Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
96	0.002764	0.1002	b1034	ycdX	-5.77	0.451964	102 -- 115	32 -- 46	alkaline phosphatase	_____________101_____________116\n_____________\|_______________\|\n5'-GGC...AAAAA_______________CGGGC...AAC-3'\n______________GGGG_AGAGGGUCUG\n______________\|::\|_\|:\|:\|\|\|\|\|\|\n______________CUUC_UUUUCCAGAC\n3'-AUU...AUGCA____A__________UUUCU...AUG-5'\n_____________\|_______________\|\n_____________47______________31\n	109 -- 115	32 -- 38	-16.8058 kcal/mol	3.54072 kcal/mol	7.24668 kcal/mol	101 116@LB@ \| \|@LB@5'-GGC...AAAAA CGGGC...AAC-3'@LB@ GGGG AGAGGGUCUG@LB@ \|::\| \|:\|:\|\|\|\|\|\|@LB@ CUUC UUUUCCAGAC@LB@3'-AUU...AUGCA A UUUCU...AUG-5'@LB@ \| \|@LB@ 47 31@LB@@LB@@LB@Energy -5.77 kcal/mol@LB@Hybridization Energy -16.8058 kcal/mol@LB@Unfolding Energy - mRNA 3.54072 kcal/mol@LB@Unfolding Energy - sRNA 7.24668 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 32 -- 46@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 32 -- 38@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)	_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@LB@
98	0.002849	0.1023	b0772	ybhC	-6.17	0.383539	27 -- 33	49 -- 55	acyl-CoA thioesterase lipoprotein	_____________26______34\n_____________\|_______\|\n5'-UCA...CGCCU_______UGCGA...AUC-3'\n______________CGAUUAC\n______________\|\|\|\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	27 -- 33	49 -- 55	-7.86935 kcal/mol	1.39337 kcal/mol	0.311712 kcal/mol	26 34@LB@ \| \|@LB@5'-UCA...CGCCU UGCGA...AUC-3'@LB@ CGAUUAC@LB@ \|\|\|\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.86935 kcal/mol@LB@Unfolding Energy - mRNA 1.39337 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 27 -- 33@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 49 -- 55@LB@
99	0.00311	0.1096	b2801	fucP	-13.12	0.004165	162 -- 172	46 -- 56	L-fucose transporter	_____________161_________173\n_____________\|___________\|\n5'-AUG...CAUAA___________CUUAA...CAC-3'\n______________CCGAUUACGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCAC\n3'-AUU...GUUUA___________UUCAU...AUG-5'\n_____________\|___________\|\n_____________57__________45\n	166 -- 172	46 -- 52	-17.4041 kcal/mol	2.44124 kcal/mol	1.86194 kcal/mol	161 173@LB@ \| \|@LB@5'-AUG...CAUAA CUUAA...CAC-3'@LB@ CCGAUUACGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCAC@LB@3'-AUU...GUUUA UUCAU...AUG-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -17.4041 kcal/mol@LB@Unfolding Energy - mRNA 2.44124 kcal/mol@LB@Unfolding Energy - sRNA 1.86194 kcal/mol@LB@@LB@Position - mRNA 162 -- 172@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 46 -- 52@LB@
100	0.003115	0.1096	b0353	mhpT	-8.28	0.132596	137 -- 146	48 -- 57	3-hydroxyphenylpropionic transporter	_____________136________147\n_____________\|__________\|\n5'-CGG...AUAGU__________CGGCU...CGG-3'\n______________UCUGAUUACG\n______________\|\|:\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	140 -- 146	48 -- 54	-13.4725 kcal/mol	3.61374 kcal/mol	1.55976 kcal/mol	136 147@LB@ \| \|@LB@5'-CGG...AUAGU CGGCU...CGG-3'@LB@ UCUGAUUACG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -8.28 kcal/mol@LB@Hybridization Energy -13.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.61374 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 137 -- 146@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 48 -- 54@LB@
101	0.00315	0.1097	b1822	rlmA	-7.85	0.169074	182 -- 190	1 -- 9	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________181_______191\n_____________\|_________\|\n5'-AAG...CUUUA_________CGGAG...GGU-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	184 -- 190	1 -- 7	-13.1594 kcal/mol	3.20778 kcal/mol	2.12872 kcal/mol	181 191@LB@ \| \|@LB@5'-AAG...CUUUA CGGAG...GGU-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -13.1594 kcal/mol@LB@Unfolding Energy - mRNA 3.20778 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 182 -- 190@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
102	0.003218	0.1101	b3816	corA	-9.85	0.049984	130 -- 160	4 -- 37	magnesium/nickel/cobalt transporter	_____________129_________________________________161\n_____________\|___________________________________\|\n5'-ACC...UUAAU_________CCCA________GUU___G_______ACCGA...AAC-3'\n______________GGUCUGAAA________AUUU___UCU_UGUGCCC\n______________\|\|\|\|\|\|\|\|\|________\|\|:\|___:\|\|_\|\|\|:\|\|\|\n______________CCAGACUUU________UAGA___GGA_ACAUGGG\n3'-AUU...AUUUU_________CUAUCUUG____AU____G_______AUG-5'\n_____________\|___________________________________\|\n_____________38__________________________________3\n	154 -- 160	4 -- 10	-28.4013 kcal/mol	7.22925 kcal/mol	11.3428 kcal/mol	129 161@LB@ \| \|@LB@5'-ACC...UUAAU CCCA GUU G ACCGA...AAC-3'@LB@ GGUCUGAAA AUUU UCU UGUGCCC@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| :\|\| \|\|\|:\|\|\|@LB@ CCAGACUUU UAGA GGA ACAUGGG@LB@3'-AUU...AUUUU CUAUCUUG AU G AUG-5'@LB@ \| \|@LB@ 38 3@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -28.4013 kcal/mol@LB@Unfolding Energy - mRNA 7.22925 kcal/mol@LB@Unfolding Energy - sRNA 11.3428 kcal/mol@LB@@LB@Position - mRNA 130 -- 160@LB@Position - sRNA 4 -- 37@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 4 -- 10@LB@
103	0.003241	0.1101	b0837	yliI	-8.40	0.123505	223 -- 230	4 -- 11	soluble aldose sugar dehydrogenase	_____________222______231\n_____________\|________\|\n5'-GUC...UUUCC________CUUAU...AAC-3'\n______________UUGUGCCC\n______________:\|\|\|:\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	224 -- 230	4 -- 10	-12.324 kcal/mol	0.491988 kcal/mol	3.45361 kcal/mol	222 231@LB@ \| \|@LB@5'-GUC...UUUCC CUUAU...AAC-3'@LB@ UUGUGCCC@LB@ :\|\|\|:\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.324 kcal/mol@LB@Unfolding Energy - mRNA 0.491988 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 223 -- 230@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 4 -- 10@LB@
104	0.003257	0.1101	b0858	ybjO	-8.07	0.149394	228 -- 257	2 -- 30	DUF2593 family inner membrane protein	_____________227______________________________258\n_____________\|________________________________\|\n5'-AUG...UUUUU____A__________C_____A__CU_G____AAUGU...UUA-3'\n______________AAGA___AACAUCUU_AUCUC_UG__C_CCUG\n______________\|\|\|\|___\|\|\|\|\|\|\|\|_\|:\|\|\|_\|\|__\|_\|\|\|:\n______________UUCU___UUGUAGAA_UGGAG_AC__G_GGAU\n3'-AUU...AGACU____AUC_________________AU______G-5'\n_____________\|________________________________\|\n_____________31_______________________________1\n	234 -- 240	16 -- 22	-20.5501 kcal/mol	4.45089 kcal/mol	8.05308 kcal/mol	227 258@LB@ \| \|@LB@5'-AUG...UUUUU A C A CU G AAUGU...UUA-3'@LB@ AAGA AACAUCUU AUCUC UG C CCUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\| \|\| \| \|\|\|:@LB@ UUCU UUGUAGAA UGGAG AC G GGAU@LB@3'-AUU...AGACU AUC AU G-5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.5501 kcal/mol@LB@Unfolding Energy - mRNA 4.45089 kcal/mol@LB@Unfolding Energy - sRNA 8.05308 kcal/mol@LB@@LB@Position - mRNA 228 -- 257@LB@Position - sRNA 2 -- 30@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 16 -- 22@LB@
105	0.003348	0.1101	b2218	rcsC	-11.03	0.021992	174 -- 214	1 -- 37	hybrid sensory kinase in two-component regulatory system with RcsB and YojN	_____________173_______________________________________215\n_____________\|_________________________________________\|\n5'-AGC...CCAUC____ACCU____C_____U__GCC______AAA________UUCUU...CCG-3'\n______________GGUC____GAGG_GGAGC_UC___CCUUUG___UACCUUGC\n______________\|\|\|\|____:\|\|:_:\|\|:\|_\|\|___\|\|\|:\|\|___\|\|\|\|:\|:\|\n______________CCAG____UUCU_UCUUG_AG___GGAGAC___AUGGGAUG\n3'-AUU...AUUUU____ACU_____A_____U__AAU_________________-5'\n_____________\|________________________________________\|\n_____________38_______________________________________1\n	208 -- 214	1 -- 7	-33.3544 kcal/mol	10.9963 kcal/mol	11.3499 kcal/mol	173 215@LB@ \| \|@LB@5'-AGC...CCAUC ACCU C U GCC AAA UUCUU...CCG-3'@LB@ GGUC GAGG GGAGC UC CCUUUG UACCUUGC@LB@ \|\|\|\| :\|\|: :\|\|:\| \|\| \|\|\|:\|\| \|\|\|\|:\|:\|@LB@ CCAG UUCU UCUUG AG GGAGAC AUGGGAUG@LB@3'-AUU...AUUUU ACU A U AAU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -33.3544 kcal/mol@LB@Unfolding Energy - mRNA 10.9963 kcal/mol@LB@Unfolding Energy - sRNA 11.3499 kcal/mol@LB@@LB@Position - mRNA 174 -- 214@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@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