Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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	Additional homologs
48	0.001595	0.1153	b4567	yjjZ	-9.54	0.291590	92 -- 131	37 -- 74	uncharacterized protein		_____________91_______________________________________132\n_____________\|________________________________________\|\n5'-CGG...UGAUU____AU_________AG___UACC__AUAG__A_______AUCUG...GGA-3'\n______________GCUA__CAUAGCGAU__GUU____CG____CA_GGGAUUU\n______________:\|\|\|__\|\|:\|\|\|:\|\|__\|\|\|____\|:____\|\|_\|\|\|\|\|\|\|\n______________UGAU__GUGUCGUUA__CAA____GU____GU_CCCUAAA\n3'-UUU...GUUUC____GU_________AG___CAAA__GA____C_______GGUAC...GCA-5'\n_____________\|________________________________________\|\n_____________75_______________________________________36\n	125 -- 131	37 -- 43	-26.8907 kcal/mol	12.5776 kcal/mol	4.77887 kcal/mol	91 132@LB@ \| \|@LB@5'-CGG...UGAUU AU AG UACC AUAG A AUCUG...GGA-3'@LB@ GCUA CAUAGCGAU GUU CG CA GGGAUUU@LB@ :\|\|\| \|\|:\|\|\|:\|\| \|\|\| \|: \|\| \|\|\|\|\|\|\|@LB@ UGAU GUGUCGUUA CAA GU GU CCCUAAA@LB@3'-UUU...GUUUC GU AG CAAA GA C GGUAC...GCA-5'@LB@ \| \|@LB@ 75 36@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -26.8907 kcal/mol@LB@Unfolding Energy - mRNA 12.5776 kcal/mol@LB@Unfolding Energy - sRNA 4.77887 kcal/mol@LB@@LB@Position - mRNA 92 -- 131@LB@Position - sRNA 37 -- 74@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 37 -- 43@LB@
156	0.007591	0.1668	b1044	ymdA	-16.39	0.008687	226 -- 252	46 -- 73	uncharacterized protein		_____________225__________________________253\n_____________\|____________________________\|\n5'-UGA...CUCUC______U____________U________UUAUU...UUU-3'\n______________UUAUGC_CGGCAGUUUGUU_UUUC_CUU\n______________:\|\|::\|_\|:\|\|\|:\|\|:\|\|\|_\|\|\|\|_\|\|:\n______________GAUGUG_GUCGUUAAGCAA_AAAG_GAG\n3'-UUU...UUUCU______U____________C____U___UCCCC...GCA-5'\n_____________\|____________________________\|\n_____________74___________________________45\n	236 -- 242	57 -- 63	-24.6333 kcal/mol	4.51706 kcal/mol	3.72492 kcal/mol	225 253@LB@ \| \|@LB@5'-UGA...CUCUC U U UUAUU...UUU-3'@LB@ UUAUGC CGGCAGUUUGUU UUUC CUU@LB@ :\|\|::\| \|:\|\|\|:\|\|:\|\|\| \|\|\|\| \|\|:@LB@ GAUGUG GUCGUUAAGCAA AAAG GAG@LB@3'-UUU...UUUCU U C U UCCCC...GCA-5'@LB@ \| \|@LB@ 74 45@LB@@LB@@LB@Energy -16.39 kcal/mol@LB@Hybridization Energy -24.6333 kcal/mol@LB@Unfolding Energy - mRNA 4.51706 kcal/mol@LB@Unfolding Energy - sRNA 3.72492 kcal/mol@LB@@LB@Position - mRNA 226 -- 252@LB@Position - sRNA 46 -- 73@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 57 -- 63@LB@
100	0.004525	0.1538	b2550	yphH	-8.03	0.477033	31 -- 47	39 -- 54	putative DNA-binding transcriptional regulator		_____________30_________________48\n_____________\|__________________\|\n5'-AGG...GCCCG_______A___UC_____CUCAA...UGG-3'\n______________GUUUCAU__GG__GGGAU\n______________\|\|\|\|\|\|:__:\|__\|\|\|\|\|\n______________CAAAGUG__UC__CCCUA\n3'-UUU...AGCAA_______AG_________AAGGU...GCA-5'\n_____________\|__________________\|\n_____________55_________________38\n	31 -- 37	48 -- 54	-12.873 kcal/mol	2.94673 kcal/mol	1.89674 kcal/mol	30 48@LB@ \| \|@LB@5'-AGG...GCCCG A UC CUCAA...UGG-3'@LB@ GUUUCAU GG GGGAU@LB@ \|\|\|\|\|\|: :\| \|\|\|\|\|@LB@ CAAAGUG UC CCCUA@LB@3'-UUU...AGCAA AG AAGGU...GCA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -8.03 kcal/mol@LB@Hybridization Energy -12.873 kcal/mol@LB@Unfolding Energy - mRNA 2.94673 kcal/mol@LB@Unfolding Energy - sRNA 1.89674 kcal/mol@LB@@LB@Position - mRNA 31 -- 47@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 48 -- 54@LB@
144	0.006569	0.1605	b2900	yqfB	-12.46	0.083290	200 -- 238	34 -- 70	UPF0267 family protein		_____________199_______________________________________239\n_____________\|_________________________________________\|\n5'-UUC...AGUAC________CAAA__ACA________UUUUUCAAC_______GGAUG...UCA-3'\n______________CAUGCAGC____CG_____UCACUU_________GUUUCCA\n______________\|\|::\|\|\|\|____\|\|_____\|\|\|\|\|:_________:\|\|\|\|\|\|\n______________GUGUGUCG____GC_____AGUGAG_________UAAAGGU\n3'-UUU...CUGAU________UUAA__AACAA______UCCCC___________ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________71________________________________________33\n	232 -- 238	34 -- 40	-21.1736 kcal/mol	3.92715 kcal/mol	4.79237 kcal/mol	199 239@LB@ \| \|@LB@5'-UUC...AGUAC CAAA ACA UUUUUCAAC GGAUG...UCA-3'@LB@ CAUGCAGC CG UCACUU GUUUCCA@LB@ \|\|::\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|@LB@ GUGUGUCG GC AGUGAG UAAAGGU@LB@3'-UUU...CUGAU UUAA AACAA UCCCC ACGAA...GCA-5'@LB@ \| \|@LB@ 71 33@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.1736 kcal/mol@LB@Unfolding Energy - mRNA 3.92715 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 200 -- 238@LB@Position - sRNA 34 -- 70@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 34 -- 40@LB@
80	0.003376	0.1462	b3098	yqjD	-10.12	0.233597	155 -- 204	31 -- 75	membrane-anchored ribosome-binding protein		_____________154_________________________________________________205\n_____________\|___________________________________________________\|\n5'-UCA...CGCGC______UA__UCA____A___CACUAC_______CCU__A__AAA______CGAAA...AAG-3'\n______________GACUAC__AC___CAAU__GU______UUACUCA___GG_GA___CUAUGU\n______________\|\|\|\|\|\|__\|\|___\|\|\|\|__\|\|______\|:\|\|\|\|\|___\|\|_\|\|___\|:\|\|\|:\n______________CUGAUG__UG___GUUA__CA______AGUGAGU___CC_CU___GGUACG\n3'-UUU...CGUUU______UG__UC_____AG__ACAA_________C_______AAA______AAUAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________76__________________________________________________30\n	181 -- 187	45 -- 51	-24.4421 kcal/mol	7.05998 kcal/mol	7.26183 kcal/mol	154 205@LB@ \| \|@LB@5'-UCA...CGCGC UA UCA A CACUAC CCU A AAA CGAAA...AAG-3'@LB@ GACUAC AC CAAU GU UUACUCA GG GA CUAUGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\| \|:\|\|\|\|\| \|\| \|\| \|:\|\|\|:@LB@ CUGAUG UG GUUA CA AGUGAGU CC CU GGUACG@LB@3'-UUU...CGUUU UG UC AG ACAA C AAA AAUAU...GCA-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -24.4421 kcal/mol@LB@Unfolding Energy - mRNA 7.05998 kcal/mol@LB@Unfolding Energy - sRNA 7.26183 kcal/mol@LB@@LB@Position - mRNA 155 -- 204@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 45 -- 51@LB@
122	0.005462	0.1553	b3143	yraI	-10.36	0.212908	69 -- 81	40 -- 51	putative periplasmic pilin chaperone	b0939 b4316 b0531	_____________68____________82\n_____________\|_____________\|\n5'-GGA...AGAAA____CC_______AGCAG...UGA-3'\n______________UCAC__CAGGGGA\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________AGUG__GUCCCCU\n3'-UUU...AACAA____A________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	75 -- 81	40 -- 46	-16.6795 kcal/mol	4.56539 kcal/mol	1.76028 kcal/mol	68 82@LB@ \| \|@LB@5'-GGA...AGAAA CC AGCAG...UGA-3'@LB@ UCAC CAGGGGA@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG GUCCCCU@LB@3'-UUU...AACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.6795 kcal/mol@LB@Unfolding Energy - mRNA 4.56539 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 40 -- 46@LB@
90	0.004009	0.1538	b3152	yraR	-13.99	0.037452	47 -- 72	45 -- 75	putative nucleoside-diphosphate-sugar epimerase		_____________46______________________________73\n_____________\|_______________________________\|\n5'-ACU...UCAGU_____AA___________UC___________UGCUU...CGA-3'\n______________GAUUA___ACGGCAAUUU______UUACUCA\n______________\|\|:\|\|___\|\|:\|\|\|\|\|\|:______\|:\|\|\|\|\|\n______________CUGAU___UGUCGUUAAG______AGUGAGU\n3'-UUU...CGUUU_____GUG__________CAACAA_______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	66 -- 72	45 -- 51	-19.6514 kcal/mol	1.92306 kcal/mol	3.74078 kcal/mol	46 73@LB@ \| \|@LB@5'-ACU...UCAGU AA UC UGCUU...CGA-3'@LB@ GAUUA ACGGCAAUUU UUACUCA@LB@ \|\|:\|\| \|\|:\|\|\|\|\|\|: \|:\|\|\|\|\|@LB@ CUGAU UGUCGUUAAG AGUGAGU@LB@3'-UUU...CGUUU GUG CAACAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -19.6514 kcal/mol@LB@Unfolding Energy - mRNA 1.92306 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 47 -- 72@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 45 -- 51@LB@
37	0.0006599	0.0618	b3399	yrfG	-16.99	0.005777	176 -- 197	35 -- 56	GMP/IMP nucleotidase		_____________175____________________198\n_____________\|______________________\|\n5'-UAG...GCAAA___C_______U__A_______CUCAU...AGC-3'\n______________UUG_UUCACUC_GG_GAUUUCC\n______________\|\|\|_\|\|\|\|\|\|\|_\|\|_\|\|\|\|\|\|\|\n______________AAC_AAGUGAG_CC_CUAAAGG\n3'-UUU...UAAGC___A_______U__C_______UACGA...GCA-5'\n_____________\|______________________\|\n_____________57_____________________34\n	191 -- 197	35 -- 41	-24.095 kcal/mol	5.08619 kcal/mol	2.02101 kcal/mol	175 198@LB@ \| \|@LB@5'-UAG...GCAAA C U A CUCAU...AGC-3'@LB@ UUG UUCACUC GG GAUUUCC@LB@ \|\|\| \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ AAC AAGUGAG CC CUAAAGG@LB@3'-UUU...UAAGC A U C UACGA...GCA-5'@LB@ \| \|@LB@ 57 34@LB@@LB@@LB@Energy -16.99 kcal/mol@LB@Hybridization Energy -24.095 kcal/mol@LB@Unfolding Energy - mRNA 5.08619 kcal/mol@LB@Unfolding Energy - sRNA 2.02101 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 35 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 35 -- 41@LB@
171	0.008374	0.1723	b4485	ytfR	-15.31	0.017344	177 -- 203	32 -- 71	putative sugar ABC transporter ATPase		_____________176_______________________________________204\n_____________\|_________________________________________\|\n5'-CCU...UGGGA_____________________A___________AA______ACGAC...GCC-3'\n______________GCACGC____________UUU_CAC_CGGGGGA___CCAUG\n______________:\|\|\|:\|____________\|\|\|_\|\|\|_\|:\|\|\|\|\|___\|\|\|\|\|\n______________UGUGUG____________AAA_GUG_GUCCCCU___GGUAC\n3'-UUU...UCUGA______UCGUUAAGCAAC_______A_______AAA_____GAAUA...GCA-5'\n_____________\|_________________________________________\|\n_____________72________________________________________31\n	190 -- 196	40 -- 46	-27.8319 kcal/mol	5.2959 kcal/mol	7.22604 kcal/mol	176 204@LB@ \| \|@LB@5'-CCU...UGGGA A AA ACGAC...GCC-3'@LB@ GCACGC UUU CAC CGGGGGA CCAUG@LB@ :\|\|\|:\| \|\|\| \|\|\| \|:\|\|\|\|\| \|\|\|\|\|@LB@ UGUGUG AAA GUG GUCCCCU GGUAC@LB@3'-UUU...UCUGA UCGUUAAGCAAC A AAA GAAUA...GCA-5'@LB@ \| \|@LB@ 72 31@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.8319 kcal/mol@LB@Unfolding Energy - mRNA 5.2959 kcal/mol@LB@Unfolding Energy - sRNA 7.22604 kcal/mol@LB@@LB@Position - mRNA 177 -- 203@LB@Position - sRNA 32 -- 71@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
172	0.008479	0.1735	b4395	ytjC	-10.99	0.163500	244 -- 268	34 -- 71	phosphatase		_____________243____________________________________269\n_____________\|______________________________________\|\n5'-UCC...GUGGA____CG________________________________GUCUG...AGC-3'\n______________ACGC__AGCGA__CGU______AUUCAGGG_____CCA\n______________\|\|:\|__\|\|\|:\|__\|\|\|______\|:\|\|\|\|\|\|_____\|\|\|\n______________UGUG__UCGUU__GCA______UGAGUCCC_____GGU\n3'-UUU...UCUGA____UG_____AA___ACAAAG________CUAAA___ACGAA...GCA-5'\n_____________\|______________________________________\|\n_____________72_____________________________________33\n	259 -- 265	42 -- 48	-22.1302 kcal/mol	6.3498 kcal/mol	4.79237 kcal/mol	243 269@LB@ \| \|@LB@5'-UCC...GUGGA CG GUCUG...AGC-3'@LB@ ACGC AGCGA CGU AUUCAGGG CCA@LB@ \|\|:\| \|\|\|:\| \|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UGUG UCGUU GCA UGAGUCCC GGU@LB@3'-UUU...UCUGA UG AA ACAAAG CUAAA ACGAA...GCA-5'@LB@ \| \|@LB@ 72 33@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -22.1302 kcal/mol@LB@Unfolding Energy - mRNA 6.3498 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 244 -- 268@LB@Position - sRNA 34 -- 71@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@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