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
180	0.007734	0.1511	b3617	kbl	-7.53	0.200168	193 -- 210	43 -- 60	glycine C-acetyltransferase		_____________192________________211\n_____________\|__________________\|\n5'-UUU...CUGGA_____GCAA_________AAUUU...AAG-3'\n______________GAAUC____UGCGUGGAG\n______________:\|\|\|\|____\|:\|\|\|\|:\|\|\n______________UUUAG____AUGCACUUC\n3'-AUU...GUCGG_____GCUA_________AUUUU...AUG-5'\n_____________\|__________________\|\n_____________61_________________42\n	204 -- 210	43 -- 49	-15.3085 kcal/mol	4.51554 kcal/mol	3.27548 kcal/mol	192 211@LB@ \| \|@LB@5'-UUU...CUGGA GCAA AAUUU...AAG-3'@LB@ GAAUC UGCGUGGAG@LB@ :\|\|\|\| \|:\|\|\|\|:\|\|@LB@ UUUAG AUGCACUUC@LB@3'-AUU...GUCGG GCUA AUUUU...AUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -15.3085 kcal/mol@LB@Unfolding Energy - mRNA 4.51554 kcal/mol@LB@Unfolding Energy - sRNA 3.27548 kcal/mol@LB@@LB@Position - mRNA 193 -- 210@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 43 -- 49@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@
132	0.004657	0.1239	b1200	dhaK	-7.52	0.201505	172 -- 179	1 -- 8	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit		_____________171______180\n_____________\|________\|\n5'-UUC...AUCCA________CGUAA...UGU-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	173 -- 179	1 -- 7	-12.1513 kcal/mol	2.5392 kcal/mol	2.11603 kcal/mol	171 180@LB@ \| \|@LB@5'-UUC...AUCCA CGUAA...UGU-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -12.1513 kcal/mol@LB@Unfolding Energy - mRNA 2.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 172 -- 179@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
184	0.00812	0.1553	b4371	rsmC	-7.50	0.203534	191 -- 216	4 -- 25	16S rRNA m(2)G1207 methyltransferase SAM-dependent		_____________190________________________217\n_____________\|__________________________\|\n5'-AUC...AUUGA________CC__G____CAUU_____CGGCA...UGC-3'\n______________GGAGCAUU__AU_UCUG____UACCC\n______________:\|\|:\|\|\|:__\|:_\|\|\|\|____\|\|\|\|\|\n______________UCUUGUAG__UG_AGAC____AUGGG\n3'-AUU...UUCUA________AA__G_____________AUG-5'\n_____________\|__________________________\|\n_____________26_________________________3\n	192 -- 198	18 -- 24	-20.5319 kcal/mol	5.03265 kcal/mol	8.0209 kcal/mol	190 217@LB@ \| \|@LB@5'-AUC...AUUGA CC G CAUU CGGCA...UGC-3'@LB@ GGAGCAUU AU UCUG UACCC@LB@ :\|\|:\|\|\|: \|: \|\|\|\| \|\|\|\|\|@LB@ UCUUGUAG UG AGAC AUGGG@LB@3'-AUU...UUCUA AA G AUG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -20.5319 kcal/mol@LB@Unfolding Energy - mRNA 5.03265 kcal/mol@LB@Unfolding Energy - sRNA 8.0209 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 18 -- 24@LB@
54	0.0007615	0.04961	b0313	betI	-7.44	0.209816	47 -- 68	32 -- 57	choline-inducible betIBA-betT divergent operon transcriptional repressor		_____________46_________________________69\n_____________\|__________________________\|\n5'-CAG...CCUUU___C________U_____________UCAUC...CGC-3'\n______________UCC___UGC_UG__GUGAAAGGUCUG\n______________\|\|\|___\|:\|_\|\|__\|\|:\|\|\|\|\|\|\|\|\|\n______________AGG___AUG_AC__CAUUUUCCAGAC\n3'-AUU...GGUUU___CUA___C__UU____________UUUCU...AUG-5'\n_____________\|__________________________\|\n_____________58_________________________31\n	62 -- 68	32 -- 38	-22.1015 kcal/mol	6.64828 kcal/mol	7.92091 kcal/mol	46 69@LB@ \| \|@LB@5'-CAG...CCUUU C U UCAUC...CGC-3'@LB@ UCC UGC UG GUGAAAGGUCUG@LB@ \|\|\| \|:\| \|\| \|\|:\|\|\|\|\|\|\|\|\|@LB@ AGG AUG AC CAUUUUCCAGAC@LB@3'-AUU...GGUUU CUA C UU UUUCU...AUG-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -22.1015 kcal/mol@LB@Unfolding Energy - mRNA 6.64828 kcal/mol@LB@Unfolding Energy - sRNA 7.92091 kcal/mol@LB@@LB@Position - mRNA 47 -- 68@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 32 -- 38@LB@
176	0.007357	0.147	b2905	gcvT	-7.40	0.214118	198 -- 224	6 -- 30	aminomethyltransferase tetrahydrofolate-dependent subunit (T protein) of glycine cleavage complex		_____________197__________________________225\n_____________\|____________________________\|\n5'-CUG...AGGAC_______CAC____GACU__________GAACA...AAA-3'\n______________AAGAUGG___AACA_____CCUUUGUAC\n______________\|\|\|\|\|:\|___\|\|\|\|_____\|\|\|:\|\|\|\|\|\n______________UUCUAUC___UUGU_____GGAGACAUG\n3'-AUU...AGACU______________AGAAU_________GGAUG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	218 -- 224	6 -- 12	-21.3805 kcal/mol	5.97871 kcal/mol	8.02863 kcal/mol	197 225@LB@ \| \|@LB@5'-CUG...AGGAC CAC GACU GAACA...AAA-3'@LB@ AAGAUGG AACA CCUUUGUAC@LB@ \|\|\|\|\|:\| \|\|\|\| \|\|\|:\|\|\|\|\|@LB@ UUCUAUC UUGU GGAGACAUG@LB@3'-AUU...AGACU AGAAU GGAUG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 5.97871 kcal/mol@LB@Unfolding Energy - sRNA 8.02863 kcal/mol@LB@@LB@Position - mRNA 198 -- 224@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 6 -- 12@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@
130	0.004431	0.1199	b3355	prkB	-7.29	0.227256	214 -- 220	52 -- 58	putative phosphoribulokinase		_____________213_____221\n_____________\|_______\|\n5'-GGC...CAAAC_______CAUUG...AUC-3'\n______________AUCCGGU\n______________\|\|\|\|\|:\|\n______________UAGGCUA\n3'-AUU...CGGUU_______AUGCA...AUG-5'\n_____________\|_______\|\n_____________59______51\n	214 -- 220	52 -- 58	-8.26146 kcal/mol	0.695321 kcal/mol	0.296688 kcal/mol	213 221@LB@ \| \|@LB@5'-GGC...CAAAC CAUUG...AUC-3'@LB@ AUCCGGU@LB@ \|\|\|\|\|:\|@LB@ UAGGCUA@LB@3'-AUU...CGGUU AUGCA...AUG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -8.26146 kcal/mol@LB@Unfolding Energy - mRNA 0.695321 kcal/mol@LB@Unfolding Energy - sRNA 0.296688 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 52 -- 58@LB@
141	0.00519	0.1284	b3550	yiaC	-7.29	0.227336	55 -- 76	1 -- 22	GNAT family putative N-acetyltransferase		_____________54______________________77\n_____________\|_______________________\|\n5'-AAU...CAUCU_____C______CGAC_______CUAAG...GGC-3'\n______________ACGUC__GCCUC____GCCCUAU\n______________\|\|:\|\|__:\|\|\|\|____:\|\|\|\|\|:\n______________UGUAG__UGGAG____UGGGAUG\n3'-AUU...UAUCU_____AA_____ACA________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	70 -- 76	1 -- 7	-20.6815 kcal/mol	5.4259 kcal/mol	7.99236 kcal/mol	54 77@LB@ \| \|@LB@5'-AAU...CAUCU C CGAC CUAAG...GGC-3'@LB@ ACGUC GCCUC GCCCUAU@LB@ \|\|:\|\| :\|\|\|\| :\|\|\|\|\|:@LB@ UGUAG UGGAG UGGGAUG@LB@3'-AUU...UAUCU AA ACA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -20.6815 kcal/mol@LB@Unfolding Energy - mRNA 5.4259 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 55 -- 76@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 1 -- 7@LB@
178	0.007695	0.1511	b4567	yjjZ	-7.25	0.231371	185 -- 218	2 -- 33	uncharacterized protein		_____________184_________________________________219\n_____________\|___________________________________\|\n5'-CGG...AUCAA_______GAU___AU___G____AA______G___GGCAG...GGA-3'\n______________UGAAAGA___GAA__CAU_UUGC__C_GUAC_CUG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|_\|\|:\|__\|_\|\|\|\|_\|\|:\n______________ACUUUCU___CUU__GUA_AAUG__G_CAUG_GAU\n3'-AUU...UCCAG_______AU_________G____GA_A____G___G-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	185 -- 191	27 -- 33	-22.8177 kcal/mol	6.54395 kcal/mol	9.04499 kcal/mol	184 219@LB@ \| \|@LB@5'-CGG...AUCAA GAU AU G AA G GGCAG...GGA-3'@LB@ UGAAAGA GAA CAU UUGC C GUAC CUG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\| \| \|\|\|\| \|\|:@LB@ ACUUUCU CUU GUA AAUG G CAUG GAU@LB@3'-AUU...UCCAG AU G GA A G G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -22.8177 kcal/mol@LB@Unfolding Energy - mRNA 6.54395 kcal/mol@LB@Unfolding Energy - sRNA 9.04499 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 27 -- 33@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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