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
51	0.01855	0.29	ct_758	murD	-8.46	0.066834	21 -- 39	25 -- 51	UDP-N-acetylmuramoylalanine--D-glutamate ligase	_____________20__________________________40\n_____________\|___________________________\|\n5'-CUG...GUGAU___________________________AAAUU...ACA-3'\n______________UGUACA________AGUCGGAAGUUAU\n______________\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|:\|\|\|\n______________ACAUGU________UCAGUCUUCGAUA\n3'-UUU...GGGAC______UUGUGAUC_____________AGGUA...GAA-5'\n_____________\|___________________________\|\n_____________52__________________________24\n	33 -- 39	25 -- 31	-21.2974 kcal/mol	1.17475 kcal/mol	11.6617 kcal/mol	20 40@LB@ \| \|@LB@5'-CUG...GUGAU AAAUU...ACA-3'@LB@ UGUACA AGUCGGAAGUUAU@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|\|:\|\|\|@LB@ ACAUGU UCAGUCUUCGAUA@LB@3'-UUU...GGGAC UUGUGAUC AGGUA...GAA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -21.2974 kcal/mol@LB@Unfolding Energy - mRNA 1.17475 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 21 -- 39@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 25 -- 31@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@
53	0.01942	0.29	ct_580	N/A	-10.14	0.025883	244 -- 280	22 -- 57	S-adenosylmethionine/S-adenosylhomocysteine transporter	_____________243___________________________________281\n_____________\|_____________________________________\|\n5'-GUU...ACAAA___G_____U_____C___UU__GACAU_________CUUAA...CUU-3'\n______________CCU_UGUGU_UAAAC_CUG__GU_____GGCUAUUUU\n______________\|\|:_\|\|\|\|\|_:\|\|\|\|_\|\|:__\|\|_____:\|\|\|\|\|\|::\n______________GGG_ACACA_GUUUG_GAU__CA_____UCGAUAAGG\n3'-UUU...GAAGG___G_____U_____U___CU__GUCU__________UACCG...GAA-5'\n_____________\|_____________________________________\|\n_____________58____________________________________21\n	273 -- 279	23 -- 29	-28.6785 kcal/mol	5.85369 kcal/mol	12.6861 kcal/mol	243 281@LB@ \| \|@LB@5'-GUU...ACAAA G U C UU GACAU CUUAA...CUU-3'@LB@ CCU UGUGU UAAAC CUG GU GGCUAUUUU@LB@ \|\|: \|\|\|\|\| :\|\|\|\| \|\|: \|\| :\|\|\|\|\|\|::@LB@ GGG ACACA GUUUG GAU CA UCGAUAAGG@LB@3'-UUU...GAAGG G U U CU GUCU UACCG...GAA-5'@LB@ \| \|@LB@ 58 21@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -28.6785 kcal/mol@LB@Unfolding Energy - mRNA 5.85369 kcal/mol@LB@Unfolding Energy - sRNA 12.6861 kcal/mol@LB@@LB@Position - mRNA 244 -- 280@LB@Position - sRNA 22 -- 57@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 23 -- 29@LB@
54	0.02089	0.29	ct_119	incA	-7.14	0.134009	237 -- 243	52 -- 58	inclusion membrane protein A	_____________236_____244\n_____________\|_______\|\n5'-UCC...CAUCU_______CACCU...AGA-3'\n______________CCCCCUG\n______________\|\|\|\|\|\|\|\n______________GGGGGAC\n3'-UUU...UGAAG_______ACAUG...GAA-5'\n_____________\|_______\|\n_____________59______51\n	237 -- 243	52 -- 58	-14.4133 kcal/mol	0.279731 kcal/mol	6.99083 kcal/mol	236 244@LB@ \| \|@LB@5'-UCC...CAUCU CACCU...AGA-3'@LB@ CCCCCUG@LB@ \|\|\|\|\|\|\|@LB@ GGGGGAC@LB@3'-UUU...UGAAG ACAUG...GAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -14.4133 kcal/mol@LB@Unfolding Energy - mRNA 0.279731 kcal/mol@LB@Unfolding Energy - sRNA 6.99083 kcal/mol@LB@@LB@Position - mRNA 237 -- 243@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 52 -- 58@LB@
55	0.02093	0.29	ct_785	rl34	-4.69	0.410747	264 -- 270	80 -- 86	50S ribosomal protein L34	_____________263_____271\n_____________\|_______\|\n5'-ACA...CUCGC_______CAAAA...GCC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	264 -- 270	80 -- 86	-8.67787 kcal/mol	2.92801 kcal/mol	1.06449 kcal/mol	263 271@LB@ \| \|@LB@5'-ACA...CUCGC CAAAA...GCC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -8.67787 kcal/mol@LB@Unfolding Energy - mRNA 2.92801 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 264 -- 270@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 80 -- 86@LB@
56	0.02215	0.29	ct_104	fabI	-6.34	0.199539	263 -- 271	80 -- 88	enoyl-(acyl carrier protein) reductase	_____________262_______272\n_____________\|_________\|\n5'-UUU...AACGG_________GGGCA...CAG-3'\n______________GUAUGGCUG\n______________:\|\|:\|\|\|\|:\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	265 -- 271	80 -- 86	-10.7973 kcal/mol	3.36368 kcal/mol	1.09753 kcal/mol	262 272@LB@ \| \|@LB@5'-UUU...AACGG GGGCA...CAG-3'@LB@ GUAUGGCUG@LB@ :\|\|:\|\|\|\|:@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.7973 kcal/mol@LB@Unfolding Energy - mRNA 3.36368 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 80 -- 86@LB@
57	0.02238	0.29	ct_132	N/A	-4.44	0.450895	20 -- 27	53 -- 60		_____________19_______28\n_____________\|________\|\n5'-GAU...AUGGA________AAAAA...ACA-3'\n______________UCUCCCCU\n______________\|\|:\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	21 -- 27	53 -- 59	-12.9803 kcal/mol	2.08802 kcal/mol	6.45136 kcal/mol	19 28@LB@ \| \|@LB@5'-GAU...AUGGA AAAAA...ACA-3'@LB@ UCUCCCCU@LB@ \|\|:\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -4.44 kcal/mol@LB@Hybridization Energy -12.9803 kcal/mol@LB@Unfolding Energy - mRNA 2.08802 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 20 -- 27@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 53 -- 59@LB@
58	0.02303	0.29	ct_184	N/A	-4.35	0.465673	5 -- 18	18 -- 35	Holliday junction resolvase	_____________4__________________19\n_____________\|__________________\|\n_______5'-ACGU_______AA_________AUUAA...UGC-3'\n______________UUAGAAG______CAUGG\n______________\|:\|\|\|\|\|______\|\|\|\|\|\n______________AGUCUUC______GUACC\n3'-UUU...AUCUC_______GAUAAG_____GCAAU...GAA-5'\n_____________\|__________________\|\n_____________36_________________17\n	5 -- 11	29 -- 35	-12.193 kcal/mol	2.86148 kcal/mol	4.97803 kcal/mol	4 19@LB@ \| \|@LB@ 5'-ACGU AA AUUAA...UGC-3'@LB@ UUAGAAG CAUGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGUCUUC GUACC@LB@3'-UUU...AUCUC GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -12.193 kcal/mol@LB@Unfolding Energy - mRNA 2.86148 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 5 -- 18@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@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@
60	0.02363	0.29	ct_796	glyQ	-6.44	0.189870	236 -- 248	21 -- 33	glycine--tRNA ligase	_____________235___________249\n_____________\|_____________\|\n5'-UAG...AUGAU__C__________AACUU...AAG-3'\n______________GG_AGCUAUUCUA\n______________:\|_\|\|\|\|\|\|\|\|:\|\n______________UC_UCGAUAAGGU\n3'-UUU...CUCAG__U__________ACCGC...GAA-5'\n_____________\|_____________\|\n_____________34____________20\n	241 -- 247	22 -- 28	-13.5001 kcal/mol	2.33043 kcal/mol	4.73034 kcal/mol	235 249@LB@ \| \|@LB@5'-UAG...AUGAU C AACUU...AAG-3'@LB@ GG AGCUAUUCUA@LB@ :\| \|\|\|\|\|\|\|\|:\|@LB@ UC UCGAUAAGGU@LB@3'-UUU...CUCAG U ACCGC...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -6.44 kcal/mol@LB@Hybridization Energy -13.5001 kcal/mol@LB@Unfolding Energy - mRNA 2.33043 kcal/mol@LB@Unfolding Energy - sRNA 4.73034 kcal/mol@LB@@LB@Position - mRNA 236 -- 248@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 241 -- 247@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