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
57	0.007764	0.4472	b0585	fes	-12.40	0.029926	182 -- 237	1 -- 55	enterobactin/ferrienterobactin esterase	_____________181___________________________________________________________238\n_____________\|_____________________________________________________________\|\n5'-CAU...GCACA_______U__G____________U_______CGU____AGU__GA_____GAGC_______AGUCG...GGU-3'\n______________GUAAACA_GG_GUU_____AUGG_GUGACGG___UAAA___AG__AGUGA____UGGUGGC\n______________\|\|\|\|\|\|\|_\|:_:\|\|_____\|\|\|:_:\|\|\|\|\|\|___\|\|\|\|___\|\|__\|:\|\|\|____\|\|:\|:\|\|\n______________CAUUUGU_CU_UAA_____UACU_UACUGCC___AUUU___UC__UUACU____ACUAUCG\n3'-UUU...AUCCC__________G___GUCUU____________AUU____AUU__AA________________-5'\n_____________\|____________________________________________________________\|\n_____________56___________________________________________________________1\n	231 -- 237	1 -- 7	-34.1879 kcal/mol	15.4551 kcal/mol	6.33758 kcal/mol	181 238@LB@ \| \|@LB@5'-CAU...GCACA U G U CGU AGU GA GAGC AGUCG...GGU-3'@LB@ GUAAACA GG GUU AUGG GUGACGG UAAA AG AGUGA UGGUGGC@LB@ \|\|\|\|\|\|\| \|: :\|\| \|\|\|: :\|\|\|\|\|\| \|\|\|\| \|\| \|:\|\|\| \|\|:\|:\|\|@LB@ CAUUUGU CU UAA UACU UACUGCC AUUU UC UUACU ACUAUCG@LB@3'-UUU...AUCCC G GUCUU AUU AUU AA -5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -34.1879 kcal/mol@LB@Unfolding Energy - mRNA 15.4551 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 182 -- 237@LB@Position - sRNA 1 -- 55@LB@Position Seed - mRNA 231 -- 237@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@
64	0.008913	0.4523	b4231	yjfF	-11.33	0.051476	106 -- 140	1 -- 41	putative sugar ABC transporter permease	_____________105_______________________________________141\n_____________\|_________________________________________\|\n5'-CGG...CCGCC_________CCA_______________C_____________UUUGC...GAG-3'\n______________AGAGAUGAA____GGUGGUGA___AAG__GGUGGUGGU_GC\n______________\|\|\|:\|\|\|\|\|____\|\|\|::\|:\|___\|\|\|__::\|\|:\|\|:\|_\|\|\n______________UCUUUACUU____CCAUUAUU___UUC__UUACUACUA_CG\n3'-UUU...GUAAG_________ACUG________UAU___AA_________U__-5'\n_____________\|________________________________________\|\n_____________42_______________________________________1\n	132 -- 138	4 -- 10	-27.205 kcal/mol	9.83395 kcal/mol	6.043 kcal/mol	105 141@LB@ \| \|@LB@5'-CGG...CCGCC CCA C UUUGC...GAG-3'@LB@ AGAGAUGAA GGUGGUGA AAG GGUGGUGGU GC@LB@ \|\|\|:\|\|\|\|\| \|\|\|::\|:\| \|\|\| ::\|\|:\|\|:\| \|\|@LB@ UCUUUACUU CCAUUAUU UUC UUACUACUA CG@LB@3'-UUU...GUAAG ACUG UAU AA U -5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -27.205 kcal/mol@LB@Unfolding Energy - mRNA 9.83395 kcal/mol@LB@Unfolding Energy - sRNA 6.043 kcal/mol@LB@@LB@Position - mRNA 106 -- 140@LB@Position - sRNA 1 -- 41@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 4 -- 10@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@
70	0.01004	0.4523	b1658	purR	-15.06	0.006831	174 -- 223	1 -- 65	transcriptional repressor hypoxanthine-binding	_____________173________________________________________________________________224\n_____________\|__________________________________________________________________\|\n5'-UUU...GGAGC______UA____C______GU_________G_______AAC______A__________________GAAAC...GCA-3'\n______________UGAAGU__GGGU___UGGA______GAAAU_GAAUGGC___AAUAAA__________GAUG_UAGC\n______________\|\|\|\|:\|__\|\|\|\|___::\|\|______\|\|\|\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|__________\|\|\|\|_\|\|\|\|\n______________ACUUUA__CCCA___GUCU______CUUUA_CUUACUG___UUAUUU__________CUAC_AUCG\n3'-UUU...GGCCA______UC____UUU____GUAAGU_____________CCA______AUUUCAAUUA____U____-5'\n_____________\|_________________________________________________________________\|\n_____________66________________________________________________________________1\n	199 -- 205	29 -- 35	-29.7477 kcal/mol	7.45199 kcal/mol	7.23987 kcal/mol	173 224@LB@ \| \|@LB@5'-UUU...GGAGC UA C GU G AAC A GAAAC...GCA-3'@LB@ UGAAGU GGGU UGGA GAAAU GAAUGGC AAUAAA GAUG UAGC@LB@ \|\|\|\|:\| \|\|\|\| ::\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ ACUUUA CCCA GUCU CUUUA CUUACUG UUAUUU CUAC AUCG@LB@3'-UUU...GGCCA UC UUU GUAAGU CCA AUUUCAAUUA U -5'@LB@ \| \|@LB@ 66 1@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -29.7477 kcal/mol@LB@Unfolding Energy - mRNA 7.45199 kcal/mol@LB@Unfolding Energy - sRNA 7.23987 kcal/mol@LB@@LB@Position - mRNA 174 -- 223@LB@Position - sRNA 1 -- 65@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 29 -- 35@LB@
79	0.01117	0.4523	b1593	ynfK	-13.04	0.021217	188 -- 210	1 -- 21	putative dethiobiotin synthetase	_____________187_____________________211\n_____________\|_______________________\|\n5'-CAC...AUAAC________________CUGA___GUUUC...CGG-3'\n______________GGUGGAGUUAGUGAUG____AGC\n______________::\|::\|\|\|\|\|:\|\|\|\|\|____\|\|\|\n______________UUAUUUCAAUUACUAC____UCG\n3'-UUU...AUUAU________________UA_____-5'\n_____________\|______________________\|\n_____________22_____________________1\n	197 -- 203	6 -- 12	-19.4081 kcal/mol	6.29658 kcal/mol	0.0669945 kcal/mol	187 211@LB@ \| \|@LB@5'-CAC...AUAAC CUGA GUUUC...CGG-3'@LB@ GGUGGAGUUAGUGAUG AGC@LB@ ::\|::\|\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ UUAUUUCAAUUACUAC UCG@LB@3'-UUU...AUUAU UA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 6.29658 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
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@
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@
84	0.01184	0.4627	b3101	yqjF	-11.66	0.043663	211 -- 235	1 -- 23	putative quinol oxidase subunit	_____________210_______________________236\n_____________\|_________________________\|\n5'-CAG...AAAAU____A__U_______UAC_______GCGCA...GUA-3'\n______________UAGA_GA_GUUGGUG___UGGUAGC\n______________\|\|:\|_:\|_\|\|\|::\|\|___\|\|:\|\|\|\|\n______________AUUU_UU_CAAUUAC___ACUAUCG\n3'-UUU...CCAUU____A__U_______U_________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	229 -- 235	1 -- 7	-15.9826 kcal/mol	4.21954 kcal/mol	0.105066 kcal/mol	210 236@LB@ \| \|@LB@5'-CAG...AAAAU A U UAC GCGCA...GUA-3'@LB@ UAGA GA GUUGGUG UGGUAGC@LB@ \|\|:\| :\| \|\|\|::\|\| \|\|:\|\|\|\|@LB@ AUUU UU CAAUUAC ACUAUCG@LB@3'-UUU...CCAUU A U U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -15.9826 kcal/mol@LB@Unfolding Energy - mRNA 4.21954 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.013	0.4962	b0451	amtB	-9.48	0.122870	5 -- 23	1 -- 22	ammonium transporter	_____________4______________________24\n_____________\|______________________\|\n_______5'-CCAA_______AAU____________GAUUG...CGU-3'\n______________AAGUAAA_____UGAUG_UGGC\n______________\|\|:\|\|\|\|_____\|\|\|\|\|_\|:\|\|\n______________UUUAUUU_____ACUAC_AUCG\n3'-UUU...CAUUA_______CAAUU_____U____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	16 -- 22	-11.4865 kcal/mol	1.90989 kcal/mol	0.0989066 kcal/mol	4 24@LB@ \| \|@LB@ 5'-CCAA AAU GAUUG...CGU-3'@LB@ AAGUAAA UGAUG UGGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|:\|\|@LB@ UUUAUUU ACUAC AUCG@LB@3'-UUU...CAUUA CAAUU U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.4865 kcal/mol@LB@Unfolding Energy - mRNA 1.90989 kcal/mol@LB@Unfolding Energy - sRNA 0.0989066 kcal/mol@LB@@LB@Position - mRNA 5 -- 23@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 16 -- 22@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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