Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
52	0.0006076	0.04117	b1119	nagK	-11.33	0.051615	175 -- 204	40 -- 71	N-acetyl-D-glucosamine kinase	_____________174_______________________________205\n_____________\|_________________________________\|\n5'-UCA...UAAAG______CA______C______C___________AUUAC...GUG-3'\n______________GCAGUA__UUAAAA_AAGGAG____GGCAAUGU\n______________\|\|\|\|\|\|__\|:\|\|\|\|_\|\|\|\|\|:____\|:\|\|\|\|:\|\n______________CGUCAU__AGUUUU_UUCCUU____CUGUUAUA\n3'-UUU...CGAUA______UA_____________CAUU________CCUCG...ACG-5'\n_____________\|_________________________________\|\n_____________72________________________________39\n	197 -- 203	41 -- 47	-22.8361 kcal/mol	5.88825 kcal/mol	5.61718 kcal/mol	174 205@LB@ \| \|@LB@5'-UCA...UAAAG CA C C AUUAC...GUG-3'@LB@ GCAGUA UUAAAA AAGGAG GGCAAUGU@LB@ \|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\|: \|:\|\|\|\|:\|@LB@ CGUCAU AGUUUU UUCCUU CUGUUAUA@LB@3'-UUU...CGAUA UA CAUU CCUCG...ACG-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -22.8361 kcal/mol@LB@Unfolding Energy - mRNA 5.88825 kcal/mol@LB@Unfolding Energy - sRNA 5.61718 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 41 -- 47@LB@
53	0.0006788	0.04512	b3949	frwC	-10.17	0.100438	200 -- 218	68 -- 90	putative enzyme IIC component of PTS	_____________199_____________________219\n_____________\|_______________________\|\n5'-UUG...CAGCU_______G_______________AUCCU...UGG-3'\n______________UAUGAAU_AGUUG____GUGCAG\n______________\|\|:\|\|\|\|_\|:\|\|\|____:\|\|\|\|\|\n______________AUGCUUA_UUAAC____UACGUC\n3'-UUU...GCAGC_______G_____ACGA______AUUAA...ACG-5'\n_____________\|_______________________\|\n_____________91______________________67\n	200 -- 206	84 -- 90	-18.2816 kcal/mol	3.60123 kcal/mol	4.51505 kcal/mol	199 219@LB@ \| \|@LB@5'-UUG...CAGCU G AUCCU...UGG-3'@LB@ UAUGAAU AGUUG GUGCAG@LB@ \|\|:\|\|\|\| \|:\|\|\| :\|\|\|\|\|@LB@ AUGCUUA UUAAC UACGUC@LB@3'-UUU...GCAGC G ACGA AUUAA...ACG-5'@LB@ \| \|@LB@ 91 67@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -18.2816 kcal/mol@LB@Unfolding Energy - mRNA 3.60123 kcal/mol@LB@Unfolding Energy - sRNA 4.51505 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 68 -- 90@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 84 -- 90@LB@
54	0.0007167	0.04676	b0147	ligT	-15.11	0.004153	163 -- 244	1 -- 81	2'-5' RNA ligase	_____________162_________________________________________________________________________________________245\n_____________\|___________________________________________________________________________________________\|\n5'-CCA...GCCAC_____A__AUC___________UAACC_______CCU__C____CU__AC_____________CUUU___AUC__________________AGAAA...CGG-3'\n______________AUUGU_GC___GCGGUAAUUCA_______GAGUG___CA_AUGU__GA__CGCAACGUCUGUU____GCU___GAC_______UUACCUGC\n______________\|\|\|\|\|_\|\|___\|\|:\|\|\|\|\|\|\|\|_______:\|\|\|:___\|\|_\|\|:\|__\|\|__\|\|\|\|\|\|\|:\|::\|:____\|\|\|___\|\|\|_______\|:\|\|\|\|\|\|\n______________UAACA_CG___CGUCAUUAAGU_______UUCAU___GU_UAUA__CU__GCGUUGCGGGUAG____CGA___CUG_______AGUGGACG\n3'-UUU...UUAGU________AUA___________UUUUUCC_____UCU_______C___C_____________________A_____CAACGUA________-5'\n_____________\|__________________________________________________________________________________________\|\n_____________82_________________________________________________________________________________________1\n	238 -- 244	1 -- 7	-55.1488 kcal/mol	19.3452 kcal/mol	20.694 kcal/mol	162 245@LB@ \| \|@LB@5'-CCA...GCCAC A AUC UAACC CCU C CU AC CUUU AUC AGAAA...CGG-3'@LB@ AUUGU GC GCGGUAAUUCA GAGUG CA AUGU GA CGCAACGUCUGUU GCU GAC UUACCUGC@LB@ \|\|\|\|\| \|\| \|\|:\|\|\|\|\|\|\|\| :\|\|\|: \|\| \|\|:\| \|\| \|\|\|\|\|\|\|:\|::\|: \|\|\| \|\|\| \|:\|\|\|\|\|\|@LB@ UAACA CG CGUCAUUAAGU UUCAU GU UAUA CU GCGUUGCGGGUAG CGA CUG AGUGGACG@LB@3'-UUU...UUAGU AUA UUUUUCC UCU C C A CAACGUA -5'@LB@ \| \|@LB@ 82 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -55.1488 kcal/mol@LB@Unfolding Energy - mRNA 19.3452 kcal/mol@LB@Unfolding Energy - sRNA 20.694 kcal/mol@LB@@LB@Position - mRNA 163 -- 244@LB@Position - sRNA 1 -- 81@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 1 -- 7@LB@
55	0.0007336	0.04699	b0585	fes	-14.13	0.008457	197 -- 228	46 -- 77	enterobactin/ferrienterobactin esterase	_____________196________________________________229\n_____________\|__________________________________\|\n5'-CAU...GGUUA__G____A___CG_________U___________GCUGG...GGU-3'\n______________UG_UGUG_CGG____UUAAAAG_AGGAAGUGAGA\n______________\|\|_\|:\|\|_\|:\|____\|:\|\|\|\|:_\|\|\|\|\|\|\|:\|\|\|\n______________AC_AUAC_GUC____AGUUUUU_UCCUUCAUUCU\n3'-UUU...UUAAC__G________AUUA___________________GUUAU...ACG-5'\n_____________\|__________________________________\|\n_____________78_________________________________45\n	222 -- 228	46 -- 52	-26.4508 kcal/mol	7.03406 kcal/mol	5.29333 kcal/mol	196 229@LB@ \| \|@LB@5'-CAU...GGUUA G A CG U GCUGG...GGU-3'@LB@ UG UGUG CGG UUAAAAG AGGAAGUGAGA@LB@ \|\| \|:\|\| \|:\| \|:\|\|\|\|: \|\|\|\|\|\|\|:\|\|\|@LB@ AC AUAC GUC AGUUUUU UCCUUCAUUCU@LB@3'-UUU...UUAAC G AUUA GUUAU...ACG-5'@LB@ \| \|@LB@ 78 45@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -26.4508 kcal/mol@LB@Unfolding Energy - mRNA 7.03406 kcal/mol@LB@Unfolding Energy - sRNA 5.29333 kcal/mol@LB@@LB@Position - mRNA 197 -- 228@LB@Position - sRNA 46 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 46 -- 52@LB@
56	0.0007477	0.04704	b2777	queE	-11.99	0.034574	197 -- 232	45 -- 77	7-carboxy-7-deazaguanine synthase; queosine biosynthesis	_____________196___________________________________233\n_____________\|_____________________________________\|\n5'-AAU...GAGAA____________CC____UU__C_A__U__UCC____CCUGC...UUG-3'\n______________UGCUAUGCAGUA___CGA__AA_G_GA_GU___AGAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|___\|:\|__\|\|_\|_\|\|_\|\|___\|\|\|\|\n______________ACGAUACGUCAU___GUU__UU_C_CU_CA___UCUG\n3'-UUU...UUAAC____________UAA___UU_______U__U______UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________78____________________________________44\n	202 -- 208	66 -- 72	-23.7263 kcal/mol	6.13303 kcal/mol	5.60521 kcal/mol	196 233@LB@ \| \|@LB@5'-AAU...GAGAA CC UU C A U UCC CCUGC...UUG-3'@LB@ UGCUAUGCAGUA CGA AA G GA GU AGAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \|:\| \|\| \| \|\| \|\| \|\|\|\|@LB@ ACGAUACGUCAU GUU UU C CU CA UCUG@LB@3'-UUU...UUAAC UAA UU U U UUAUA...ACG-5'@LB@ \| \|@LB@ 78 44@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -23.7263 kcal/mol@LB@Unfolding Energy - mRNA 6.13303 kcal/mol@LB@Unfolding Energy - sRNA 5.60521 kcal/mol@LB@@LB@Position - mRNA 197 -- 232@LB@Position - sRNA 45 -- 77@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 66 -- 72@LB@
57	0.0009345	0.05776	b3755	yieP	-11.62	0.043293	183 -- 203	41 -- 61	putative transcriptional regulator	_____________182____________________204\n_____________\|______________________\|\n5'-UUC...AAAAA___________A__________CCUUU...CCG-3'\n______________GAAAAAGGAAG_UAAG_UAAUG\n______________:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|_:\|\|\|:\n______________UUUUUUCCUUC_AUUC_GUUAU\n3'-UUU...UUAAG________________U_____ACCUC...ACG-5'\n_____________\|______________________\|\n_____________62_____________________40\n	187 -- 193	51 -- 57	-16.3745 kcal/mol	2.38082 kcal/mol	2.36907 kcal/mol	182 204@LB@ \| \|@LB@5'-UUC...AAAAA A CCUUU...CCG-3'@LB@ GAAAAAGGAAG UAAG UAAUG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|:@LB@ UUUUUUCCUUC AUUC GUUAU@LB@3'-UUU...UUAAG U ACCUC...ACG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.3745 kcal/mol@LB@Unfolding Energy - mRNA 2.38082 kcal/mol@LB@Unfolding Energy - sRNA 2.36907 kcal/mol@LB@@LB@Position - mRNA 183 -- 203@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
58	0.0009751	0.05816	b3809	dapF	-9.70	0.129467	46 -- 52	1 -- 7	diaminopimelate epimerase	_____________45______53\n_____________\|_______\|\n5'-UCU...UUUCC_______AGAUA...UGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	46 -- 52	1 -- 7	-13.4276 kcal/mol	1.39772 kcal/mol	2.34039 kcal/mol	45 53@LB@ \| \|@LB@5'-UCU...UUUCC AGAUA...UGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.4276 kcal/mol@LB@Unfolding Energy - mRNA 1.39772 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
59	0.0009764	0.05816	b0593	entC	-14.06	0.008887	219 -- 262	19 -- 57	isochorismate synthase 1	_____________218____________________________________________263\n_____________\|______________________________________________\|\n5'-GGC...UGGCU_________CAGC____C______CAACACUU______A_______UUUCU...CAG-3'\n______________GAGGAAGUA____AGAC___AUGG________GCGCCC_AUCGCUU\n______________:\|\|\|\|\|\|\|\|____\|\|\|\|___\|\|\|\|________:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUCCUUCAU____UCUG___UACC________UGCGGG_UAGCGAA\n3'-UUU...GUUUU_________________UUA____UCGCGU________________CUGCA...ACG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________18\n	256 -- 262	19 -- 25	-38.3486 kcal/mol	10.4998 kcal/mol	13.7965 kcal/mol	218 263@LB@ \| \|@LB@5'-GGC...UGGCU CAGC C CAACACUU A UUUCU...CAG-3'@LB@ GAGGAAGUA AGAC AUGG GCGCCC AUCGCUU@LB@ :\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCCUUCAU UCUG UACC UGCGGG UAGCGAA@LB@3'-UUU...GUUUU UUA UCGCGU CUGCA...ACG-5'@LB@ \| \|@LB@ 58 18@LB@@LB@@LB@Energy -14.06 kcal/mol@LB@Hybridization Energy -38.3486 kcal/mol@LB@Unfolding Energy - mRNA 10.4998 kcal/mol@LB@Unfolding Energy - sRNA 13.7965 kcal/mol@LB@@LB@Position - mRNA 219 -- 262@LB@Position - sRNA 19 -- 57@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 19 -- 25@LB@
60	0.001013	0.05816	b2207	napD	-8.99	0.186283	27 -- 46	75 -- 92	assembly protein for periplasmic nitrate reductase	_____________26___________________47\n_____________\|____________________\|\n5'-GUU...CCUGG_____C_________AA___CGCCG...AAG-3'\n______________CGUAU_AGUCAGUUG__UGC\n______________\|\|\|\|:_\|:\|\|\|:\|\|\|__\|\|\|\n______________GCAUG_UUAGUUAAC__ACG\n3'-UUU...CCGCA_____C______________AUACG...ACG-5'\n_____________\|____________________\|\n_____________93___________________74\n	35 -- 41	78 -- 84	-16.0375 kcal/mol	4.6767 kcal/mol	2.37539 kcal/mol	26 47@LB@ \| \|@LB@5'-GUU...CCUGG C AA CGCCG...AAG-3'@LB@ CGUAU AGUCAGUUG UGC@LB@ \|\|\|\|: \|:\|\|\|:\|\|\| \|\|\|@LB@ GCAUG UUAGUUAAC ACG@LB@3'-UUU...CCGCA C AUACG...ACG-5'@LB@ \| \|@LB@ 93 74@LB@@LB@@LB@Energy -8.99 kcal/mol@LB@Hybridization Energy -16.0375 kcal/mol@LB@Unfolding Energy - mRNA 4.6767 kcal/mol@LB@Unfolding Energy - sRNA 2.37539 kcal/mol@LB@@LB@Position - mRNA 27 -- 46@LB@Position - sRNA 75 -- 92@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 78 -- 84@LB@
61	0.001027	0.05816	b0443	fadM	-9.40	0.151451	193 -- 205	69 -- 81	long-chain acyl-CoA thioesterase III	_____________192___________206\n_____________\|_____________\|\n5'-GUU...AGGUU____C________AACAC...AUG-3'\n______________AUUG_GCUAUGCA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UAAC_CGAUACGU\n3'-UUU...UUAGU____A________CAUUA...ACG-5'\n_____________\|_____________\|\n_____________82____________68\n	199 -- 205	69 -- 75	-15.9471 kcal/mol	4.72824 kcal/mol	1.82028 kcal/mol	192 206@LB@ \| \|@LB@5'-GUU...AGGUU C AACAC...AUG-3'@LB@ AUUG GCUAUGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAAC CGAUACGU@LB@3'-UUU...UUAGU A CAUUA...ACG-5'@LB@ \| \|@LB@ 82 68@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -15.9471 kcal/mol@LB@Unfolding Energy - mRNA 4.72824 kcal/mol@LB@Unfolding Energy - sRNA 1.82028 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 69 -- 81@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@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:

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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

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