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
80	0.02888	0.29	ct_821	sucC	-7.97	0.087313	257 -- 264	53 -- 60	succinyl-CoA ligase subunit beta	_____________256______265\n_____________\|________\|\n5'-UCG...CCUAU________AUCAC...CAG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	258 -- 264	53 -- 59	-16.0066 kcal/mol	1.58949 kcal/mol	6.45136 kcal/mol	256 265@LB@ \| \|@LB@5'-UCG...CCUAU AUCAC...CAG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -16.0066 kcal/mol@LB@Unfolding Energy - mRNA 1.58949 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 53 -- 59@LB@
134	0.05433	0.3262	ct_581	thrS	-7.17	0.132364	52 -- 64	21 -- 33	threonine--tRNA ligase	_____________51___________65\n_____________\|____________\|\n5'-AAA...CUAAA_______CC___GAACU...CAG-3'\n______________AGAAGCU__UCC\n______________\|\|\|\|\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________20\n	52 -- 58	27 -- 33	-13.855 kcal/mol	1.83194 kcal/mol	4.72509 kcal/mol	51 65@LB@ \| \|@LB@5'-AAA...CUAAA CC GAACU...CAG-3'@LB@ AGAAGCU UCC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -13.855 kcal/mol@LB@Unfolding Energy - mRNA 1.83194 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 52 -- 64@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 27 -- 33@LB@
97	0.03496	0.2959	ct_539	trxA	-6.38	0.195495	87 -- 94	80 -- 87	thioredoxin	_____________86_______95\n_____________\|________\|\n5'-AUG...GAGGU________ACUGG...UGC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	88 -- 94	80 -- 86	-10.4005 kcal/mol	2.9242 kcal/mol	1.09752 kcal/mol	86 95@LB@ \| \|@LB@5'-AUG...GAGGU ACUGG...UGC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -10.4005 kcal/mol@LB@Unfolding Energy - mRNA 2.9242 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 87 -- 94@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 80 -- 86@LB@
108	0.04117	0.3134	ct_817	tyrP_1	-6.29	0.204127	20 -- 34	17 -- 30	tyrosine-specific transport protein	_____________19______________35\n_____________\|_______________\|\n5'-CGA...AUCAU____UACA_______UUUAC...UCC-3'\n______________GGCU____CCAUGGC\n______________:\|\|\|____\|\|\|\|\|\|\|\n______________UCGA____GGUACCG\n3'-UUU...AGUCU____UAA________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________31______________16\n	28 -- 34	17 -- 23	-15.6862 kcal/mol	4.66372 kcal/mol	4.73426 kcal/mol	19 35@LB@ \| \|@LB@5'-CGA...AUCAU UACA UUUAC...UCC-3'@LB@ GGCU CCAUGGC@LB@ :\|\|\| \|\|\|\|\|\|\|@LB@ UCGA GGUACCG@LB@3'-UUU...AGUCU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -6.29 kcal/mol@LB@Hybridization Energy -15.6862 kcal/mol@LB@Unfolding Energy - mRNA 4.66372 kcal/mol@LB@Unfolding Energy - sRNA 4.73426 kcal/mol@LB@@LB@Position - mRNA 20 -- 34@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 17 -- 23@LB@
177	0.07605	0.3532	ct_428	ubiE	-3.67	0.587989	9 -- 17	20 -- 28	demethylmenaquinone methyltransferase	_____________8_________18\n_____________\|_________\|\n___5'-UUCUUCAA_________UUCAG...AUA-3'\n______________CUAUUUCAU\n______________\|\|\|\|\|:\|\|\|\n______________GAUAAGGUA\n3'-UUU...UCUUC_________CCGCA...GAA-5'\n_____________\|_________\|\n_____________29________19\n	10 -- 16	21 -- 27	-8.26525 kcal/mol	0.050804 kcal/mol	4.54807 kcal/mol	8 18@LB@ \| \|@LB@ 5'-UUCUUCAA UUCAG...AUA-3'@LB@ CUAUUUCAU@LB@ \|\|\|\|\|:\|\|\|@LB@ GAUAAGGUA@LB@3'-UUU...UCUUC CCGCA...GAA-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -8.26525 kcal/mol@LB@Unfolding Energy - mRNA 0.050804 kcal/mol@LB@Unfolding Energy - sRNA 4.54807 kcal/mol@LB@@LB@Position - mRNA 9 -- 17@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 21 -- 27@LB@
4	0.0004436	0.07439	ct_864	xerD	-16.31	0.000480	24 -- 38	17 -- 31	site-specific tyrosine recombinase XerD	_____________23______________39\n_____________\|_______________\|\n5'-CAU...AUGGA_______________ACCUU...AUU-3'\n______________GAGCUAUUCCAUGGU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UUCGAUAAGGUACCG\n3'-UUU...CAGUC_______________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	32 -- 38	17 -- 23	-24.2689 kcal/mol	3.09995 kcal/mol	4.86101 kcal/mol	23 39@LB@ \| \|@LB@5'-CAU...AUGGA ACCUU...AUU-3'@LB@ GAGCUAUUCCAUGGU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UUCGAUAAGGUACCG@LB@3'-UUU...CAGUC CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -16.31 kcal/mol@LB@Hybridization Energy -24.2689 kcal/mol@LB@Unfolding Energy - mRNA 3.09995 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 17 -- 23@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@
59	0.02324	0.29	ct_106	yceC	-7.97	0.086897	139 -- 180	3 -- 31	tRNA pseudouridine synthase A	_____________138__________________________________________181\n_____________\|____________________________________________\|\n5'-CUC...GAAAA__________UAUCA______AAUUCUCGUAAAAUC________ACACU...CCG-3'\n______________AAGCUGUUCU_______UAGA_______________GUACCAAC\n______________\|\|\|\|\|:\|\|\|:_______\|\|\|\|_______________:\|\|\|\|\|\|\|\n______________UUCGAUAAGG_______AUCU_______________UAUGGUUG\n3'-UUU...CAGUC__________UACCGCA___________________________AA-5'\n_____________\|____________________________________________\|\n_____________32___________________________________________2\n	174 -- 180	3 -- 9	-21.8491 kcal/mol	5.39956 kcal/mol	8.47511 kcal/mol	138 181@LB@ \| \|@LB@5'-CUC...GAAAA UAUCA AAUUCUCGUAAAAUC ACACU...CCG-3'@LB@ AAGCUGUUCU UAGA GUACCAAC@LB@ \|\|\|\|\|:\|\|\|: \|\|\|\| :\|\|\|\|\|\|\|@LB@ UUCGAUAAGG AUCU UAUGGUUG@LB@3'-UUU...CAGUC UACCGCA AA-5'@LB@ \| \|@LB@ 32 2@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -21.8491 kcal/mol@LB@Unfolding Energy - mRNA 5.39956 kcal/mol@LB@Unfolding Energy - sRNA 8.47511 kcal/mol@LB@@LB@Position - mRNA 139 -- 180@LB@Position - sRNA 3 -- 31@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 3 -- 9@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@LB@
148	0.06134	0.3407	ct_434	ygbB	-10.66	0.019089	186 -- 200	41 -- 57	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________185_______________201\n_____________\|_________________\|\n5'-GGU...CCUGU_____U___________AUGAC...AUC-3'\n______________CCCCU___UGCAAGCAC\n______________\|\|\|\|\|___\|:\|\|\|:\|\|\|\n______________GGGGA___AUGUUUGUG\n3'-UUU...GAAGG_____CAC_________AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	194 -- 200	41 -- 47	-19.7128 kcal/mol	1.2348 kcal/mol	7.82241 kcal/mol	185 201@LB@ \| \|@LB@5'-GGU...CCUGU U AUGAC...AUC-3'@LB@ CCCCU UGCAAGCAC@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\|@LB@ GGGGA AUGUUUGUG@LB@3'-UUU...GAAGG CAC AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.7128 kcal/mol@LB@Unfolding Energy - mRNA 1.2348 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 194 -- 200@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)

Job resubmission

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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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