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
168	0.07022	0.3436	ct_336	ptsI	-3.01	0.707290	114 -- 124	23 -- 33	phosphoenolpyruvate-protein phosphotransferase	_____________113_________125\n_____________\|___________\|\n5'-GUU...GGCGA__UU_______AUAUA...UGU-3'\n______________GG__GCUGUUC\n______________:\|__\|\|\|:\|\|\|\n______________UC__CGAUAAG\n3'-UUU...CUCAG__UU_______GUACC...GAA-5'\n_____________\|___________\|\n_____________34__________22\n	118 -- 124	23 -- 29	-10.9545 kcal/mol	3.2189 kcal/mol	4.72321 kcal/mol	113 125@LB@ \| \|@LB@5'-GUU...GGCGA UU AUAUA...UGU-3'@LB@ GG GCUGUUC@LB@ :\| \|\|\|:\|\|\|@LB@ UC CGAUAAG@LB@3'-UUU...CUCAG UU GUACC...GAA-5'@LB@ \| \|@LB@ 34 22@LB@@LB@@LB@Energy -3.01 kcal/mol@LB@Hybridization Energy -10.9545 kcal/mol@LB@Unfolding Energy - mRNA 3.2189 kcal/mol@LB@Unfolding Energy - sRNA 4.72321 kcal/mol@LB@@LB@Position - mRNA 114 -- 124@LB@Position - sRNA 23 -- 33@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 23 -- 29@LB@
82	0.02927	0.29	ct_342	rs21	-5.39	0.307662	118 -- 125	14 -- 21	30S ribosomal protein S21	_____________117______126\n_____________\|________\|\n5'-UUA...UAAAA________ACAAU...AGU-3'\n______________GUGGUGUU\n______________:\|\|\|:\|\|\|\n______________UACCGCAA\n3'-UUU...UAAGG________UCUUA...GAA-5'\n_____________\|________\|\n_____________22_______13\n	119 -- 125	14 -- 20	-8.72589 kcal/mol	2.15057 kcal/mol	1.18847 kcal/mol	117 126@LB@ \| \|@LB@5'-UUA...UAAAA ACAAU...AGU-3'@LB@ GUGGUGUU@LB@ :\|\|\|:\|\|\|@LB@ UACCGCAA@LB@3'-UUU...UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -8.72589 kcal/mol@LB@Unfolding Energy - mRNA 2.15057 kcal/mol@LB@Unfolding Energy - sRNA 1.18847 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 14 -- 20@LB@
155	0.06493	0.3424	ct_355	N/A	-6.27	0.205473	16 -- 22	80 -- 86		_____________15______23\n_____________\|_______\|\n5'-GUU...UUCUG_______GGUCC...CCU-3'\n______________ACGGCUG\n______________\|\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	16 -- 22	80 -- 86	-10.68 kcal/mol	3.341 kcal/mol	1.06449 kcal/mol	15 23@LB@ \| \|@LB@5'-GUU...UUCUG GGUCC...CCU-3'@LB@ ACGGCUG@LB@ \|\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -10.68 kcal/mol@LB@Unfolding Energy - mRNA 3.341 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 16 -- 22@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
10	0.001873	0.154	ct_367	aroL	-15.55	0.000817	132 -- 208	3 -- 59	shikimate kinase	_____________131_______________________________________________________________________________209\n_____________\|_________________________________________________________________________________\|\n5'-UGU...ACAAA_______CUGUAACACACA___________________UUCCA__________AUUGCA___C____CACUAC________GUUCG...UGC-3'\n______________CCCUCCU____________GUGUAUAAAUA__AGAGUU______UAUUUCGUG______GCG__AGA______AUGCCAAC\n______________\|\|\|:\|\|\|____________\|\|\|\|\|:\|\|\|:\|__\|\|\|\|\|:______\|\|\|\|:\|:\|\|______\|\|\|__\|\|\|______\|\|:\|\|\|\|\|\n______________GGGGGGA____________CACAUGUUUGU__UCUCAG______AUAAGGUAC______CGC__UCU______UAUGGUUG\n3'-UUU...CUGAA______________________________GA______UCUUCG__________________AA_________________AA-5'\n_____________\|_________________________________________________________________________________\|\n_____________60________________________________________________________________________________2\n	202 -- 208	3 -- 9	-46.252 kcal/mol	13.1534 kcal/mol	17.5467 kcal/mol	131 209@LB@ \| \|@LB@5'-UGU...ACAAA CUGUAACACACA UUCCA AUUGCA C CACUAC GUUCG...UGC-3'@LB@ CCCUCCU GUGUAUAAAUA AGAGUU UAUUUCGUG GCG AGA AUGCCAAC@LB@ \|\|\|:\|\|\| \|\|\|\|\|:\|\|\|:\| \|\|\|\|\|: \|\|\|\|:\|:\|\| \|\|\| \|\|\| \|\|:\|\|\|\|\|@LB@ GGGGGGA CACAUGUUUGU UCUCAG AUAAGGUAC CGC UCU UAUGGUUG@LB@3'-UUU...CUGAA GA UCUUCG AA AA-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -46.252 kcal/mol@LB@Unfolding Energy - mRNA 13.1534 kcal/mol@LB@Unfolding Energy - sRNA 17.5467 kcal/mol@LB@@LB@Position - mRNA 132 -- 208@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 3 -- 9@LB@
68	0.02545	0.29	ct_369	aroB	-8.93	0.051509	264 -- 292	1 -- 31	3-dehydroquinate synthase	_____________263_____________________________293\n_____________\|_______________________________\|\n5'-GGC...ACCCU_________GCUU_______UC_________CCCUCUCA-3'\n______________AAGCUGUUU_____CGUU_G__UACCGACUU\n______________\|\|\|\|\|:\|\|:_____\|\|\|\|_\|__\|\|\|\|:\|\|\|\|\n______________UUCGAUAAG_____GCAA_C__AUGGUUGAA\n3'-UUU...CAGUC_________GUACC____U_UU_________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	286 -- 292	1 -- 7	-23.4181 kcal/mol	6.00993 kcal/mol	8.47514 kcal/mol	263 293@LB@ \| \|@LB@5'-GGC...ACCCU GCUU UC CCCUCUCA-3'@LB@ AAGCUGUUU CGUU G UACCGACUU@LB@ \|\|\|\|\|:\|\|: \|\|\|\| \| \|\|\|\|:\|\|\|\|@LB@ UUCGAUAAG GCAA C AUGGUUGAA@LB@3'-UUU...CAGUC GUACC U UU -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -8.93 kcal/mol@LB@Hybridization Energy -23.4181 kcal/mol@LB@Unfolding Energy - mRNA 6.00993 kcal/mol@LB@Unfolding Energy - sRNA 8.47514 kcal/mol@LB@@LB@Position - mRNA 264 -- 292@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 1 -- 7@LB@
70	0.02698	0.29	ct_381	artJ	-6.76	0.162330	168 -- 194	31 -- 57	arginine ABC transporter substrate-binding protein ArtJ	_____________167__________________________195\n_____________\|____________________________\|\n5'-AUU...UAUAG______CC__UA__C_____________GUGAG...GUG-3'\n______________UCCCUG__GU__GA_CAUU_GAGUCGGA\n______________:\|\|\|\|\|__\|\|__:\|_\|\|:\|_\|\|\|\|\|:\|\|\n______________GGGGAC__CA__UU_GUGA_CUCAGUCU\n3'-UUU...GAAGG______A___UG__U____U________UCGAU...GAA-5'\n_____________\|____________________________\|\n_____________58___________________________30\n	188 -- 194	31 -- 37	-25.975 kcal/mol	9.18513 kcal/mol	10.0297 kcal/mol	167 195@LB@ \| \|@LB@5'-AUU...UAUAG CC UA C GUGAG...GUG-3'@LB@ UCCCUG GU GA CAUU GAGUCGGA@LB@ :\|\|\|\|\| \|\| :\| \|\|:\| \|\|\|\|\|:\|\|@LB@ GGGGAC CA UU GUGA CUCAGUCU@LB@3'-UUU...GAAGG A UG U U UCGAU...GAA-5'@LB@ \| \|@LB@ 58 30@LB@@LB@@LB@Energy -6.76 kcal/mol@LB@Hybridization Energy -25.975 kcal/mol@LB@Unfolding Energy - mRNA 9.18513 kcal/mol@LB@Unfolding Energy - sRNA 10.0297 kcal/mol@LB@@LB@Position - mRNA 168 -- 194@LB@Position - sRNA 31 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 31 -- 37@LB@
103	0.03832	0.3036	ct_382	aroG	-9.59	0.035559	138 -- 150	48 -- 60	3-deoxy-7-phosphoheptulonate synthase	_____________137___________151\n_____________\|_____________\|\n5'-UUU...UUUUC_____________UAUGA...CUA-3'\n______________UCUUCCCUGUGUG\n______________\|\|::\|\|\|\|\|\|\|\|:\n______________AGGGGGGACACAU\n3'-UUU...ACUGA_____________GUUUG...GAA-5'\n_____________\|_____________\|\n_____________61____________47\n	144 -- 150	48 -- 54	-20.2814 kcal/mol	1.44568 kcal/mol	9.24642 kcal/mol	137 151@LB@ \| \|@LB@5'-UUU...UUUUC UAUGA...CUA-3'@LB@ UCUUCCCUGUGUG@LB@ \|\|::\|\|\|\|\|\|\|\|:@LB@ AGGGGGGACACAU@LB@3'-UUU...ACUGA GUUUG...GAA-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -20.2814 kcal/mol@LB@Unfolding Energy - mRNA 1.44568 kcal/mol@LB@Unfolding Energy - sRNA 9.24642 kcal/mol@LB@@LB@Position - mRNA 138 -- 150@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 48 -- 54@LB@
178	0.07667	0.3541	ct_386	N/A	-3.82	0.559485	134 -- 140	82 -- 88		_____________133_____141\n_____________\|_______\|\n5'-CUU...UUUGG_______ACUAC...AGA-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	134 -- 140	82 -- 88	-6.88346 kcal/mol	1.9622 kcal/mol	1.09753 kcal/mol	133 141@LB@ \| \|@LB@5'-CUU...UUUGG ACUAC...AGA-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -3.82 kcal/mol@LB@Hybridization Energy -6.88346 kcal/mol@LB@Unfolding Energy - mRNA 1.9622 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 134 -- 140@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 82 -- 88@LB@
137	0.05536	0.3262	ct_389	N/A	-5.69	0.269629	175 -- 181	80 -- 86		_____________174_____182\n_____________\|_______\|\n5'-GUU...AUAAC_______UCUCA...GCC-3'\n______________GCGGCUG\n______________:\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	175 -- 181	80 -- 86	-10.4159 kcal/mol	3.66497 kcal/mol	1.06449 kcal/mol	174 182@LB@ \| \|@LB@5'-GUU...AUAAC UCUCA...GCC-3'@LB@ GCGGCUG@LB@ :\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -10.4159 kcal/mol@LB@Unfolding Energy - mRNA 3.66497 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 175 -- 181@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 80 -- 86@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@

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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