Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein		_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
91	0.01869	0.6177	b3432	glgB	-9.43	0.053684	93 -- 103	45 -- 56	1 4-alpha-glucan branching enzyme		_____________92___________104\n_____________\|____________\|\n5'-CAU...GACGA____________UGCAC...GAC-3'\n______________CG_CAGAGAGGA\n______________\|\|_\|\|:\|\|\|\|\|\|\n______________GC_GUUUCUCCU\n3'-UUU...ACCGG__A_________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	97 -- 103	45 -- 51	-14.5586 kcal/mol	4.18817 kcal/mol	0.938337 kcal/mol	92 104@LB@ \| \|@LB@5'-CAU...GACGA UGCAC...GAC-3'@LB@ CG CAGAGAGGA@LB@ \|\| \|\|:\|\|\|\|\|\|@LB@ GC GUUUCUCCU@LB@3'-UUU...ACCGG A UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -14.5586 kcal/mol@LB@Unfolding Energy - mRNA 4.18817 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 93 -- 103@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 45 -- 51@LB@
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
98	0.0193	0.6177	b2705	srlD	-10.75	0.028892	101 -- 114	40 -- 53	sorbitol-6-phosphate dehydrogenase		_____________100____________115\n_____________\|______________\|\n5'-CAC...UUAAA_____C________CGGGC...AUA-3'\n______________CGAAG_GGAAUUUC\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________GUUUC_CCUUAAAG\n3'-UUU...GGGCA_____U________UAAAA...ACA-5'\n_____________\|______________\|\n_____________54_____________39\n	108 -- 114	40 -- 46	-15.1517 kcal/mol	3.39572 kcal/mol	1.00568 kcal/mol	100 115@LB@ \| \|@LB@5'-CAC...UUAAA C CGGGC...AUA-3'@LB@ CGAAG GGAAUUUC@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUUC CCUUAAAG@LB@3'-UUU...GGGCA U UAAAA...ACA-5'@LB@ \| \|@LB@ 54 39@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.1517 kcal/mol@LB@Unfolding Energy - mRNA 3.39572 kcal/mol@LB@Unfolding Energy - sRNA 1.00568 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 40 -- 53@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 40 -- 46@LB@
159	0.0318	0.6177	b2532	trmJ	-7.64	0.122614	101 -- 114	44 -- 55	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________100____________115\n_____________\|______________\|\n5'-CGU...UGGAU________AC____AAACG...UGU-3'\n______________GUUAAAGA__GGGA\n______________\|\|:\|\|\|\|\|__\|\|:\|\n______________CAGUUUCU__CCUU\n3'-UUU...CCGGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________56_____________43\n	102 -- 108	48 -- 54	-10.9175 kcal/mol	2.33739 kcal/mol	0.941432 kcal/mol	100 115@LB@ \| \|@LB@5'-CGU...UGGAU AC AAACG...UGU-3'@LB@ GUUAAAGA GGGA@LB@ \|\|:\|\|\|\|\| \|\|:\|@LB@ CAGUUUCU CCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -10.9175 kcal/mol@LB@Unfolding Energy - mRNA 2.33739 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 48 -- 54@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase		_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
113	0.02257	0.6177	b0915	lpxK	-7.55	0.127690	105 -- 116	46 -- 56	lipid A 4'kinase		_____________104__________117\n_____________\|____________\|\n5'-GAA...GUGGU_________U__UGUCA...GCU-3'\n______________CGUCGAGGA_GG\n______________\|\|\|\|:\|:\|\|_\|\|\n______________GCAGUUUCU_CC\n3'-UUU...ACCGG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________57___________45\n	107 -- 113	48 -- 54	-12.734 kcal/mol	4.25329 kcal/mol	0.93204 kcal/mol	104 117@LB@ \| \|@LB@5'-GAA...GUGGU U UGUCA...GCU-3'@LB@ CGUCGAGGA GG@LB@ \|\|\|\|:\|:\|\| \|\|@LB@ GCAGUUUCU CC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -7.55 kcal/mol@LB@Hybridization Energy -12.734 kcal/mol@LB@Unfolding Energy - mRNA 4.25329 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 105 -- 116@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@LB@
194	0.04051	0.6177	b0814	ompX	-6.96	0.165642	107 -- 118	50 -- 61	outer membrane protein X		_____________106__________119\n_____________\|____________\|\n5'-CUG...UGAAA____________CAUCA...CAC-3'\n______________UGGCCCGUUAGA\n______________\|\|\|\|\|\|\|\|:\|:\|\n______________ACCGGGCAGUUU\n3'-UUU...CGAUA____________CUCCU...ACA-5'\n_____________\|____________\|\n_____________62___________49\n	111 -- 117	51 -- 57	-20.1081 kcal/mol	2.98628 kcal/mol	10.1573 kcal/mol	106 119@LB@ \| \|@LB@5'-CUG...UGAAA CAUCA...CAC-3'@LB@ UGGCCCGUUAGA@LB@ \|\|\|\|\|\|\|\|:\|:\|@LB@ ACCGGGCAGUUU@LB@3'-UUU...CGAUA CUCCU...ACA-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -20.1081 kcal/mol@LB@Unfolding Energy - mRNA 2.98628 kcal/mol@LB@Unfolding Energy - sRNA 10.1573 kcal/mol@LB@@LB@Position - mRNA 107 -- 118@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 51 -- 57@LB@
62	0.01306	0.6177	b4034	malE	-9.62	0.049140	112 -- 120	45 -- 53	maltose transporter subunit		_____________111_______121\n_____________\|_________\|\n5'-AGG...AGGGG_________UGGAA...UGG-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	114 -- 120	45 -- 51	-12.5673 kcal/mol	2.02865 kcal/mol	0.917553 kcal/mol	111 121@LB@ \| \|@LB@5'-AGG...AGGGG UGGAA...UGG-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -12.5673 kcal/mol@LB@Unfolding Energy - mRNA 2.02865 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 112 -- 120@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 45 -- 51@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB		_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@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