Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
191	0.02237	0.3833	b1658	purR	-11.05	0.172432	254 -- 265	163 -- 174	transcriptional repressor hypoxanthine-binding	_____________253_______________266\n_____________\|_________________\|\n5'-UUU...CUACA___GU____________CAACA...GCA-3'\n______________ACU__GUCACACGUGAU\n______________\|\|\|__\|\|\|\|\|\|\|:\|\|\|\|\n______________UGA__CAGUGUGUACUA\n3'-UUU...GGUUA___GU____________CGUCC...UAG-5'\n_____________\|_________________\|\n_____________175_______________162\n	259 -- 265	163 -- 169	-20.3148 kcal/mol	3.57431 kcal/mol	4.30742 kcal/mol	253 266@LB@ \| \|@LB@5'-UUU...CUACA GU CAACA...GCA-3'@LB@ ACU GUCACACGUGAU@LB@ \|\|\| \|\|\|\|\|\|\|:\|\|\|\|@LB@ UGA CAGUGUGUACUA@LB@3'-UUU...GGUUA GU CGUCC...UAG-5'@LB@ \| \|@LB@ 175 162@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -20.3148 kcal/mol@LB@Unfolding Energy - mRNA 3.57431 kcal/mol@LB@Unfolding Energy - sRNA 4.30742 kcal/mol@LB@@LB@Position - mRNA 254 -- 265@LB@Position - sRNA 163 -- 174@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 163 -- 169@LB@
192	0.02246	0.3833	b4340	yjiR	-11.68	0.128907	36 -- 62	126 -- 153	putative DNA-binding transcriptional regulator/putative aminotransferase	_____________35_______63\n_____________\|________\|\n5'-AGC...CAGAG________AUCCA...GUC-3'\n______________GCUUCAUC\n______________\|\|\|\|\|\|\|\|\n______________CGAAGUAG\n3'-UUU...GGGAA________-5'\n_____________\|_______\|\n_____________154_____126\n	50 -- 56	1 -- 7	-12.7164 kcal/mol	1.73081 kcal/mol	0.703102 kcal/mol	35 63@LB@ \| \|@LB@5'-AGC...CAGAG AUCCA...GUC-3'@LB@ GCUUCAUC@LB@ \|\|\|\|\|\|\|\|@LB@ CGAAGUAG@LB@3'-UUU...GGGAA -5'@LB@ \| \|@LB@ 154 126@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -12.7164 kcal/mol@LB@Unfolding Energy - mRNA 1.73081 kcal/mol@LB@Unfolding Energy - sRNA 0.703102 kcal/mol@LB@@LB@Position - mRNA 36 -- 62@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 1 -- 7@LB@
193	0.0225	0.3833	b3751	rbsB	-14.76	0.030308	38 -- 56	74 -- 93	D-ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor	_____________37________________________________________________57\n_____________\|_________________________________________________\|\n___5'-GCGGUACG_____GG______GAAAA_____CA___U____________________UUAAU...UCU-3'\n______________AGUCU__CGGGCG_____GGUCG__UUG_UGGGACGUU_GAUCGGCGCA\n______________\|\|\|\|:__\|::\|\|:_____::\|\|\|__\|\|\|_\|\|\|\|\|\|\|:\|_:\|:\|::\|\|\|\|\n______________UCAGG__GUUCGU_____UUAGC__AAC_ACCCUGCGA_UUGGUUGCGU\n3'-UUU...CGUAG_____AA______ACCAA____________________A__________UGGUC...UAG-5'\n_____________\|_________________________________________________\|\n_____________94________________________________________________73\n	40 -- 46	85 -- 91	-47.7546 kcal/mol	17.619 kcal/mol	19.1533 kcal/mol	37 57@LB@ \| \|@LB@ 5'-GCGGUACG GG GAAAA CA U UUAAU...UCU-3'@LB@ AGUCU CGGGCG GGUCG UUG UGGGACGUU GAUCGGCGCA@LB@ \|\|\|\|: \|::\|\|: ::\|\|\| \|\|\| \|\|\|\|\|\|\|:\| :\|:\|::\|\|\|\|@LB@ UCAGG GUUCGU UUAGC AAC ACCCUGCGA UUGGUUGCGU@LB@3'-UUU...CGUAG AA ACCAA A UGGUC...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -47.7546 kcal/mol@LB@Unfolding Energy - mRNA 17.619 kcal/mol@LB@Unfolding Energy - sRNA 19.1533 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 85 -- 91@LB@
194	0.02283	0.3833	b3823	rhtC	-9.67	0.316154	216 -- 300	113 -- 178	threonine efflux pump	_____________215___________________301\n_____________\|_____________________\|\n5'-AGA...UAUUU____CC_______________CAUUG...GUU-3'\n______________CUCA__GUCGC_CAUGGUGCA\n______________\|\|\|\|__\|\|\|:\|_\|\|\|\|:\|\|\|\|\n______________GAGU__CAGUG_GUACUACGU\n3'-UUU...GUUAU___________U_________CCGUU...UAG-5'\n_____________\|_____________________\|\n_____________179___________________112\n	228 -- 234	161 -- 167	-23.3741 kcal/mol	7.13181 kcal/mol	4.79874 kcal/mol	215 301@LB@ \| \|@LB@5'-AGA...UAUUU CC CAUUG...GUU-3'@LB@ CUCA GUCGC CAUGGUGCA@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|:\|\|\|\|@LB@ GAGU CAGUG GUACUACGU@LB@3'-UUU...GUUAU U CCGUU...UAG-5'@LB@ \| \|@LB@ 179 112@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -23.3741 kcal/mol@LB@Unfolding Energy - mRNA 7.13181 kcal/mol@LB@Unfolding Energy - sRNA 4.79874 kcal/mol@LB@@LB@Position - mRNA 216 -- 300@LB@Position - sRNA 113 -- 178@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 161 -- 167@LB@
195	0.02319	0.3833	b1233	ychJ	-7.86	0.620262	61 -- 80	1 -- 18	UPF0225 family protein	_____________60____________________________________81\n_____________\|_____________________________________\|\n5'-CUU...GCUAC_______________A___CUACU_____________ACGCC...UCA-3'\n______________UGCUCGGUUA_ACAU_GUG_____CAGGC_GGUUAAU\n______________\|:\|\|\|:\|\|:\|_\|\|\|\|_:\|\|_____\|\|\|\|\|_:\|\|:\|\|:\n______________AUGAGUCAGU_UGUA_UAC_____GUCCG_UCAGUUG\n3'-UUU...UGGUU__________G____C_____________U_______AAAGU...UAG-5'\n_____________\|_____________________________________\|\n_____________19____________________________________0\n	139 -- 145	171 -- 177	-29.0991 kcal/mol	9.80481 kcal/mol	8.18679 kcal/mol	60 81@LB@ \| \|@LB@5'-CUU...GCUAC A CUACU ACGCC...UCA-3'@LB@ UGCUCGGUUA ACAU GUG CAGGC GGUUAAU@LB@ \|:\|\|\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\| :\|\|:\|\|:@LB@ AUGAGUCAGU UGUA UAC GUCCG UCAGUUG@LB@3'-UUU...UGGUU G C U AAAGU...UAG-5'@LB@ \| \|@LB@ 19 0@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -29.0991 kcal/mol@LB@Unfolding Energy - mRNA 9.80481 kcal/mol@LB@Unfolding Energy - sRNA 8.18679 kcal/mol@LB@@LB@Position - mRNA 61 -- 80@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 171 -- 177@LB@
196	0.0235	0.3833	b3105	yhaJ	-11.17	0.163135	292 -- 299	86 -- 93	LysR family putative transcriptional regulator	_____________291______300\n_____________\|________\|\n5'-CGG...UGAGC________G-3'\n______________UGGGACGC\n______________\|\|\|\|\|\|\|\|\n______________ACCCUGCG\n3'-UUU...GCAAC________AAUUG...UAG-5'\n_____________\|________\|\n_____________94_______85\n	293 -- 299	86 -- 92	-14.7688 kcal/mol	2.10679 kcal/mol	4.21973 kcal/mol	291 300@LB@ \| \|@LB@5'-CGG...UGAGC G-3'@LB@ UGGGACGC@LB@ \|\|\|\|\|\|\|\|@LB@ ACCCUGCG@LB@3'-UUU...GCAAC AAUUG...UAG-5'@LB@ \| \|@LB@ 94 85@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -14.7688 kcal/mol@LB@Unfolding Energy - mRNA 2.10679 kcal/mol@LB@Unfolding Energy - sRNA 4.21973 kcal/mol@LB@@LB@Position - mRNA 292 -- 299@LB@Position - sRNA 86 -- 93@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 86 -- 92@LB@
197	0.02355	0.3833	b2764	cysJ	-10.17	0.255883	3 -- 30	98 -- 123	sulfite reductase alpha subunit flavoprotein	_____________2________31\n_____________\|________\|\n5'-UUC...AACAG________ACUGG...UUG-3'\n______________CUUUGCUU\n______________\|:\|\|\|\|\|\|\n______________GGAACGAA\n3'-UUU...GUGGG________GUAG-5'\n_____________\|________\|\n_____________124______97\n	176 -- 182	5 -- 11	-8.59037 kcal/mol	0.881795 kcal/mol	1.04254 kcal/mol	2 31@LB@ \| \|@LB@5'-UUC...AACAG ACUGG...UUG-3'@LB@ CUUUGCUU@LB@ \|:\|\|\|\|\|\|@LB@ GGAACGAA@LB@3'-UUU...GUGGG GUAG-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -8.59037 kcal/mol@LB@Unfolding Energy - mRNA 0.881795 kcal/mol@LB@Unfolding Energy - sRNA 1.04254 kcal/mol@LB@@LB@Position - mRNA 3 -- 30@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 5 -- 11@LB@
198	0.0236	0.3833	b1110	ycfJ	-10.00	0.275196	69 -- 84	142 -- 161	uncharacterized protein	_____________68__________________85\n_____________\|___________________\|\n5'-ACU...CCAGC_______GC___UU_____UUCUG...AAU-3'\n______________CAUUCCC__GCU__UCAUC\n______________\|\|::\|\|\|__\|\|\|__\|\|\|\|\|\n______________GUGGGGG__CGA__AGUAG\n3'-UUU...ACCCC_______AA__________-5'\n_____________\|__________________\|\n_____________162________________142\n	113 -- 119	11 -- 17	-18.8572 kcal/mol	2.50144 kcal/mol	7.16879 kcal/mol	68 85@LB@ \| \|@LB@5'-ACU...CCAGC GC UU UUCUG...AAU-3'@LB@ CAUUCCC GCU UCAUC@LB@ \|\|::\|\|\| \|\|\| \|\|\|\|\|@LB@ GUGGGGG CGA AGUAG@LB@3'-UUU...ACCCC AA -5'@LB@ \| \|@LB@ 162 142@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -18.8572 kcal/mol@LB@Unfolding Energy - mRNA 2.50144 kcal/mol@LB@Unfolding Energy - sRNA 7.16879 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 142 -- 161@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 11 -- 17@LB@
199	0.02363	0.3833	b4141	yjeH	-8.04	0.585705	57 -- 67	64 -- 74	putative transporter	_____________56_____________68\n_____________\|______________\|\n5'-CAG...AAAUC___G_______C__AAAUU...CUG-3'\n______________UAC_CAGUUGC_CA\n______________\|\|\|_\|\|\|\|::\|_\|\|\n______________AUG_GUCAGUG_GU\n3'-UUU...UGGUU___A_______U__ACUAC...UAG-5'\n_____________\|______________\|\n_____________75_____________63\n	163 -- 169	170 -- 176	-11.2481 kcal/mol	2.09942 kcal/mol	0.433965 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAUC G C AAAUU...CUG-3'@LB@ UAC CAGUUGC CA@LB@ \|\|\| \|\|\|\|::\| \|\|@LB@ AUG GUCAGUG GU@LB@3'-UUU...UGGUU A U ACUAC...UAG-5'@LB@ \| \|@LB@ 75 63@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -11.2481 kcal/mol@LB@Unfolding Energy - mRNA 2.09942 kcal/mol@LB@Unfolding Energy - sRNA 0.433965 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 64 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 170 -- 176@LB@
200	0.02363	0.3833	b3068	mug	-12.10	0.106144	279 -- 297	1 -- 19	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________278__________________298\n_____________\|____________________\|\n5'-UGG...GGACU___UU_______________CGG-3'\n______________GGU__UCCCUUUGCU_CAUC\n______________\|\|:__:\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCG__GGGGGAACGA_GUAG\n3'-UUU...GUACC___U___________A____-5'\n_____________\|___________________\|\n_____________20__________________1\n	287 -- 293	6 -- 12	-22.9494 kcal/mol	3.41941 kcal/mol	8.43224 kcal/mol	278 298@LB@ \| \|@LB@5'-UGG...GGACU UU CGG-3'@LB@ GGU UCCCUUUGCU CAUC@LB@ \|\|: :\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCG GGGGGAACGA GUAG@LB@3'-UUU...GUACC U A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.9494 kcal/mol@LB@Unfolding Energy - mRNA 3.41941 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 6 -- 12@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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