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
31	0.0009469	0.09599	b0166	dapD	-11.60	0.005180	96 -- 124	11 -- 40	2 3 4 5-tetrahydropyridine-2-carboxylate N-succinyltransferase	_____________95_____________________________125\n_____________\|______________________________\|\n5'-UUG...GGCGU________UAACGA_______G________GCAUC...AGG-3'\n______________GCGCUUAA_______GUUGCA_CAGGAAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|:\|\|_\|\|\|\|\|\|:\|\n______________CGUGAAUU_______CAAUGU_GUCCUUUA\n3'-UUU...UUCUU________UUUUAAG______G________GACUA...CAA-5'\n_____________\|______________________________\|\n_____________41_____________________________10\n	97 -- 103	33 -- 39	-29.7713 kcal/mol	8.96001 kcal/mol	9.20882 kcal/mol	95 125@LB@ \| \|@LB@5'-UUG...GGCGU UAACGA G GCAUC...AGG-3'@LB@ GCGCUUAA GUUGCA CAGGAAGU@LB@ \|\|:\|\|\|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ CGUGAAUU CAAUGU GUCCUUUA@LB@3'-UUU...UUCUU UUUUAAG G GACUA...CAA-5'@LB@ \| \|@LB@ 41 10@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -29.7713 kcal/mol@LB@Unfolding Energy - mRNA 8.96001 kcal/mol@LB@Unfolding Energy - sRNA 9.20882 kcal/mol@LB@@LB@Position - mRNA 96 -- 124@LB@Position - sRNA 11 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 33 -- 39@LB@
32	0.0009536	0.09599	b0637	rsfS	-12.32	0.003012	197 -- 230	23 -- 59	ribosomal silencing factor	_____________196___________________________________231\n_____________\|_____________________________________\|\n5'-AUU...GGGGA________A_______________CC____U______AUCGA...UCA-3'\n______________AAACUUGC__GGGUA__AAGCACU__AGGA_UUUGUU\n______________\|\|\|\|\|\|\|\|__::\|:\|__\|\|\|\|\|\|\|__\|::\|_\|\|:\|\|\|\n______________UUUGAACG__UUCGU__UUCGUGA__UUUU_AAGCAA\n3'-UUU...CCUAC________AA_____UC_______AU____U______UGUGG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________22\n	211 -- 217	36 -- 42	-25.7611 kcal/mol	7.16036 kcal/mol	6.27609 kcal/mol	196 231@LB@ \| \|@LB@5'-AUU...GGGGA A CC U AUCGA...UCA-3'@LB@ AAACUUGC GGGUA AAGCACU AGGA UUUGUU@LB@ \|\|\|\|\|\|\|\| ::\|:\| \|\|\|\|\|\|\| \|::\| \|\|:\|\|\|@LB@ UUUGAACG UUCGU UUCGUGA UUUU AAGCAA@LB@3'-UUU...CCUAC AA UC AU U UGUGG...CAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -12.32 kcal/mol@LB@Hybridization Energy -25.7611 kcal/mol@LB@Unfolding Energy - mRNA 7.16036 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 197 -- 230@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@LB@
33	0.001071	0.1045	b2058	wcaB	-10.41	0.012241	46 -- 64	25 -- 42	putative acyl transferase	_____________45__________________65\n_____________\|___________________\|\n5'-ACC...ACCGC______AA___C_______ACCGC...AGA-3'\n______________AAGCAC__AGA_AAAUUCG\n______________\|\|\|\|\|\|__\|:\|_\|\|\|\|\|\|\|\n______________UUCGUG__UUU_UUUAAGC\n3'-UUU...CGUUC______AA___________AAUGU...CAA-5'\n_____________\|___________________\|\n_____________43__________________24\n	58 -- 64	25 -- 31	-12.8013 kcal/mol	0.745291 kcal/mol	1.64855 kcal/mol	45 65@LB@ \| \|@LB@5'-ACC...ACCGC AA C ACCGC...AGA-3'@LB@ AAGCAC AGA AAAUUCG@LB@ \|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ UUCGUG UUU UUUAAGC@LB@3'-UUU...CGUUC AA AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -12.8013 kcal/mol@LB@Unfolding Energy - mRNA 0.745291 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 46 -- 64@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 25 -- 31@LB@
34	0.001265	0.1198	b0826	moeB	-10.82	0.009172	276 -- 295	26 -- 46	molybdopterin synthase sulfurylase	_____________275___________________296\n_____________\|_____________________\|\n5'-CUU...ACGGC_____________________UCGCG-3'\n______________CAGGAGGCGC_UGAAAGAUUC\n______________\|\|:\|\|:\|\|:\|_\|:\|\|\|:\|\|\|\|\n______________GUUCUUCGUG_AUUUUUUAAG\n3'-UUU...AAUUC__________A__________CAAUG...CAA-5'\n_____________\|_____________________\|\n_____________47____________________25\n	289 -- 295	26 -- 32	-23.0973 kcal/mol	6.15128 kcal/mol	6.13041 kcal/mol	275 296@LB@ \| \|@LB@5'-CUU...ACGGC UCGCG-3'@LB@ CAGGAGGCGC UGAAAGAUUC@LB@ \|\|:\|\|:\|\|:\| \|:\|\|\|:\|\|\|\|@LB@ GUUCUUCGUG AUUUUUUAAG@LB@3'-UUU...AAUUC A CAAUG...CAA-5'@LB@ \| \|@LB@ 47 25@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -23.0973 kcal/mol@LB@Unfolding Energy - mRNA 6.15128 kcal/mol@LB@Unfolding Energy - sRNA 6.13041 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 26 -- 46@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 26 -- 32@LB@
35	0.001338	0.121	b0405	queA	-9.92	0.017135	73 -- 106	26 -- 60	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	_____________72____________________________________107\n_____________\|_____________________________________\|\n5'-GGG...UCCGC_____GG___A__U_____U_________________AUCGA...GGC-3'\n______________GAGAU__GCU_AA_GCAGG_GAGC___UAAAAAAUUC\n______________\|\|:\|:__\|\|\|_\|\|_\|\|\|:\|_:\|\|\|___\|\|\|\|\|\|\|\|\|\|\n______________CUUUG__CGA_UU_CGUUC_UUCG___AUUUUUUAAG\n3'-UUU...CCCUA_____AA___A_____________UGA__________CAAUG...CAA-5'\n_____________\|_____________________________________\|\n_____________61____________________________________25\n	100 -- 106	26 -- 32	-25.4572 kcal/mol	9.25896 kcal/mol	6.27609 kcal/mol	72 107@LB@ \| \|@LB@5'-GGG...UCCGC GG A U U AUCGA...GGC-3'@LB@ GAGAU GCU AA GCAGG GAGC UAAAAAAUUC@LB@ \|\|:\|: \|\|\| \|\| \|\|\|:\| :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CUUUG CGA UU CGUUC UUCG AUUUUUUAAG@LB@3'-UUU...CCCUA AA A UGA CAAUG...CAA-5'@LB@ \| \|@LB@ 61 25@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -25.4572 kcal/mol@LB@Unfolding Energy - mRNA 9.25896 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 73 -- 106@LB@Position - sRNA 26 -- 60@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 26 -- 32@LB@
36	0.001384	0.121	b2573	rpoE	-5.96	0.197133	163 -- 178	25 -- 41	RNA polymerase sigma E factor	_____________162_______________179\n_____________\|_________________\|\n5'-ACA...UCGAU_____GU__________GUUUG...UGG-3'\n______________AGCGC___GGAAAUUUG\n______________\|\|\|:\|___::\|\|\|\|\|:\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	172 -- 178	25 -- 31	-12.5895 kcal/mol	4.97735 kcal/mol	1.64839 kcal/mol	162 179@LB@ \| \|@LB@5'-ACA...UCGAU GU GUUUG...UGG-3'@LB@ AGCGC GGAAAUUUG@LB@ \|\|\|:\| ::\|\|\|\|\|:\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -5.96 kcal/mol@LB@Hybridization Energy -12.5895 kcal/mol@LB@Unfolding Energy - mRNA 4.97735 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 25 -- 31@LB@
37	0.00139	0.121	b2222	atoA	-4.53	0.397320	265 -- 276	25 -- 38	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________264____________277\n_____________\|______________\|\n5'-CGC...CGUUA______________GUUUA...AUU-3'\n______________ACUUAGGGA__UCG\n______________\|\|\|\|\|:::\|__\|\|\|\n______________UGAAUUUUU__AGC\n3'-UUU...CUUCG_________UA___AAUGU...CAA-5'\n_____________\|______________\|\n_____________39_____________24\n	266 -- 272	31 -- 37	-7.73128 kcal/mol	1.76584 kcal/mol	1.4343 kcal/mol	264 277@LB@ \| \|@LB@5'-CGC...CGUUA GUUUA...AUU-3'@LB@ ACUUAGGGA UCG@LB@ \|\|\|\|\|:::\| \|\|\|@LB@ UGAAUUUUU AGC@LB@3'-UUU...CUUCG UA AAUGU...CAA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -4.53 kcal/mol@LB@Hybridization Energy -7.73128 kcal/mol@LB@Unfolding Energy - mRNA 1.76584 kcal/mol@LB@Unfolding Energy - sRNA 1.4343 kcal/mol@LB@@LB@Position - mRNA 265 -- 276@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 31 -- 37@LB@
38	0.00143	0.1212	b3315	rplV	-7.95	0.062235	2 -- 19	23 -- 40	50S ribosomal subunit protein L22	_____________1__________________20\n_____________\|__________________\|\n__________5'-C________UCCCG_____CAACG...UGG-3'\n______________GCACUUGG_____UCGUU\n______________\|\|\|\|\|\|::_____\|\|\|\|\|\n______________CGUGAAUU_____AGCAA\n3'-UUU...UUCUU________UUUUA_____UGUGG...CAA-5'\n_____________\|__________________\|\n_____________41_________________22\n	3 -- 9	33 -- 39	-14.4443 kcal/mol	4.84591 kcal/mol	1.64885 kcal/mol	1 20@LB@ \| \|@LB@ 5'-C UCCCG CAACG...UGG-3'@LB@ GCACUUGG UCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|@LB@ CGUGAAUU AGCAA@LB@3'-UUU...UUCUU UUUUA UGUGG...CAA-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -14.4443 kcal/mol@LB@Unfolding Energy - mRNA 4.84591 kcal/mol@LB@Unfolding Energy - sRNA 1.64885 kcal/mol@LB@@LB@Position - mRNA 2 -- 19@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 33 -- 39@LB@
39	0.00159	0.1292	b1637	tyrS	-8.51	0.043578	178 -- 203	5 -- 27	tyrosyl-tRNA synthetase	_____________177________________________204\n_____________\|__________________________\|\n5'-CAU...UGCAG_________A__U_______U_____GCAAG...CGA-3'\n______________UCGUUAUAU_CA_GGAGAUU_UGAUG\n______________\|\|\|\|\|\|:\|:_\|\|_\|\|\|:\|\|:_\|\|\|\|\|\n______________AGCAAUGUG_GU_CCUUUAG_ACUAC\n3'-UUU...UUUUA__________________________ACAA-5'\n_____________\|__________________________\|\n_____________28_________________________4\n	191 -- 197	10 -- 16	-22.7194 kcal/mol	5.60368 kcal/mol	8.60118 kcal/mol	177 204@LB@ \| \|@LB@5'-CAU...UGCAG A U U GCAAG...CGA-3'@LB@ UCGUUAUAU CA GGAGAUU UGAUG@LB@ \|\|\|\|\|\|:\|: \|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ AGCAAUGUG GU CCUUUAG ACUAC@LB@3'-UUU...UUUUA ACAA-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -22.7194 kcal/mol@LB@Unfolding Energy - mRNA 5.60368 kcal/mol@LB@Unfolding Energy - sRNA 8.60118 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
40	0.001639	0.1292	b0156	erpA	-9.82	0.018424	105 -- 133	14 -- 48	iron-sulfur cluster insertion protein	_____________104_________________________________134\n_____________\|___________________________________\|\n5'-UAG...CAGCC________________________AA_________UAUUA...UAC-3'\n______________AGCGAGAA_UACUUGAA_____CG__AUACCAGGG\n______________\|\|\|:\|\|\|\|_:\|\|\|\|:\|\|_____\|\|__\|:\|\|\|\|\|\|:\n______________UCGUUCUU_GUGAAUUU_____GC__UGUGGUCCU\n3'-UUU...CGAAU________C________UUUAA__AA_________UUAGA...CAA-5'\n_____________\|___________________________________\|\n_____________49__________________________________13\n	127 -- 133	14 -- 20	-29.1703 kcal/mol	5.55319 kcal/mol	13.801 kcal/mol	104 134@LB@ \| \|@LB@5'-UAG...CAGCC AA UAUUA...UAC-3'@LB@ AGCGAGAA UACUUGAA CG AUACCAGGG@LB@ \|\|\|:\|\|\|\| :\|\|\|\|:\|\| \|\| \|:\|\|\|\|\|\|:@LB@ UCGUUCUU GUGAAUUU GC UGUGGUCCU@LB@3'-UUU...CGAAU C UUUAA AA UUAGA...CAA-5'@LB@ \| \|@LB@ 49 13@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -29.1703 kcal/mol@LB@Unfolding Energy - mRNA 5.55319 kcal/mol@LB@Unfolding Energy - sRNA 13.801 kcal/mol@LB@@LB@Position - mRNA 105 -- 133@LB@Position - sRNA 14 -- 48@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 14 -- 20@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