Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase	_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
30	0.001614	0.1727	b3607	cysE	-13.31	0.031682	13 -- 32	63 -- 81	serine acetyltransferase	_____________12___________________33\n_____________\|____________________\|\n5'-CGG...GAAAU______A____A________AUCAA...CGA-3'\n______________GCCAAU_ACCG_GGAAAUUU\n______________\|\|\|\|\|:_\|\|\|:_\|\|\|\|\|\|:\|\n______________CGGUUG_UGGU_CCUUUAGA\n3'-UUU...UGACG___________C________ACCGA...GUG-5'\n_____________\|____________________\|\n_____________82___________________62\n	26 -- 32	63 -- 69	-21.8966 kcal/mol	1.53041 kcal/mol	7.0543 kcal/mol	12 33@LB@ \| \|@LB@5'-CGG...GAAAU A A AUCAA...CGA-3'@LB@ GCCAAU ACCG GGAAAUUU@LB@ \|\|\|\|\|: \|\|\|: \|\|\|\|\|\|:\|@LB@ CGGUUG UGGU CCUUUAGA@LB@3'-UUU...UGACG C ACCGA...GUG-5'@LB@ \| \|@LB@ 82 62@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -21.8966 kcal/mol@LB@Unfolding Energy - mRNA 1.53041 kcal/mol@LB@Unfolding Energy - sRNA 7.0543 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 63 -- 81@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 63 -- 69@LB@
159	0.009346	0.2062	b3661	nlpA	-7.63	0.365650	232 -- 240	1 -- 9	cytoplasmic membrane lipoprotein-28	_____________231_______241\n_____________\|_________\|\n5'-UGU...GACAG_________UAUUG...ACA-3'\n______________GGGCCGCAU\n______________:\|\|\|\|\|\|\|:\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	234 -- 240	1 -- 7	-16.6231 kcal/mol	3.46198 kcal/mol	5.10726 kcal/mol	231 241@LB@ \| \|@LB@5'-UGU...GACAG UAUUG...ACA-3'@LB@ GGGCCGCAU@LB@ :\|\|\|\|\|\|\|:@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -16.6231 kcal/mol@LB@Unfolding Energy - mRNA 3.46198 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 232 -- 240@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.004911	0.1855	b3732	atpD	-9.01	0.211333	117 -- 128	1 -- 11	F1 sector of membrane-bound ATP synthase beta subunit	_____________116__________129\n_____________\|____________\|\n5'-GGC...GCUCG_______A____UACUC...AAA-3'\n______________UCAGGCC_GCAU\n______________\|\|\|\|\|\|\|_\|\|\|:\n______________AGUCCGG_CGUG\n3'-UUU...CAAAA____________-5'\n_____________\|___________\|\n_____________12__________1\n	117 -- 123	5 -- 11	-17.8068 kcal/mol	3.15312 kcal/mol	5.60325 kcal/mol	116 129@LB@ \| \|@LB@5'-GGC...GCUCG A UACUC...AAA-3'@LB@ UCAGGCC GCAU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ AGUCCGG CGUG@LB@3'-UUU...CAAAA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -17.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.15312 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 117 -- 128@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 5 -- 11@LB@
2	1.572e-09	2.767e-06	b3749	rbsA	-20.95	0.000983	43 -- 64	65 -- 86	D-ribose ABC transporter ATPase	_____________42_____________________65\n_____________\|______________________\|\n5'-UAA...GAGCA_____AAA______________ACCAU...UGG-3'\n______________GCUGC___AACACCAGGGAAAU\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGACG___UUGUGGUCCCUUUA\n3'-UUU...GCUUA_____CGG______________GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	58 -- 64	65 -- 71	-31.8331 kcal/mol	3.49898 kcal/mol	7.38332 kcal/mol	42 65@LB@ \| \|@LB@5'-UAA...GAGCA AAA ACCAU...UGG-3'@LB@ GCUGC AACACCAGGGAAAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGACG UUGUGGUCCCUUUA@LB@3'-UUU...GCUUA CGG GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -20.95 kcal/mol@LB@Hybridization Energy -31.8331 kcal/mol@LB@Unfolding Energy - mRNA 3.49898 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 43 -- 64@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 65 -- 71@LB@
146	0.008611	0.2059	b3750	rbsC	-8.88	0.223197	137 -- 159	56 -- 77	D-ribose ABC transporter permease	_____________136_______________________160\n_____________\|_________________________\|\n5'-GAU...AGGCC_____________G_UAA_______CGCUG...UCU-3'\n______________AC_CCA_GGAAGU_U___UGGCUGC\n______________\|\|_\|\|\|_\|\|\|\|:\|_\|___\|\|\|\|\|\|\|\n______________UG_GGU_CCUUUA_A___ACCGACG\n3'-UUU...GCGGU__U___C______G___________CGGCA...GUG-5'\n_____________\|_________________________\|\n_____________78________________________55\n	153 -- 159	56 -- 62	-22.4095 kcal/mol	5.11916 kcal/mol	8.4081 kcal/mol	136 160@LB@ \| \|@LB@5'-GAU...AGGCC G UAA CGCUG...UCU-3'@LB@ AC CCA GGAAGU U UGGCUGC@LB@ \|\| \|\|\| \|\|\|\|:\| \| \|\|\|\|\|\|\|@LB@ UG GGU CCUUUA A ACCGACG@LB@3'-UUU...GCGGU U C G CGGCA...GUG-5'@LB@ \| \|@LB@ 78 55@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -22.4095 kcal/mol@LB@Unfolding Energy - mRNA 5.11916 kcal/mol@LB@Unfolding Energy - sRNA 8.4081 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 56 -- 77@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 56 -- 62@LB@
109	0.005919	0.1855	b3807	cyaY	-12.33	0.049473	23 -- 64	29 -- 73	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________22__________________________________________________65\n_____________\|___________________________________________________\|\n5'-UGA...AGAAA________GACG___UGUAA_______C_____________A_________AUCUU...AAA-3'\n______________CAGGGAAA____UGG_____CUGCGCC_UA_______AUGA_GAG__ACAA\n______________\|\|\|\|\|\|\|\|____\|\|\|_____\|\|\|\|\|\|\|_\|\|_______\|\|\|\|_\|\|\|__\|\|\|\|\n______________GUCCCUUU____ACC_____GACGCGG_AU_______UACU_CUC__UGUU\n3'-UUU...UUGUG________AGA________________C__UUAAUAA____A___AA____CCCGU...GUG-5'\n_____________\|___________________________________________________\|\n_____________74__________________________________________________28\n	43 -- 49	53 -- 59	-33.7794 kcal/mol	12.1445 kcal/mol	9.30637 kcal/mol	22 65@LB@ \| \|@LB@5'-UGA...AGAAA GACG UGUAA C A AUCUU...AAA-3'@LB@ CAGGGAAA UGG CUGCGCC UA AUGA GAG ACAA@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\| \|\|\| \|\|\|\|@LB@ GUCCCUUU ACC GACGCGG AU UACU CUC UGUU@LB@3'-UUU...UUGUG AGA C UUAAUAA A AA CCCGU...GUG-5'@LB@ \| \|@LB@ 74 28@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -33.7794 kcal/mol@LB@Unfolding Energy - mRNA 12.1445 kcal/mol@LB@Unfolding Energy - sRNA 9.30637 kcal/mol@LB@@LB@Position - mRNA 23 -- 64@LB@Position - sRNA 29 -- 73@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 53 -- 59@LB@
62	0.003053	0.1727	b3812	yigB	-11.80	0.062766	182 -- 199	65 -- 83	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis	_____________181_________________200\n_____________\|___________________\|\n5'-CUG...UCCAC__________G________AAUGC...GAG-3'\n______________GCGCCAA_AC_GGGGAAAU\n______________\|\|\|\|\|\|\|_\|\|_:\|\|\|\|\|\|\|\n______________CGCGGUU_UG_UCCCUUUA\n3'-UUU...UAUGA_______G__G________GAACC...GUG-5'\n_____________\|___________________\|\n_____________84__________________64\n	193 -- 199	65 -- 71	-28.1563 kcal/mol	8.99645 kcal/mol	7.35968 kcal/mol	181 200@LB@ \| \|@LB@5'-CUG...UCCAC G AAUGC...GAG-3'@LB@ GCGCCAA AC GGGGAAAU@LB@ \|\|\|\|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ CGCGGUU UG UCCCUUUA@LB@3'-UUU...UAUGA G G GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -28.1563 kcal/mol@LB@Unfolding Energy - mRNA 8.99645 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 65 -- 71@LB@
131	0.007315	0.1966	b3824	rhtB	-9.48	0.174149	77 -- 100	63 -- 87	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________76________________________101\n_____________\|_________________________\|\n5'-ACG...CUUUU______UGA_________U______GCCUC...ACC-3'\n______________UGCUGC___AACAUCGGG__AAUCU\n______________\|:\|\|\|\|___\|\|\|\|:\|:\|\|__\|\|\|\|\|\n______________AUGACG___UUGUGGUCC__UUAGA\n3'-UUU...CGCUU______CGG_________CU_____ACCGA...GUG-5'\n_____________\|_________________________\|\n_____________88________________________62\n	88 -- 94	70 -- 76	-24.9255 kcal/mol	8.06413 kcal/mol	7.38606 kcal/mol	76 101@LB@ \| \|@LB@5'-ACG...CUUUU UGA U GCCUC...ACC-3'@LB@ UGCUGC AACAUCGGG AAUCU@LB@ \|:\|\|\|\| \|\|\|\|:\|:\|\| \|\|\|\|\|@LB@ AUGACG UUGUGGUCC UUAGA@LB@3'-UUU...CGCUU CGG CU ACCGA...GUG-5'@LB@ \| \|@LB@ 88 62@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.9255 kcal/mol@LB@Unfolding Energy - mRNA 8.06413 kcal/mol@LB@Unfolding Energy - sRNA 7.38606 kcal/mol@LB@@LB@Position - mRNA 77 -- 100@LB@Position - sRNA 63 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 70 -- 76@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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