Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein	_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase	_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@LB@
164	0.03346	0.6177	b1449	curA	-5.87	0.264423	114 -- 122	45 -- 53	curcumin/dihydrocurcumin reductase NADPH-dependent	_____________113_______123\n_____________\|_________\|\n5'-CGG...UGUUG_________UGUGA...UCG-3'\n______________CAGAGGGGA\n______________\|\|:\|\|:\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	116 -- 122	45 -- 51	-11.6619 kcal/mol	4.87234 kcal/mol	0.917553 kcal/mol	113 123@LB@ \| \|@LB@5'-CGG...UGUUG UGUGA...UCG-3'@LB@ CAGAGGGGA@LB@ \|\|:\|\|:\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -11.6619 kcal/mol@LB@Unfolding Energy - mRNA 4.87234 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 114 -- 122@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 45 -- 51@LB@
161	0.03295	0.6177	b1630	rsxD	-5.86	0.265655	34 -- 42	49 -- 57	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex	_____________33________43\n_____________\|_________\|\n5'-AGC...AGCUG_________CGGCU...CAG-3'\n______________CCGUCGAAG\n______________\|\|\|\|\|:\|\|\|\n______________GGCAGUUUC\n3'-UUU...AACCG_________UCCUU...ACA-5'\n_____________\|_________\|\n_____________58________48\n	36 -- 42	49 -- 55	-12.0908 kcal/mol	3.50131 kcal/mol	2.72876 kcal/mol	33 43@LB@ \| \|@LB@5'-AGC...AGCUG CGGCU...CAG-3'@LB@ CCGUCGAAG@LB@ \|\|\|\|\|:\|\|\|@LB@ GGCAGUUUC@LB@3'-UUU...AACCG UCCUU...ACA-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.0908 kcal/mol@LB@Unfolding Energy - mRNA 3.50131 kcal/mol@LB@Unfolding Energy - sRNA 2.72876 kcal/mol@LB@@LB@Position - mRNA 34 -- 42@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 49 -- 55@LB@
191	0.0398	0.6177	b4335	yjiM	-5.72	0.281824	283 -- 290	47 -- 54	putative 2-hydroxyglutaryl-CoA dehydratase	_____________282______291\n_____________\|________\|\n5'-CGG...GGAUC________CGCGG...UUC-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	284 -- 290	47 -- 53	-8.85878 kcal/mol	2.24401 kcal/mol	0.897871 kcal/mol	282 291@LB@ \| \|@LB@5'-CGG...GGAUC CGCGG...UUC-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -8.85878 kcal/mol@LB@Unfolding Energy - mRNA 2.24401 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 47 -- 53@LB@
145	0.02855	0.6177	b2252	ais	-5.71	0.282709	182 -- 202	38 -- 55	putative LPS core heptose(II)-phosphate phosphatase	_____________181___________________203\n_____________\|_____________________\|\n5'-ACC...CGCUU___UAU___U_______A___GUUAG...GGA-3'\n______________GUC___AGG_GGAGUUU_CGU\n______________\|\|\|___\|:\|_\|\|\|:\|\|\|_\|:\|\n______________CAG___UUC_CCUUAAA_GUA\n3'-UUU...CCGGG___U_____U___________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	192 -- 198	41 -- 47	-12.7294 kcal/mol	5.84979 kcal/mol	1.17036 kcal/mol	181 203@LB@ \| \|@LB@5'-ACC...CGCUU UAU U A GUUAG...GGA-3'@LB@ GUC AGG GGAGUUU CGU@LB@ \|\|\| \|:\| \|\|\|:\|\|\| \|:\|@LB@ CAG UUC CCUUAAA GUA@LB@3'-UUU...CCGGG U U AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -5.71 kcal/mol@LB@Hybridization Energy -12.7294 kcal/mol@LB@Unfolding Energy - mRNA 5.84979 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 182 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 41 -- 47@LB@
140	0.02703	0.6177	b3447	ggt	-5.41	0.319095	66 -- 81	38 -- 54	gamma-glutamyltranspeptidase	_____________65________________82\n_____________\|_________________\|\n5'-GUU...AAGAA________UC_______CGCGU...CGU-3'\n______________UCAGA_AG__GUUUCAU\n______________\|\|\|:\|_\|\|__:\|\|\|\|\|\|\n______________AGUUU_UC__UAAAGUA\n3'-UUU...CGGGC_____C__CU_______AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	75 -- 81	38 -- 44	-8.61894 kcal/mol	2.03989 kcal/mol	1.17036 kcal/mol	65 82@LB@ \| \|@LB@5'-GUU...AAGAA UC CGCGU...CGU-3'@LB@ UCAGA AG GUUUCAU@LB@ \|\|\|:\| \|\| :\|\|\|\|\|\|@LB@ AGUUU UC UAAAGUA@LB@3'-UUU...CGGGC C CU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -5.41 kcal/mol@LB@Hybridization Energy -8.61894 kcal/mol@LB@Unfolding Energy - mRNA 2.03989 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 66 -- 81@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 38 -- 44@LB@
190	0.03948	0.6177	b2914	rpiA	-5.25	0.339968	76 -- 83	45 -- 52	ribose 5-phosphate isomerase constitutive	_____________75_______84\n_____________\|________\|\n5'-GAA...GGGCG________UGCCU...CAC-3'\n______________AAAGGGGA\n______________\|\|\|\|:\|\|\|\n______________UUUCUCCU\n3'-UUU...GGCAG________UAAAG...ACA-5'\n_____________\|________\|\n_____________53_______44\n	77 -- 83	45 -- 51	-8.77639 kcal/mol	2.67801 kcal/mol	0.850469 kcal/mol	75 84@LB@ \| \|@LB@5'-GAA...GGGCG UGCCU...CAC-3'@LB@ AAAGGGGA@LB@ \|\|\|\|:\|\|\|@LB@ UUUCUCCU@LB@3'-UUU...GGCAG UAAAG...ACA-5'@LB@ \| \|@LB@ 53 44@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -8.77639 kcal/mol@LB@Unfolding Energy - mRNA 2.67801 kcal/mol@LB@Unfolding Energy - sRNA 0.850469 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 45 -- 52@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 45 -- 51@LB@
133	0.02604	0.6177	b0876	ybjD	-5.23	0.342712	179 -- 199	45 -- 55	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________178___________________200\n_____________\|_____________________\|\n5'-CGU...GAUAA____CAUAUUUCUG_______UAUGA...GGG-3'\n______________GUCA__________GAGGGGA\n______________\|\|\|\|__________:\|\|:\|\|\|\n______________CAGU__________UUCUCCU\n3'-UUU...CCGGG_____________________UAAAG...ACA-5'\n_____________\|_____________________\|\n_____________56____________________44\n	193 -- 199	45 -- 51	-10.7419 kcal/mol	4.58374 kcal/mol	0.930875 kcal/mol	178 200@LB@ \| \|@LB@5'-CGU...GAUAA CAUAUUUCUG UAUGA...GGG-3'@LB@ GUCA GAGGGGA@LB@ \|\|\|\| :\|\|:\|\|\|@LB@ CAGU UUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -10.7419 kcal/mol@LB@Unfolding Energy - mRNA 4.58374 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 199@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 45 -- 51@LB@
163	0.03345	0.6177	b1235	rssB	-5.20	0.346272	186 -- 195	44 -- 55	PcnB-degradosome interaction factor; response regulator	_____________185__________196\n_____________\|____________\|\n5'-AAU...AGCCA____________AGAAC...CAA-3'\n______________GUC__AGGGGAG\n______________\|\|\|__\|\|:\|\|\|:\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-10.1709 kcal/mol	4.02871 kcal/mol	0.941432 kcal/mol	185 196@LB@ \| \|@LB@5'-AAU...AGCCA AGAAC...CAA-3'@LB@ GUC AGGGGAG@LB@ \|\|\| \|\|:\|\|\|:@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -5.20 kcal/mol@LB@Hybridization Energy -10.1709 kcal/mol@LB@Unfolding Energy - mRNA 4.02871 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@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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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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