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
31	0.00291	0.3081	b1205	ychH	-11.03	0.059536	152 -- 163	53 -- 64	DUF2583 family putative inner membrane protein	_____________151__________164\n_____________\|____________\|\n5'-CAA...CAUAA____G_______UUCCC...UAC-3'\n______________GGAA_AGGGGUA\n______________\|:\|\|_\|\|\|\|\|\|\|\n______________CUUU_UCCCCAU\n3'-UUU...GCCAA____A_______UUGUC...UCG-5'\n_____________\|____________\|\n_____________65___________52\n	157 -- 163	53 -- 59	-13.5677 kcal/mol	2.46117 kcal/mol	0.0747267 kcal/mol	151 164@LB@ \| \|@LB@5'-CAA...CAUAA G UUCCC...UAC-3'@LB@ GGAA AGGGGUA@LB@ \|:\|\| \|\|\|\|\|\|\|@LB@ CUUU UCCCCAU@LB@3'-UUU...GCCAA A UUGUC...UCG-5'@LB@ \| \|@LB@ 65 52@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.5677 kcal/mol@LB@Unfolding Energy - mRNA 2.46117 kcal/mol@LB@Unfolding Energy - sRNA 0.0747267 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 53 -- 64@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 53 -- 59@LB@
68	0.00983	0.4523	b1321	ycjX	-10.80	0.066674	34 -- 41	55 -- 62	DUF463 family protein puatative P-loop NTPase	_____________33_______42\n_____________\|________\|\n5'-UGA...UAAAU________ACAUA...CAG-3'\n______________AGUAGGGG\n______________\|:\|\|\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	35 -- 41	55 -- 61	-12.2037 kcal/mol	1.3787 kcal/mol	0.0270923 kcal/mol	33 42@LB@ \| \|@LB@5'-UGA...UAAAU ACAUA...CAG-3'@LB@ AGUAGGGG@LB@ \|:\|\|\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -12.2037 kcal/mol@LB@Unfolding Energy - mRNA 1.3787 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 34 -- 41@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 55 -- 61@LB@
135	0.02191	0.526	b1342	ydaN	-17.19	0.001818	129 -- 197	1 -- 58	putative Zn(II) transporter	_____________128______________________________________________________________________198\n_____________\|________________________________________________________________________\|\n5'-CGU...GUAAU_______UG_______GCGUAACAGGGC______GCUA____UACA________UGC___________A___ACUGU...AUG-3'\n______________GGGGUGA__AGAUGUU____________CAGAAG_____GAC______AAAUAA___GUUGAUGAUGG_GGC\n______________\|\|\|\|\|:\|__\|\|\|::\|\|____________\|\|\|\|\|:_____\|\|\|______\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|:_:\|\|\n______________CCCCAUU__UCUGUAA____________GUCUUU_____CUG______UUUAUU___CAAUUACUACU_UCG\n3'-UUU...UUUAU_______UG_________________________ACUUA___CCAUUA______U_____________A___-5'\n_____________\|_______________________________________________________________________\|\n_____________59______________________________________________________________________1\n	187 -- 193	5 -- 11	-40.4273 kcal/mol	16.9018 kcal/mol	6.33758 kcal/mol	128 198@LB@ \| \|@LB@5'-CGU...GUAAU UG GCGUAACAGGGC GCUA UACA UGC A ACUGU...AUG-3'@LB@ GGGGUGA AGAUGUU CAGAAG GAC AAAUAA GUUGAUGAUGG GGC@LB@ \|\|\|\|\|:\| \|\|\|::\|\| \|\|\|\|\|: \|\|\| \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|: :\|\|@LB@ CCCCAUU UCUGUAA GUCUUU CUG UUUAUU CAAUUACUACU UCG@LB@3'-UUU...UUUAU UG ACUUA CCAUUA U A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -17.19 kcal/mol@LB@Hybridization Energy -40.4273 kcal/mol@LB@Unfolding Energy - mRNA 16.9018 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 129 -- 197@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 5 -- 11@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter	_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@LB@
40	0.004127	0.3349	b1659	ydhB	-12.78	0.024485	130 -- 177	1 -- 61	LysR family putative transcriptional regulator	_____________129_______________________________________________________________178\n_____________\|_________________________________________________________________\|\n5'-CGA...AAAGU______A_____AU_____________________________UU_______________C____UUCAA...UCA-3'\n______________GUAGGG_GUGAA__UAG_UGUU_____GUGAA__ACGGUAAUA___________UGAUGA_UGGU\n______________:\|\|\|\|\|_\|\|:\|\|__:\|\|_::\|\|_____:\|\|\|\|__\|\|\|\|\|\|\|\|\|___________\|\|\|\|\|\|_\|:\|:\n______________UAUCCC_CAUUU__GUC_GUAA_____UACUU__UGCCAUUAU___________ACUACU_AUCG\n3'-UUU...AACUU_________________U____GUCUU_____AC_________UUAUUUCAAUU___________-5'\n_____________\|________________________________________________________________\|\n_____________62_______________________________________________________________1\n	158 -- 164	22 -- 28	-31.01 kcal/mol	11.8895 kcal/mol	6.344 kcal/mol	129 178@LB@ \| \|@LB@5'-CGA...AAAGU A AU UU C UUCAA...UCA-3'@LB@ GUAGGG GUGAA UAG UGUU GUGAA ACGGUAAUA UGAUGA UGGU@LB@ :\|\|\|\|\| \|\|:\|\| :\|\| ::\|\| :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|:@LB@ UAUCCC CAUUU GUC GUAA UACUU UGCCAUUAU ACUACU AUCG@LB@3'-UUU...AACUU U GUCUU AC UUAUUUCAAUU -5'@LB@ \| \|@LB@ 62 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -31.01 kcal/mol@LB@Unfolding Energy - mRNA 11.8895 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 130 -- 177@LB@Position - sRNA 1 -- 61@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 22 -- 28@LB@
93	0.0151	0.5059	b1675	ydhZ	-8.81	0.164498	185 -- 226	5 -- 54	uncharacterized protein	_____________184________________________________________________227\n_____________\|__________________________________________________\|\n5'-CUU...CAUGA___________AA____UG___AAU___AC____________________ACUGU...AGC-3'\n______________UAAAUAGGUAU__AGAA__GGA___CGG____AAA_AGAG_____GAUGA\n______________\|\|\|\|:\|\|::\|\|__\|\|\|\|__\|:\|___\|\|\|____\|\|\|_\|:\|\|_____\|\|\|\|\|\n______________AUUUGUCUGUA__UCUU__CUU___GCC____UUU_UUUC_____CUACU\n3'-UUU...UCCCC___________AG____UA___ACU___AUUA___A____AAUUA_____AUCG-5'\n_____________\|__________________________________________________\|\n_____________55_________________________________________________4\n	186 -- 192	47 -- 53	-19.2855 kcal/mol	4.14282 kcal/mol	6.33746 kcal/mol	184 227@LB@ \| \|@LB@5'-CUU...CAUGA AA UG AAU AC ACUGU...AGC-3'@LB@ UAAAUAGGUAU AGAA GGA CGG AAA AGAG GAUGA@LB@ \|\|\|\|:\|\|::\|\| \|\|\|\| \|:\| \|\|\| \|\|\| \|:\|\| \|\|\|\|\|@LB@ AUUUGUCUGUA UCUU CUU GCC UUU UUUC CUACU@LB@3'-UUU...UCCCC AG UA ACU AUUA A AAUUA AUCG-5'@LB@ \| \|@LB@ 55 4@LB@@LB@@LB@Energy -8.81 kcal/mol@LB@Hybridization Energy -19.2855 kcal/mol@LB@Unfolding Energy - mRNA 4.14282 kcal/mol@LB@Unfolding Energy - sRNA 6.33746 kcal/mol@LB@@LB@Position - mRNA 185 -- 226@LB@Position - sRNA 5 -- 54@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
46	0.00512	0.3601	b2012	yeeD	-13.46	0.016912	185 -- 206	3 -- 23	putative TusA family sulfurtransferase	_____________184____________________207\n_____________\|______________________\|\n5'-GAU...CAAAU__________G___A_______AUUAA...UAG-3'\n______________UAAGUAAGGU_UAA_GAUGGUG\n______________\|\|\|:\|\|\|:\|\|_\|\|\|_\|\|\|\|:\|:\n______________AUUUAUUUCA_AUU_CUACUAU\n3'-UUU...CCAUU______________A_______CG-5'\n_____________\|______________________\|\n_____________24_____________________2\n	200 -- 206	3 -- 9	-15.4658 kcal/mol	1.89879 kcal/mol	0.104738 kcal/mol	184 207@LB@ \| \|@LB@5'-GAU...CAAAU G A AUUAA...UAG-3'@LB@ UAAGUAAGGU UAA GAUGGUG@LB@ \|\|\|:\|\|\|:\|\| \|\|\| \|\|\|\|:\|:@LB@ AUUUAUUUCA AUU CUACUAU@LB@3'-UUU...CCAUU A CG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -15.4658 kcal/mol@LB@Unfolding Energy - mRNA 1.89879 kcal/mol@LB@Unfolding Energy - sRNA 0.104738 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 3 -- 9@LB@
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein	______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
149	0.02481	0.526	b2108	yehA	-13.80	0.014025	228 -- 241	1 -- 14	putative fimbrial-like adhesin protein	_____________227____________242\n_____________\|______________\|\n5'-GUU...UUAUA______________UAUGC...UUG-3'\n______________UUAAUGAUGAUGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	235 -- 241	1 -- 7	-16.5389 kcal/mol	2.69058 kcal/mol	0.0473494 kcal/mol	227 242@LB@ \| \|@LB@5'-GUU...UUAUA UAUGC...UUG-3'@LB@ UUAAUGAUGAUGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -16.5389 kcal/mol@LB@Unfolding Energy - mRNA 2.69058 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 228 -- 241@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
169	0.02775	0.531	b2110	yehC	-5.87	0.481945	191 -- 199	20 -- 28	putative periplasmic pilin chaperone	_____________190_______200\n_____________\|_________\|\n5'-CAG...CUCCA_________CAUGG...CCG-3'\n______________GGUAAUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUAUUU\n3'-UUU...UACUG_________AUUUC...UCG-5'\n_____________\|_________\|\n_____________29________19\n	193 -- 199	20 -- 26	-7.96952 kcal/mol	1.36589 kcal/mol	0.737257 kcal/mol	190 200@LB@ \| \|@LB@5'-CAG...CUCCA CAUGG...CCG-3'@LB@ GGUAAUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUAUUU@LB@3'-UUU...UACUG AUUUC...UCG-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -7.96952 kcal/mol@LB@Unfolding Energy - mRNA 1.36589 kcal/mol@LB@Unfolding Energy - sRNA 0.737257 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 20 -- 26@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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