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
194	0.01194	0.2159	b3454	livF	-10.01	0.138607	25 -- 47	72 -- 86	branched-chain amino acid ABC transporter ATPase	_____________24______________________48\n_____________\|_______________________\|\n5'-AGA...GCCGA_______AAUCAUCA________CUAUC...UUG-3'\n______________ACUGCGC________CAACACCA\n______________\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________UGACGCG________GUUGUGGU\n3'-UUU...GCUUA_______________________CCCUU...GUG-5'\n_____________\|_______________________\|\n_____________87______________________71\n	41 -- 47	72 -- 78	-22.1496 kcal/mol	4.90616 kcal/mol	7.23529 kcal/mol	24 48@LB@ \| \|@LB@5'-AGA...GCCGA AAUCAUCA CUAUC...UUG-3'@LB@ ACUGCGC CAACACCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACGCG GUUGUGGU@LB@3'-UUU...GCUUA CCCUU...GUG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -22.1496 kcal/mol@LB@Unfolding Energy - mRNA 4.90616 kcal/mol@LB@Unfolding Energy - sRNA 7.23529 kcal/mol@LB@@LB@Position - mRNA 25 -- 47@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 72 -- 78@LB@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease	_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
54	0.002681	0.1727	b3201	lptB	-14.37	0.019597	275 -- 293	64 -- 82	lipopolysaccharide export ABC transporter ATPase	_____________274_________________294\n_____________\|___________________\|\n5'-UUC...CUGAC_______U___________GUCGGUC-3'\n______________CGUCAAC_CCGGGGAAAUU\n______________\|\|:\|\|\|\|_\|\|:\|\|\|\|\|\|\|:\n______________GCGGUUG_GGUCCCUUUAG\n3'-UUU...AUGAC_______U___________AACCG...GUG-5'\n_____________\|___________________\|\n_____________83__________________63\n	287 -- 293	64 -- 70	-27.6824 kcal/mol	6.24463 kcal/mol	7.07066 kcal/mol	274 294@LB@ \| \|@LB@5'-UUC...CUGAC U GUCGGUC-3'@LB@ CGUCAAC CCGGGGAAAUU@LB@ \|\|:\|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ GCGGUUG GGUCCCUUUAG@LB@3'-UUU...AUGAC U AACCG...GUG-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -14.37 kcal/mol@LB@Hybridization Energy -27.6824 kcal/mol@LB@Unfolding Energy - mRNA 6.24463 kcal/mol@LB@Unfolding Energy - sRNA 7.07066 kcal/mol@LB@@LB@Position - mRNA 275 -- 293@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 64 -- 70@LB@
135	0.007679	0.1993	b0096	lpxC	-11.14	0.084212	289 -- 298	76 -- 85	UDP-3-O-acyl N-acetylglucosamine deacetylase	_____________288________299\n_____________\|__________\|\n5'-GAA...ACGCC__________CA-3'\n______________CUGCGCCGGC\n______________\|\|\|\|\|\|\|::\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	292 -- 298	76 -- 82	-18.1767 kcal/mol	1.93848 kcal/mol	5.09564 kcal/mol	288 299@LB@ \| \|@LB@5'-GAA...ACGCC CA-3'@LB@ CUGCGCCGGC@LB@ \|\|\|\|\|\|\|::\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.93848 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 76 -- 82@LB@
53	0.002649	0.1727	b2289	lrhA	-9.83	0.149509	112 -- 119	68 -- 75	transcriptional repressor of flagellar motility and chemotaxis genes	_____________111______120\n_____________\|________\|\n5'-CUG...AAACU________GGCAC...CCG-3'\n______________GCCAGGGA\n______________:\|\|\|\|\|\|\|\n______________UGGUCCCU\n3'-UUU...GGUUG________UUAGA...GUG-5'\n_____________\|________\|\n_____________76_______67\n	113 -- 119	68 -- 74	-14.981 kcal/mol	1.464 kcal/mol	3.68273 kcal/mol	111 120@LB@ \| \|@LB@5'-CUG...AAACU GGCAC...CCG-3'@LB@ GCCAGGGA@LB@ :\|\|\|\|\|\|\|@LB@ UGGUCCCU@LB@3'-UUU...GGUUG UUAGA...GUG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.981 kcal/mol@LB@Unfolding Energy - mRNA 1.464 kcal/mol@LB@Unfolding Energy - sRNA 3.68273 kcal/mol@LB@@LB@Position - mRNA 112 -- 119@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 68 -- 74@LB@
174	0.01024	0.2071	b0889	lrp	-11.01	0.089440	79 -- 112	38 -- 78	leucine-responsive global transcriptional regulator	_____________78________________________________________113\n_____________\|_________________________________________\|\n5'-GUG...CCGUA_________C______________________CU_C_____UUCGG...AGC-3'\n______________GAC_CCAGG___AUU___GC_GCGCCGUGAAU__U_AUGAU\n______________:\|\|_\|\|\|\|\|___\|\|:___\|\|_\|\|\|\|\|\|\|:\|\|\|__\|_\|\|\|\|\|\n______________UUG_GGUCC___UAG___CG_CGCGGCAUUUA__A_UACUA\n3'-UUU...CGCGG___U_____CUU___AAC__A___________AU_A_____CUCAA...GUG-5'\n_____________\|_________________________________________\|\n_____________79________________________________________37\n	96 -- 102	48 -- 54	-32.0055 kcal/mol	11.6338 kcal/mol	9.36467 kcal/mol	78 113@LB@ \| \|@LB@5'-GUG...CCGUA C CU C UUCGG...AGC-3'@LB@ GAC CCAGG AUU GC GCGCCGUGAAU U AUGAU@LB@ :\|\| \|\|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\|\|\| \| \|\|\|\|\|@LB@ UUG GGUCC UAG CG CGCGGCAUUUA A UACUA@LB@3'-UUU...CGCGG U CUU AAC A AU A CUCAA...GUG-5'@LB@ \| \|@LB@ 79 37@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -32.0055 kcal/mol@LB@Unfolding Energy - mRNA 11.6338 kcal/mol@LB@Unfolding Energy - sRNA 9.36467 kcal/mol@LB@@LB@Position - mRNA 79 -- 112@LB@Position - sRNA 38 -- 78@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 48 -- 54@LB@
96	0.005105	0.1855	b0870	ltaE	-12.99	0.036706	93 -- 116	68 -- 88	L-allo-threonine aldolase PLP-dependent	_____________92_______________________117\n_____________\|________________________\|\n5'-GUC...UGUAU_________G___U______C___CGCGG...ACC-3'\n______________AUGCUGCGC_CAA_CAUCAG_GGA\n______________\|\|:\|\|\|\|\|\|_\|\|\|_\|\|:\|\|\|_\|\|\|\n______________UAUGACGCG_GUU_GUGGUC_CCU\n3'-UUU...GCGCU________________________UUAGA...GUG-5'\n_____________\|________________________\|\n_____________89_______________________67\n	95 -- 101	80 -- 86	-29.0922 kcal/mol	8.72289 kcal/mol	7.38144 kcal/mol	92 117@LB@ \| \|@LB@5'-GUC...UGUAU G U C CGCGG...ACC-3'@LB@ AUGCUGCGC CAA CAUCAG GGA@LB@ \|\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\| \|\|\|@LB@ UAUGACGCG GUU GUGGUC CCU@LB@3'-UUU...GCGCU UUAGA...GUG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -29.0922 kcal/mol@LB@Unfolding Energy - mRNA 8.72289 kcal/mol@LB@Unfolding Energy - sRNA 7.38144 kcal/mol@LB@@LB@Position - mRNA 93 -- 116@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 80 -- 86@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3	_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
66	0.003275	0.1727	b0394	mak	-8.12	0.303293	18 -- 92	5 -- 77	manno(fructo)kinase	_____________17_______________________________________________________________________________93\n_____________\|________________________________________________________________________________\|\n5'-GUU...CUUCU____G___C_______CGC____AA_A_G_____CC____AAUUUUUGA_______________GAUAA____CAC____UUGUC...GUG-3'\n______________GCAC_CAG_GAAAUCU___GGCU__G_C_GUAAA__AUUA_________AC_____CACAGCAU_____UUUC___GGCC\n______________:\|\|\|_\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|__\|_\|_\|\|\|\|\|__\|\|\|\|_________\|\|_____\|\|\|\|\|\|\|:_____\|\|\|\|___\|\|\|\|\n______________UGUG_GUC_CUUUAGA___CCGA__C_G_CAUUU__UAAU_________UG_____GUGUCGUG_____AAAG___CCGG\n3'-UUU...GCGGU________C_______A______CG___G_____AA____ACUACUCAA__UUCCC________ACAA_____U______CGUG-5'\n_____________\|________________________________________________________________________________\|\n_____________78_______________________________________________________________________________4\n	70 -- 76	18 -- 24	-46.4183 kcal/mol	15.5654 kcal/mol	22.7286 kcal/mol	17 93@LB@ \| \|@LB@5'-GUU...CUUCU G C CGC AA A G CC AAUUUUUGA GAUAA CAC UUGUC...GUG-3'@LB@ GCAC CAG GAAAUCU GGCU G C GUAAA AUUA AC CACAGCAU UUUC GGCC@LB@ :\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| \| \| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ UGUG GUC CUUUAGA CCGA C G CAUUU UAAU UG GUGUCGUG AAAG CCGG@LB@3'-UUU...GCGGU C A CG G AA ACUACUCAA UUCCC ACAA U CGUG-5'@LB@ \| \|@LB@ 78 4@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -46.4183 kcal/mol@LB@Unfolding Energy - mRNA 15.5654 kcal/mol@LB@Unfolding Energy - sRNA 22.7286 kcal/mol@LB@@LB@Position - mRNA 18 -- 92@LB@Position - sRNA 5 -- 77@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 18 -- 24@LB@
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator	_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@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