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
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@
6	0.000543	0.07439	ct_280	nqr4	-8.45	0.067322	89 -- 131	2 -- 35	Na(+)-translocating NADH-quinone reductase subunit D	_____________88___________________________________________132\n_____________\|____________________________________________\|\n5'-GAC...GAAUU__________C___GACUUGUA_________CC_______UU__CUCAU...CGG-3'\n______________UCAGGAGCUA_UUU________AUGGUGUUA__GAAU_CC__CU\n______________\|\|\|\|:\|\|\|\|\|_\|::________\|\|\|\|:\|\|\|\|__\|\|\|\|_\|\|__\|\|\n______________AGUCUUCGAU_AGG________UACCGCAAU__CUUA_GG__GA\n3'-UUU...AUCUC__________A__________________________U__UU__A-5'\n_____________\|____________________________________________\|\n_____________36___________________________________________1\n	113 -- 119	13 -- 19	-28.603 kcal/mol	11.5634 kcal/mol	8.59199 kcal/mol	88 132@LB@ \| \|@LB@5'-GAC...GAAUU C GACUUGUA CC UU CUCAU...CGG-3'@LB@ UCAGGAGCUA UUU AUGGUGUUA GAAU CC CU@LB@ \|\|\|\|:\|\|\|\|\| \|:: \|\|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|@LB@ AGUCUUCGAU AGG UACCGCAAU CUUA GG GA@LB@3'-UUU...AUCUC A U UU A-5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -28.603 kcal/mol@LB@Unfolding Energy - mRNA 11.5634 kcal/mol@LB@Unfolding Energy - sRNA 8.59199 kcal/mol@LB@@LB@Position - mRNA 89 -- 131@LB@Position - sRNA 2 -- 35@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 13 -- 19@LB@
46	0.01681	0.29	ct_425	N/A	-8.97	0.050526	259 -- 284	2 -- 23		_____________258_________________________285\n_____________\|___________________________\|\n5'-CUU...UUCUA__________UC_____UUCU______AAUUU...AAG-3'\n______________CC_UGGCGUU__GAAUA____UCAGCU\n______________\|\|_\|\|\|\|\|\|\|__\|\|\|\|\|____:\|\|:\|\|\n______________GG_ACCGCAA__CUUAU____GGUUGA\n3'-UUU...GAUAA__U_______U________________A-5'\n_____________\|___________________________\|\n_____________24__________________________1\n	261 -- 267	14 -- 20	-21.0816 kcal/mol	4.01638 kcal/mol	8.09761 kcal/mol	258 285@LB@ \| \|@LB@5'-CUU...UUCUA UC UUCU AAUUU...AAG-3'@LB@ CC UGGCGUU GAAUA UCAGCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|\|:\|\|@LB@ GG ACCGCAA CUUAU GGUUGA@LB@3'-UUU...GAUAA U U A-5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -21.0816 kcal/mol@LB@Unfolding Energy - mRNA 4.01638 kcal/mol@LB@Unfolding Energy - sRNA 8.09761 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 2 -- 23@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 14 -- 20@LB@
164	0.06834	0.3424	ct_716	N/A	-9.26	0.042990	10 -- 57	2 -- 60		_____________9____________________________________________________________58\n_____________\|____________________________________________________________\|\n5'-UCA...GAGCU________UACU_____GC_________U_________GAUAUCAU______________AGGAG...UAG-3'\n______________UCUCUCCU_____CAAA__CUA___UCA_GAAGCUAUU________________CCAACU\n______________\|\|:\|:\|\|\|_____\|\|\|\|__\|\|\|___\|\|\|_\|\|\|\|\|\|\|\|\|________________\|\|\|\|\|\|\n______________AGGGGGGA_____GUUU__GAU___AGU_CUUCGAUAA________________GGUUGA\n3'-UUU...ACUGA________CACAU____GU___CUC_____________GGUACCGCAAUCUUAU______A-5'\n_____________\|____________________________________________________________\|\n_____________61___________________________________________________________1\n	37 -- 43	24 -- 30	-32.8059 kcal/mol	5.03112 kcal/mol	18.5194 kcal/mol	9 58@LB@ \| \|@LB@5'-UCA...GAGCU UACU GC U GAUAUCAU AGGAG...UAG-3'@LB@ UCUCUCCU CAAA CUA UCA GAAGCUAUU CCAACU@LB@ \|\|:\|:\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA GUUU GAU AGU CUUCGAUAA GGUUGA@LB@3'-UUU...ACUGA CACAU GU CUC GGUACCGCAAUCUUAU A-5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -32.8059 kcal/mol@LB@Unfolding Energy - mRNA 5.03112 kcal/mol@LB@Unfolding Energy - sRNA 18.5194 kcal/mol@LB@@LB@Position - mRNA 10 -- 57@LB@Position - sRNA 2 -- 60@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 24 -- 30@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@
20	0.004812	0.1918	ct_026	rs16	-8.27	0.073959	26 -- 51	3 -- 33	30S ribosomal protein S16	_____________25______________________________52\n_____________\|_______________________________\|\n5'-CUG...ACGAA________________AA_________G___CGGAU...AUA-3'\n______________AGGAGUUA____GUGG__UU_GAGUAU_AGC\n______________\|\|:\|\|:\|\|____:\|\|\|__\|\|_\|\|:\|\|:_\|:\|\n______________UCUUCGAU____UACC__AA_CUUAUG_UUG\n3'-UUU...CUCAG________AAGG____GC__U______G___AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	27 -- 33	26 -- 32	-20.5759 kcal/mol	3.70935 kcal/mol	8.59196 kcal/mol	25 52@LB@ \| \|@LB@5'-CUG...ACGAA AA G CGGAU...AUA-3'@LB@ AGGAGUUA GUGG UU GAGUAU AGC@LB@ \|\|:\|\|:\|\| :\|\|\| \|\| \|\|:\|\|: \|:\|@LB@ UCUUCGAU UACC AA CUUAUG UUG@LB@3'-UUU...CUCAG AAGG GC U G AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -20.5759 kcal/mol@LB@Unfolding Energy - mRNA 3.70935 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 26 -- 51@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 26 -- 32@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@
92	0.03292	0.2942	ct_558	lipA	-15.60	0.000793	187 -- 244	3 -- 58	lipoyl synthase	_____________186_________________________________________________________245\n_____________\|___________________________________________________________\|\n5'-ACU...AUAUG_______CUAAA_____ACC__U______UCUC_______UAAAAAAUCU______C__CAGAU...AAA-3'\n______________CCCCCUG_____AAAUG___GA_UCAGAA____CUAUUCC___________AUACC_GC\n______________\|\|\|\|\|\|\|_____\|\|\|::___\|\|_\|\|\|\|\|\|____\|\|\|\|\|\|\|___________\|\|\|\|\|_:\|\n______________GGGGGAC_____UUUGU___CU_AGUCUU____GAUAAGG___________UAUGG_UG\n3'-UUU...UGAAG_______ACAUG_____GAU__C______C__________UACCGCAAUCU_____U__AA-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	220 -- 226	22 -- 28	-35.9268 kcal/mol	3.77883 kcal/mol	16.5523 kcal/mol	186 245@LB@ \| \|@LB@5'-ACU...AUAUG CUAAA ACC U UCUC UAAAAAAUCU C CAGAU...AAA-3'@LB@ CCCCCUG AAAUG GA UCAGAA CUAUUCC AUACC GC@LB@ \|\|\|\|\|\|\| \|\|\|:: \|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|@LB@ GGGGGAC UUUGU CU AGUCUU GAUAAGG UAUGG UG@LB@3'-UUU...UGAAG ACAUG GAU C C UACCGCAAUCU U AA-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -15.60 kcal/mol@LB@Hybridization Energy -35.9268 kcal/mol@LB@Unfolding Energy - mRNA 3.77883 kcal/mol@LB@Unfolding Energy - sRNA 16.5523 kcal/mol@LB@@LB@Position - mRNA 187 -- 244@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 22 -- 28@LB@
112	0.04461	0.3262	ct_089	lcrE	-7.82	0.094118	129 -- 157	3 -- 33	low calcium response protein E	_____________128_____________________________158\n_____________\|_______________________________\|\n5'-CGG...UACCA_______UUA_____AAA_____________CUUUG...UUA-3'\n______________AGAAGUU___CC_UG___UUAGAAU_CCAGC\n______________\|\|\|\|\|:\|___\|\|_\|\|___\|\|\|\|\|\|\|_\|\|\|:\|\n______________UCUUCGA___GG_AC___AAUCUUA_GGUUG\n3'-UUU...CUCAG_______UAA__U__CGC_______U_____AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	129 -- 135	27 -- 33	-21.9416 kcal/mol	5.52555 kcal/mol	8.59196 kcal/mol	128 158@LB@ \| \|@LB@5'-CGG...UACCA UUA AAA CUUUG...UUA-3'@LB@ AGAAGUU CC UG UUAGAAU CCAGC@LB@ \|\|\|\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ UCUUCGA GG AC AAUCUUA GGUUG@LB@3'-UUU...CUCAG UAA U CGC U AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -21.9416 kcal/mol@LB@Unfolding Energy - mRNA 5.52555 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 129 -- 157@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 27 -- 33@LB@
118	0.04846	0.3262	ct_515	rs8	-12.50	0.006183	13 -- 43	3 -- 33	30S ribosomal protein S8	_____________12_______________________________44\n_____________\|________________________________\|\n5'-GGA...GACGA___U________UU__________UG______AAAUC...UGC-3'\n______________GGA_GUUAUUCC__UGGU_UUAGA__AUCAGC\n______________:\|\|_\|:\|\|\|\|\|\|__\|\|\|:_\|\|\|\|\|__\|:\|\|:\|\n______________UCU_CGAUAAGG__ACCG_AAUCU__UGGUUG\n3'-UUU...CUCAG___U________U_____C_____UA______AA-5'\n_____________\|________________________________\|\n_____________34_______________________________2\n	18 -- 24	22 -- 28	-29.6343 kcal/mol	8.5463 kcal/mol	8.59196 kcal/mol	12 44@LB@ \| \|@LB@5'-GGA...GACGA U UU UG AAAUC...UGC-3'@LB@ GGA GUUAUUCC UGGU UUAGA AUCAGC@LB@ :\|\| \|:\|\|\|\|\|\| \|\|\|: \|\|\|\|\| \|:\|\|:\|@LB@ UCU CGAUAAGG ACCG AAUCU UGGUUG@LB@3'-UUU...CUCAG U U C UA AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -29.6343 kcal/mol@LB@Unfolding Energy - mRNA 8.5463 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 13 -- 43@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 22 -- 28@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