Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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_000913 Escherichia coli str. K-12 substr. MG1655

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
37	0.0006972	0.06333	b1594	mlc	-9.54	0.201866	190 -- 226	24 -- 50	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor	_____________189___________________________________227\n_____________\|_____________________________________\|\n5'-AAA...AUAUA____GUAUGC_______G___AAAAC____CUG____CAUUG...GUA-3'\n______________GGGA______GGUGGUU_CUG_____CAGC___GGCA\n______________:\|\|\|______\|\|\|\|\|\|\|_\|\|\|_____\|\|\|\|___:\|\|\|\n______________UCCU______CCACCAA_GAC_____GUCG___UCGU\n3'-UUU...CCGAU_________________G___CAU______A______AAAAU...UCG-5'\n_____________\|_____________________________________\|\n_____________51____________________________________23\n	200 -- 206	40 -- 46	-27.1319 kcal/mol	12.9802 kcal/mol	4.6134 kcal/mol	189 227@LB@ \| \|@LB@5'-AAA...AUAUA GUAUGC G AAAAC CUG CAUUG...GUA-3'@LB@ GGGA GGUGGUU CUG CAGC GGCA@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\|\| :\|\|\|@LB@ UCCU CCACCAA GAC GUCG UCGU@LB@3'-UUU...CCGAU G CAU A AAAAU...UCG-5'@LB@ \| \|@LB@ 51 23@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -27.1319 kcal/mol@LB@Unfolding Energy - mRNA 12.9802 kcal/mol@LB@Unfolding Energy - sRNA 4.6134 kcal/mol@LB@@LB@Position - mRNA 190 -- 226@LB@Position - sRNA 24 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
146	0.006865	0.158	b2701	mltB	-8.70	0.277719	77 -- 106	9 -- 36	membrane-bound lytic murein transglycosylase B	_____________76______________________________107\n_____________\|_______________________________\|\n5'-AGA...UAAAA________G__G_GAAUGAGU__A_______AAAGU...GAA-3'\n______________GG_AUAGC_AG_G________UG_GUUAUGU\n______________\|\|_\|:\|\|\|_\|\|_:________\|\|_\|\|\|\|\|\|\|\n______________CC_UGUCG_UC_U________AC_CAAUACA\n3'-UUU...AAGGA__A_____A__G_AAAAU_____C_______AAAAGUCG-5'\n_____________\|_______________________________\|\n_____________37______________________________8\n	100 -- 106	9 -- 15	-15.8871 kcal/mol	5.69864 kcal/mol	1.48926 kcal/mol	76 107@LB@ \| \|@LB@5'-AGA...UAAAA G G GAAUGAGU A AAAGU...GAA-3'@LB@ GG AUAGC AG G UG GUUAUGU@LB@ \|\| \|:\|\|\| \|\| : \|\| \|\|\|\|\|\|\|@LB@ CC UGUCG UC U AC CAAUACA@LB@3'-UUU...AAGGA A A G AAAAU C AAAAGUCG-5'@LB@ \| \|@LB@ 37 8@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -15.8871 kcal/mol@LB@Unfolding Energy - mRNA 5.69864 kcal/mol@LB@Unfolding Energy - sRNA 1.48926 kcal/mol@LB@@LB@Position - mRNA 77 -- 106@LB@Position - sRNA 9 -- 36@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 9 -- 15@LB@
185	0.01059	0.1919	b3856	mobB	-14.40	0.016564	123 -- 150	1 -- 31	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________122______________________________151\n_____________\|________________________________\|\n5'-GUG...CGUCU________GUC____C_____A__________GAUCA...CCA-3'\n______________GGCUGGCG____AUG_GGUUG____UUUCAGC\n______________:\|\|\|:\|\|:____\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\n______________UCGAUCGU____UAC_CCAAU____AAAGUCG\n3'-UUU...CCAUG________AAAA_________ACAA_______-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	144 -- 150	1 -- 7	-26.2194 kcal/mol	10.3308 kcal/mol	1.48722 kcal/mol	122 151@LB@ \| \|@LB@5'-GUG...CGUCU GUC C A GAUCA...CCA-3'@LB@ GGCUGGCG AUG GGUUG UUUCAGC@LB@ :\|\|\|:\|\|: \|\|\| \|\|\|\|: \|\|\|\|\|\|\|@LB@ UCGAUCGU UAC CCAAU AAAGUCG@LB@3'-UUU...CCAUG AAAA ACAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -26.2194 kcal/mol@LB@Unfolding Energy - mRNA 10.3308 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 123 -- 150@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 1 -- 7@LB@
10	2.916e-05	0.0098	b1890	motA	-14.10	0.019983	224 -- 242	28 -- 46	proton conductor component of flagella motor	_____________223_________________243\n_____________\|___________________\|\n5'-GAC...UACCU___U_____C_________UUCGG...AAC-3'\n______________GGU_GUUCU_GGUACAGUU\n______________\|\|\|_\|\|\|\|:_\|\|\|\|\|\|\|:\|\n______________CCA_CAAGG_CCAUGUCGA\n3'-UUU...UUCCU___C_____A_________UCGUA...UCG-5'\n_____________\|___________________\|\n_____________47__________________27\n	236 -- 242	28 -- 34	-23.9025 kcal/mol	5.49413 kcal/mol	4.3041 kcal/mol	223 243@LB@ \| \|@LB@5'-GAC...UACCU U C UUCGG...AAC-3'@LB@ GGU GUUCU GGUACAGUU@LB@ \|\|\| \|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CCA CAAGG CCAUGUCGA@LB@3'-UUU...UUCCU C A UCGUA...UCG-5'@LB@ \| \|@LB@ 47 27@LB@@LB@@LB@Energy -14.10 kcal/mol@LB@Hybridization Energy -23.9025 kcal/mol@LB@Unfolding Energy - mRNA 5.49413 kcal/mol@LB@Unfolding Energy - sRNA 4.3041 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 28 -- 46@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 28 -- 34@LB@
104	0.003825	0.1236	b0081	mraZ	-12.90	0.040525	169 -- 210	15 -- 49	RsmH methytransferase inhibitor	_____________168________________________________________211\n_____________\|__________________________________________\|\n5'-GAU...AUUGU____CAAA____GAAUAAGG____A_________GUUCC___GAGCA...AAA-3'\n______________GGGG____GUGG________GGUG_GGCUGGCAU_____GGG\n______________\|\|:\|____\|\|\|\|________\|\|\|:_:\|\|\|:\|\|\|\|_____\|\|\|\n______________CCUC____CACC________CCAU_UCGAUCGUA_____CCC\n3'-UUU...CGAUU____________AAGGA_______G_________AAAUA___AAUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________50_________________________________________14\n	196 -- 202	23 -- 29	-32.8076 kcal/mol	15.3299 kcal/mol	4.57366 kcal/mol	168 211@LB@ \| \|@LB@5'-GAU...AUUGU CAAA GAAUAAGG A GUUCC GAGCA...AAA-3'@LB@ GGGG GUGG GGUG GGCUGGCAU GGG@LB@ \|\|:\| \|\|\|\| \|\|\|: :\|\|\|:\|\|\|\| \|\|\|@LB@ CCUC CACC CCAU UCGAUCGUA CCC@LB@3'-UUU...CGAUU AAGGA G AAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -32.8076 kcal/mol@LB@Unfolding Energy - mRNA 15.3299 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 23 -- 29@LB@
180	0.01039	0.1919	b1778	msrB	-9.69	0.189810	88 -- 95	29 -- 36	methionine sulfoxide reductase B	_____________87_______96\n_____________\|________\|\n5'-CUU...AUUUA________CAUUU...GUC-3'\n______________GGUGCAGC\n______________\|\|\|:\|\|\|\|\n______________CCAUGUCG\n3'-UUU...AAGGA________AUCGU...UCG-5'\n_____________\|________\|\n_____________37_______28\n	89 -- 95	29 -- 35	-13.558 kcal/mol	2.69806 kcal/mol	1.16901 kcal/mol	87 96@LB@ \| \|@LB@5'-CUU...AUUUA CAUUU...GUC-3'@LB@ GGUGCAGC@LB@ \|\|\|:\|\|\|\|@LB@ CCAUGUCG@LB@3'-UUU...AAGGA AUCGU...UCG-5'@LB@ \| \|@LB@ 37 28@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -13.558 kcal/mol@LB@Unfolding Energy - mRNA 2.69806 kcal/mol@LB@Unfolding Energy - sRNA 1.16901 kcal/mol@LB@@LB@Position - mRNA 88 -- 95@LB@Position - sRNA 29 -- 36@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 29 -- 35@LB@
43	0.0008959	0.07003	b3068	mug	-12.52	0.050096	232 -- 248	1 -- 17	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________231_______________249\n_____________\|_________________\|\n5'-UGG...GUUAC____C_______G____AUCAA...CGG-3'\n______________GGGU_GUGUUUU_CGGU\n______________\|\|\|\|_:\|\|\|\|\|\|_\|:\|:\n______________CCCA_UACAAAA_GUCG\n3'-UUU...AAAUA____A_______A____-5'\n_____________\|________________\|\n_____________18_______________1\n	237 -- 243	6 -- 12	-17.5569 kcal/mol	4.10869 kcal/mol	0.931609 kcal/mol	231 249@LB@ \| \|@LB@5'-UGG...GUUAC C G AUCAA...CGG-3'@LB@ GGGU GUGUUUU CGGU@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|:@LB@ CCCA UACAAAA GUCG@LB@3'-UUU...AAAUA A A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -17.5569 kcal/mol@LB@Unfolding Energy - mRNA 4.10869 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 232 -- 248@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 6 -- 12@LB@
66	0.001771	0.09017	b0924	mukB	-12.08	0.063147	4 -- 24	1 -- 22	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________3______________________25\n_____________\|______________________\|\n________5'-UGG________CCACGACAG_____AAGUU...CUG-3'\n______________UUUAUGGG__________CAGC\n______________\|\|\|\|\|\|\|\|__________\|\|\|\|\n______________AAAUACCC__________GUCG\n3'-UUU...UCGUA________AAUACAAAAA____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	15 -- 21	-14.8798 kcal/mol	1.84387 kcal/mol	0.958674 kcal/mol	3 25@LB@ \| \|@LB@ 5'-UGG CCACGACAG AAGUU...CUG-3'@LB@ UUUAUGGG CAGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|@LB@ AAAUACCC GUCG@LB@3'-UUU...UCGUA AAUACAAAAA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -14.8798 kcal/mol@LB@Unfolding Energy - mRNA 1.84387 kcal/mol@LB@Unfolding Energy - sRNA 0.958674 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 15 -- 21@LB@
62	0.00164	0.08891	b0922	mukF	-17.51	0.001582	1 -- 30	14 -- 38	chromosome condensin MukBEF kleisin-like subunit binds calcium	______________1_____________________________31\n______________\|_____________________________\|\n___________5'-____AAGAA__U________AA________AAGAC...UGG-3'\n______________CUGG_____GC_GGUUGGCA__UUAUGGGU\n______________\|\|\|\|_____:\|_:\|:\|:\|\|\|__\|\|\|\|\|\|\|\|\n______________GACC_____UG_UCGAUCGU__AAUACCCA\n3'-UUU...CCAAG____A_______________AA________AUACA...UCG-5'\n_____________\|______________________________\|\n_____________39_____________________________13\n	24 -- 30	14 -- 20	-25.2653 kcal/mol	3.2564 kcal/mol	4.5012 kcal/mol	1 31@LB@ \| \|@LB@ 5'- AAGAA U AA AAGAC...UGG-3'@LB@ CUGG GC GGUUGGCA UUAUGGGU@LB@ \|\|\|\| :\| :\|:\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GACC UG UCGAUCGU AAUACCCA@LB@3'-UUU...CCAAG A AA AUACA...UCG-5'@LB@ \| \|@LB@ 39 13@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -25.2653 kcal/mol@LB@Unfolding Energy - mRNA 3.2564 kcal/mol@LB@Unfolding Energy - sRNA 4.5012 kcal/mol@LB@@LB@Position - mRNA 1 -- 30@LB@Position - sRNA 14 -- 38@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 14 -- 20@LB@
86	0.002806	0.1082	b1107	nagZ	-13.13	0.035629	98 -- 119	25 -- 47	beta N-acetyl-glucosaminidase	_____________97______________________120\n_____________\|_______________________\|\n5'-AUU...AAGCA_________GA_____C______GACAA...CGC-3'\n______________GGGUGGUUU___GUAC_GCUGGC\n______________:\|\|\|\|\|\|\|:___\|\|\|\|_\|\|\|:\|\|\n______________UCCACCAAG___CAUG_CGAUCG\n3'-UUU...AUUCC_________GAC____U______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	100 -- 106	39 -- 45	-29.3426 kcal/mol	11.6523 kcal/mol	4.55753 kcal/mol	97 120@LB@ \| \|@LB@5'-AUU...AAGCA GA C GACAA...CGC-3'@LB@ GGGUGGUUU GUAC GCUGGC@LB@ :\|\|\|\|\|\|\|: \|\|\|\| \|\|\|:\|\|@LB@ UCCACCAAG CAUG CGAUCG@LB@3'-UUU...AUUCC GAC U UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -29.3426 kcal/mol@LB@Unfolding Energy - mRNA 11.6523 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 98 -- 119@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 39 -- 45@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