Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
13	4.485e-05	0.01183	b0511	ybbW	-13.60	0.002717	173 -- 210	18 -- 58	putative allantoin transporter		_____________172________________________________________211\n_____________\|__________________________________________\|\n5'-UGG...ACGUU_______________AU____________UUU__________AGAGA...UUA-3'\n______________AUUCGA_UACGUGAA__UAAGAGG___GA___AUGGAACAUC\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|:\|\|\|___\|\|___\|\|:\|\|\|\|\|\|\|\n______________UAGGCU_AUGCACUU__AUUUUCC___CU___UAUCUUGUAG\n3'-AUU...CGGUU______A________C________AGA__UUC__________AAUGG...AUG-5'\n_____________\|__________________________________________\|\n_____________59_________________________________________17\n	204 -- 210	18 -- 24	-34.0515 kcal/mol	8.25655 kcal/mol	12.1809 kcal/mol	172 211@LB@ \| \|@LB@5'-UGG...ACGUU AU UUU AGAGA...UUA-3'@LB@ AUUCGA UACGUGAA UAAGAGG GA AUGGAACAUC@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|:\|\|\| \|\| \|\|:\|\|\|\|\|\|\|@LB@ UAGGCU AUGCACUU AUUUUCC CU UAUCUUGUAG@LB@3'-AUU...CGGUU A C AGA UUC AAUGG...AUG-5'@LB@ \| \|@LB@ 59 17@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -34.0515 kcal/mol@LB@Unfolding Energy - mRNA 8.25655 kcal/mol@LB@Unfolding Energy - sRNA 12.1809 kcal/mol@LB@@LB@Position - mRNA 173 -- 210@LB@Position - sRNA 18 -- 58@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein		_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
182	0.007896	0.1519	b0686	ybfF	-7.34	0.221050	164 -- 170	2 -- 8	acyl-CoA esterase		_____________163_____171\n_____________\|_______\|\n5'-CUU...CAUAA_______ACCCG...GCG-3'\n______________UACCCUA\n______________\|\|\|\|\|\|\|\n______________AUGGGAU\n3'-AUU...GAGAC_______G-5'\n_____________\|_______\|\n_____________9_______1\n	164 -- 170	2 -- 8	-9.7212 kcal/mol	0.292492 kcal/mol	2.11083 kcal/mol	163 171@LB@ \| \|@LB@5'-CUU...CAUAA ACCCG...GCG-3'@LB@ UACCCUA@LB@ \|\|\|\|\|\|\|@LB@ AUGGGAU@LB@3'-AUU...GAGAC G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -9.7212 kcal/mol@LB@Unfolding Energy - mRNA 0.292492 kcal/mol@LB@Unfolding Energy - sRNA 2.11083 kcal/mol@LB@@LB@Position - mRNA 164 -- 170@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 2 -- 8@LB@
150	0.00611	0.1406	b0735	ybgE	-10.35	0.035619	38 -- 71	5 -- 31	putative inner membrane protein in cydABX-ybgE operon		_____________37_________________________________72\n_____________\|__________________________________\|\n5'-CUG...CCAAA_______UU______AAC___CACUC________AAGUA...UUU-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	65 -- 71	5 -- 11	-23.0678 kcal/mol	4.68737 kcal/mol	8.05162 kcal/mol	37 72@LB@ \| \|@LB@5'-CUG...CCAAA UU AAC CACUC AAGUA...UUU-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.35 kcal/mol@LB@Hybridization Energy -23.0678 kcal/mol@LB@Unfolding Energy - mRNA 4.68737 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 38 -- 71@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 5 -- 11@LB@
98	0.002849	0.1023	b0772	ybhC	-6.17	0.383539	27 -- 33	49 -- 55	acyl-CoA thioesterase lipoprotein		_____________26______34\n_____________\|_______\|\n5'-UCA...CGCCU_______UGCGA...AUC-3'\n______________CGAUUAC\n______________\|\|\|\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	27 -- 33	49 -- 55	-7.86935 kcal/mol	1.39337 kcal/mol	0.311712 kcal/mol	26 34@LB@ \| \|@LB@5'-UCA...CGCCU UGCGA...AUC-3'@LB@ CGAUUAC@LB@ \|\|\|\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.86935 kcal/mol@LB@Unfolding Energy - mRNA 1.39337 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 27 -- 33@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 49 -- 55@LB@
2	0	0	b0796	ybiH	-7.52	0.201543	119 -- 140	54 -- 76	DUF1956 domain-containing tetR family putative transcriptional regulator	b1013	_____________118_____________________141\n_____________\|_______________________\|\n5'-CGG...GCGUU________UC_______UA____GACAA...CCA-3'\n______________GCUAAAAU__UUAGCCA___CUG\n______________\|\|\|\|\|\|\|\|__\|:\|\|\|\|\|___\|:\|\n______________CGAUUUUA__AGUCGGU___GGC\n3'-AUU...CCCGC________UA_______UUA___UAAUG...AUG-5'\n_____________\|_______________________\|\n_____________77______________________53\n	129 -- 135	60 -- 66	-19.7488 kcal/mol	5.88928 kcal/mol	6.3634 kcal/mol	118 141@LB@ \| \|@LB@5'-CGG...GCGUU UC UA GACAA...CCA-3'@LB@ GCUAAAAU UUAGCCA CUG@LB@ \|\|\|\|\|\|\|\| \|:\|\|\|\|\| \|:\|@LB@ CGAUUUUA AGUCGGU GGC@LB@3'-AUU...CCCGC UA UUA UAAUG...AUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -19.7488 kcal/mol@LB@Unfolding Energy - mRNA 5.88928 kcal/mol@LB@Unfolding Energy - sRNA 6.3634 kcal/mol@LB@@LB@Position - mRNA 119 -- 140@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 60 -- 66@LB@
191	0.008587	0.1558	b0823	ybiW	-9.49	0.063221	47 -- 54	1 -- 8	putative pyruvate formate lyase	b3951	_____________46_______55\n_____________\|________\|\n5'-ACC...UUUUC________CACAC...CGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	48 -- 54	1 -- 7	-12.4662 kcal/mol	0.878635 kcal/mol	2.11603 kcal/mol	46 55@LB@ \| \|@LB@5'-ACC...UUUUC CACAC...CGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -12.4662 kcal/mol@LB@Unfolding Energy - mRNA 0.878635 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 47 -- 54@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 1 -- 7@LB@
104	0.003257	0.1101	b0858	ybjO	-8.07	0.149394	228 -- 257	2 -- 30	DUF2593 family inner membrane protein		_____________227______________________________258\n_____________\|________________________________\|\n5'-AUG...UUUUU____A__________C_____A__CU_G____AAUGU...UUA-3'\n______________AAGA___AACAUCUU_AUCUC_UG__C_CCUG\n______________\|\|\|\|___\|\|\|\|\|\|\|\|_\|:\|\|\|_\|\|__\|_\|\|\|:\n______________UUCU___UUGUAGAA_UGGAG_AC__G_GGAU\n3'-AUU...AGACU____AUC_________________AU______G-5'\n_____________\|________________________________\|\n_____________31_______________________________1\n	234 -- 240	16 -- 22	-20.5501 kcal/mol	4.45089 kcal/mol	8.05308 kcal/mol	227 258@LB@ \| \|@LB@5'-AUG...UUUUU A C A CU G AAUGU...UUA-3'@LB@ AAGA AACAUCUU AUCUC UG C CCUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\| \|\| \| \|\|\|:@LB@ UUCU UUGUAGAA UGGAG AC G GGAU@LB@3'-AUU...AGACU AUC AU G-5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.5501 kcal/mol@LB@Unfolding Energy - mRNA 4.45089 kcal/mol@LB@Unfolding Energy - sRNA 8.05308 kcal/mol@LB@@LB@Position - mRNA 228 -- 257@LB@Position - sRNA 2 -- 30@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 16 -- 22@LB@
106	0.003365	0.1101	b0955	ycbZ	-10.52	0.031644	269 -- 288	48 -- 66	putative peptidase		_____________268__________________289\n_____________\|____________________\|\n5'-UUG...UUUGC_______C_________A__AAAAC...CUU-3'\n______________UCAGCCA_AUUUGAUUG_CG\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|:_\|\|\n______________AGUCGGU_UAGGCUAAU_GC\n3'-AUU...UUAUA_______U____________ACUUC...AUG-5'\n_____________\|____________________\|\n_____________67___________________47\n	279 -- 285	50 -- 56	-21.5915 kcal/mol	3.60671 kcal/mol	7.48271 kcal/mol	268 289@LB@ \| \|@LB@5'-UUG...UUUGC C A AAAAC...CUU-3'@LB@ UCAGCCA AUUUGAUUG CG@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|: \|\|@LB@ AGUCGGU UAGGCUAAU GC@LB@3'-AUU...UUAUA U ACUUC...AUG-5'@LB@ \| \|@LB@ 67 47@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -21.5915 kcal/mol@LB@Unfolding Energy - mRNA 3.60671 kcal/mol@LB@Unfolding Energy - sRNA 7.48271 kcal/mol@LB@@LB@Position - mRNA 269 -- 288@LB@Position - sRNA 48 -- 66@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 50 -- 56@LB@
96	0.002764	0.1002	b1034	ycdX	-5.77	0.451964	102 -- 115	32 -- 46	alkaline phosphatase		_____________101_____________116\n_____________\|_______________\|\n5'-GGC...AAAAA_______________CGGGC...AAC-3'\n______________GGGG_AGAGGGUCUG\n______________\|::\|_\|:\|:\|\|\|\|\|\|\n______________CUUC_UUUUCCAGAC\n3'-AUU...AUGCA____A__________UUUCU...AUG-5'\n_____________\|_______________\|\n_____________47______________31\n	109 -- 115	32 -- 38	-16.8058 kcal/mol	3.54072 kcal/mol	7.24668 kcal/mol	101 116@LB@ \| \|@LB@5'-GGC...AAAAA CGGGC...AAC-3'@LB@ GGGG AGAGGGUCUG@LB@ \|::\| \|:\|:\|\|\|\|\|\|@LB@ CUUC UUUUCCAGAC@LB@3'-AUU...AUGCA A UUUCU...AUG-5'@LB@ \| \|@LB@ 47 31@LB@@LB@@LB@Energy -5.77 kcal/mol@LB@Hybridization Energy -16.8058 kcal/mol@LB@Unfolding Energy - mRNA 3.54072 kcal/mol@LB@Unfolding Energy - sRNA 7.24668 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 32 -- 46@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 32 -- 38@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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