Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
166	0.01216	0.2504	b4485	ytfR	-12.60	0.094393	18 -- 41	9 -- 34	putative sugar ABC transporter ATPase	_____________17_________________________42\n_____________\|__________________________\|\n5'-CCU...UGAUA________GAA_______________AGAAA...GCC-3'\n______________CCGCAAAA____GA_AUUAGAGAAGA\n______________\|\|:\|\|\|\|\|____\|\|_\|\|:\|:\|\|\|\|:\|\n______________GGUGUUUU____CU_UAGUUUCUUUU\n3'-UUU...CCCGA________ACCC__G___________CGUCACCG-5'\n_____________\|__________________________\|\n_____________35_________________________8\n	35 -- 41	9 -- 15	-17.8797 kcal/mol	1.35017 kcal/mol	3.92941 kcal/mol	17 42@LB@ \| \|@LB@5'-CCU...UGAUA GAA AGAAA...GCC-3'@LB@ CCGCAAAA GA AUUAGAGAAGA@LB@ \|\|:\|\|\|\|\| \|\| \|\|:\|:\|\|\|\|:\|@LB@ GGUGUUUU CU UAGUUUCUUUU@LB@3'-UUU...CCCGA ACCC G CGUCACCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -17.8797 kcal/mol@LB@Unfolding Energy - mRNA 1.35017 kcal/mol@LB@Unfolding Energy - sRNA 3.92941 kcal/mol@LB@@LB@Position - mRNA 18 -- 41@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@LB@
134	0.009704	0.2504	b1444	patD	-10.55	0.224369	279 -- 297	10 -- 25	gamma-aminobutyraldehyde dehydrogenase	_____________278_________________298\n_____________\|___________________\|\n5'-UCG...CAACG_________UUACU_____UUG-3'\n______________GGGGACGUU_____GGAAA\n______________\|\|\|\|\|\|:\|:_____:\|\|\|\|\n______________CCCCUGUAG_____UCUUU\n3'-UUU...UUUUA_________UU________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	281 -- 287	17 -- 23	-18.1658 kcal/mol	6.94606 kcal/mol	0.670388 kcal/mol	278 298@LB@ \| \|@LB@5'-UCG...CAACG UUACU UUG-3'@LB@ GGGGACGUU GGAAA@LB@ \|\|\|\|\|\|:\|: :\|\|\|\|@LB@ CCCCUGUAG UCUUU@LB@3'-UUU...UUUUA UU UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -18.1658 kcal/mol@LB@Unfolding Energy - mRNA 6.94606 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 17 -- 23@LB@
161	0.01187	0.2504	b0093	ftsQ	-14.15	0.043981	32 -- 43	18 -- 29	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________31___________44\n_____________\|____________\|\n5'-GCU...GCAAA____________AUUGA...CCG-3'\n______________GGAUGGGGACGU\n______________::\|\|\|\|\|\|\|\|:\|\n______________UUUACCCCUGUA\n3'-UUU...GGUGU____________GUUUC...CCG-5'\n_____________\|____________\|\n_____________30___________17\n	37 -- 43	18 -- 24	-18.9266 kcal/mol	4.11166 kcal/mol	0.665542 kcal/mol	31 44@LB@ \| \|@LB@5'-GCU...GCAAA AUUGA...CCG-3'@LB@ GGAUGGGGACGU@LB@ ::\|\|\|\|\|\|\|\|:\|@LB@ UUUACCCCUGUA@LB@3'-UUU...GGUGU GUUUC...CCG-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -18.9266 kcal/mol@LB@Unfolding Energy - mRNA 4.11166 kcal/mol@LB@Unfolding Energy - sRNA 0.665542 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 18 -- 24@LB@
171	0.01235	0.2504	b1092	fabD	-9.75	0.300248	258 -- 270	47 -- 59	malonyl-CoA-[acyl-carrier-protein] transacylase	_____________257___________271\n_____________\|_____________\|\n5'-AAC...UGCUG_____U_______CGAGC...UUG-3'\n______________GCUGA_AUGGCGG\n______________:\|:\|\|_\|\|\|\|\|\|\|\n______________UGGCU_UACCGCC\n3'-UUU...GAACU_____U_______CCAAC...CCG-5'\n_____________\|_____________\|\n_____________60____________46\n	264 -- 270	47 -- 53	-17.9053 kcal/mol	4.19285 kcal/mol	3.96442 kcal/mol	257 271@LB@ \| \|@LB@5'-AAC...UGCUG U CGAGC...UUG-3'@LB@ GCUGA AUGGCGG@LB@ :\|:\|\| \|\|\|\|\|\|\|@LB@ UGGCU UACCGCC@LB@3'-UUU...GAACU U CCAAC...CCG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -17.9053 kcal/mol@LB@Unfolding Energy - mRNA 4.19285 kcal/mol@LB@Unfolding Energy - sRNA 3.96442 kcal/mol@LB@@LB@Position - mRNA 258 -- 270@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 47 -- 53@LB@
164	0.01206	0.2504	b0882	clpA	-9.12	0.369525	95 -- 107	48 -- 60	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________94____________108\n_____________\|_____________\|\n5'-UUU...GCAGA____A________AUGGU...CGC-3'\n______________AACC_AAGUGGCG\n______________\|\|\|\|_\|\|:\|\|\|\|\|\n______________UUGG_UUUACCGC\n3'-UUU...GGAAC____C________CCCAA...CCG-5'\n_____________\|_____________\|\n_____________61____________47\n	101 -- 107	48 -- 54	-16.8445 kcal/mol	3.76103 kcal/mol	3.96136 kcal/mol	94 108@LB@ \| \|@LB@5'-UUU...GCAGA A AUGGU...CGC-3'@LB@ AACC AAGUGGCG@LB@ \|\|\|\| \|\|:\|\|\|\|\|@LB@ UUGG UUUACCGC@LB@3'-UUU...GGAAC C CCCAA...CCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -16.8445 kcal/mol@LB@Unfolding Energy - mRNA 3.76103 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 48 -- 54@LB@
186	0.01333	0.2514	b0084	ftsI	-11.80	0.135121	196 -- 214	1 -- 22	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________195____________________215\n_____________\|______________________\|\n5'-GUU...AACGC_______U__________C___GAAAA...UGG-3'\n______________GACG_CA___GAAAGCAG_GGC\n______________\|\|\|:_\|\|___:\|\|\|\|\|\|\|_\|\|\|\n______________CUGU_GU___UUUUCGUC_CCG\n3'-UUU...UACCC____A__UUC________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	204 -- 210	5 -- 11	-21.3841 kcal/mol	8.04628 kcal/mol	1.54023 kcal/mol	195 215@LB@ \| \|@LB@5'-GUU...AACGC U C GAAAA...UGG-3'@LB@ GACG CA GAAAGCAG GGC@LB@ \|\|\|: \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CUGU GU UUUUCGUC CCG@LB@3'-UUU...UACCC A UUC A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -21.3841 kcal/mol@LB@Unfolding Energy - mRNA 8.04628 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein	_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@LB@
195	0.01413	0.2529	b2527	hscB	-14.38	0.038945	62 -- 81	1 -- 21	HscA co-chaperone J domain-containing protein Hsc56; IscU-specific chaperone HscAB	_____________61____________________82\n_____________\|_____________________\|\n5'-GGU...CCCGA__________U__________UGCGG...CUG-3'\n______________ACGUCAAAGA_GAGU_GUGGU\n______________\|\|:\|\|\|\|\|\|\|_:\|\|:_\|\|\|\|:\n______________UGUAGUUUCU_UUCG_CACCG\n3'-UUU...ACCCC__________U____U_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	65 -- 71	12 -- 18	-23.3701 kcal/mol	7.47956 kcal/mol	1.51103 kcal/mol	61 82@LB@ \| \|@LB@5'-GGU...CCCGA U UGCGG...CUG-3'@LB@ ACGUCAAAGA GAGU GUGGU@LB@ \|\|:\|\|\|\|\|\|\| :\|\|: \|\|\|\|:@LB@ UGUAGUUUCU UUCG CACCG@LB@3'-UUU...ACCCC U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.3701 kcal/mol@LB@Unfolding Energy - mRNA 7.47956 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 12 -- 18@LB@
189	0.01393	0.2529	b0934	ssuC	-14.25	0.041816	137 -- 153	1 -- 17	aliphatic sulfonate ABC transporter permease	_____________136_______________154\n_____________\|_________________\|\n5'-UGC...AUCCG_____C___________GAAUG...GGC-3'\n______________CAAGG_GAAGCGGUGGC\n______________\|\|\|:\|_:\|\|\|\|:\|\|\|\|\|\n______________GUUUC_UUUCGUCACCG\n3'-UUU...CUGUA_____U___________-5'\n_____________\|________________\|\n_____________18_______________1\n	147 -- 153	1 -- 7	-24.8998 kcal/mol	9.21593 kcal/mol	1.43853 kcal/mol	136 154@LB@ \| \|@LB@5'-UGC...AUCCG C GAAUG...GGC-3'@LB@ CAAGG GAAGCGGUGGC@LB@ \|\|\|:\| :\|\|\|\|:\|\|\|\|\|@LB@ GUUUC UUUCGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.25 kcal/mol@LB@Hybridization Energy -24.8998 kcal/mol@LB@Unfolding Energy - mRNA 9.21593 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 137 -- 153@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 1 -- 7@LB@
192	0.01406	0.2529	b4220	tamA	-13.04	0.076745	183 -- 206	1 -- 23	translocation and assembly module for autotransporter export outer membrane subunit	_____________182______________________207\n_____________\|________________________\|\n5'-CGC...AAAAA_______C_______AAU___C__UAUAU...GAC-3'\n______________GGAUAUU_AGGAGAA___GUG_GC\n______________\|\|\|:\|\|:_\|:\|\|:\|\|___\|\|\|_\|\|\n______________CCUGUAG_UUCUUUU___CAC_CG\n3'-UUU...UUACC_______U_______CGU______-5'\n_____________\|_______________________\|\n_____________24______________________1\n	191 -- 197	9 -- 15	-18.7095 kcal/mol	4.09087 kcal/mol	1.57928 kcal/mol	182 207@LB@ \| \|@LB@5'-CGC...AAAAA C AAU C UAUAU...GAC-3'@LB@ GGAUAUU AGGAGAA GUG GC@LB@ \|\|\|:\|\|: \|:\|\|:\|\| \|\|\| \|\|@LB@ CCUGUAG UUCUUUU CAC CG@LB@3'-UUU...UUACC U CGU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -18.7095 kcal/mol@LB@Unfolding Energy - mRNA 4.09087 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 183 -- 206@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 9 -- 15@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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