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
150	0.02489	0.526	b2088	insE1	-9.25	0.136086	235 -- 276	1 -- 55	IS3 transposase A	b0298 b0373 b0540 b1027	_____________234_____________________________________________________277\n_____________\|_______________________________________________________\|\n5'-ACC...ACCCC_______________CC_______UU__C____________CCC___________UUGCU...CUG-3'\n______________GUAAACAG_CAUUCG____UGAAU__CG______AGUGAAG____UGA____AGC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|:____\|\|\|\|\|__\|\|______\|:\|:\|\|\|____\|\|\|____\|\|\|\n______________CAUUUGUC_GUAAGU____ACUUA__GC______UUAUUUC____ACU____UCG\n3'-UUU...AUCCC________U______CUUU_____CU__CAUUAU_______AAUU___ACUA___-5'\n_____________\|______________________________________________________\|\n_____________56_____________________________________________________1\n	261 -- 267	15 -- 21	-23.7484 kcal/mol	8.16492 kcal/mol	6.33758 kcal/mol	234 277@LB@ \| \|@LB@5'-ACC...ACCCC CC UU C CCC UUGCU...CUG-3'@LB@ GUAAACAG CAUUCG UGAAU CG AGUGAAG UGA AGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\| \|\| \|:\|:\|\|\| \|\|\| \|\|\|@LB@ CAUUUGUC GUAAGU ACUUA GC UUAUUUC ACU UCG@LB@3'-UUU...AUCCC U CUUU CU CAUUAU AAUU ACUA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.7484 kcal/mol@LB@Unfolding Energy - mRNA 8.16492 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 235 -- 276@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 15 -- 21@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@
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@
121	0.01924	0.5155	b0074	leuA	-11.43	0.049038	243 -- 261	39 -- 56	2-isopropylmalate synthase		_____________242_________________262\n_____________\|___________________\|\n5'-CAU...GCGAC______________A____CAAGC...UGG-3'\n______________GGUGAACAGGCGUU_CAGG\n______________\|\|\|:\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________CCAUUUGUCUGUAA_GUCU\n3'-UUU...UAUCC___________________UUACU...UCG-5'\n_____________\|___________________\|\n_____________57__________________38\n	247 -- 253	46 -- 52	-24.0317 kcal/mol	6.35652 kcal/mol	6.24929 kcal/mol	242 262@LB@ \| \|@LB@5'-CAU...GCGAC A CAAGC...UGG-3'@LB@ GGUGAACAGGCGUU CAGG@LB@ \|\|\|:\|\|\|\|\|:\|:\|\| \|\|\|:@LB@ CCAUUUGUCUGUAA GUCU@LB@3'-UUU...UAUCC UUACU...UCG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -24.0317 kcal/mol@LB@Unfolding Energy - mRNA 6.35652 kcal/mol@LB@Unfolding Energy - sRNA 6.24929 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 46 -- 52@LB@
130	0.02079	0.5217	b3455	livG	-10.98	0.060940	96 -- 122	4 -- 29	branched-chain amino acid ABC transporter ATPase		_____________95__________________________123\n_____________\|___________________________\|\n5'-AUG...AUGCU_______UU_____U_C__________CUGGC...UCG-3'\n______________CGGUGGU__GAUGG_G_UGAUGAUGAU\n______________\|\|\|\|::\|__:\|\|::_\|_\|:\|\|\|\|\|\|\|\|\n______________GCCAUUA__UUAUU_C_AUUACUACUA\n3'-UUU...UUACU_______U______U_A__________UCG-5'\n_____________\|___________________________\|\n_____________30__________________________3\n	116 -- 122	4 -- 10	-20.0623 kcal/mol	6.95142 kcal/mol	2.12698 kcal/mol	95 123@LB@ \| \|@LB@5'-AUG...AUGCU UU U C CUGGC...UCG-3'@LB@ CGGUGGU GAUGG G UGAUGAUGAU@LB@ \|\|\|\|::\| :\|\|:: \| \|:\|\|\|\|\|\|\|\|@LB@ GCCAUUA UUAUU C AUUACUACUA@LB@3'-UUU...UUACU U U A UCG-5'@LB@ \| \|@LB@ 30 3@LB@@LB@@LB@Energy -10.98 kcal/mol@LB@Hybridization Energy -20.0623 kcal/mol@LB@Unfolding Energy - mRNA 6.95142 kcal/mol@LB@Unfolding Energy - sRNA 2.12698 kcal/mol@LB@@LB@Position - mRNA 96 -- 122@LB@Position - sRNA 4 -- 29@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 4 -- 10@LB@
72	0.01058	0.4523	b3458	livK	-8.91	0.157650	183 -- 215	28 -- 63	leucine transporter subunit		_____________182___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AUCAC________AUUUUU____UAU______CG________AAAAC...CGA-3'\n______________GAAUGGGG_______GAC_____GAAA__GAAUG_CG\n______________:\|\|\|:\|\|\|_______\|\|\|_____\|\|\|\|__\|\|\|\|\|_\|\|\n______________UUUAUCCC_______CUG_____CUUU__CUUAC_GC\n3'-UUU...CCAAC________CAUUUGU___UAAGU____A______U__CAUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________64____________________________________27\n	184 -- 190	56 -- 62	-20.644 kcal/mol	5.44449 kcal/mol	6.29422 kcal/mol	182 216@LB@ \| \|@LB@5'-UGU...AUCAC AUUUUU UAU CG AAAAC...CGA-3'@LB@ GAAUGGGG GAC GAAA GAAUG CG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UUUAUCCC CUG CUUU CUUAC GC@LB@3'-UUU...CCAAC CAUUUGU UAAGU A U CAUUA...UCG-5'@LB@ \| \|@LB@ 64 27@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -20.644 kcal/mol@LB@Unfolding Energy - mRNA 5.44449 kcal/mol@LB@Unfolding Energy - sRNA 6.29422 kcal/mol@LB@@LB@Position - mRNA 183 -- 215@LB@Position - sRNA 28 -- 63@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 56 -- 62@LB@
97	0.01584	0.5059	b0116	lpd	-10.63	0.072174	157 -- 204	5 -- 49	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase		_____________156_______________________________________________205\n_____________\|_________________________________________________\|\n5'-CCG...CUGAA_____A_____U____CC_C___A________UAUA___GUC_______GUACU...UAA-3'\n______________AGACG__CGGG_AUGA__G_CGG_GAUAAAUA____GAG___AUGAUGA\n______________\|\|\|\|:__\|:\|:_\|\|\|\|__\|_\|\|\|_:\|\|\|\|\|\|\|____:\|\|___\|\|\|\|\|\|\|\n______________UCUGU__GUCU_UACU__C_GCC_UUAUUUAU____UUC___UACUACU\n3'-UUU...AUUUG_____AA____U____UA_U___A_______________AAU_______AUCG-5'\n_____________\|_________________________________________________\|\n_____________50________________________________________________4\n	198 -- 204	5 -- 11	-27.6335 kcal/mol	10.6788 kcal/mol	6.32229 kcal/mol	156 205@LB@ \| \|@LB@5'-CCG...CUGAA A U CC C A UAUA GUC GUACU...UAA-3'@LB@ AGACG CGGG AUGA G CGG GAUAAAUA GAG AUGAUGA@LB@ \|\|\|\|: \|:\|: \|\|\|\| \| \|\|\| :\|\|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|@LB@ UCUGU GUCU UACU C GCC UUAUUUAU UUC UACUACU@LB@3'-UUU...AUUUG AA U UA U A AAU AUCG-5'@LB@ \| \|@LB@ 50 4@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -27.6335 kcal/mol@LB@Unfolding Energy - mRNA 10.6788 kcal/mol@LB@Unfolding Energy - sRNA 6.32229 kcal/mol@LB@@LB@Position - mRNA 157 -- 204@LB@Position - sRNA 5 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
133	0.02154	0.526	b1105	lpoB	-10.17	0.089721	187 -- 196	50 -- 59	OM lipoprotein stimulator of MrcB transpeptidase		_____________186________197\n_____________\|__________\|\n5'-UUA...UUGUA__________CUUGA...AAC-3'\n______________AGGGGUGAAU\n______________\|\|\|\|\|\|:\|\|:\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	190 -- 196	50 -- 56	-15.1396 kcal/mol	4.24097 kcal/mol	0.728772 kcal/mol	186 197@LB@ \| \|@LB@5'-UUA...UUGUA CUUGA...AAC-3'@LB@ AGGGGUGAAU@LB@ \|\|\|\|\|\|:\|\|:@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -15.1396 kcal/mol@LB@Unfolding Energy - mRNA 4.24097 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 187 -- 196@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
1	2.411e-07	0.0007914	b0889	lrp	-21.69	0.000065	168 -- 212	1 -- 64	leucine-responsive global transcriptional regulator		_____________167_______________________________________________________________213\n_____________\|_________________________________________________________________\|\n5'-GUG...AGACA_________AA_______AUA_____________________________________A______AAGAA...AGC-3'\n______________GGAGUAGGG______GGA____CAGAGA_____GAC_______AAUAA___UAAUGGU_GAUAGC\n______________\|:\|:\|\|\|\|\|______:\|\|____\|\|\|\|:\|_____\|\|\|_______\|\|\|\|\|___\|\|\|\|\|:\|_\|\|\|\|\|\|\n______________CUUUAUCCC______UCU____GUCUUU_____CUG_______UUAUU___AUUACUA_CUAUCG\n3'-UUU...GCCAA_________CAUUUG___GUAA______ACUUA___CCAUUAU_____UCA______________-5'\n_____________\|________________________________________________________________\|\n_____________65_______________________________________________________________1\n	199 -- 205	7 -- 13	-30.6118 kcal/mol	2.57614 kcal/mol	6.344 kcal/mol	167 213@LB@ \| \|@LB@5'-GUG...AGACA AA AUA A AAGAA...AGC-3'@LB@ GGAGUAGGG GGA CAGAGA GAC AAUAA UAAUGGU GAUAGC@LB@ \|:\|:\|\|\|\|\| :\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|@LB@ CUUUAUCCC UCU GUCUUU CUG UUAUU AUUACUA CUAUCG@LB@3'-UUU...GCCAA CAUUUG GUAA ACUUA CCAUUAU UCA -5'@LB@ \| \|@LB@ 65 1@LB@@LB@@LB@Energy -21.69 kcal/mol@LB@Hybridization Energy -30.6118 kcal/mol@LB@Unfolding Energy - mRNA 2.57614 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 1 -- 64@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@LB@
69	0.009861	0.4523	b0879	macB	-12.35	0.030572	144 -- 182	1 -- 59	macrolide ABC transporter peremase/ATPase		_____________143___________________________________________________________183\n_____________\|_____________________________________________________________\|\n5'-AAU...GUCAA____CUUG_____________________________________________________CAAAC...CGG-3'\n______________AGGG____AAGCGGGC_______GAUGAA_G_UGGUGAU____________UGGUGA_GGC\n______________\|\|\|\|____\|\|:\|:\|:\|_______:\|\|\|\|\|_\|_:\|\|\|:\|\|____________\|\|:\|\|\|_:\|\|\n______________UCCC____UUUGUCUG_______UUACUU_C_GCCAUUA____________ACUACU_UCG\n3'-UUU...CUUUA____CA__________UAAGUCU______A_U_______UUUAUUUCAAUU______A___-5'\n_____________\|____________________________________________________________\|\n_____________60___________________________________________________________1\n	167 -- 173	23 -- 29	-29.0987 kcal/mol	10.4067 kcal/mol	6.33764 kcal/mol	143 183@LB@ \| \|@LB@5'-AAU...GUCAA CUUG CAAAC...CGG-3'@LB@ AGGG AAGCGGGC GAUGAA G UGGUGAU UGGUGA GGC@LB@ \|\|\|\| \|\|:\|:\|:\| :\|\|\|\|\| \| :\|\|\|:\|\| \|\|:\|\|\| :\|\|@LB@ UCCC UUUGUCUG UUACUU C GCCAUUA ACUACU UCG@LB@3'-UUU...CUUUA CA UAAGUCU A U UUUAUUUCAAUU A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -29.0987 kcal/mol@LB@Unfolding Energy - mRNA 10.4067 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 144 -- 182@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 23 -- 29@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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