Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
142	0.02338	0.5385	b1126	potA	-10.56	0.084569	277 -- 295	14 -- 34	spermidine/putrescine ABC transporter ATPase	_____________276___________________296\n_____________\|_____________________\|\n5'-CAA...CAAAU_______U_____________CAUUC-3'\n______________GCUUUGA_GGU__AAAGAGGU\n______________:\|\|\|::\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________UGAAGUU_CCA__UUUCUCCA\n3'-CGC...GUCAC_______C___AU________CGGCG...AAG-5'\n_____________\|_____________________\|\n_____________35____________________13\n	289 -- 295	14 -- 20	-18.1028 kcal/mol	4.21038 kcal/mol	3.33169 kcal/mol	276 296@LB@ \| \|@LB@5'-CAA...CAAAU U CAUUC-3'@LB@ GCUUUGA GGU AAAGAGGU@LB@ :\|\|\|::\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAAGUU CCA UUUCUCCA@LB@3'-CGC...GUCAC C AU CGGCG...AAG-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -18.1028 kcal/mol@LB@Unfolding Energy - mRNA 4.21038 kcal/mol@LB@Unfolding Energy - sRNA 3.33169 kcal/mol@LB@@LB@Position - mRNA 277 -- 295@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 14 -- 20@LB@
38	0.006978	0.5385	b3738	atpB	-10.53	0.085759	128 -- 143	69 -- 84	F0 sector of membrane-bound ATP synthase subunit a	_____________127______________144\n_____________\|________________\|\n5'-CAU...GAUCG______G_________GCUGG...ACC-3'\n______________UUACGU_GGUUUUGGU\n______________\|:\|\|\|\|_\|\|:\|\|\|:\|\|\n______________AGUGCA_CCGAAAUCA\n3'-CGC...UUUCA______A_________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	137 -- 143	69 -- 75	-16.8893 kcal/mol	5.79988 kcal/mol	0.563592 kcal/mol	127 144@LB@ \| \|@LB@5'-CAU...GAUCG G GCUGG...ACC-3'@LB@ UUACGU GGUUUUGGU@LB@ \|:\|\|\|\| \|\|:\|\|\|:\|\|@LB@ AGUGCA CCGAAAUCA@LB@3'-CGC...UUUCA A AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -16.8893 kcal/mol@LB@Unfolding Energy - mRNA 5.79988 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 128 -- 143@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 69 -- 75@LB@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@LB@
63	0.01271	0.5385	b3306	rpsH	-10.49	0.086924	89 -- 100	56 -- 67	30S ribosomal subunit protein S8	_____________88___________101\n_____________\|____________\|\n5'-AGC...CGGAA____________CCGUA...AAG-3'\n______________GUUCGGGUUGAG\n______________:\|\|\|\|:\|\|\|\|\|\|\n______________UAAGCUCAACUC\n3'-CGC...AUCAA____________UUUGA...AAG-5'\n_____________\|____________\|\n_____________68___________55\n	94 -- 100	56 -- 62	-16.8063 kcal/mol	4.74141 kcal/mol	1.57281 kcal/mol	88 101@LB@ \| \|@LB@5'-AGC...CGGAA CCGUA...AAG-3'@LB@ GUUCGGGUUGAG@LB@ :\|\|\|\|:\|\|\|\|\|\|@LB@ UAAGCUCAACUC@LB@3'-CGC...AUCAA UUUGA...AAG-5'@LB@ \| \|@LB@ 68 55@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -16.8063 kcal/mol@LB@Unfolding Energy - mRNA 4.74141 kcal/mol@LB@Unfolding Energy - sRNA 1.57281 kcal/mol@LB@@LB@Position - mRNA 89 -- 100@LB@Position - sRNA 56 -- 67@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 56 -- 62@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@LB@
16	0.002981	0.5385	b3428	glgP	-10.45	0.088230	278 -- 289	76 -- 86	glycogen phosphorylase	_____________277__________290\n_____________\|____________\|\n5'-CCA...CUGAU_______A____AAAGG...CGG-3'\n______________GUUUACG_UUGG\n______________\|\|\|:\|\|\|_\|\|\|\|\n______________CAAGUGC_AACC\n3'-CGC...GUUUU____________GAAAU...AAG-5'\n_____________\|____________\|\n_____________87___________75\n	278 -- 284	80 -- 86	-12.981 kcal/mol	2.0211 kcal/mol	0.505081 kcal/mol	277 290@LB@ \| \|@LB@5'-CCA...CUGAU A AAAGG...CGG-3'@LB@ GUUUACG UUGG@LB@ \|\|\|:\|\|\| \|\|\|\|@LB@ CAAGUGC AACC@LB@3'-CGC...GUUUU GAAAU...AAG-5'@LB@ \| \|@LB@ 87 75@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -12.981 kcal/mol@LB@Unfolding Energy - mRNA 2.0211 kcal/mol@LB@Unfolding Energy - sRNA 0.505081 kcal/mol@LB@@LB@Position - mRNA 278 -- 289@LB@Position - sRNA 76 -- 86@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 80 -- 86@LB@
147	0.02477	0.5467	b3259	prmA	-10.37	0.091190	111 -- 125	72 -- 88	methyltransferase for 50S ribosomal subunit protein L11	_____________110_______________126\n_____________\|_________________\|\n5'-GCC...CUACU_________________CCUGG...AGG-3'\n______________AAGUUUGC__UGGCUUU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\|\|\n______________UUCAAGUG__ACCGAAA\n3'-CGC...GCGUU________CA_______UCAAU...AAG-5'\n_____________\|_________________\|\n_____________89________________71\n	119 -- 125	72 -- 78	-14.8408 kcal/mol	3.95141 kcal/mol	0.517175 kcal/mol	110 126@LB@ \| \|@LB@5'-GCC...CUACU CCUGG...AGG-3'@LB@ AAGUUUGC UGGCUUU@LB@ \|\|\|\|\|::\| \|\|\|\|\|\|\|@LB@ UUCAAGUG ACCGAAA@LB@3'-CGC...GCGUU CA UCAAU...AAG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -14.8408 kcal/mol@LB@Unfolding Energy - mRNA 3.95141 kcal/mol@LB@Unfolding Energy - sRNA 0.517175 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 72 -- 78@LB@
36	0.006672	0.5385	b3956	ppc	-10.31	0.093393	270 -- 282	76 -- 88	phosphoenolpyruvate carboxylase	_____________269___________283\n_____________\|_____________\|\n5'-CUU...CCAUC___GA________GAGAA...AAC-3'\n______________AAG__UGCGUUGG\n______________\|\|\|__::\|\|\|\|\|\|\n______________UUC__GUGCAACC\n3'-CGC...GCGUU___AA________GAAAU...AAG-5'\n_____________\|_____________\|\n_____________89____________75\n	276 -- 282	76 -- 82	-12.0501 kcal/mol	1.22517 kcal/mol	0.512479 kcal/mol	269 283@LB@ \| \|@LB@5'-CUU...CCAUC GA GAGAA...AAC-3'@LB@ AAG UGCGUUGG@LB@ \|\|\| ::\|\|\|\|\|\|@LB@ UUC GUGCAACC@LB@3'-CGC...GCGUU AA GAAAU...AAG-5'@LB@ \| \|@LB@ 89 75@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -12.0501 kcal/mol@LB@Unfolding Energy - mRNA 1.22517 kcal/mol@LB@Unfolding Energy - sRNA 0.512479 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 76 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 76 -- 82@LB@
195	0.03428	0.5559	b0434	yajG	-10.30	0.093744	131 -- 149	66 -- 84	putative lipoprotein	_____________130__________________150\n_____________\|____________________\|\n5'-UGG...UCCCC___C_______AAU______GAUGG...UGC-3'\n______________UCG_CGUUGGC____GUUAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AGU_GCAACCG____CAAUA\n3'-CGC...UUUCA___________AAAU_____AGCUC...AAG-5'\n_____________\|____________________\|\n_____________85___________________65\n	135 -- 141	75 -- 81	-17.0927 kcal/mol	6.21917 kcal/mol	0.5705 kcal/mol	130 150@LB@ \| \|@LB@5'-UGG...UCCCC C AAU GAUGG...UGC-3'@LB@ UCG CGUUGGC GUUAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AGU GCAACCG CAAUA@LB@3'-CGC...UUUCA AAAU AGCUC...AAG-5'@LB@ \| \|@LB@ 85 65@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -17.0927 kcal/mol@LB@Unfolding Energy - mRNA 6.21917 kcal/mol@LB@Unfolding Energy - sRNA 0.5705 kcal/mol@LB@@LB@Position - mRNA 131 -- 149@LB@Position - sRNA 66 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 75 -- 81@LB@
47	0.009854	0.5385	b3408	feoA	-10.27	0.095129	159 -- 188	52 -- 83	ferrous iron transporter protein A	_____________158_________________________________189\n_____________\|___________________________________\|\n5'-AGC...CGCCC____A_______________C___UAA________AAGUA...CUG-3'\n______________CAUG__GGU___AGUUA_UC_AGU___UGAGAAAC\n______________\|\|:\|__\|\|:___\|\|\|\|\|_\|\|_\|\|\|___\|\|\|\|\|\|\|\|\n______________GUGC__CCG___UCAAU_AG_UCA___ACUCUUUG\n3'-CGC...UUCAA____AA___AAA_____A__C______________AGAGC...AAG-5'\n_____________\|___________________________________\|\n_____________84__________________________________51\n	182 -- 188	52 -- 58	-20.9255 kcal/mol	6.25891 kcal/mol	4.4004 kcal/mol	158 189@LB@ \| \|@LB@5'-AGC...CGCCC A C UAA AAGUA...CUG-3'@LB@ CAUG GGU AGUUA UC AGU UGAGAAAC@LB@ \|\|:\| \|\|: \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUGC CCG UCAAU AG UCA ACUCUUUG@LB@3'-CGC...UUCAA AA AAA A C AGAGC...AAG-5'@LB@ \| \|@LB@ 84 51@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -20.9255 kcal/mol@LB@Unfolding Energy - mRNA 6.25891 kcal/mol@LB@Unfolding Energy - sRNA 4.4004 kcal/mol@LB@@LB@Position - mRNA 159 -- 188@LB@Position - sRNA 52 -- 83@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 52 -- 58@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