Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
81	0.01129	0.4523	b1718	infC	-12.35	0.030679	105 -- 150	1 -- 56	translation initiation factor IF-3	_____________104______________________________________________________151\n_____________\|________________________________________________________\|\n5'-UUG...GCCGU___________C________GCAUG__________________GAUC_________UGCAA...AGC-3'\n______________GGUAA__AGAC___UGGGAA_____GACG____UAAAUGAAGU____GA_GA_AGC\n______________\|\|\|\|\|__\|\|\|\|___::\|:\|\|_____\|\|\|\|____\|\|\|\|\|:\|\|\|\|____\|\|_\|\|_\|\|\|\n______________CCAUU__UCUG___GUCUUU_____CUGC____AUUUAUUUCA____CU_CU_UCG\n3'-UUU...UAUCC_____UG____UAA______ACUUA____CAUU__________AUUA__A__A___-5'\n_____________\|_______________________________________________________\|\n_____________57______________________________________________________1\n	133 -- 139	14 -- 20	-27.0853 kcal/mol	8.40012 kcal/mol	6.33758 kcal/mol	104 151@LB@ \| \|@LB@5'-UUG...GCCGU C GCAUG GAUC UGCAA...AGC-3'@LB@ GGUAA AGAC UGGGAA GACG UAAAUGAAGU GA GA AGC@LB@ \|\|\|\|\| \|\|\|\| ::\|:\|\| \|\|\|\| \|\|\|\|\|:\|\|\|\| \|\| \|\| \|\|\|@LB@ CCAUU UCUG GUCUUU CUGC AUUUAUUUCA CU CU UCG@LB@3'-UUU...UAUCC UG UAA ACUUA CAUU AUUA A A -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -27.0853 kcal/mol@LB@Unfolding Energy - mRNA 8.40012 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 105 -- 150@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 14 -- 20@LB@
82	0.0113	0.4523	b3747	kup	-9.05	0.148352	64 -- 70	53 -- 59	potassium transporter	_____________63______71\n_____________\|_______\|\n5'-AAA...AAAGG_______UUUUU...GUG-3'\n______________GGGGGUA\n______________:\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	64 -- 70	53 -- 59	-11.6233 kcal/mol	2.51972 kcal/mol	0.0564539 kcal/mol	63 71@LB@ \| \|@LB@5'-AAA...AAAGG UUUUU...GUG-3'@LB@ GGGGGUA@LB@ :\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -11.6233 kcal/mol@LB@Unfolding Energy - mRNA 2.51972 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 53 -- 59@LB@
83	0.0117	0.4626	b1071	flgM	-8.58	0.180603	153 -- 179	1 -- 25	anti-sigma factor for FliA (sigma 28)	_____________152_________________________180\n_____________\|___________________________\|\n5'-CCA...UUGCC__________CAACAC_____AAA___GCCCU...CAA-3'\n______________GAUAAAUAAG______AUGAU___AGC\n______________:\|\|\|\|\|\|\|\|:______\|\|\|\|\|___\|\|\|\n______________UUAUUUAUUU______UACUA___UCG\n3'-UUU...UGCCA__________CAAU_______CUA___-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	156 -- 162	16 -- 22	-10.1551 kcal/mol	1.46038 kcal/mol	0.112205 kcal/mol	152 180@LB@ \| \|@LB@5'-CCA...UUGCC CAACAC AAA GCCCU...CAA-3'@LB@ GAUAAAUAAG AUGAU AGC@LB@ :\|\|\|\|\|\|\|\|: \|\|\|\|\| \|\|\|@LB@ UUAUUUAUUU UACUA UCG@LB@3'-UUU...UGCCA CAAU CUA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -10.1551 kcal/mol@LB@Unfolding Energy - mRNA 1.46038 kcal/mol@LB@Unfolding Energy - sRNA 0.112205 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 16 -- 22@LB@
84	0.01184	0.4627	b3101	yqjF	-11.66	0.043663	211 -- 235	1 -- 23	putative quinol oxidase subunit	_____________210_______________________236\n_____________\|_________________________\|\n5'-CAG...AAAAU____A__U_______UAC_______GCGCA...GUA-3'\n______________UAGA_GA_GUUGGUG___UGGUAGC\n______________\|\|:\|_:\|_\|\|\|::\|\|___\|\|:\|\|\|\|\n______________AUUU_UU_CAAUUAC___ACUAUCG\n3'-UUU...CCAUU____A__U_______U_________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	229 -- 235	1 -- 7	-15.9826 kcal/mol	4.21954 kcal/mol	0.105066 kcal/mol	210 236@LB@ \| \|@LB@5'-CAG...AAAAU A U UAC GCGCA...GUA-3'@LB@ UAGA GA GUUGGUG UGGUAGC@LB@ \|\|:\| :\| \|\|\|::\|\| \|\|:\|\|\|\|@LB@ AUUU UU CAAUUAC ACUAUCG@LB@3'-UUU...CCAUU A U U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -15.9826 kcal/mol@LB@Unfolding Energy - mRNA 4.21954 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.01268	0.4896	b1827	kdgR	-11.91	0.038409	291 -- 299	56 -- 64	KDG regulon transcriptional repressor	_____________290_______300\n_____________\|_________\|\n5'-GCC...AGCGC_________A-3'\n______________GAAAUAGGG\n______________\|\|\|\|\|\|\|\|\|\n______________CUUUAUCCC\n3'-UUU...GCCAA_________CAUUU...UCG-5'\n_____________\|_________\|\n_____________65________55\n	293 -- 299	56 -- 62	-12.6296 kcal/mol	0.690209 kcal/mol	0.02823 kcal/mol	290 300@LB@ \| \|@LB@5'-GCC...AGCGC A-3'@LB@ GAAAUAGGG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUUAUCCC@LB@3'-UUU...GCCAA CAUUU...UCG-5'@LB@ \| \|@LB@ 65 55@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -12.6296 kcal/mol@LB@Unfolding Energy - mRNA 0.690209 kcal/mol@LB@Unfolding Energy - sRNA 0.02823 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 56 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 56 -- 62@LB@
86	0.013	0.4962	b0451	amtB	-9.48	0.122870	5 -- 23	1 -- 22	ammonium transporter	_____________4______________________24\n_____________\|______________________\|\n_______5'-CCAA_______AAU____________GAUUG...CGU-3'\n______________AAGUAAA_____UGAUG_UGGC\n______________\|\|:\|\|\|\|_____\|\|\|\|\|_\|:\|\|\n______________UUUAUUU_____ACUAC_AUCG\n3'-UUU...CAUUA_______CAAUU_____U____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	16 -- 22	-11.4865 kcal/mol	1.90989 kcal/mol	0.0989066 kcal/mol	4 24@LB@ \| \|@LB@ 5'-CCAA AAU GAUUG...CGU-3'@LB@ AAGUAAA UGAUG UGGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|:\|\|@LB@ UUUAUUU ACUAC AUCG@LB@3'-UUU...CAUUA CAAUU U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.4865 kcal/mol@LB@Unfolding Energy - mRNA 1.90989 kcal/mol@LB@Unfolding Energy - sRNA 0.0989066 kcal/mol@LB@@LB@Position - mRNA 5 -- 23@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 16 -- 22@LB@
87	0.01323	0.4992	b1951	rcsA	-11.40	0.049597	149 -- 196	25 -- 65	transcriptional regulator of colanic acid capsular biosynthesis	_____________148______________________________________________197\n_____________\|________________________________________________\|\n5'-GUU...CAUGA_______UUCA______G___AUUAU____ACGCAU_______G____UGCCA...UUG-3'\n______________UGAAAUA____GGUAAG_GGA_____CGUU______UGAGUGA_GGUA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|:_:\|\|_____\|:\|\|______\|\|\|:\|\|\|_\|\|\|\|\n______________ACUUUAU____CCAUUU_UCU_____GUAA______ACUUACU_CCAU\n3'-UUU...GGCCA_______CC________G____________GUCUUU_______G____UAUUU...UCG-5'\n_____________\|________________________________________________\|\n_____________66_______________________________________________24\n	149 -- 155	59 -- 65	-29.5865 kcal/mol	10.9819 kcal/mol	7.2015 kcal/mol	148 197@LB@ \| \|@LB@5'-GUU...CAUGA UUCA G AUUAU ACGCAU G UGCCA...UUG-3'@LB@ UGAAAUA GGUAAG GGA CGUU UGAGUGA GGUA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: :\|\| \|:\|\| \|\|\|:\|\|\| \|\|\|\|@LB@ ACUUUAU CCAUUU UCU GUAA ACUUACU CCAU@LB@3'-UUU...GGCCA CC G GUCUUU G UAUUU...UCG-5'@LB@ \| \|@LB@ 66 24@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -29.5865 kcal/mol@LB@Unfolding Energy - mRNA 10.9819 kcal/mol@LB@Unfolding Energy - sRNA 7.2015 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 25 -- 65@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 59 -- 65@LB@
88	0.01388	0.5059	b3809	dapF	-7.53	0.274407	192 -- 207	1 -- 17	diaminopimelate epimerase	_____________191_______________208\n_____________\|_________________\|\n5'-UCU...GAUUG____A_______C____UCUCG...UGG-3'\n______________GAGU_AAUGAUG__AGU\n______________:\|\|\|_\|\|\|\|\|\|\|__\|\|:\n______________UUCA_UUACUAC__UCG\n3'-UUU...UUUAU____A_______UA___-5'\n_____________\|________________\|\n_____________18_______________1\n	197 -- 203	6 -- 12	-9.99588 kcal/mol	2.41483 kcal/mol	0.0529402 kcal/mol	191 208@LB@ \| \|@LB@5'-UCU...GAUUG A C UCUCG...UGG-3'@LB@ GAGU AAUGAUG AGU@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|:@LB@ UUCA UUACUAC UCG@LB@3'-UUU...UUUAU A UA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -9.99588 kcal/mol@LB@Unfolding Energy - mRNA 2.41483 kcal/mol@LB@Unfolding Energy - sRNA 0.0529402 kcal/mol@LB@@LB@Position - mRNA 192 -- 207@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
89	0.01433	0.5059	b0636	rlmH	-12.18	0.033475	189 -- 207	1 -- 19	23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent	_____________188__________________208\n_____________\|____________________\|\n5'-CGG...AACUC___________C________UGCAA...UCG-3'\n______________UGGAGUUAAUG_GUGA_AGC\n______________\|::\|\|\|\|\|\|\|\|_:\|\|\|_\|\|\|\n______________AUUUCAAUUAC_UACU_UCG\n3'-UUU...UAUUU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	193 -- 199	9 -- 15	-16.4949 kcal/mol	4.25175 kcal/mol	0.0638423 kcal/mol	188 208@LB@ \| \|@LB@5'-CGG...AACUC C UGCAA...UCG-3'@LB@ UGGAGUUAAUG GUGA AGC@LB@ \|::\|\|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ AUUUCAAUUAC UACU UCG@LB@3'-UUU...UAUUU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -16.4949 kcal/mol@LB@Unfolding Energy - mRNA 4.25175 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 9 -- 15@LB@
90	0.01478	0.5059	b0740	tolB	-11.20	0.054749	186 -- 207	1 -- 21	periplasmic protein	_____________185_____________________208\n_____________\|_______________________\|\n5'-UCC...GUCCA_______GAGAU___________AGGCA...CCG-3'\n______________GAUAAGG_____AUGAUGA_AGC\n______________:\|\|\|\|:\|_____\|\|\|\|\|\|\|_\|\|\|\n______________UUAUUUC_____UACUACU_UCG\n3'-UUU...AUUAU_______AAU_________A___-5'\n_____________\|______________________\|\n_____________22_____________________1\n	198 -- 204	5 -- 11	-16.1118 kcal/mol	4.84175 kcal/mol	0.0669945 kcal/mol	185 208@LB@ \| \|@LB@5'-UCC...GUCCA GAGAU AGGCA...CCG-3'@LB@ GAUAAGG AUGAUGA AGC@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UUAUUUC UACUACU UCG@LB@3'-UUU...AUUAU AAU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -16.1118 kcal/mol@LB@Unfolding Energy - mRNA 4.84175 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 186 -- 207@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 198 -- 204@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)

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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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