Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
71	0.001933	0.09081	b2044	wcaL	-10.40	0.140507	12 -- 21	24 -- 33	putative glycosyl transferase	_____________11_________22\n_____________\|__________\|\n5'-GGG...AUGCA________G_CUACC...AGA-3'\n______________GCAGCUGG_A\n______________:\|\|\|\|\|:\|_\|\n______________UGUCGAUC_U\n3'-UUU...GACCA________G_AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	13 -- 19	26 -- 32	-13.1871 kcal/mol	1.35791 kcal/mol	1.42716 kcal/mol	11 22@LB@ \| \|@LB@5'-GGG...AUGCA G CUACC...AGA-3'@LB@ GCAGCUGG A@LB@ :\|\|\|\|\|:\| \|@LB@ UGUCGAUC U@LB@3'-UUU...GACCA G AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -13.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.35791 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 26 -- 32@LB@
69	0.001909	0.09081	b1830	prc	-10.38	0.141777	185 -- 217	2 -- 49	carboxy-terminal protease for penicillin-binding protein 3	_____________184______________________________________________218\n_____________\|________________________________________________\|\n5'-CGA...GAAAC_______________GC__________GAAC_________________GCUUA...CGG-3'\n______________GGAGG_____CC_GG__CAG___GCAU__________AUGUUUUUUAG\n______________\|\|\|\|\|_____\|\|_\|\|__\|\|\|___\|\|\|\|__________\|\|\|\|\|\|\|\|:\|\|\n______________CCUCC_____GG_CC__GUC___CGUA__________UACAAAAAGUC\n3'-UUU...CGAUU_____ACCAA__A__AU___GAU____AAAUACCCAA___________G-5'\n_____________\|________________________________________________\|\n_____________50_______________________________________________1\n	211 -- 217	2 -- 8	-24.9215 kcal/mol	9.93043 kcal/mol	4.60955 kcal/mol	184 218@LB@ \| \|@LB@5'-CGA...GAAAC GC GAAC GCUUA...CGG-3'@LB@ GGAGG CC GG CAG GCAU AUGUUUUUUAG@LB@ \|\|\|\|\| \|\| \|\| \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ CCUCC GG CC GUC CGUA UACAAAAAGUC@LB@3'-UUU...CGAUU ACCAA A AU GAU AAAUACCCAA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -24.9215 kcal/mol@LB@Unfolding Energy - mRNA 9.93043 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 185 -- 217@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
56	0.001349	0.08097	b0287	yagU	-10.29	0.147287	182 -- 196	14 -- 37	DUF1440 family inner membrane acid resistance protein	_____________181______________________197\n_____________\|________________________\|\n5'-AAC...CAUAA________________________AGAUA...GGG-3'\n______________UGGUACA___AGCA______GGGU\n______________\|\|\|\|\|\|\|___\|\|\|\|______\|\|\|\|\n______________ACCAUGU___UCGU______CCCA\n3'-UUU...CAAGG_______CGA____AAAAUA____AUACA...UCG-5'\n_____________\|________________________\|\n_____________38_______________________13\n	182 -- 188	31 -- 37	-16.1787 kcal/mol	3.22484 kcal/mol	2.65978 kcal/mol	181 197@LB@ \| \|@LB@5'-AAC...CAUAA AGAUA...GGG-3'@LB@ UGGUACA AGCA GGGU@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ ACCAUGU UCGU CCCA@LB@3'-UUU...CAAGG CGA AAAAUA AUACA...UCG-5'@LB@ \| \|@LB@ 38 13@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -16.1787 kcal/mol@LB@Unfolding Energy - mRNA 3.22484 kcal/mol@LB@Unfolding Energy - sRNA 2.65978 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 14 -- 37@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
16	0.000101	0.02121	b3428	glgP	-10.27	0.148738	91 -- 131	1 -- 46	glycogen phosphorylase	_____________90_____________________________________________132\n_____________\|______________________________________________\|\n5'-CCA...ACUGU__C_____G__CA___UCA____________CA____GA_______UGGCA...CGG-3'\n______________GG_GGUUU_UG__ACG___GGC____UAUGG___AUG__UUUUAGC\n______________\|\|_\|\|\|\|:_\|\|__\|\|:___:\|\|____\|\|\|\|\|___\|\|\|__\|\|\|:\|\|\|\n______________CC_CCAAG_AC__UGU___UCG____AUACC___UAC__AAAGUCG\n3'-UUU...UUCCU__A_____G__CA___CGA___UAAA_____CAA___AA_______-5'\n_____________\|_____________________________________________\|\n_____________47____________________________________________1\n	125 -- 131	1 -- 7	-28.7783 kcal/mol	13.8975 kcal/mol	4.60935 kcal/mol	90 132@LB@ \| \|@LB@5'-CCA...ACUGU C G CA UCA CA GA UGGCA...CGG-3'@LB@ GG GGUUU UG ACG GGC UAUGG AUG UUUUAGC@LB@ \|\| \|\|\|\|: \|\| \|\|: :\|\| \|\|\|\|\| \|\|\| \|\|\|:\|\|\|@LB@ CC CCAAG AC UGU UCG AUACC UAC AAAGUCG@LB@3'-UUU...UUCCU A G CA CGA UAAA CAA AA -5'@LB@ \| \|@LB@ 47 1@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -28.7783 kcal/mol@LB@Unfolding Energy - mRNA 13.8975 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 91 -- 131@LB@Position - sRNA 1 -- 46@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 1 -- 7@LB@
193	0.01107	0.1919	b3532	bcsB	-10.24	0.150531	226 -- 241	15 -- 35	regulator of cellulose synthase cyclic di-GMP binding	_____________225___________________242\n_____________\|_____________________\|\n5'-AAG...GAUUU_______G_____________GAUGA...UCA-3'\n______________GUGCAGU__GC____UAUGGG\n______________\|\|:\|\|\|:__\|\|____\|\|\|\|\|\|\n______________CAUGUCG__CG____AUACCC\n3'-UUU...AGGAC_______AU__UAAA______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________36____________________14\n	226 -- 232	29 -- 35	-18.7324 kcal/mol	7.03896 kcal/mol	1.4496 kcal/mol	225 242@LB@ \| \|@LB@5'-AAG...GAUUU G GAUGA...UCA-3'@LB@ GUGCAGU GC UAUGGG@LB@ \|\|:\|\|\|: \|\| \|\|\|\|\|\|@LB@ CAUGUCG CG AUACCC@LB@3'-UUU...AGGAC AU UAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -18.7324 kcal/mol@LB@Unfolding Energy - mRNA 7.03896 kcal/mol@LB@Unfolding Energy - sRNA 1.4496 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 29 -- 35@LB@
120	0.005024	0.1407	b2564	pdxJ	-10.23	0.151404	275 -- 296	21 -- 43	pyridoxine 5'-phosphate synthase	_____________274_____________________297\n_____________\|_______________________\|\n5'-AAA...UACCC__A___________GCC______AUUG-3'\n______________GG_UCC_GGUGCAG___GCGUUU\n______________\|\|_\|\|\|_\|\|\|:\|\|\|___\|\|:\|\|\|\n______________CC_AGG_CCAUGUC___CGUAAA\n3'-UUU...CUCCA__A___A_______GAU______AUACC...UCG-5'\n_____________\|_______________________\|\n_____________44______________________20\n	281 -- 287	30 -- 36	-24.4803 kcal/mol	9.69131 kcal/mol	4.55861 kcal/mol	274 297@LB@ \| \|@LB@5'-AAA...UACCC A GCC AUUG-3'@LB@ GG UCC GGUGCAG GCGUUU@LB@ \|\| \|\|\| \|\|\|:\|\|\| \|\|:\|\|\|@LB@ CC AGG CCAUGUC CGUAAA@LB@3'-UUU...CUCCA A A GAU AUACC...UCG-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -24.4803 kcal/mol@LB@Unfolding Energy - mRNA 9.69131 kcal/mol@LB@Unfolding Energy - sRNA 4.55861 kcal/mol@LB@@LB@Position - mRNA 275 -- 296@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 30 -- 36@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein	_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
94	0.003268	0.1162	b2687	luxS	-10.18	0.155002	189 -- 196	42 -- 49	S-ribosylhomocysteine lyase	_____________188______197\n_____________\|________\|\n5'-GAA...UUACC________CUAAA...UCA-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	190 -- 196	42 -- 48	-16.7111 kcal/mol	3.76521 kcal/mol	2.77009 kcal/mol	188 197@LB@ \| \|@LB@5'-GAA...UUACC CUAAA...UCA-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -16.7111 kcal/mol@LB@Unfolding Energy - mRNA 3.76521 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
88	0.002837	0.1082	b4377	yjjU	-10.09	0.160689	120 -- 144	1 -- 33	putative patatin-like family phospholipase	_____________119________________________________145\n_____________\|__________________________________\|\n5'-AGG...GUCCA____A___________C_________________GAAUA...GAC-3'\n______________GCGG_CUGGC_UUUUG_GG________UUUUAGC\n______________:\|:\|_\|\|:\|\|_\|\|\|\|:_\|\|________\|\|\|:\|\|\|\n______________UGUC_GAUCG_AAAAU_CC________AAAGUCG\n3'-UUU...GACCA__________U_____A__CAAUACAA_______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	138 -- 144	1 -- 7	-20.956 kcal/mol	9.37145 kcal/mol	1.49313 kcal/mol	119 145@LB@ \| \|@LB@5'-AGG...GUCCA A C GAAUA...GAC-3'@LB@ GCGG CUGGC UUUUG GG UUUUAGC@LB@ :\|:\| \|\|:\|\| \|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ UGUC GAUCG AAAAU CC AAAGUCG@LB@3'-UUU...GACCA U A CAAUACAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -20.956 kcal/mol@LB@Unfolding Energy - mRNA 9.37145 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 120 -- 144@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 1 -- 7@LB@
164	0.008548	0.1748	b0461	tomB	-9.85	0.177976	15 -- 39	9 -- 30	Hha toxicity attenuator; conjugation-related protein	_____________14________________________40\n_____________\|_________________________\|\n5'-UGC...UUAGU________GAAAAA___A__CC___CCCGC...AUC-3'\n______________GCUAGUAU______GUG_GU__UGU\n______________\|\|\|\|\|:\|\|______:\|\|_\|\|__\|\|\|\n______________CGAUCGUA______UAC_CA__ACA\n3'-UUU...CAUGU________AAA______C__AU___AAAAGUCG-5'\n_____________\|_________________________\|\n_____________31________________________8\n	16 -- 22	23 -- 29	-13.2091 kcal/mol	1.89111 kcal/mol	1.4702 kcal/mol	14 40@LB@ \| \|@LB@5'-UGC...UUAGU GAAAAA A CC CCCGC...AUC-3'@LB@ GCUAGUAU GUG GU UGU@LB@ \|\|\|\|\|:\|\| :\|\| \|\| \|\|\|@LB@ CGAUCGUA UAC CA ACA@LB@3'-UUU...CAUGU AAA C AU AAAAGUCG-5'@LB@ \| \|@LB@ 31 8@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.2091 kcal/mol@LB@Unfolding Energy - mRNA 1.89111 kcal/mol@LB@Unfolding Energy - sRNA 1.4702 kcal/mol@LB@@LB@Position - mRNA 15 -- 39@LB@Position - sRNA 9 -- 30@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 23 -- 29@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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