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
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@
157	0.02559	0.526	b2057	wcaC	-8.75	0.168472	165 -- 205	16 -- 58	putative glycosyl transferase		_____________164___________________________________________206\n_____________\|_____________________________________________\|\n5'-GUC...GCGCU__U__________AAA____CGC_______A_____U________UAUUU...CAC-3'\n______________GG_GGUGGG_AGA_____AG____GAGUGA_GGUAA_UAAAUGAA\n______________\|\|_\|\|\|:::_\|\|\|_____\|\|____\|\|:\|\|\|_\|\|\|\|\|_\|\|\|\|\|:\|\|\n______________CC_CCAUUU_UCU_____UC____CUUACU_CCAUU_AUUUAUUU\n3'-UUU...UUUAU_________G___GUAAG__UUUA______G______________CAAUU...UCG-5'\n_____________\|_____________________________________________\|\n_____________59____________________________________________15\n	199 -- 205	16 -- 22	-25.2337 kcal/mol	10.162 kcal/mol	6.32308 kcal/mol	164 206@LB@ \| \|@LB@5'-GUC...GCGCU U AAA CGC A U UAUUU...CAC-3'@LB@ GG GGUGGG AGA AG GAGUGA GGUAA UAAAUGAA@LB@ \|\| \|\|\|::: \|\|\| \|\| \|\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|\|@LB@ CC CCAUUU UCU UC CUUACU CCAUU AUUUAUUU@LB@3'-UUU...UUUAU G GUAAG UUUA G CAAUU...UCG-5'@LB@ \| \|@LB@ 59 15@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -25.2337 kcal/mol@LB@Unfolding Energy - mRNA 10.162 kcal/mol@LB@Unfolding Energy - sRNA 6.32308 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 16 -- 58@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
13	0.0005091	0.1286	b2062	wza	-15.65	0.004784	187 -- 207	5 -- 27	colanic acid export protein; outer membrane auxillary lipoprotein		_____________186_____________________208\n_____________\|_______________________\|\n5'-AAA...CCAAA____________C__________AAUCC...GCA-3'\n______________GUGAUAAAUAAA___AAUGAUGA\n______________\|\|:\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CAUUAUUUAUUU___UUACUACU\n3'-UUU...ACUGC____________CAA________AUCG-5'\n_____________\|_______________________\|\n_____________28______________________4\n	201 -- 207	5 -- 11	-18.4073 kcal/mol	2.04721 kcal/mol	0.709121 kcal/mol	186 208@LB@ \| \|@LB@5'-AAA...CCAAA C AAUCC...GCA-3'@LB@ GUGAUAAAUAAA AAUGAUGA@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CAUUAUUUAUUU UUACUACU@LB@3'-UUU...ACUGC CAA AUCG-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -18.4073 kcal/mol@LB@Unfolding Energy - mRNA 2.04721 kcal/mol@LB@Unfolding Energy - sRNA 0.709121 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@LB@
24	0.001422	0.1946	b0065	yabI	-15.22	0.006192	70 -- 99	1 -- 29	DedA family inner membrane protein		_____________69______________________________100\n_____________\|_______________________________\|\n5'-UGA...CGUGC____U_____GAA_____G____________CGUCA...GUU-3'\n______________CGGU_GUGAA___AAAGU_AAUGAUG_UAGC\n______________\|\|\|\|_:\|:\|\|___\|\|\|\|\|_\|\|\|\|\|\|\|_\|\|\|\|\n______________GCCA_UAUUU___UUUCA_UUACUAC_AUCG\n3'-UUU...UUACU____U_____A_______A_______U____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	89 -- 95	6 -- 12	-22.6746 kcal/mol	5.32597 kcal/mol	2.12711 kcal/mol	69 100@LB@ \| \|@LB@5'-UGA...CGUGC U GAA G CGUCA...GUU-3'@LB@ CGGU GUGAA AAAGU AAUGAUG UAGC@LB@ \|\|\|\| :\|:\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ GCCA UAUUU UUUCA UUACUAC AUCG@LB@3'-UUU...UUACU U A A U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.22 kcal/mol@LB@Hybridization Energy -22.6746 kcal/mol@LB@Unfolding Energy - mRNA 5.32597 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 70 -- 99@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 6 -- 12@LB@
196	0.0332	0.554	b0128	yadH	-11.13	0.056665	104 -- 121	39 -- 55	putative ABC transporter permease		_____________103________________122\n_____________\|__________________\|\n5'-UUA...GUUAA_______G__________UAUUA...UCA-3'\n______________GUGAGCA_GGCAUUCAGG\n______________\|\|:\|:\|\|_\|:\|\|\|\|\|\|\|:\n______________CAUUUGU_CUGUAAGUCU\n3'-UUU...AUCCC__________________UUACU...UCG-5'\n_____________\|__________________\|\n_____________56_________________38\n	114 -- 120	40 -- 46	-20.6932 kcal/mol	3.311 kcal/mol	6.24918 kcal/mol	103 122@LB@ \| \|@LB@5'-UUA...GUUAA G UAUUA...UCA-3'@LB@ GUGAGCA GGCAUUCAGG@LB@ \|\|:\|:\|\| \|:\|\|\|\|\|\|\|:@LB@ CAUUUGU CUGUAAGUCU@LB@3'-UUU...AUCCC UUACU...UCG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -20.6932 kcal/mol@LB@Unfolding Energy - mRNA 3.311 kcal/mol@LB@Unfolding Energy - sRNA 6.24918 kcal/mol@LB@@LB@Position - mRNA 104 -- 121@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 40 -- 46@LB@
200	0.03384	0.5555	b0316	yahB	-11.86	0.039401	41 -- 57	47 -- 61	putative DNA-bindng transcriptional regulator	b0504	_____________40________________58\n_____________\|_________________\|\n5'-CUG...ACUGC__________UUU____AUAUG...CUU-3'\n______________GUGGGGGUAA___CAGA\n______________:\|:\|\|\|\|\|\|\|___\|\|\|\|\n______________UAUCCCCAUU___GUCU\n3'-UUU...AACUU__________U______GUAAG...UCG-5'\n_____________\|_________________\|\n_____________62________________46\n	44 -- 50	52 -- 58	-17.391 kcal/mol	3.44789 kcal/mol	2.08204 kcal/mol	40 58@LB@ \| \|@LB@5'-CUG...ACUGC UUU AUAUG...CUU-3'@LB@ GUGGGGGUAA CAGA@LB@ :\|:\|\|\|\|\|\|\| \|\|\|\|@LB@ UAUCCCCAUU GUCU@LB@3'-UUU...AACUU U GUAAG...UCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -17.391 kcal/mol@LB@Unfolding Energy - mRNA 3.44789 kcal/mol@LB@Unfolding Energy - sRNA 2.08204 kcal/mol@LB@@LB@Position - mRNA 41 -- 57@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 52 -- 58@LB@
191	0.03238	0.5507	b0445	ybaE	-8.08	0.221556	124 -- 136	4 -- 16	putative ABC transporter periplasmic binding protein		_____________123___________137\n_____________\|_____________\|\n5'-CGU...GACAC_____________UGAGU...GUU-3'\n______________GGUUAAUGGUGAU\n______________:\|\|\|\|\|\|\|:\|\|\|\|\n______________UCAAUUACUACUA\n3'-UUU...UUAUU_____________UCG-5'\n_____________\|_____________\|\n_____________17____________3\n	130 -- 136	4 -- 10	-14.6304 kcal/mol	6.50117 kcal/mol	0.0488422 kcal/mol	123 137@LB@ \| \|@LB@5'-CGU...GACAC UGAGU...GUU-3'@LB@ GGUUAAUGGUGAU@LB@ :\|\|\|\|\|\|\|:\|\|\|\|@LB@ UCAAUUACUACUA@LB@3'-UUU...UUAUU UCG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -14.6304 kcal/mol@LB@Unfolding Energy - mRNA 6.50117 kcal/mol@LB@Unfolding Energy - sRNA 0.0488422 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 4 -- 10@LB@
105	0.01645	0.5059	b0454	ybaZ	-8.45	0.190978	84 -- 93	47 -- 56	excision repair protein alkyltransferase-like protein ATL		_____________83_________94\n_____________\|__________\|\n5'-AGG...GACCU__________GUAGC...UUC-3'\n______________GGUAAACAGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUCU\n3'-UUU...UAUCC__________GUAAG...UCG-5'\n_____________\|__________\|\n_____________57_________46\n	87 -- 93	47 -- 53	-13.2019 kcal/mol	2.68818 kcal/mol	2.06629 kcal/mol	83 94@LB@ \| \|@LB@5'-AGG...GACCU GUAGC...UUC-3'@LB@ GGUAAACAGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUCU@LB@3'-UUU...UAUCC GUAAG...UCG-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.2019 kcal/mol@LB@Unfolding Energy - mRNA 2.68818 kcal/mol@LB@Unfolding Energy - sRNA 2.06629 kcal/mol@LB@@LB@Position - mRNA 84 -- 93@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 47 -- 53@LB@
181	0.02995	0.5424	b0601	ybdM	-11.52	0.046768	198 -- 207	55 -- 64	Spo0J family protein ParB-like nuclease domain		_____________197________208\n_____________\|__________\|\n5'-UUG...CGUCA__________AUACU...GCA-3'\n______________GGAAUGGGGG\n______________\|:\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	201 -- 207	55 -- 61	-14.9628 kcal/mol	3.4127 kcal/mol	0.0291912 kcal/mol	197 208@LB@ \| \|@LB@5'-UUG...CGUCA AUACU...GCA-3'@LB@ GGAAUGGGGG@LB@ \|:\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -14.9628 kcal/mol@LB@Unfolding Energy - mRNA 3.4127 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 198 -- 207@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 55 -- 61@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@

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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