Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
138	0.01576	0.3813	b3361	fic	-10.85	0.137765	79 -- 110	27 -- 60	stationary phase-induced protein putative toxin	_____________78__________________________________111\n_____________\|___________________________________\|\n5'-CGC...CGUCU________UUC_______UAA____AA________CCAGU...AAC-3'\n______________CUGGGAGC______AGCG___UCGU__UUUUCAGG\n______________\|\|\|\|:\|\|\|______\|\|\|:___\|\|\|\|__:\|\|\|\|\|\|\|\n______________GACCUUCG______UCGU___AGCA__GAAAGUCC\n3'-UUU...AUUAU________UUACAC____UAC____C_________AAGAG...GCG-5'\n_____________\|___________________________________\|\n_____________61__________________________________26\n	104 -- 110	27 -- 33	-28.8548 kcal/mol	10.0238 kcal/mol	7.97931 kcal/mol	78 111@LB@ \| \|@LB@5'-CGC...CGUCU UUC UAA AA CCAGU...AAC-3'@LB@ CUGGGAGC AGCG UCGU UUUUCAGG@LB@ \|\|\|\|:\|\|\| \|\|\|: \|\|\|\| :\|\|\|\|\|\|\|@LB@ GACCUUCG UCGU AGCA GAAAGUCC@LB@3'-UUU...AUUAU UUACAC UAC C AAGAG...GCG-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -28.8548 kcal/mol@LB@Unfolding Energy - mRNA 10.0238 kcal/mol@LB@Unfolding Energy - sRNA 7.97931 kcal/mol@LB@@LB@Position - mRNA 79 -- 110@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 27 -- 33@LB@
191	0.0243	0.4226	b4511	ybdZ	-10.65	0.148355	2 -- 30	16 -- 45	stimulator of EntF adenylation activity MbtH-like	_____________1_________________________________31\n_____________\|_________________________________\|\n__________5'-C_____________GGAAG_____A_________CCGAU...UAC-3'\n______________GCA___UUGUGCU_____CGGGU__UUCGCGAG\n______________\|\|\|___\|:\|\|\|\|\|_____\|:\|\|\|__\|:\|\|\|\|\|\|\n______________CGU___AGCACGA_____GUCCA__AGGCGCUC\n3'-UUU...ACACU___UAC_______AA________AG________CCAGA...GCG-5'\n_____________\|_________________________________\|\n_____________46________________________________15\n	24 -- 30	16 -- 22	-30.8687 kcal/mol	10.0459 kcal/mol	10.1709 kcal/mol	1 31@LB@ \| \|@LB@ 5'-C GGAAG A CCGAU...UAC-3'@LB@ GCA UUGUGCU CGGGU UUCGCGAG@LB@ \|\|\| \|:\|\|\|\|\| \|:\|\|\| \|:\|\|\|\|\|\|@LB@ CGU AGCACGA GUCCA AGGCGCUC@LB@3'-UUU...ACACU UAC AA AG CCAGA...GCG-5'@LB@ \| \|@LB@ 46 15@LB@@LB@@LB@Energy -10.65 kcal/mol@LB@Hybridization Energy -30.8687 kcal/mol@LB@Unfolding Energy - mRNA 10.0459 kcal/mol@LB@Unfolding Energy - sRNA 10.1709 kcal/mol@LB@@LB@Position - mRNA 2 -- 30@LB@Position - sRNA 16 -- 45@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 16 -- 22@LB@
48	0.004482	0.2905	b4045	yjbJ	-14.69	0.031336	242 -- 268	42 -- 68	stress-induced protein UPF0337 family	_____________241___________________________269\n_____________\|_____________________________\|\n5'-CGU...UUUAA________G__AAA_______________ACUGA...AAG-3'\n______________AGGUAA_A_UG___GAGCAAUG_GGGCAA\n______________\|:\|\|\|\|_\|_\|\|___:\|\|\|\|\|\|\|_\|:\|\|\|\|\n______________UUCAUU_U_AC___UUCGUUAC_CUCGUU\n3'-UUU...ACCGA______A_G__C__________A______ACAGC...GCG-5'\n_____________\|_____________________________\|\n_____________69____________________________41\n	256 -- 262	49 -- 55	-22.1594 kcal/mol	4.16538 kcal/mol	3.30492 kcal/mol	241 269@LB@ \| \|@LB@5'-CGU...UUUAA G AAA ACUGA...AAG-3'@LB@ AGGUAA A UG GAGCAAUG GGGCAA@LB@ \|:\|\|\|\| \| \|\| :\|\|\|\|\|\|\| \|:\|\|\|\|@LB@ UUCAUU U AC UUCGUUAC CUCGUU@LB@3'-UUU...ACCGA A G C A ACAGC...GCG-5'@LB@ \| \|@LB@ 69 41@LB@@LB@@LB@Energy -14.69 kcal/mol@LB@Hybridization Energy -22.1594 kcal/mol@LB@Unfolding Energy - mRNA 4.16538 kcal/mol@LB@Unfolding Energy - sRNA 3.30492 kcal/mol@LB@@LB@Position - mRNA 242 -- 268@LB@Position - sRNA 42 -- 68@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 49 -- 55@LB@
19	0.001375	0.2431	b0722	sdhD	-16.32	0.016452	168 -- 195	12 -- 41	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________167_____________________________196\n_____________\|_______________________________\|\n5'-UCC...AUUAC_____________C_____________A___CUCGU...UGG-3'\n______________UGUCGUGCUUUCA__UUCU_CGC_AGG_GUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|_\|\|\|_\|\|\|_\|\|\|\n______________ACAGCACGAAAGU__AAGA_GCG_UCC_CAG\n3'-UUU...UCGUU_____________CC____G___C_______AAGGA...GCG-5'\n_____________\|_______________________________\|\n_____________42______________________________11\n	174 -- 180	29 -- 35	-35.0246 kcal/mol	7.60237 kcal/mol	11.1071 kcal/mol	167 196@LB@ \| \|@LB@5'-UCC...AUUAC C A CUCGU...UGG-3'@LB@ UGUCGUGCUUUCA UUCU CGC AGG GUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|@LB@ ACAGCACGAAAGU AAGA GCG UCC CAG@LB@3'-UUU...UCGUU CC G C AAGGA...GCG-5'@LB@ \| \|@LB@ 42 11@LB@@LB@@LB@Energy -16.32 kcal/mol@LB@Hybridization Energy -35.0246 kcal/mol@LB@Unfolding Energy - mRNA 7.60237 kcal/mol@LB@Unfolding Energy - sRNA 11.1071 kcal/mol@LB@@LB@Position - mRNA 168 -- 195@LB@Position - sRNA 12 -- 41@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 29 -- 35@LB@
88	0.008994	0.3393	b0721	sdhC	-13.41	0.051766	40 -- 58	43 -- 60	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________39__________________59\n_____________\|___________________\|\n5'-UCC...CGCAU_____________UUU___UGACG...CCG-3'\n______________CUGGAAGCAGUGU___GCA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|___\|\|\|\n______________GACCUUCGUUACA___CGU\n3'-UUU...AUUAU_____________CU____UACAG...GCG-5'\n_____________\|___________________\|\n_____________61__________________42\n	46 -- 52	48 -- 54	-24.0509 kcal/mol	7.34137 kcal/mol	3.29917 kcal/mol	39 59@LB@ \| \|@LB@5'-UCC...CGCAU UUU UGACG...CCG-3'@LB@ CUGGAAGCAGUGU GCA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\|@LB@ GACCUUCGUUACA CGU@LB@3'-UUU...AUUAU CU UACAG...GCG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -13.41 kcal/mol@LB@Hybridization Energy -24.0509 kcal/mol@LB@Unfolding Energy - mRNA 7.34137 kcal/mol@LB@Unfolding Energy - sRNA 3.29917 kcal/mol@LB@@LB@Position - mRNA 40 -- 58@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 48 -- 54@LB@
128	0.01397	0.3627	b1656	sodB	-9.64	0.214388	197 -- 205	38 -- 46	superoxide dismutase Fe	_____________196_______206\n_____________\|_________\|\n5'-UCU...AGAGU_________AUUCG...AGA-3'\n______________AGCAAUGUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCGUUACAG\n3'-UUU...UACAC_________CACGA...GCG-5'\n_____________\|_________\|\n_____________47________37\n	199 -- 205	38 -- 44	-13.5738 kcal/mol	2.78264 kcal/mol	1.15511 kcal/mol	196 206@LB@ \| \|@LB@5'-UCU...AGAGU AUUCG...AGA-3'@LB@ AGCAAUGUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCGUUACAG@LB@3'-UUU...UACAC CACGA...GCG-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -13.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.78264 kcal/mol@LB@Unfolding Energy - sRNA 1.15511 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
177	0.02193	0.4113	b4136	dsbD	-10.49	0.157561	37 -- 60	42 -- 62	thiol:disulfide interchange protein and activator of DsbC	_____________36_______________________61\n_____________\|________________________\|\n5'-UGC...UCUAU_______AA_____GCUG______GAAUA...CGG-3'\n______________UACUGGG__GGUAA____GAGCAA\n______________\|\|\|\|\|\|:__:\|:\|\|____\|\|\|\|\|\|\n______________AUGACCU__UCGUU____CUCGUU\n3'-UUU...UCAUU______________ACA_______ACAGC...GCG-5'\n_____________\|________________________\|\n_____________63_______________________41\n	37 -- 43	56 -- 62	-20.3754 kcal/mol	6.58529 kcal/mol	3.30151 kcal/mol	36 61@LB@ \| \|@LB@5'-UGC...UCUAU AA GCUG GAAUA...CGG-3'@LB@ UACUGGG GGUAA GAGCAA@LB@ \|\|\|\|\|\|: :\|:\|\| \|\|\|\|\|\|@LB@ AUGACCU UCGUU CUCGUU@LB@3'-UUU...UCAUU ACA ACAGC...GCG-5'@LB@ \| \|@LB@ 63 41@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -20.3754 kcal/mol@LB@Unfolding Energy - mRNA 6.58529 kcal/mol@LB@Unfolding Energy - sRNA 3.30151 kcal/mol@LB@@LB@Position - mRNA 37 -- 60@LB@Position - sRNA 42 -- 62@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 56 -- 62@LB@
37	0.003144	0.2776	b3743	asnC	-18.99	0.005660	240 -- 261	40 -- 60	transcriptional activator of asnA; autorepressor	_____________239____________________262\n_____________\|______________________\|\n5'-AUU...GCAUC_________UUAA_________CGCGC...GCG-3'\n______________CUGGAAGCA____UGGGCAAUG\n______________\|\|\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\|\n______________GACCUUCGU____ACUCGUUAC\n3'-UUU...AUUAU_________UAC__________AGCAC...GCG-5'\n_____________\|______________________\|\n_____________61_____________________39\n	255 -- 261	40 -- 46	-27.3577 kcal/mol	5.06736 kcal/mol	3.29985 kcal/mol	239 262@LB@ \| \|@LB@5'-AUU...GCAUC UUAA CGCGC...GCG-3'@LB@ CUGGAAGCA UGGGCAAUG@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GACCUUCGU ACUCGUUAC@LB@3'-UUU...AUUAU UAC AGCAC...GCG-5'@LB@ \| \|@LB@ 61 39@LB@@LB@@LB@Energy -18.99 kcal/mol@LB@Hybridization Energy -27.3577 kcal/mol@LB@Unfolding Energy - mRNA 5.06736 kcal/mol@LB@Unfolding Energy - sRNA 3.29985 kcal/mol@LB@@LB@Position - mRNA 240 -- 261@LB@Position - sRNA 40 -- 60@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 40 -- 46@LB@
100	0.01027	0.3393	b0661	miaB	-11.26	0.118120	162 -- 200	37 -- 86	tRNA-i(6)A37 methylthiotransferase	_____________161_________________________________________________201\n_____________\|___________________________________________________\|\n5'-CGC...UAUGC___CU_______________C________UC____________________AUGAC...AAC-3'\n______________GCC__GCAUUC__CUGGCUA_____UAUU____GCAA___GAGCAA_GUCG\n______________\|\|\|__\|\|\|::\|__\|\|\|\|\|\|\|_____\|\|:\|____\|\|\|\|___\|\|\|\|\|\|_\|\|\|\|\n______________CGG__CGUGGG__GACCGAU_____AUGA____CGUU___CUCGUU_CAGC\n_______3'-UUUU___U_______CC_______UCAUU____CCUU____ACA______A____ACGAA...GCG-5'\n_____________\|___________________________________________________\|\n_____________87__________________________________________________36\n	173 -- 179	68 -- 74	-35.2592 kcal/mol	9.08526 kcal/mol	14.9108 kcal/mol	161 201@LB@ \| \|@LB@5'-CGC...UAUGC CU C UC AUGAC...AAC-3'@LB@ GCC GCAUUC CUGGCUA UAUU GCAA GAGCAA GUCG@LB@ \|\|\| \|\|\|::\| \|\|\|\|\|\|\| \|\|:\| \|\|\|\| \|\|\|\|\|\| \|\|\|\|@LB@ CGG CGUGGG GACCGAU AUGA CGUU CUCGUU CAGC@LB@ 3'-UUUU U CC UCAUU CCUU ACA A ACGAA...GCG-5'@LB@ \| \|@LB@ 87 36@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -35.2592 kcal/mol@LB@Unfolding Energy - mRNA 9.08526 kcal/mol@LB@Unfolding Energy - sRNA 14.9108 kcal/mol@LB@@LB@Position - mRNA 162 -- 200@LB@Position - sRNA 37 -- 86@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 68 -- 74@LB@
194	0.02479	0.4226	b1260	trpA	-8.29	0.338830	290 -- 297	41 -- 48	tryptophan synthase alpha subunit	_____________289______298\n_____________\|________\|\n5'-GCC...GGCAU________CAU-3'\n______________UGAGCAGU\n______________\|\|\|\|\|\|:\|\n______________ACUCGUUA\n3'-UUU...GUUAC________CAGCA...GCG-5'\n_____________\|________\|\n_____________49_______40\n	291 -- 297	41 -- 47	-10.1831 kcal/mol	0.772851 kcal/mol	1.11967 kcal/mol	289 298@LB@ \| \|@LB@5'-GCC...GGCAU CAU-3'@LB@ UGAGCAGU@LB@ \|\|\|\|\|\|:\|@LB@ ACUCGUUA@LB@3'-UUU...GUUAC CAGCA...GCG-5'@LB@ \| \|@LB@ 49 40@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -10.1831 kcal/mol@LB@Unfolding Energy - mRNA 0.772851 kcal/mol@LB@Unfolding Energy - sRNA 1.11967 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 41 -- 48@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 41 -- 47@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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