Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
8	0.000167	0.07068	b0814	ompX	-11.11	0.078421	202 -- 223	1 -- 22	outer membrane protein X		_____________201____________________224\n_____________\|______________________\|\n5'-CUG...GGUUA___AAAA__U___A________AGCAC...CAC-3'\n______________UGA____AA_UGC_UGUCUUUC\n______________\|\|\|____\|\|_\|\|\|_:\|\|\|\|\|\|\|\n______________ACU____UU_ACG_GCAGAAAG\n3'-UUU...CUACU___AUUG__U___C________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	217 -- 223	1 -- 7	-15.5509 kcal/mol	3.18554 kcal/mol	1.25963 kcal/mol	201 224@LB@ \| \|@LB@5'-CUG...GGUUA AAAA U A AGCAC...CAC-3'@LB@ UGA AA UGC UGUCUUUC@LB@ \|\|\| \|\| \|\|\| :\|\|\|\|\|\|\|@LB@ ACU UU ACG GCAGAAAG@LB@3'-UUU...CUACU AUUG U C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.5509 kcal/mol@LB@Unfolding Energy - mRNA 3.18554 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 202 -- 223@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@LB@
5	7.362e-05	0.04801	b0741	pal	-13.90	0.024968	103 -- 115	3 -- 16	peptidoglycan-associated outer membrane lipoprotein		_____________102____________116\n_____________\|______________\|\n5'-GGA...CGUUU______________CCGGC...GCG-3'\n______________CAAA_GCGCGUCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________GUUU_CGCGCAGAA\n3'-UUU...CUAUU____A_________AG-5'\n_____________\|______________\|\n_____________17_____________2\n	109 -- 115	3 -- 9	-18.0761 kcal/mol	2.94526 kcal/mol	1.22934 kcal/mol	102 116@LB@ \| \|@LB@5'-GGA...CGUUU CCGGC...GCG-3'@LB@ CAAA GCGCGUCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GUUU CGCGCAGAA@LB@3'-UUU...CUAUU A AG-5'@LB@ \| \|@LB@ 17 2@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -18.0761 kcal/mol@LB@Unfolding Energy - mRNA 2.94526 kcal/mol@LB@Unfolding Energy - sRNA 1.22934 kcal/mol@LB@@LB@Position - mRNA 103 -- 115@LB@Position - sRNA 3 -- 16@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 3 -- 9@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)		_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@LB@
147	0.01411	0.3104	b0441	ppiD	-10.51	0.099467	81 -- 98	3 -- 21	periplasmic folding chaperone has an inactive PPIase domain		_____________80__________________99\n_____________\|___________________\|\n5'-GUA...UAUUC______UUUC_________GUGGG...ACC-3'\n______________GGUGAC_____UGCGUCUU\n______________\|:\|:\|\|_____:\|\|\|\|\|\|\|\n______________CUAUUG_____GCGCAGAA\n3'-UUU...UACUA______UUUAC________AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	92 -- 98	3 -- 9	-17.0331 kcal/mol	5.27038 kcal/mol	1.257 kcal/mol	80 99@LB@ \| \|@LB@5'-GUA...UAUUC UUUC GUGGG...ACC-3'@LB@ GGUGAC UGCGUCUU@LB@ \|:\|:\|\| :\|\|\|\|\|\|\|@LB@ CUAUUG GCGCAGAA@LB@3'-UUU...UACUA UUUAC AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -17.0331 kcal/mol@LB@Unfolding Energy - mRNA 5.27038 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 81 -- 98@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 3 -- 9@LB@
104	0.01032	0.3104	b1714	pheS	-13.82	0.025875	273 -- 287	5 -- 21	phenylalanine tRNA synthetase alpha subunit		_____________272_______________288\n_____________\|_________________\|\n5'-UUG...CGUUA_________________GAAUA...GUA-3'\n______________GAUAAU__GUGCGCGUC\n______________\|\|\|\|\|:__:\|\|\|\|\|\|\|\|\n______________CUAUUG__UACGCGCAG\n3'-UUU...UACUA______UU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	281 -- 287	5 -- 11	-20.2911 kcal/mol	5.22554 kcal/mol	1.24955 kcal/mol	272 288@LB@ \| \|@LB@5'-UUG...CGUUA GAAUA...GUA-3'@LB@ GAUAAU GUGCGCGUC@LB@ \|\|\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CUAUUG UACGCGCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -20.2911 kcal/mol@LB@Unfolding Energy - mRNA 5.22554 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 273 -- 287@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 5 -- 11@LB@
132	0.01286	0.3104	b3176	glmM	-8.35	0.224806	246 -- 258	8 -- 20	phosphoglucosamine mutase		_____________245___________259\n_____________\|_____________\|\n5'-GUU...GUCGU____G________CGAUC...CGG-3'\n______________GUAG_GGAUGCGC\n______________:\|\|:_::\|\|\|\|\|\|\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	252 -- 258	8 -- 14	-14.3134 kcal/mol	4.73041 kcal/mol	1.23367 kcal/mol	245 259@LB@ \| \|@LB@5'-GUU...GUCGU G CGAUC...CGG-3'@LB@ GUAG GGAUGCGC@LB@ :\|\|: ::\|\|\|\|\|\|@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.35 kcal/mol@LB@Hybridization Energy -14.3134 kcal/mol@LB@Unfolding Energy - mRNA 4.73041 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 8 -- 14@LB@
154	0.01456	0.3104	b2048	cpsG	-9.02	0.175967	42 -- 71	4 -- 44	phosphomannomutase		_____________41________________________________________72\n_____________\|_________________________________________\|\n5'-GGG...GGCUC___________GA___________UG_______________CGCGG...GCG-3'\n______________UUAUCUC_GAA_____GGAUGAUG_________GUGCGUUU\n______________\|:\|\|\|\|\|_\|\|\|_____\|\|\|\|\|\|\|\|_________\|:\|\|\|\|:\|\n______________AGUAGAG_CUU_____CCUACUAC_________CGCGCAGA\n3'-UUU...UUUAA_______A___AAGUC________UAUUGUUUA________AAG-5'\n_____________\|_________________________________________\|\n_____________45________________________________________3\n	65 -- 71	4 -- 10	-28.9111 kcal/mol	10.4373 kcal/mol	9.45546 kcal/mol	41 72@LB@ \| \|@LB@5'-GGG...GGCUC GA UG CGCGG...GCG-3'@LB@ UUAUCUC GAA GGAUGAUG GUGCGUUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|:\|@LB@ AGUAGAG CUU CCUACUAC CGCGCAGA@LB@3'-UUU...UUUAA A AAGUC UAUUGUUUA AAG-5'@LB@ \| \|@LB@ 45 3@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -28.9111 kcal/mol@LB@Unfolding Energy - mRNA 10.4373 kcal/mol@LB@Unfolding Energy - sRNA 9.45546 kcal/mol@LB@@LB@Position - mRNA 42 -- 71@LB@Position - sRNA 4 -- 44@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 4 -- 10@LB@
156	0.01464	0.3104	b4105	phnD	-8.45	0.216438	196 -- 209	4 -- 18	phosphonate ABC transporter periplasmic binding protein		_____________195_____________210\n_____________\|_______________\|\n5'-CCG...AGGAA________AA_____AAGAU...UGA-3'\n______________AACGAAUG__CG_CU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\n______________UUGUUUAC__GC_GA\n3'-UUU...UACUA________GC__A__AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	197 -- 203	11 -- 17	-10.9184 kcal/mol	1.23392 kcal/mol	1.22995 kcal/mol	195 210@LB@ \| \|@LB@5'-CCG...AGGAA AA AAGAU...UGA-3'@LB@ AACGAAUG CG CU@LB@ \|\|\|:\|\|\|\| \|\| \|\|@LB@ UUGUUUAC GC GA@LB@3'-UUU...UACUA GC A AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -10.9184 kcal/mol@LB@Unfolding Energy - mRNA 1.23392 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 196 -- 209@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 11 -- 17@LB@
22	0.001004	0.1545	b0583	entD	-18.10	0.004183	41 -- 63	1 -- 22	phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex		_____________40______________________64\n_____________\|_______________________\|\n5'-AUA...CAGAU__U____A___________G___AUGCC...UGC-3'\n______________UG_UGAC_AAGUGCGCGUC_UUC\n______________\|\|_\|:\|\|_\|\|:\|\|\|\|\|\|\|\|_\|\|\|\n______________AC_AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU__U________________A___-5'\n_____________\|______________________\|\n_____________23_____________________1\n	53 -- 59	5 -- 11	-24.6004 kcal/mol	5.24265 kcal/mol	1.25963 kcal/mol	40 64@LB@ \| \|@LB@5'-AUA...CAGAU U A G AUGCC...UGC-3'@LB@ UG UGAC AAGUGCGCGUC UUC@LB@ \|\| \|:\|\| \|\|:\|\|\|\|\|\|\|\| \|\|\|@LB@ AC AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -18.10 kcal/mol@LB@Hybridization Energy -24.6004 kcal/mol@LB@Unfolding Energy - mRNA 5.24265 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 41 -- 63@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@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

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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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