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@
179	0.02973	0.5424	b2812	tcdA	-11.60	0.044907	209 -- 228	1 -- 28	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________208___________________________229\n_____________\|_____________________________\|\n5'-GUG...UCUGU_______________________C_____GUCAG...UUU-3'\n______________GGUAAU_________UAGUGAUG_AUGGC\n______________\|\|\|\|\|\|_________\|\|:\|\|\|\|\|_\|\|:\|\|\n______________CCAUUA_________AUUACUAC_UAUCG\n3'-UUU...UACUG______UUUAUUUCA______________-5'\n_____________\|____________________________\|\n_____________29___________________________1\n	216 -- 222	6 -- 12	-16.3639 kcal/mol	3.995 kcal/mol	0.766821 kcal/mol	208 229@LB@ \| \|@LB@5'-GUG...UCUGU C GUCAG...UUU-3'@LB@ GGUAAU UAGUGAUG AUGGC@LB@ \|\|\|\|\|\| \|\|:\|\|\|\|\| \|\|:\|\|@LB@ CCAUUA AUUACUAC UAUCG@LB@3'-UUU...UACUG UUUAUUUCA -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.3639 kcal/mol@LB@Unfolding Energy - mRNA 3.995 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
153	0.02513	0.526	b2745	truD	-9.91	0.100940	94 -- 116	1 -- 24	tRNA(Glu) pseudouridine(13) synthase	_____________93_______________________117\n_____________\|________________________\|\n5'-AAC...GCCAU________U_____C_____A___CACUA...UGG-3'\n______________AUGGAUGA_GUUAA__GUGA_AGC\n______________\|\|::\|\|:\|_\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UAUUUAUU_CAAUU__UACU_UCG\n3'-UUU...GCCAU________U_____AC____A___-5'\n_____________\|_______________________\|\n_____________25______________________1\n	95 -- 101	17 -- 23	-14.0384 kcal/mol	4.01581 kcal/mol	0.108605 kcal/mol	93 117@LB@ \| \|@LB@5'-AAC...GCCAU U C A CACUA...UGG-3'@LB@ AUGGAUGA GUUAA GUGA AGC@LB@ \|\|::\|\|:\| \|\|\|\|\| :\|\|\| \|\|\|@LB@ UAUUUAUU CAAUU UACU UCG@LB@3'-UUU...GCCAU U AC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.0384 kcal/mol@LB@Unfolding Energy - mRNA 4.01581 kcal/mol@LB@Unfolding Energy - sRNA 0.108605 kcal/mol@LB@@LB@Position - mRNA 94 -- 116@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 17 -- 23@LB@
76	0.01084	0.4523	b3990	thiH	-9.70	0.111440	16 -- 25	55 -- 64	tyrosine lyase involved in thiamine-thiazole moiety synthesis	_____________15_________26\n_____________\|__________\|\n5'-GCC...CGCUG__________CCGAC...AUG-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	19 -- 25	55 -- 61	-15.2995 kcal/mol	5.57445 kcal/mol	0.0291912 kcal/mol	15 26@LB@ \| \|@LB@5'-GCC...CGCUG CCGAC...AUG-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -15.2995 kcal/mol@LB@Unfolding Energy - mRNA 5.57445 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 16 -- 25@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 55 -- 61@LB@
26	0.001686	0.211	b0091	murC	-10.53	0.075719	174 -- 220	1 -- 48	UDP-N-acetylmuramate:L-alanine ligase	_____________173______________________________________________221\n_____________\|________________________________________________\|\n5'-CAG...CGUAU__AUUUA______U___________A_______UACACAACAAU____AAAAC...GCG-3'\n______________GA_____AGAAGU_AAUGGC_GUAA_GAAUGAA___________UGGC\n______________\|\|_____\|\|\|\|:\|_\|\|\|\|:\|_\|\|\|\|_:\|\|\|:\|\|___________\|:\|\|\n______________CU_____UCUUUA_UUACUG_CAUU_UUUAUUU___________AUCG\n3'-UUU...UUUGU__GUAAG______C______C____A_______CAAUUACUACU____-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	199 -- 205	16 -- 22	-22.2946 kcal/mol	5.44296 kcal/mol	6.32011 kcal/mol	173 221@LB@ \| \|@LB@5'-CAG...CGUAU AUUUA U A UACACAACAAU AAAAC...GCG-3'@LB@ GA AGAAGU AAUGGC GUAA GAAUGAA UGGC@LB@ \|\| \|\|\|\|:\| \|\|\|\|:\| \|\|\|\| :\|\|\|:\|\| \|:\|\|@LB@ CU UCUUUA UUACUG CAUU UUUAUUU AUCG@LB@3'-UUU...UUUGU GUAAG C C A CAAUUACUACU -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -22.2946 kcal/mol@LB@Unfolding Energy - mRNA 5.44296 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 174 -- 220@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
5	3.022e-05	0.01984	b4553	ysaB	-16.91	0.002179	166 -- 209	3 -- 54	uncharacterized protein	_____________165__________________________________________________210\n_____________\|____________________________________________________\|\n5'-UCA...AUAAA___UA____UCACCUGCAAACCA_____________________________AACGC...AUC-3'\n______________UAA__AGAC______________GACGGUAAU________UUAAUGAUGAUG\n______________\|\|\|__\|\|\|\|______________\|\|\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\|\|\|:\n______________AUU__UCUG______________CUGCCAUUA________AAUUACUACUAU\n3'-UUU...UCCCC___UG____UAAGUCUUUACUUA_________UUUAUUUC____________CG-5'\n_____________\|____________________________________________________\|\n_____________55___________________________________________________2\n	203 -- 209	3 -- 9	-28.2861 kcal/mol	5.03949 kcal/mol	6.3375 kcal/mol	165 210@LB@ \| \|@LB@5'-UCA...AUAAA UA UCACCUGCAAACCA AACGC...AUC-3'@LB@ UAA AGAC GACGGUAAU UUAAUGAUGAUG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|:@LB@ AUU UCUG CUGCCAUUA AAUUACUACUAU@LB@3'-UUU...UCCCC UG UAAGUCUUUACUUA UUUAUUUC CG-5'@LB@ \| \|@LB@ 55 2@LB@@LB@@LB@Energy -16.91 kcal/mol@LB@Hybridization Energy -28.2861 kcal/mol@LB@Unfolding Energy - mRNA 5.03949 kcal/mol@LB@Unfolding Energy - sRNA 6.3375 kcal/mol@LB@@LB@Position - mRNA 166 -- 209@LB@Position - sRNA 3 -- 54@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 3 -- 9@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@
104	0.01633	0.5059	b3057	bacA	-10.04	0.095309	188 -- 194	54 -- 60	undecaprenyl pyrophosphate phosphatase	_____________187_____195\n_____________\|_______\|\n5'-UUC...UAAUU_______UUAUU...UUG-3'\n______________UAGGGGU\n______________\|\|\|\|\|\|\|\n______________AUCCCCA\n3'-UUU...ACUUU_______UUUGU...UCG-5'\n_____________\|_______\|\n_____________61______53\n	188 -- 194	54 -- 60	-11.2865 kcal/mol	1.18126 kcal/mol	0.0661814 kcal/mol	187 195@LB@ \| \|@LB@5'-UUC...UAAUU UUAUU...UUG-3'@LB@ UAGGGGU@LB@ \|\|\|\|\|\|\|@LB@ AUCCCCA@LB@3'-UUU...ACUUU UUUGU...UCG-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -11.2865 kcal/mol@LB@Unfolding Energy - mRNA 1.18126 kcal/mol@LB@Unfolding Energy - sRNA 0.0661814 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 54 -- 60@LB@
56	0.007094	0.4159	b1242	ychE	-10.14	0.091024	67 -- 90	1 -- 23	UPF0056 family inner membrane protein	_____________66_______________________91\n_____________\|________________________\|\n5'-CAU...ACAAC_______CAA___C_A________AAUUU...GCA-3'\n______________UAGAUAA___UAA_G_AUGAUAGC\n______________\|\|:\|\|\|\|___\|\|\|_\|_\|\|\|\|\|\|\|\|\n______________AUUUAUU___AUU_C_UACUAUCG\n3'-UUU...CCAUU_______UCA___A__________-5'\n_____________\|_______________________\|\n_____________24______________________1\n	84 -- 90	1 -- 7	-13.9916 kcal/mol	3.74778 kcal/mol	0.105066 kcal/mol	66 91@LB@ \| \|@LB@5'-CAU...ACAAC CAA C A AAUUU...GCA-3'@LB@ UAGAUAA UAA G AUGAUAGC@LB@ \|\|:\|\|\|\| \|\|\| \| \|\|\|\|\|\|\|\|@LB@ AUUUAUU AUU C UACUAUCG@LB@3'-UUU...CCAUU UCA A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.9916 kcal/mol@LB@Unfolding Energy - mRNA 3.74778 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 67 -- 90@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 1 -- 7@LB@
143	0.02405	0.526	b3292	zntR	-11.17	0.055543	275 -- 285	1 -- 12	zntA gene transcriptional activator	_____________274__________286\n_____________\|____________\|\n5'-UGA...CAGCA____________AUGAA...CUG-3'\n______________GAUGAUGG_AGC\n______________:\|\|\|\|\|\|:_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	276 -- 282	5 -- 11	-12.3439 kcal/mol	1.13072 kcal/mol	0.0394463 kcal/mol	274 286@LB@ \| \|@LB@5'-UGA...CAGCA AUGAA...CUG-3'@LB@ GAUGAUGG AGC@LB@ :\|\|\|\|\|\|: \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -12.3439 kcal/mol@LB@Unfolding Energy - mRNA 1.13072 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 275 -- 285@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 276 -- 282@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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