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
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@
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@
25	0.0007384	0.09021	b3434	yhgN	-11.94	0.004015	159 -- 197	7 -- 41	UPF0056 family inner membrane protein	_____________158_____________________________________198\n_____________\|_______________________________________\|\n5'-UUU...UUGUU_____GC_______CCG__GCAAU_______________GUUAU...CGA-3'\n______________AGCAC__AGAAAGU___CG_____UAUCAGGGAAUUUGA\n______________\|\|\|\|\|__\|:\|\|\|:\|___\|\|_____:\|:\|\|\|\|:\|\|\|:\|\|\|\n______________UCGUG__UUUUUUA___GC_____GUGGUCCUUUAGACU\n3'-UUU...GUUCU_____AA_______A____AAU_________________ACACAA-5'\n_____________\|_______________________________________\|\n_____________42______________________________________6\n	188 -- 194	10 -- 16	-30.001 kcal/mol	8.83552 kcal/mol	9.22092 kcal/mol	158 198@LB@ \| \|@LB@5'-UUU...UUGUU GC CCG GCAAU GUUAU...CGA-3'@LB@ AGCAC AGAAAGU CG UAUCAGGGAAUUUGA@LB@ \|\|\|\|\| \|:\|\|\|:\| \|\| :\|:\|\|\|\|:\|\|\|:\|\|\|@LB@ UCGUG UUUUUUA GC GUGGUCCUUUAGACU@LB@3'-UUU...GUUCU AA A AAU ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -11.94 kcal/mol@LB@Hybridization Energy -30.001 kcal/mol@LB@Unfolding Energy - mRNA 8.83552 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 159 -- 197@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 10 -- 16@LB@
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@LB@
117	0.009786	0.2694	b1706	ydiU	-6.16	0.177349	6 -- 27	36 -- 55	UPF0061 family protein	_____________5______________________28\n_____________\|______________________\|\n______5'-UGCAA____AUCAUU____________GAUAC...AUA-3'\n______________UUGC______GCGGGAGGCAUU\n______________\|\|\|\|______\|\|::\|\|:\|\|\|:\|\n______________AACG______CGUUCUUCGUGA\n3'-UUU...CUUUG____AAUU______________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	21 -- 27	36 -- 42	-19.2761 kcal/mol	6.93839 kcal/mol	6.17795 kcal/mol	5 28@LB@ \| \|@LB@ 5'-UGCAA AUCAUU GAUAC...AUA-3'@LB@ UUGC GCGGGAGGCAUU@LB@ \|\|\|\| \|\|::\|\|:\|\|\|:\|@LB@ AACG CGUUCUUCGUGA@LB@3'-UUU...CUUUG AAUU AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.16 kcal/mol@LB@Hybridization Energy -19.2761 kcal/mol@LB@Unfolding Energy - mRNA 6.93839 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 36 -- 42@LB@
177	0.02045	0.3721	b3148	yraN	-6.85	0.120614	263 -- 276	37 -- 54	UPF0102 family protein	_____________262________________277\n_____________\|__________________\|\n5'-GGU...GGCGA__________________AAGCG...GCA-3'\n______________UGC____GUGGGAAGCAC\n______________\|\|\|____\|:::\|\|\|\|\|\|\|\n______________ACG____CGUUCUUCGUG\n3'-UUU...UUUGA___AAUU___________AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	270 -- 276	37 -- 43	-17.1481 kcal/mol	4.14332 kcal/mol	6.1584 kcal/mol	262 277@LB@ \| \|@LB@5'-GGU...GGCGA AAGCG...GCA-3'@LB@ UGC GUGGGAAGCAC@LB@ \|\|\| \|:::\|\|\|\|\|\|\|@LB@ ACG CGUUCUUCGUG@LB@3'-UUU...UUUGA AAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -17.1481 kcal/mol@LB@Unfolding Energy - mRNA 4.14332 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 37 -- 43@LB@
122	0.01076	0.2828	b1908	yecA	-7.65	0.074805	79 -- 96	18 -- 40	UPF0149 family protein	_____________78_______________________97\n_____________\|________________________\|\n5'-UAC...UGCCU__A_____________________CUCCU...UGG-3'\n______________GC_ACUUG______UCGUUACACC\n______________\|\|_\|\|\|\|:______\|\|\|\|\|\|\|\|\|\|\n______________CG_UGAAU______AGCAAUGUGG\n3'-UUU...UUCUU________UUUUUA__________UCCUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________17\n	90 -- 96	18 -- 24	-19.1188 kcal/mol	2.30438 kcal/mol	9.1639 kcal/mol	78 97@LB@ \| \|@LB@5'-UAC...UGCCU A CUCCU...UGG-3'@LB@ GC ACUUG UCGUUACACC@LB@ \|\| \|\|\|\|: \|\|\|\|\|\|\|\|\|\|@LB@ CG UGAAU AGCAAUGUGG@LB@3'-UUU...UUCUU UUUUUA UCCUU...CAA-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -19.1188 kcal/mol@LB@Unfolding Energy - mRNA 2.30438 kcal/mol@LB@Unfolding Energy - sRNA 9.1639 kcal/mol@LB@@LB@Position - mRNA 79 -- 96@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 18 -- 24@LB@
43	0.001794	0.1344	b0631	ybeD	-7.18	0.099343	171 -- 193	16 -- 40	UPF0250 family protein	_____________170________________________194\n_____________\|__________________________\|\n5'-GCU...GAGUU__U______UUA______________AGCUG...AAG-3'\n______________GC_AUUUAA______CGUUACGCCGG\n______________\|\|_\|:\|\|\|\|______\|\|\|\|\|\|:\|\|:\|\n______________CG_UGAAUU______GCAAUGUGGUC\n3'-UUU...UUCUU_________UUUUAA___________CUUUA...CAA-5'\n_____________\|__________________________\|\n_____________41_________________________15\n	187 -- 193	16 -- 22	-19.4847 kcal/mol	3.10673 kcal/mol	9.1996 kcal/mol	170 194@LB@ \| \|@LB@5'-GCU...GAGUU U UUA AGCUG...AAG-3'@LB@ GC AUUUAA CGUUACGCCGG@LB@ \|\| \|:\|\|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ CG UGAAUU GCAAUGUGGUC@LB@3'-UUU...UUCUU UUUUAA CUUUA...CAA-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -19.4847 kcal/mol@LB@Unfolding Energy - mRNA 3.10673 kcal/mol@LB@Unfolding Energy - sRNA 9.1996 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 16 -- 22@LB@
171	0.01957	0.3668	b2498	upp	-5.84	0.210430	244 -- 265	42 -- 61	uracil phosphoribosyltransferase	_____________243____________________266\n_____________\|______________________\|\n5'-GGC...CAAGC_______GA___G_________UAUCA...CCG-3'\n______________UGGGACU__UGC_UGAGCAAGA\n______________\|\|::\|\|\|__\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACUUUGA__ACG_AUUCGUUCU\n3'-UUU...GCCCU____________A_________UCGUG...CAA-5'\n_____________\|______________________\|\n_____________62_____________________41\n	259 -- 265	42 -- 48	-21.1169 kcal/mol	8.03919 kcal/mol	7.23689 kcal/mol	243 266@LB@ \| \|@LB@5'-GGC...CAAGC GA G UAUCA...CCG-3'@LB@ UGGGACU UGC UGAGCAAGA@LB@ \|\|::\|\|\| \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACUUUGA ACG AUUCGUUCU@LB@3'-UUU...GCCCU A UCGUG...CAA-5'@LB@ \| \|@LB@ 62 41@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -21.1169 kcal/mol@LB@Unfolding Energy - mRNA 8.03919 kcal/mol@LB@Unfolding Energy - sRNA 7.23689 kcal/mol@LB@@LB@Position - mRNA 244 -- 265@LB@Position - sRNA 42 -- 61@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@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)

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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

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