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	Additional homologs
68	0.001174	0.05856	b1253	yciA	-8.30	0.130708	128 -- 145	3 -- 21	acyl-CoA esterase		_____________127__________________146\n_____________\|____________________\|\n5'-UUU...CGCUG______________UC____CAGGA...GGU-3'\n______________UAUCU__CCUCUGU__UCCU\n______________:\|\|\|\|__\|\|\|\|\|\|\|__:\|\|\|\n______________GUAGA__GGAGACA__GGGA\n3'-AUU...AUCUU_____AU_______U_____UG-5'\n_____________\|____________________\|\n_____________22___________________2\n	133 -- 139	8 -- 14	-17.321 kcal/mol	1.04882 kcal/mol	7.99052 kcal/mol	127 146@LB@ \| \|@LB@5'-UUU...CGCUG UC CAGGA...GGU-3'@LB@ UAUCU CCUCUGU UCCU@LB@ :\|\|\|\| \|\|\|\|\|\|\| :\|\|\|@LB@ GUAGA GGAGACA GGGA@LB@3'-AUU...AUCUU AU U UG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -8.30 kcal/mol@LB@Hybridization Energy -17.321 kcal/mol@LB@Unfolding Energy - mRNA 1.04882 kcal/mol@LB@Unfolding Energy - sRNA 7.99052 kcal/mol@LB@@LB@Position - mRNA 128 -- 145@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 8 -- 14@LB@
182	0.007896	0.1519	b0686	ybfF	-7.34	0.221050	164 -- 170	2 -- 8	acyl-CoA esterase		_____________163_____171\n_____________\|_______\|\n5'-CUU...CAUAA_______ACCCG...GCG-3'\n______________UACCCUA\n______________\|\|\|\|\|\|\|\n______________AUGGGAU\n3'-AUU...GAGAC_______G-5'\n_____________\|_______\|\n_____________9_______1\n	164 -- 170	2 -- 8	-9.7212 kcal/mol	0.292492 kcal/mol	2.11083 kcal/mol	163 171@LB@ \| \|@LB@5'-CUU...CAUAA ACCCG...GCG-3'@LB@ UACCCUA@LB@ \|\|\|\|\|\|\|@LB@ AUGGGAU@LB@3'-AUU...GAGAC G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -9.7212 kcal/mol@LB@Unfolding Energy - mRNA 0.292492 kcal/mol@LB@Unfolding Energy - sRNA 2.11083 kcal/mol@LB@@LB@Position - mRNA 164 -- 170@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 2 -- 8@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@
11	3.674e-05	0.01134	b2099	yegU	-10.44	0.033453	166 -- 229	3 -- 59	ADP-ribosylglycohydrolase family protein		_____________165_________________________________________________________________230\n_____________\|___________________________________________________________________\|\n5'-GUG...UCGAU____G____AU____U___CAC______AAGUUAAA_____AC________AU______G_______UUAUG...CAC-3'\n______________GAUC_CGAU__UGCG_UGA___AAGGGG________UGAAA___AGAACGU____UCUC_GUGCUCU\n______________:\|\|\|_\|\|\|\|__\|:\|\|_\|\|\|___\|\|::\|\|________\|\|\|\|\|___\|\|\|\|\|:\|____:\|\|\|_\|\|:\|:\|\|\n______________UUAG_GCUA__AUGC_ACU___UUUUCC________ACUUU___UCUUGUA____GGAG_CAUGGGA\n3'-AUU...UCGGU___________________UCA______AG___________CUA_______GAAU____A_______UG-5'\n_____________\|___________________________________________________________________\|\n_____________60__________________________________________________________________2\n	223 -- 229	3 -- 9	-36.2809 kcal/mol	13.1575 kcal/mol	12.7026 kcal/mol	165 230@LB@ \| \|@LB@5'-GUG...UCGAU G AU U CAC AAGUUAAA AC AU G UUAUG...CAC-3'@LB@ GAUC CGAU UGCG UGA AAGGGG UGAAA AGAACGU UCUC GUGCUCU@LB@ :\|\|\| \|\|\|\| \|:\|\| \|\|\| \|\|::\|\| \|\|\|\|\| \|\|\|\|\|:\| :\|\|\| \|\|:\|:\|\|@LB@ UUAG GCUA AUGC ACU UUUUCC ACUUU UCUUGUA GGAG CAUGGGA@LB@3'-AUU...UCGGU UCA AG CUA GAAU A UG-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -36.2809 kcal/mol@LB@Unfolding Energy - mRNA 13.1575 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 166 -- 229@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 3 -- 9@LB@
31	0.0003178	0.03519	b3588	aldB	-11.98	0.010708	83 -- 100	1 -- 16	aldehyde dehydrogenase B		_____________82_________________101\n_____________\|__________________\|\n5'-GAA...UCAAC__________A___U___CCGUA...GGG-3'\n______________UAUCUCUGUA_CCC_UGC\n______________\|\|:\|\|\|\|\|\|\|_\|\|\|_\|:\|\n______________AUGGAGACAU_GGG_AUG\n3'-AUU...GUAGA__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	86 -- 92	7 -- 13	-19.6311 kcal/mol	1.07825 kcal/mol	6.59719 kcal/mol	82 101@LB@ \| \|@LB@5'-GAA...UCAAC A U CCGUA...GGG-3'@LB@ UAUCUCUGUA CCC UGC@LB@ \|\|:\|\|\|\|\|\|\| \|\|\| \|:\|@LB@ AUGGAGACAU GGG AUG@LB@3'-AUU...GUAGA -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.6311 kcal/mol@LB@Unfolding Energy - mRNA 1.07825 kcal/mol@LB@Unfolding Energy - sRNA 6.59719 kcal/mol@LB@@LB@Position - mRNA 83 -- 100@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 7 -- 13@LB@
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@
176	0.007357	0.147	b2905	gcvT	-7.40	0.214118	198 -- 224	6 -- 30	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex		_____________197__________________________225\n_____________\|____________________________\|\n5'-CUG...AGGAC_______CAC____GACU__________GAACA...AAA-3'\n______________AAGAUGG___AACA_____CCUUUGUAC\n______________\|\|\|\|\|:\|___\|\|\|\|_____\|\|\|:\|\|\|\|\|\n______________UUCUAUC___UUGU_____GGAGACAUG\n3'-AUU...AGACU______________AGAAU_________GGAUG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	218 -- 224	6 -- 12	-21.3805 kcal/mol	5.97871 kcal/mol	8.02863 kcal/mol	197 225@LB@ \| \|@LB@5'-CUG...AGGAC CAC GACU GAACA...AAA-3'@LB@ AAGAUGG AACA CCUUUGUAC@LB@ \|\|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\|\|\|@LB@ UUCUAUC UUGU GGAGACAUG@LB@3'-AUU...AGACU AGAAU GGAUG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 5.97871 kcal/mol@LB@Unfolding Energy - sRNA 8.02863 kcal/mol@LB@@LB@Position - mRNA 198 -- 224@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 6 -- 12@LB@
26	0.0002109	0.02687	b4122	fumB	-13.50	0.002989	276 -- 286	47 -- 57	anaerobic class I fumarate hydratase (fumarase B)	b1612	_____________275_________287\n_____________\|___________\|\n5'-UCC...UCACU___________UAGCG...ACU-3'\n______________UCCGAUUACGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AGGCUAAUGCA\n3'-AUU...GGUUU___________CUUCA...AUG-5'\n_____________\|___________\|\n_____________58__________46\n	280 -- 286	47 -- 53	-16.5827 kcal/mol	1.51899 kcal/mol	1.56839 kcal/mol	275 287@LB@ \| \|@LB@5'-UCC...UCACU UAGCG...ACU-3'@LB@ UCCGAUUACGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AGGCUAAUGCA@LB@3'-AUU...GGUUU CUUCA...AUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -16.5827 kcal/mol@LB@Unfolding Energy - mRNA 1.51899 kcal/mol@LB@Unfolding Energy - sRNA 1.56839 kcal/mol@LB@@LB@Position - mRNA 276 -- 286@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 47 -- 53@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase		_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@LB@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA		_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@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