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
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@
61	0.008575	0.4523	b3464	ftsY	-13.38	0.017655	71 -- 119	2 -- 50	Signal Recognition Particle (SRP) receptor	_____________70__________________________________________________120\n_____________\|___________________________________________________\|\n5'-CCC...UCCGC______ACACAUACUUGCA_______AU______U________________ACUAU...CGG-3'\n______________CAGAUA_____________GGCGGUG__GUGAAU_AAGUUAA__GUGAUAG\n______________\|\|\|\|:\|_____________\|:\|\|\|\|:__:\|:\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|\|\|\n______________GUCUGU_____________CUGCCAU__UAUUUA_UUCAAUU__UACUAUC\n3'-UUU...CAUUU______AAGUCUUUACUUA_______________U_______AC_______G-5'\n_____________\|___________________________________________________\|\n_____________51__________________________________________________1\n	113 -- 119	2 -- 8	-30.4135 kcal/mol	10.695 kcal/mol	6.33478 kcal/mol	70 120@LB@ \| \|@LB@5'-CCC...UCCGC ACACAUACUUGCA AU U ACUAU...CGG-3'@LB@ CAGAUA GGCGGUG GUGAAU AAGUUAA GUGAUAG@LB@ \|\|\|\|:\| \|:\|\|\|\|: :\|:\|\|\| \|\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ GUCUGU CUGCCAU UAUUUA UUCAAUU UACUAUC@LB@3'-UUU...CAUUU AAGUCUUUACUUA U AC G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -30.4135 kcal/mol@LB@Unfolding Energy - mRNA 10.695 kcal/mol@LB@Unfolding Energy - sRNA 6.33478 kcal/mol@LB@@LB@Position - mRNA 71 -- 119@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 2 -- 8@LB@
103	0.01627	0.5059	b3527	yhjJ	-12.72	0.025178	191 -- 250	1 -- 59	putative periplasmic M16 family chaperone	_____________190_____________________________________________________________________251\n_____________\|_______________________________________________________________________\|\n5'-CUC...UGAUC______UC___U___GGGCACAAAAA____ACUUUUAGCG____________________C__________CACUG...GGC-3'\n______________AGGGGU__ACA_GCA___________UUCG__________GGCGGU___________UUG_UGAUGAUGGC\n______________\|\|\|\|\|\|__\|\|\|_:\|\|___________\|\|\|:__________\|:\|\|\|\|___________\|\|:_\|\|\|\|\|\|\|:\|\|\n______________UCCCCA__UGU_UGU___________AAGU__________CUGCCA___________AAU_ACUACUAUCG\n3'-UUU...CUUUA______UU___C__________________CUUUACUUA_______UUAUUUAUUUC___U__________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	244 -- 250	1 -- 7	-34.0873 kcal/mol	15.0257 kcal/mol	6.33764 kcal/mol	190 251@LB@ \| \|@LB@5'-CUC...UGAUC UC U GGGCACAAAAA ACUUUUAGCG C CACUG...GGC-3'@LB@ AGGGGU ACA GCA UUCG GGCGGU UUG UGAUGAUGGC@LB@ \|\|\|\|\|\| \|\|\| :\|\| \|\|\|: \|:\|\|\|\| \|\|: \|\|\|\|\|\|\|:\|\|@LB@ UCCCCA UGU UGU AAGU CUGCCA AAU ACUACUAUCG@LB@3'-UUU...CUUUA UU C CUUUACUUA UUAUUUAUUUC U -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -34.0873 kcal/mol@LB@Unfolding Energy - mRNA 15.0257 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 191 -- 250@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 1 -- 7@LB@
192	0.03268	0.5507	b3532	bcsB	-10.41	0.080313	186 -- 199	1 -- 12	regulator of cellulose synthase cyclic di-GMP binding	_____________185____________200\n_____________\|______________\|\n5'-AAG...UCAAC__________AC__GAUGA...UCA-3'\n______________AAUGAUGAUA__GC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________UUACUACUAU__CG\n3'-UUU...UUCAA______________-5'\n_____________\|_____________\|\n_____________13____________1\n	189 -- 195	3 -- 9	-11.9692 kcal/mol	1.52301 kcal/mol	0.0394463 kcal/mol	185 200@LB@ \| \|@LB@5'-AAG...UCAAC AC GAUGA...UCA-3'@LB@ AAUGAUGAUA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UUACUACUAU CG@LB@3'-UUU...UUCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -11.9692 kcal/mol@LB@Unfolding Energy - mRNA 1.52301 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 3 -- 9@LB@
39	0.003905	0.3287	b3541	dppD	-12.54	0.027771	124 -- 154	26 -- 56	dipeptide/heme ABC transporter ATPas	_____________123_______________________________155\n_____________\|_________________________________\|\n5'-UUU...CUGAC_______U________ACCU_____________CUGCG...GCG-3'\n______________GGU__GC_GGCAUUUA____GAUGGGUGACGGU\n______________\|\|\|__:\|_\|:\|\|\|\|:\|____:\|\|\|::\|\|\|\|\|\|\|\n______________CCA__UG_CUGUAAGU____UUACUUACUGCCA\n3'-UUU...UAUCC___UU__U________CU_______________UUAUU...UCG-5'\n_____________\|_________________________________\|\n_____________57________________________________25\n	148 -- 154	26 -- 32	-28.6535 kcal/mol	9.81942 kcal/mol	6.29593 kcal/mol	123 155@LB@ \| \|@LB@5'-UUU...CUGAC U ACCU CUGCG...GCG-3'@LB@ GGU GC GGCAUUUA GAUGGGUGACGGU@LB@ \|\|\| :\| \|:\|\|\|\|:\| :\|\|\|::\|\|\|\|\|\|\|@LB@ CCA UG CUGUAAGU UUACUUACUGCCA@LB@3'-UUU...UAUCC UU U CU UUAUU...UCG-5'@LB@ \| \|@LB@ 57 25@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -28.6535 kcal/mol@LB@Unfolding Energy - mRNA 9.81942 kcal/mol@LB@Unfolding Energy - sRNA 6.29593 kcal/mol@LB@@LB@Position - mRNA 124 -- 154@LB@Position - sRNA 26 -- 56@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 26 -- 32@LB@
151	0.02491	0.526	b3575	yiaK	-7.81	0.245984	13 -- 22	1 -- 10	2 3-diketo-L-gulonate reductase NADH-dependent	_____________12_________23\n_____________\|__________\|\n5'-UUU...CGUCC__________GCAAA...UCG-3'\n______________UGAUGGUAGC\n______________\|\|\|\|\|:\|\|\|\|\n______________ACUACUAUCG\n3'-UUU...CAAUU__________-5'\n_____________\|_________\|\n_____________11________1\n	16 -- 22	1 -- 7	-14.2362 kcal/mol	6.39652 kcal/mol	0.0255427 kcal/mol	12 23@LB@ \| \|@LB@5'-UUU...CGUCC GCAAA...UCG-3'@LB@ UGAUGGUAGC@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACUACUAUCG@LB@3'-UUU...CAAUU -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -14.2362 kcal/mol@LB@Unfolding Energy - mRNA 6.39652 kcal/mol@LB@Unfolding Energy - sRNA 0.0255427 kcal/mol@LB@@LB@Position - mRNA 13 -- 22@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 1 -- 7@LB@
63	0.008816	0.4523	b3600	mtlD	-11.23	0.053963	184 -- 208	1 -- 23	mannitol-1-phosphate dehydrogenase NAD-dependent	_____________183_______________________209\n_____________\|_________________________\|\n5'-GUG...AACAU___UG_________ACU____A___AUUAC...AUC-3'\n______________UGA__AAGGUUAAU___AUGA_AGC\n______________\|:\|__\|\|:\|\|\|\|\|\|___\|\|\|\|_\|\|\|\n______________AUU__UUUCAAUUA___UACU_UCG\n3'-UUU...CCAUU___UA_________C______A___-5'\n_____________\|________________________\|\n_____________24_______________________1\n	191 -- 197	10 -- 16	-14.8386 kcal/mol	3.50103 kcal/mol	0.105066 kcal/mol	183 209@LB@ \| \|@LB@5'-GUG...AACAU UG ACU A AUUAC...AUC-3'@LB@ UGA AAGGUUAAU AUGA AGC@LB@ \|:\| \|\|:\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ AUU UUUCAAUUA UACU UCG@LB@3'-UUU...CCAUU UA C A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.8386 kcal/mol@LB@Unfolding Energy - mRNA 3.50103 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 184 -- 208@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
140	0.02319	0.526	b3615	waaH	-10.58	0.073933	178 -- 212	1 -- 47	LPS(HepIII)-glucuronic acid glycosyltransferase	_____________177______________________________________________213\n_____________\|________________________________________________\|\n5'-GAU...GGAUA____________C____U_______UU________________AC___ACCAA...GGA-3'\n______________AC_UUCAGAGGU____G_CGGUAAU___________AUGAUGA__AGC\n______________\|\|_\|\|\|\|\|\|::\|____\|_\|\|\|\|\|\|\|___________\|\|\|\|\|\|\|__\|\|\|\n______________UG_AAGUCUUUA____C_GCCAUUA___________UACUACU__UCG\n3'-UUU...UUGUC__U_________CUUA_U_______UUUAUUUCAAU_______A____-5'\n_____________\|_______________________________________________\|\n_____________48______________________________________________1\n	201 -- 207	5 -- 11	-24.9941 kcal/mol	8.09222 kcal/mol	6.32011 kcal/mol	177 213@LB@ \| \|@LB@5'-GAU...GGAUA C U UU AC ACCAA...GGA-3'@LB@ AC UUCAGAGGU G CGGUAAU AUGAUGA AGC@LB@ \|\| \|\|\|\|\|\|::\| \| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UG AAGUCUUUA C GCCAUUA UACUACU UCG@LB@3'-UUU...UUGUC U CUUA U UUUAUUUCAAU A -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -24.9941 kcal/mol@LB@Unfolding Energy - mRNA 8.09222 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
18	0.0008759	0.1482	b3626	waaR	-11.62	0.044565	224 -- 238	11 -- 25	lipopolysaccharide 1 2-glucosyltransferase; UDP-glucose:(glucosyl)LPS alpha-1 2-glucosyltransferase	_____________223_____________239\n_____________\|_______________\|\n5'-UGG...AUAGA_______________AGCCU...GUG-3'\n______________GAUAGAUAAAGUUAA\n______________:\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________UUAUUUAUUUCAAUU\n3'-UUU...UGCCA_______________ACUAC...UCG-5'\n_____________\|_______________\|\n_____________26______________10\n	232 -- 238	11 -- 17	-12.9968 kcal/mol	1.27318 kcal/mol	0.10636 kcal/mol	223 239@LB@ \| \|@LB@5'-UGG...AUAGA AGCCU...GUG-3'@LB@ GAUAGAUAAAGUUAA@LB@ :\|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ UUAUUUAUUUCAAUU@LB@3'-UUU...UGCCA ACUAC...UCG-5'@LB@ \| \|@LB@ 26 10@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -12.9968 kcal/mol@LB@Unfolding Energy - mRNA 1.27318 kcal/mol@LB@Unfolding Energy - sRNA 0.10636 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 11 -- 25@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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