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
88	0.03104	0.29	ct_766	miaA	-2.38	0.813549	82 -- 88	27 -- 33	tRNA dimethylallyltransferase	_____________81______89\n_____________\|_______\|\n5'-AUA...UAAUG_______UUGUA...UGU-3'\n______________GGAAGCU\n______________:\|\|\|\|\|\|\n______________UCUUCGA\n3'-UUU...CUCAG_______UAAGG...GAA-5'\n_____________\|_______\|\n_____________34______26\n	82 -- 88	27 -- 33	-8.83329 kcal/mol	1.86027 kcal/mol	4.59825 kcal/mol	81 89@LB@ \| \|@LB@5'-AUA...UAAUG UUGUA...UGU-3'@LB@ GGAAGCU@LB@ :\|\|\|\|\|\|@LB@ UCUUCGA@LB@3'-UUU...CUCAG UAAGG...GAA-5'@LB@ \| \|@LB@ 34 26@LB@@LB@@LB@Energy -2.38 kcal/mol@LB@Hybridization Energy -8.83329 kcal/mol@LB@Unfolding Energy - mRNA 1.86027 kcal/mol@LB@Unfolding Energy - sRNA 4.59825 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 27 -- 33@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 27 -- 33@LB@
83	0.0294	0.29	ct_767	N/A	-5.43	0.301596	255 -- 261	54 -- 60		_____________254_____262\n_____________\|_______\|\n5'-CUC...UUUAU_______UGGAA...AAC-3'\n______________UCCCCCU\n______________\|\|\|\|\|\|:\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	255 -- 261	54 -- 60	-13.2051 kcal/mol	1.33057 kcal/mol	6.44182 kcal/mol	254 262@LB@ \| \|@LB@5'-CUC...UUUAU UGGAA...AAC-3'@LB@ UCCCCCU@LB@ \|\|\|\|\|\|:@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.43 kcal/mol@LB@Hybridization Energy -13.2051 kcal/mol@LB@Unfolding Energy - mRNA 1.33057 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 255 -- 261@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 54 -- 60@LB@
38	0.01345	0.2859	ct_769	ybeB	-11.98	0.008536	76 -- 102	17 -- 43	ribosome silencing factor	_____________75___________________________103\n_____________\|____________________________\|\n5'-CUU...GAUCU________GAA_________________AAAGA...CCC-3'\n______________CGCUAGAG___AGAGGCUAUUUU_UGGU\n______________\|:\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|::_\|\|\|:\n______________GUGAUCUC___UCUUCGAUAAGG_ACCG\n3'-UUU...UGUUU________AG_____________U____CAAUC...GAA-5'\n_____________\|____________________________\|\n_____________44___________________________16\n	91 -- 97	23 -- 29	-31.1732 kcal/mol	6.53125 kcal/mol	12.6613 kcal/mol	75 103@LB@ \| \|@LB@5'-CUU...GAUCU GAA AAAGA...CCC-3'@LB@ CGCUAGAG AGAGGCUAUUUU UGGU@LB@ \|:\|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:: \|\|\|:@LB@ GUGAUCUC UCUUCGAUAAGG ACCG@LB@3'-UUU...UGUUU AG U CAAUC...GAA-5'@LB@ \| \|@LB@ 44 16@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -31.1732 kcal/mol@LB@Unfolding Energy - mRNA 6.53125 kcal/mol@LB@Unfolding Energy - sRNA 12.6613 kcal/mol@LB@@LB@Position - mRNA 76 -- 102@LB@Position - sRNA 17 -- 43@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 23 -- 29@LB@
158	0.06677	0.3424	ct_770	fabF	-2.81	0.742017	6 -- 13	26 -- 33	3-oxoacyl-ACP synthase	_____________5________14\n_____________\|________\|\n______5'-UAUAG________AAAAA...GUG-3'\n______________AGGAGUUA\n______________\|\|:\|\|:\|\|\n______________UCUUCGAU\n3'-UUU...CUCAG________AAGGU...GAA-5'\n_____________\|________\|\n_____________34_______25\n	7 -- 13	26 -- 32	-8.27201 kcal/mol	0.759487 kcal/mol	4.69868 kcal/mol	5 14@LB@ \| \|@LB@ 5'-UAUAG AAAAA...GUG-3'@LB@ AGGAGUUA@LB@ \|\|:\|\|:\|\|@LB@ UCUUCGAU@LB@3'-UUU...CUCAG AAGGU...GAA-5'@LB@ \| \|@LB@ 34 25@LB@@LB@@LB@Energy -2.81 kcal/mol@LB@Hybridization Energy -8.27201 kcal/mol@LB@Unfolding Energy - mRNA 0.759487 kcal/mol@LB@Unfolding Energy - sRNA 4.69868 kcal/mol@LB@@LB@Position - mRNA 6 -- 13@LB@Position - sRNA 26 -- 33@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 26 -- 32@LB@
199	0.0896	0.3683	ct_774	cysQ	-5.35	0.311933	207 -- 214	53 -- 60	3'(2') 5'-bisphosphate nucleotidase	_____________206______215\n_____________\|________\|\n5'-UCA...UGUUC________CAAUG...UUC-3'\n______________UCCCUCCU\n______________\|\|\|\|:\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	208 -- 214	53 -- 59	-13.0073 kcal/mol	1.20108 kcal/mol	6.45136 kcal/mol	206 215@LB@ \| \|@LB@5'-UCA...UGUUC CAAUG...UUC-3'@LB@ UCCCUCCU@LB@ \|\|\|\|:\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -5.35 kcal/mol@LB@Hybridization Energy -13.0073 kcal/mol@LB@Unfolding Energy - mRNA 1.20108 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 207 -- 214@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 53 -- 59@LB@
174	0.07335	0.3448	ct_777	bioF	-7.25	0.126962	76 -- 92	19 -- 34	8-amino-7-oxononanoate synthase	_____________75________________93\n_____________\|_________________\|\n5'-CUG...UCAGG_______G_____U___UUGGG...UUU-3'\n______________UAGAAGC_AUUCC_AUG\n______________:\|\|\|\|\|\|_\|\|\|\|\|_\|\|\|\n______________GUCUUCG_UAAGG_UAC\n3'-UUU...UCUCA_______A_________CGCAA...GAA-5'\n_____________\|_________________\|\n_____________35________________18\n	76 -- 82	28 -- 34	-16.4612 kcal/mol	4.23516 kcal/mol	4.97732 kcal/mol	75 93@LB@ \| \|@LB@5'-CUG...UCAGG G U UUGGG...UUU-3'@LB@ UAGAAGC AUUCC AUG@LB@ :\|\|\|\|\|\| \|\|\|\|\| \|\|\|@LB@ GUCUUCG UAAGG UAC@LB@3'-UUU...UCUCA A CGCAA...GAA-5'@LB@ \| \|@LB@ 35 18@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -16.4612 kcal/mol@LB@Unfolding Energy - mRNA 4.23516 kcal/mol@LB@Unfolding Energy - sRNA 4.97732 kcal/mol@LB@@LB@Position - mRNA 76 -- 92@LB@Position - sRNA 19 -- 34@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 28 -- 34@LB@
115	0.04794	0.3262	ct_778	priA	-6.05	0.227860	46 -- 52	54 -- 60	primosomal protein N'	_____________45______53\n_____________\|_______\|\n5'-CGC...GUCAU_______AUCCU...AAA-3'\n______________UCCCCUC\n______________\|\|\|\|\|:\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	46 -- 52	54 -- 60	-12.5948 kcal/mol	0.0982726 kcal/mol	6.44182 kcal/mol	45 53@LB@ \| \|@LB@5'-CGC...GUCAU AUCCU...AAA-3'@LB@ UCCCCUC@LB@ \|\|\|\|\|:\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -6.05 kcal/mol@LB@Hybridization Energy -12.5948 kcal/mol@LB@Unfolding Energy - mRNA 0.0982726 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 54 -- 60@LB@
33	0.01042	0.2518	ct_780	N/A	-7.85	0.092931	30 -- 50	15 -- 34		_____________29____________________51\n_____________\|_____________________\|\n5'-UGU...AAAAA___C____GAA_G________GUCAA...UCA-3'\n______________CAG_AAGU___U_CAUGGCGU\n______________\|\|\|_\|\|\|:___\|_\|\|\|\|\|\|\|\|\n______________GUC_UUCG___A_GUACCGCA\n3'-UUU...UCUCA________AUA_G________AUCUU...GAA-5'\n_____________\|_____________________\|\n_____________35____________________14\n	44 -- 50	15 -- 21	-20.7959 kcal/mol	4.71518 kcal/mol	8.23265 kcal/mol	29 51@LB@ \| \|@LB@5'-UGU...AAAAA C GAA G GUCAA...UCA-3'@LB@ CAG AAGU U CAUGGCGU@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|\|@LB@ GUC UUCG A GUACCGCA@LB@3'-UUU...UCUCA AUA G AUCUU...GAA-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -20.7959 kcal/mol@LB@Unfolding Energy - mRNA 4.71518 kcal/mol@LB@Unfolding Energy - sRNA 8.23265 kcal/mol@LB@@LB@Position - mRNA 30 -- 50@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 15 -- 21@LB@
179	0.07718	0.3544	ct_781	lysS	-5.99	0.234962	194 -- 201	79 -- 86	lysine--tRNA ligase	_____________193______202\n_____________\|________\|\n5'-AAA...AAAGG________UGUCU...AUC-3'\n______________ACGGUUGA\n______________\|\|\|\|:\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	195 -- 201	79 -- 85	-9.06205 kcal/mol	1.97593 kcal/mol	1.09752 kcal/mol	193 202@LB@ \| \|@LB@5'-AAA...AAAGG UGUCU...AUC-3'@LB@ ACGGUUGA@LB@ \|\|\|\|:\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -9.06205 kcal/mol@LB@Unfolding Energy - mRNA 1.97593 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 194 -- 201@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 79 -- 85@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 80 -- 86@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching