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
81	0.02893	0.29	ct_185	zwf	-6.95	0.147965	38 -- 47	51 -- 60	glucose-6-phosphate 1-dehydrogenase	_____________37_________48\n_____________\|__________\|\n5'-AAG...GCCUG__________AUCGU...UUU-3'\n______________UCCUCCCUGU\n______________\|\|\|:\|\|\|\|\|\|\n______________AGGGGGGACA\n3'-UUU...ACUGA__________CAUGU...GAA-5'\n_____________\|__________\|\n_____________61_________50\n	41 -- 47	51 -- 57	-17.9011 kcal/mol	1.87917 kcal/mol	9.07545 kcal/mol	37 48@LB@ \| \|@LB@5'-AAG...GCCUG AUCGU...UUU-3'@LB@ UCCUCCCUGU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGGGGGGACA@LB@3'-UUU...ACUGA CAUGU...GAA-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -17.9011 kcal/mol@LB@Unfolding Energy - mRNA 1.87917 kcal/mol@LB@Unfolding Energy - sRNA 9.07545 kcal/mol@LB@@LB@Position - mRNA 38 -- 47@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 51 -- 57@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@
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@
84	0.03042	0.29	ct_726	N/A	-6.32	0.200732	30 -- 36	81 -- 87	cell division protein	_____________29______37\n_____________\|_______\|\n5'-AGG...CCCCC_______UGCUG...AUC-3'\n______________UAUGGCU\n______________\|\|:\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	30 -- 36	81 -- 87	-8.84564 kcal/mol	1.42457 kcal/mol	1.09752 kcal/mol	29 37@LB@ \| \|@LB@5'-AGG...CCCCC UGCUG...AUC-3'@LB@ UAUGGCU@LB@ \|\|:\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -8.84564 kcal/mol@LB@Unfolding Energy - mRNA 1.42457 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
85	0.03073	0.29	ct_522	rs3	-5.11	0.345416	189 -- 204	18 -- 34	30S ribosomal protein S3	_____________188_______________205\n_____________\|_________________\|\n5'-UGU...GGCAG_______AAGG______GUCAA...UCA-3'\n______________UAGGAGU_____UAUGG\n______________:\|\|:\|\|:_____:\|\|\|\|\n______________GUCUUCG_____GUACC\n3'-UUU...UCUCA_______AUAAG_____GCAAU...GAA-5'\n_____________\|_________________\|\n_____________35________________17\n	189 -- 195	28 -- 34	-12.0284 kcal/mol	1.93617 kcal/mol	4.97803 kcal/mol	188 205@LB@ \| \|@LB@5'-UGU...GGCAG AAGG GUCAA...UCA-3'@LB@ UAGGAGU UAUGG@LB@ :\|\|:\|\|: :\|\|\|\|@LB@ GUCUUCG GUACC@LB@3'-UUU...UCUCA AUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -5.11 kcal/mol@LB@Hybridization Energy -12.0284 kcal/mol@LB@Unfolding Energy - mRNA 1.93617 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
86	0.03096	0.29	ct_221	yqfU	-7.15	0.133289	38 -- 44	80 -- 86		_____________37______45\n_____________\|_______\|\n5'-AUA...GCUCA_______GAGCA...GUG-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.46136 kcal/mol	0.243281 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-AUA...GCUCA GAGCA...GUG-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -8.46136 kcal/mol@LB@Unfolding Energy - mRNA 0.243281 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 80 -- 86@LB@
87	0.03104	0.29	ct_437	fusA	-5.85	0.250219	118 -- 125	79 -- 86	elongation factor G	_____________117______126\n_____________\|________\|\n5'-AUC...AUCGC________AGCAA...UCU-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	119 -- 125	79 -- 85	-8.84241 kcal/mol	1.89322 kcal/mol	1.09752 kcal/mol	117 126@LB@ \| \|@LB@5'-AUC...AUCGC AGCAA...UCU-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.85 kcal/mol@LB@Hybridization Energy -8.84241 kcal/mol@LB@Unfolding Energy - mRNA 1.89322 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 79 -- 85@LB@
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@
89	0.03269	0.2942	ct_269	murE	-8.94	0.051230	172 -- 183	46 -- 57	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2 6-diaminopimelate ligase	_____________171__________184\n_____________\|____________\|\n5'-AUC...UGAAG____________UGUCU...UUG-3'\n______________CCCUUGUGUGCG\n______________\|\|\|:\|\|\|\|\|:\|:\n______________GGGGACACAUGU\n3'-UUU...GAAGG____________UUGUG...GAA-5'\n_____________\|____________\|\n_____________58___________45\n	176 -- 182	47 -- 53	-19.7508 kcal/mol	3.51628 kcal/mol	7.29173 kcal/mol	171 184@LB@ \| \|@LB@5'-AUC...UGAAG UGUCU...UUG-3'@LB@ CCCUUGUGUGCG@LB@ \|\|\|:\|\|\|\|\|:\|:@LB@ GGGGACACAUGU@LB@3'-UUU...GAAGG UUGUG...GAA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -19.7508 kcal/mol@LB@Unfolding Energy - mRNA 3.51628 kcal/mol@LB@Unfolding Energy - sRNA 7.29173 kcal/mol@LB@@LB@Position - mRNA 172 -- 183@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 47 -- 53@LB@
90	0.03275	0.2942	ct_332	pykF	-4.34	0.468844	109 -- 116	80 -- 87	pyruvate kinase	_____________108______117\n_____________\|________\|\n5'-UUU...GCGAU________CUAAA...GCC-3'\n______________UGCGGUUG\n______________\|:\|\|\|:\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	110 -- 116	80 -- 86	-9.21836 kcal/mol	3.78563 kcal/mol	1.09752 kcal/mol	108 117@LB@ \| \|@LB@5'-UUU...GCGAU CUAAA...GCC-3'@LB@ UGCGGUUG@LB@ \|:\|\|\|:\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -4.34 kcal/mol@LB@Hybridization Energy -9.21836 kcal/mol@LB@Unfolding Energy - mRNA 3.78563 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 109 -- 116@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 110 -- 116@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

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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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