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	Additional homologs
127	0.01998	0.5155	b2922	yggE	-8.69	0.172995	232 -- 253	1 -- 26	oxidative stress defense protein		_____________231________________________254\n_____________\|__________________________\|\n5'-GCA...GGCAU________________C_________AGCGC...CCG-3'\n______________UAAUGGGUA___UUAG_GG_GAUGGC\n______________\|\|\|\|:::\|\|___\|\|\|:_\|:_\|\|\|:\|\|\n______________AUUAUUUAU___AAUU_CU_CUAUCG\n3'-UUU...CUGCC_________UUC____A__A______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	234 -- 240	18 -- 24	-12.7828 kcal/mol	3.51669 kcal/mol	0.580494 kcal/mol	231 254@LB@ \| \|@LB@5'-GCA...GGCAU C AGCGC...CCG-3'@LB@ UAAUGGGUA UUAG GG GAUGGC@LB@ \|\|\|\|:::\|\| \|\|\|: \|: \|\|\|:\|\|@LB@ AUUAUUUAU AAUU CU CUAUCG@LB@3'-UUU...CUGCC UUC A A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -12.7828 kcal/mol@LB@Unfolding Energy - mRNA 3.51669 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 232 -- 253@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 18 -- 24@LB@
75	0.01076	0.4523	b4291	fecA	-8.60	0.179326	183 -- 193	2 -- 12	TonB-dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR-interacting protein		_____________182_________194\n_____________\|___________\|\n5'-AGC...ACAAA___________GGAAG...CUG-3'\n______________AAUGAUGAUGG\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UUACUACUAUC\n3'-UUU...UUCAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	187 -- 193	2 -- 8	-12.8036 kcal/mol	4.16536 kcal/mol	0.0386655 kcal/mol	182 194@LB@ \| \|@LB@5'-AGC...ACAAA GGAAG...CUG-3'@LB@ AAUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UUACUACUAUC@LB@3'-UUU...UUCAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.8036 kcal/mol@LB@Unfolding Energy - mRNA 4.16536 kcal/mol@LB@Unfolding Energy - sRNA 0.0386655 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 2 -- 8@LB@
146	0.02455	0.526	b0491	fetB	-8.60	0.179526	114 -- 156	14 -- 57	iron export ABC transporter permease; peroxide resistance protein		_____________113_______________________________________________157\n_____________\|_________________________________________________\|\n5'-GCC...GCUGU______C___C____AAGAC_____U___CAU_________________GAUUA...AGA-3'\n______________GGGUGA_ACA_GAUA_____GAAAU_AAU___GCGG______AUAAAGU\n______________\|\|\|\|:\|_\|\|\|_\|\|:\|_____\|\|\|\|\|_\|\|\|___:\|\|\|______\|\|\|\|\|\|\|\n______________CCCAUU_UGU_CUGU_____CUUUA_UUA___UGCC______UAUUUCA\n3'-UUU...UUAUC_______________AAGU______C___C______AUUAUU_______AUUAC...UCG-5'\n_____________\|_________________________________________________\|\n_____________58________________________________________________13\n	150 -- 156	14 -- 20	-22.3302 kcal/mol	7.40722 kcal/mol	6.32606 kcal/mol	113 157@LB@ \| \|@LB@5'-GCC...GCUGU C C AAGAC U CAU GAUUA...AGA-3'@LB@ GGGUGA ACA GAUA GAAAU AAU GCGG AUAAAGU@LB@ \|\|\|\|:\| \|\|\| \|\|:\| \|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CCCAUU UGU CUGU CUUUA UUA UGCC UAUUUCA@LB@3'-UUU...UUAUC AAGU C C AUUAUU AUUAC...UCG-5'@LB@ \| \|@LB@ 58 13@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.3302 kcal/mol@LB@Unfolding Energy - mRNA 7.40722 kcal/mol@LB@Unfolding Energy - sRNA 6.32606 kcal/mol@LB@@LB@Position - mRNA 114 -- 156@LB@Position - sRNA 14 -- 57@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 14 -- 20@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@
105	0.01645	0.5059	b0454	ybaZ	-8.45	0.190978	84 -- 93	47 -- 56	excision repair protein alkyltransferase-like protein ATL		_____________83_________94\n_____________\|__________\|\n5'-AGG...GACCU__________GUAGC...UUC-3'\n______________GGUAAACAGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUCU\n3'-UUU...UAUCC__________GUAAG...UCG-5'\n_____________\|__________\|\n_____________57_________46\n	87 -- 93	47 -- 53	-13.2019 kcal/mol	2.68818 kcal/mol	2.06629 kcal/mol	83 94@LB@ \| \|@LB@5'-AGG...GACCU GUAGC...UUC-3'@LB@ GGUAAACAGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUCU@LB@3'-UUU...UAUCC GUAAG...UCG-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.2019 kcal/mol@LB@Unfolding Energy - mRNA 2.68818 kcal/mol@LB@Unfolding Energy - sRNA 2.06629 kcal/mol@LB@@LB@Position - mRNA 84 -- 93@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 47 -- 53@LB@
120	0.01923	0.5155	b4004	zraR	-8.11	0.219313	234 -- 248	1 -- 12	fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator/sigma54 interaction protein	b2220	_____________233_____________249\n_____________\|_______________\|\n5'-GGA...UGGUG________CAU____CACUG...CGC-3'\n______________GAUGAUGA___UAGC\n______________:\|\|\|\|\|\|\|___\|\|\|\|\n______________UUACUACU___AUCG\n3'-UUU...UUCAA_______________-5'\n_____________\|______________\|\n_____________13_____________1\n	235 -- 241	5 -- 11	-11.3572 kcal/mol	3.21186 kcal/mol	0.0394463 kcal/mol	233 249@LB@ \| \|@LB@5'-GGA...UGGUG CAU CACUG...CGC-3'@LB@ GAUGAUGA UAGC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UUACUACU AUCG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -11.3572 kcal/mol@LB@Unfolding Energy - mRNA 3.21186 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 234 -- 248@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 5 -- 11@LB@
125	0.01993	0.5155	b2347	yfdC	-8.10	0.220050	281 -- 291	15 -- 25	putative inner membrane protein		_____________280_________292\n_____________\|___________\|\n5'-GCA...AUAGA___________ACCGA...UCC-3'\n______________AAUAGAUGAAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________UUAUUUAUUUC\n3'-UUU...UGCCA___________AAUUA...UCG-5'\n_____________\|___________\|\n_____________26__________14\n	285 -- 291	15 -- 21	-8.49349 kcal/mol	0.301625 kcal/mol	0.0943905 kcal/mol	280 292@LB@ \| \|@LB@5'-GCA...AUAGA ACCGA...UCC-3'@LB@ AAUAGAUGAAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ UUAUUUAUUUC@LB@3'-UUU...UGCCA AAUUA...UCG-5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -8.49349 kcal/mol@LB@Unfolding Energy - mRNA 0.301625 kcal/mol@LB@Unfolding Energy - sRNA 0.0943905 kcal/mol@LB@@LB@Position - mRNA 281 -- 291@LB@Position - sRNA 15 -- 25@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 15 -- 21@LB@
191	0.03238	0.5507	b0445	ybaE	-8.08	0.221556	124 -- 136	4 -- 16	putative ABC transporter periplasmic binding protein		_____________123___________137\n_____________\|_____________\|\n5'-CGU...GACAC_____________UGAGU...GUU-3'\n______________GGUUAAUGGUGAU\n______________:\|\|\|\|\|\|\|:\|\|\|\|\n______________UCAAUUACUACUA\n3'-UUU...UUAUU_____________UCG-5'\n_____________\|_____________\|\n_____________17____________3\n	130 -- 136	4 -- 10	-14.6304 kcal/mol	6.50117 kcal/mol	0.0488422 kcal/mol	123 137@LB@ \| \|@LB@5'-CGU...GACAC UGAGU...GUU-3'@LB@ GGUUAAUGGUGAU@LB@ :\|\|\|\|\|\|\|:\|\|\|\|@LB@ UCAAUUACUACUA@LB@3'-UUU...UUAUU UCG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -14.6304 kcal/mol@LB@Unfolding Energy - mRNA 6.50117 kcal/mol@LB@Unfolding Energy - sRNA 0.0488422 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 4 -- 10@LB@
28	0.00198	0.2275	b2821	ptrA	-8.02	0.226801	174 -- 191	5 -- 22	protease III		_____________173________________192\n_____________\|__________________\|\n5'-GCU...ACAGA____U________U____GGUCC...CCA-3'\n______________AAAU_AAGUUGAU_AUGA\n______________\|\|\|\|_\|\|\|\|\|:\|\|_\|\|\|\|\n______________UUUA_UUCAAUUA_UACU\n3'-UUU...CAUUA____U________C____AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	180 -- 186	10 -- 16	-10.4485 kcal/mol	2.32937 kcal/mol	0.0977783 kcal/mol	173 192@LB@ \| \|@LB@5'-GCU...ACAGA U U GGUCC...CCA-3'@LB@ AAAU AAGUUGAU AUGA@LB@ \|\|\|\| \|\|\|\|\|:\|\| \|\|\|\|@LB@ UUUA UUCAAUUA UACU@LB@3'-UUU...CAUUA U C AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -10.4485 kcal/mol@LB@Unfolding Energy - mRNA 2.32937 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 174 -- 191@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 10 -- 16@LB@
177	0.02886	0.5353	b2206	napA	-7.95	0.233634	77 -- 89	1 -- 13	nitrate reductase periplasmic large subunit		_____________76____________90\n_____________\|_____________\|\n5'-GAC...GAUUG_________A___AGAAG...UUG-3'\n______________UGGUGGUGG_AGC\n______________\|::\|\|:\|\|:_\|\|\|\n______________AUUACUACU_UCG\n3'-UUU...UUUCA_________A___-5'\n_____________\|____________\|\n_____________14___________1\n	79 -- 85	5 -- 11	-12.9311 kcal/mol	4.9403 kcal/mol	0.0446954 kcal/mol	76 90@LB@ \| \|@LB@5'-GAC...GAUUG A AGAAG...UUG-3'@LB@ UGGUGGUGG AGC@LB@ \|::\|\|:\|\|: \|\|\|@LB@ AUUACUACU UCG@LB@3'-UUU...UUUCA A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -12.9311 kcal/mol@LB@Unfolding Energy - mRNA 4.9403 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 79 -- 85@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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