU...AAAGC____AAU___UG__________G__AAAGC...AGC-3'\n______________CCAG___GAA____UGGCUGUG_CG\n______________\|\|\|\|___\|\|\|____\|\|\|\|\|\|:\|_\|\|\n______________GGUC___CUU____ACCGACGC_GC\n3'-UUU...GUUGU____C_____UAGA________G__AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________75________________________51\n	166 -- 172	55 -- 61	-23.8546 kcal/mol	3.76094 kcal/mol	8.7601 kcal/mol	152 176@LB@ \| \|@LB@5'-GUU...AAAGC AAU UG G AAAGC...AGC-3'@LB@ CCAG GAA UGGCUGUG CG@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:\| \|\|@LB@ GGUC CUU ACCGACGC GC@LB@3'-UUU...GUUGU C UAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -23.8546 kcal/mol@LB@Unfolding Energy - mRNA 3.76094 kcal/mol@LB@Unfolding Energy - sRNA 8.7601 kcal/mol@LB@@LB@Position - mRNA 153 -- 175@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 55 -- 61@LB@
189	0.01136	0.2116	b3413	gntX	-9.78	0.152759	211 -- 235	52 -- 76	DNA catabolic protein	_____________210_______________________236\n_____________\|_________________________\|\n5'-CCC...AACAG_______AUU__GC_____A_____AAUGC...AUA-3'\n______________UACCGGG___AU__UGGCU_UGCCG\n______________:\|\|\|:\|\|___\|\|__\|\|\|\|\|_:\|\|\|\|\n______________GUGGUCC___UA__ACCGA_GCGGC\n3'-UUU...CGGUU_______CUU__GA_____C_____AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________77________________________51\n	211 -- 217	70 -- 76	-26.9968 kcal/mol	7.94838 kcal/mol	9.26585 kcal/mol	210 236@LB@ \| \|@LB@5'-CCC...AACAG AUU GC A AAUGC...AUA-3'@LB@ UACCGGG AU UGGCU UGCCG@LB@ :\|\|\|:\|\| \|\| \|\|\|\|\| :\|\|\|\|@LB@ GUGGUCC UA ACCGA GCGGC@LB@3'-UUU...CGGUU CUU GA C AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.9968 kcal/mol@LB@Unfolding Energy - mRNA 7.94838 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 70 -- 76@LB@
191	0.01171	0.2159	b4221	tamB	-9.06	0.207346	81 -- 101	52 -- 76	translocation and assembly module for autotransporter export inner membrane subunit	_____________80_________________________102\n_____________\|__________________________\|\n5'-ACC...ACCGG__________________G_______GGAAU...AUC-3'\n______________UACCGGGG___UC__GGC_UGCGCUG\n______________:\|\|\|:\|\|\|___\|\|__\|\|\|_\|\|\|\|\|:\|\n______________GUGGUCCC___AG__CCG_ACGCGGC\n3'-UUU...CGGUU________UUU__AA___________AUUUA...GUG-5'\n_____________\|__________________________\|\n_____________77_________________________51\n	95 -- 101	52 -- 58	-29.4253 kcal/mol	11.0996 kcal/mol	9.26585 kcal/mol	80 102@LB@ \| \|@LB@5'-ACC...ACCGG G GGAAU...AUC-3'@LB@ UACCGGGG UC GGC UGCGCUG@LB@ :\|\|\|:\|\|\| \|\| \|\|\| \|\|\|\|\|:\|@LB@ GUGGUCCC AG CCG ACGCGGC@LB@3'-UUU...CGGUU UUU AA AUUUA...GUG-5'@LB@ \| \|@LB@ 77 51@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -29.4253 kcal/mol@LB@Unfolding Energy - mRNA 11.0996 kcal/mol@LB@Unfolding Energy - sRNA 9.26585 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 52 -- 76@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 52 -- 58@LB@
5	5.466e-05	0.03849	b0713	ybgL	-10.83	0.096857	234 -- 242	53 -- 61	UPF0271 family protein	_____________233_______243\n_____________\|_________\|\n5'-GCC...GCGAA_________AGCGA...AUG-3'\n______________GGCUGCGCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCGACGCGG\n3'-UUU...UAGAA_________CAUUU...GUG-5'\n_____________\|_________\|\n_____________62________52\n	236 -- 242	53 -- 59	-22.2033 kcal/mol	6.50503 kcal/mol	4.87107 kcal/mol	233 243@LB@ \| \|@LB@5'-GCC...GCGAA AGCGA...AUG-3'@LB@ GGCUGCGCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCGACGCGG@LB@3'-UUU...UAGAA CAUUU...GUG-5'@LB@ \| \|@LB@ 62 52@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 6.50503 kcal/mol@LB@Unfolding Energy - sRNA 4.87107 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 53 -- 61@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 53 -- 59@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