Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
110	0.04403	0.3262	ct_742	ygcA	-7.58	0.107160	204 -- 253	23 -- 59	rRNA methyltransferse	_____________203__________________________________________________254\n_____________\|____________________________________________________\|\n5'-AAC...AGUUG________CUAUCGUAAC___________UU___C___UGU___________AUCUC...UUG-3'\n______________CUCUCCUG__________UGUA__AACAU__UGG_GUC___GGAGGCUGUUC\n______________\|:\|:\|\|\|\|__________\|\|\|\|__\|\|\|\|:__\|:\|_\|\|\|___:\|\|:\|\|\|:\|\|\|\n______________GGGGGGAC__________ACAU__UUGUG__AUC_CAG___UCUUCGAUAAG\n3'-UUU...CUGAA______________________GU__________U_________________GUACC...GAA-5'\n_____________\|____________________________________________________\|\n_____________60___________________________________________________22\n	247 -- 253	23 -- 29	-33.6475 kcal/mol	12.386 kcal/mol	13.6844 kcal/mol	203 254@LB@ \| \|@LB@5'-AAC...AGUUG CUAUCGUAAC UU C UGU AUCUC...UUG-3'@LB@ CUCUCCUG UGUA AACAU UGG GUC GGAGGCUGUUC@LB@ \|:\|:\|\|\|\| \|\|\|\| \|\|\|\|: \|:\| \|\|\| :\|\|:\|\|\|:\|\|\|@LB@ GGGGGGAC ACAU UUGUG AUC CAG UCUUCGAUAAG@LB@3'-UUU...CUGAA GU U GUACC...GAA-5'@LB@ \| \|@LB@ 60 22@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -33.6475 kcal/mol@LB@Unfolding Energy - mRNA 12.386 kcal/mol@LB@Unfolding Energy - sRNA 13.6844 kcal/mol@LB@@LB@Position - mRNA 204 -- 253@LB@Position - sRNA 23 -- 59@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 23 -- 29@LB@
32	0.009822	0.2518	ct_649	ygfA	-6.64	0.172247	22 -- 28	80 -- 86	5-formyltetrahydrofolate cyclo-ligase	_____________21______29\n_____________\|_______\|\n5'-UAC...AAGUG_______CCGAG...AGC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	22 -- 28	80 -- 86	-8.81528 kcal/mol	1.11082 kcal/mol	1.06449 kcal/mol	21 29@LB@ \| \|@LB@5'-UAC...AAGUG CCGAG...AGC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -8.81528 kcal/mol@LB@Unfolding Energy - mRNA 1.11082 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 22 -- 28@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 80 -- 86@LB@
200	0.0896	0.3683	ct_487	yhhF	-5.19	0.334580	14 -- 20	79 -- 85	methyltransferase	_____________13______21\n_____________\|_______\|\n5'-ACG...UCCUC_______UAAUG...UUA-3'\n______________CGGUUAG\n______________\|\|\|:\|\|:\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	14 -- 20	79 -- 85	-7.01592 kcal/mol	0.727938 kcal/mol	1.09751 kcal/mol	13 21@LB@ \| \|@LB@5'-ACG...UCCUC UAAUG...UUA-3'@LB@ CGGUUAG@LB@ \|\|\|:\|\|:@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -7.01592 kcal/mol@LB@Unfolding Energy - mRNA 0.727938 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 14 -- 20@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 79 -- 85@LB@
41	0.01426	0.2859	ct_458	YhhY	-4.46	0.446972	238 -- 245	81 -- 88	acetyltransferase	_____________237______246\n_____________\|________\|\n5'-UUA...UCGGU________CCUGA...GAG-3'\n______________AUACGGUU\n______________\|\|\|\|\|\|:\|\n______________UAUGCCGA\n3'-UUU...GCCUC________UUGAG...GAA-5'\n_____________\|________\|\n_____________89_______80\n	239 -- 245	81 -- 87	-8.66821 kcal/mol	3.10635 kcal/mol	1.09753 kcal/mol	237 246@LB@ \| \|@LB@5'-UUA...UCGGU CCUGA...GAG-3'@LB@ AUACGGUU@LB@ \|\|\|\|\|\|:\|@LB@ UAUGCCGA@LB@3'-UUU...GCCUC UUGAG...GAA-5'@LB@ \| \|@LB@ 89 80@LB@@LB@@LB@Energy -4.46 kcal/mol@LB@Hybridization Energy -8.66821 kcal/mol@LB@Unfolding Energy - mRNA 3.10635 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 81 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 81 -- 87@LB@
125	0.05005	0.3262	ct_644	yohI	-5.25	0.326074	256 -- 262	53 -- 59	tRNA-dihydrouridine synthase	_____________255_____263\n_____________\|_______\|\n5'-CUG...CUACG_______AGCGG...CGG-3'\n______________CCCCCUU\n______________\|\|\|\|\|:\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	256 -- 262	53 -- 59	-11.5527 kcal/mol	0.822659 kcal/mol	5.47887 kcal/mol	255 263@LB@ \| \|@LB@5'-CUG...CUACG AGCGG...CGG-3'@LB@ CCCCCUU@LB@ \|\|\|\|\|:\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -11.5527 kcal/mol@LB@Unfolding Energy - mRNA 0.822659 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 256 -- 262@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 53 -- 59@LB@
144	0.05714	0.3262	ct_392	yprS	-4.10	0.509599	238 -- 247	22 -- 33		_____________237__________248\n_____________\|____________\|\n5'-AGG...CCCUG____________CAAUU...GUC-3'\n______________AGAGGCU__UCC\n______________\|\|\|:\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	238 -- 244	27 -- 33	-11.7781 kcal/mol	2.9519 kcal/mol	4.72509 kcal/mol	237 248@LB@ \| \|@LB@5'-AGG...CCCUG CAAUU...GUC-3'@LB@ AGAGGCU UCC@LB@ \|\|\|:\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -11.7781 kcal/mol@LB@Unfolding Energy - mRNA 2.9519 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 27 -- 33@LB@
86	0.03096	0.29	ct_221	yqfU	-7.15	0.133289	38 -- 44	80 -- 86		_____________37______45\n_____________\|_______\|\n5'-AUA...GCUCA_______GAGCA...GUG-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.46136 kcal/mol	0.243281 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-AUA...GCUCA GAGCA...GUG-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -8.46136 kcal/mol@LB@Unfolding Energy - mRNA 0.243281 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 80 -- 86@LB@
91	0.03287	0.2942	ct_674	yscC	-7.61	0.105180	32 -- 46	36 -- 57	type II secretion system protein	_____________31_____________________47\n_____________\|______________________\|\n5'-UGG...ACACA______________G_______AUUUG...CGG-3'\n______________CCCC_______AAA_GCUAGAG\n______________\|\|\|\|_______\|\|\|_:\|\|\|\|\|\|\n______________GGGG_______UUU_UGAUCUC\n3'-UUU...GAAGG____ACACAUG___G_______AGUCU...GAA-5'\n_____________\|______________________\|\n_____________58_____________________35\n	40 -- 46	36 -- 42	-18.3 kcal/mol	2.71277 kcal/mol	7.97448 kcal/mol	31 47@LB@ \| \|@LB@5'-UGG...ACACA G AUUUG...CGG-3'@LB@ CCCC AAA GCUAGAG@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\|@LB@ GGGG UUU UGAUCUC@LB@3'-UUU...GAAGG ACACAUG G AGUCU...GAA-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -18.3 kcal/mol@LB@Unfolding Energy - mRNA 2.71277 kcal/mol@LB@Unfolding Energy - sRNA 7.97448 kcal/mol@LB@@LB@Position - mRNA 32 -- 46@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 36 -- 42@LB@
175	0.07342	0.3448	ct_738	yycJ	-7.78	0.096435	160 -- 204	18 -- 50	Zn-dependent hydrolase	_____________159____________________________________________205\n_____________\|______________________________________________\|\n5'-CAU...ACCGC_____________UCCAAUUAUCAAA______C_A___A_______AAGGU...AAC-3'\n______________GU_CAAAUACUAG_____________UCAGGA_G_UUA_UCCAUGG\n______________\|\|_\|\|\|\|:\|\|\|\|\|_____________\|\|\|\|:\|_\|_:\|\|_\|\|\|\|\|\|\|\n______________CA_GUUUGUGAUC_____________AGUCUU_C_GAU_AGGUACC\n3'-UUU...GGACA__U__________UC_______________________A_______GCAAU...GAA-5'\n_____________\|______________________________________________\|\n_____________51_____________________________________________17\n	198 -- 204	18 -- 24	-28.1471 kcal/mol	7.4527 kcal/mol	12.9164 kcal/mol	159 205@LB@ \| \|@LB@5'-CAU...ACCGC UCCAAUUAUCAAA C A A AAGGU...AAC-3'@LB@ GU CAAAUACUAG UCAGGA G UUA UCCAUGG@LB@ \|\| \|\|\|\|:\|\|\|\|\| \|\|\|\|:\| \| :\|\| \|\|\|\|\|\|\|@LB@ CA GUUUGUGAUC AGUCUU C GAU AGGUACC@LB@3'-UUU...GGACA U UC A GCAAU...GAA-5'@LB@ \| \|@LB@ 51 17@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -28.1471 kcal/mol@LB@Unfolding Energy - mRNA 7.4527 kcal/mol@LB@Unfolding Energy - sRNA 12.9164 kcal/mol@LB@@LB@Position - mRNA 160 -- 204@LB@Position - sRNA 18 -- 50@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 18 -- 24@LB@
81	0.02893	0.29	ct_185	zwf	-6.95	0.147965	38 -- 47	51 -- 60	glucose-6-phosphate 1-dehydrogenase	_____________37_________48\n_____________\|__________\|\n5'-AAG...GCCUG__________AUCGU...UUU-3'\n______________UCCUCCCUGU\n______________\|\|\|:\|\|\|\|\|\|\n______________AGGGGGGACA\n3'-UUU...ACUGA__________CAUGU...GAA-5'\n_____________\|__________\|\n_____________61_________50\n	41 -- 47	51 -- 57	-17.9011 kcal/mol	1.87917 kcal/mol	9.07545 kcal/mol	37 48@LB@ \| \|@LB@5'-AAG...GCCUG AUCGU...UUU-3'@LB@ UCCUCCCUGU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGGGGGGACA@LB@3'-UUU...ACUGA CAUGU...GAA-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -17.9011 kcal/mol@LB@Unfolding Energy - mRNA 1.87917 kcal/mol@LB@Unfolding Energy - sRNA 9.07545 kcal/mol@LB@@LB@Position - mRNA 38 -- 47@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 51 -- 57@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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usability assessment

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service.

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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