Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
41	0.004182	0.3349	b3771	ilvD	-12.17	0.033695	175 -- 200	14 -- 53	dihydroxyacid dehydratase	_____________174______________________________________201\n_____________\|________________________________________\|\n5'-GCG...UUACG_________C_________________GA___________AUGCC...GUA-3'\n______________AGACAGACA_______________UGG__GUAAAUAAAGU\n______________\|:\|\|\|\|\|\|\|_______________:\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________UUUGUCUGU_______________GCC__UAUUUAUUUCA\n3'-UUU...CCCCA_________AAGUCUUUACUUACU___AU___________AUUAC...UCG-5'\n_____________\|________________________________________\|\n_____________54_______________________________________13\n	194 -- 200	14 -- 20	-22.054 kcal/mol	3.56189 kcal/mol	6.32552 kcal/mol	174 201@LB@ \| \|@LB@5'-GCG...UUACG C GA AUGCC...GUA-3'@LB@ AGACAGACA UGG GUAAAUAAAGU@LB@ \|:\|\|\|\|\|\|\| :\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ UUUGUCUGU GCC UAUUUAUUUCA@LB@3'-UUU...CCCCA AAGUCUUUACUUACU AU AUUAC...UCG-5'@LB@ \| \|@LB@ 54 13@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -22.054 kcal/mol@LB@Unfolding Energy - mRNA 3.56189 kcal/mol@LB@Unfolding Energy - sRNA 6.32552 kcal/mol@LB@@LB@Position - mRNA 175 -- 200@LB@Position - sRNA 14 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 14 -- 20@LB@
42	0.004307	0.3367	b4051	qorA	-12.29	0.031673	118 -- 140	3 -- 26	quinone oxidoreductase NADPH-dependent	_____________117______________________141\n_____________\|________________________\|\n5'-CGC...UGCCA_______________CC_______AAGAA...UCG-3'\n______________UAGUGAAUGGAGUUA__GA_GAUA\n______________\|\|:\|:\|\|\|::\|\|\|\|\|__\|\|_\|\|\|\|\n______________AUUAUUUAUUUCAAU__CU_CUAU\n3'-UUU...CUGCC_______________UA__A____CG-5'\n_____________\|________________________\|\n_____________27_______________________2\n	126 -- 132	12 -- 18	-16.4059 kcal/mol	3.53962 kcal/mol	0.580109 kcal/mol	117 141@LB@ \| \|@LB@5'-CGC...UGCCA CC AAGAA...UCG-3'@LB@ UAGUGAAUGGAGUUA GA GAUA@LB@ \|\|:\|:\|\|\|::\|\|\|\|\| \|\| \|\|\|\|@LB@ AUUAUUUAUUUCAAU CU CUAU@LB@3'-UUU...CUGCC UA A CG-5'@LB@ \| \|@LB@ 27 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -16.4059 kcal/mol@LB@Unfolding Energy - mRNA 3.53962 kcal/mol@LB@Unfolding Energy - sRNA 0.580109 kcal/mol@LB@@LB@Position - mRNA 118 -- 140@LB@Position - sRNA 3 -- 26@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 12 -- 18@LB@
43	0.004693	0.3568	b1395	paaH	-8.91	0.157263	246 -- 258	49 -- 61	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________245___________259\n_____________\|_____________\|\n5'-GGC...GCACC_______C_____UUGCU...UGU-3'\n______________AUGGGGG_AGGCA\n______________\|\|:\|\|\|\|_\|::\|\|\n______________UAUCCCC_UUUGU\n3'-UUU...AACUU_______A_____CUGUA...UCG-5'\n_____________\|_____________\|\n_____________62____________48\n	246 -- 252	55 -- 61	-14.1165 kcal/mol	4.46726 kcal/mol	0.738192 kcal/mol	245 259@LB@ \| \|@LB@5'-GGC...GCACC C UUGCU...UGU-3'@LB@ AUGGGGG AGGCA@LB@ \|\|:\|\|\|\| \|::\|\|@LB@ UAUCCCC UUUGU@LB@3'-UUU...AACUU A CUGUA...UCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -14.1165 kcal/mol@LB@Unfolding Energy - mRNA 4.46726 kcal/mol@LB@Unfolding Energy - sRNA 0.738192 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 55 -- 61@LB@
44	0.004782	0.3568	b3243	aaeR	-11.65	0.043804	4 -- 44	1 -- 57	transcriptional regulator for aaeXAB operon	_____________3_________________________________________________________45\n_____________\|_________________________________________________________\|\n________5'-AAC_________________UGU____CCU_____U_____G__________________AGGCG...UCA-3'\n______________GGG_AAACAGAC__UCA____UGA____UGGU_GUAAA_AGAG___________AGC\n______________\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|____\|\|\|____:\|\|\|_:\|\|\|\|_\|:\|\|___________\|\|\|\n______________CCC_UUUGUCUG__AGU____ACU____GCCA_UAUUU_UUUC___________UCG\n3'-UUU...UUAUC___A________UA___CUUU___UACU____U_____A____AAUUACUACUA___-5'\n_____________\|________________________________________________________\|\n_____________58_______________________________________________________1\n	8 -- 14	46 -- 52	-26.9604 kcal/mol	8.9713 kcal/mol	6.33758 kcal/mol	3 45@LB@ \| \|@LB@ 5'-AAC UGU CCU U G AGGCG...UCA-3'@LB@ GGG AAACAGAC UCA UGA UGGU GUAAA AGAG AGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\| :\|\|\|\| \|:\|\| \|\|\|@LB@ CCC UUUGUCUG AGU ACU GCCA UAUUU UUUC UCG@LB@3'-UUU...UUAUC A UA CUUU UACU U A AAUUACUACUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -26.9604 kcal/mol@LB@Unfolding Energy - mRNA 8.9713 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 4 -- 44@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 46 -- 52@LB@
45	0.005107	0.3601	b0435	bolA	-10.01	0.096403	160 -- 209	3 -- 59	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________159________________________________________________________210\n_____________\|__________________________________________________________\|\n5'-UGA...UUUAA____A___________C____CGU______U___AGG______UUUC___________CGUGA...CCG-3'\n______________AGGG_UGGAU_GACAU_UCAG_______UG_CGG____AGAUA______AUGAUGAUA\n______________\|\|\|\|_\|::\|:_\|\|\|\|\|_\|\|\|\|_______\|\|_\|\|\|____\|:\|\|\|______\|\|\|\|\|\|\|\|\|\n______________UCCC_AUUUG_CUGUA_AGUC_______AC_GCC____UUUAU______UACUACUAU\n3'-UUU...CUUUA____C_____U__________UUUACUU__U___AUUA_____UUCAAU_________CG-5'\n_____________\|__________________________________________________________\|\n_____________60_________________________________________________________2\n	203 -- 209	3 -- 9	-31.3101 kcal/mol	14.9582 kcal/mol	6.33762 kcal/mol	159 210@LB@ \| \|@LB@5'-UGA...UUUAA A C CGU U AGG UUUC CGUGA...CCG-3'@LB@ AGGG UGGAU GACAU UCAG UG CGG AGAUA AUGAUGAUA@LB@ \|\|\|\| \|::\|: \|\|\|\|\| \|\|\|\| \|\| \|\|\| \|:\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCCC AUUUG CUGUA AGUC AC GCC UUUAU UACUACUAU@LB@3'-UUU...CUUUA C U UUUACUU U AUUA UUCAAU CG-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -31.3101 kcal/mol@LB@Unfolding Energy - mRNA 14.9582 kcal/mol@LB@Unfolding Energy - sRNA 6.33762 kcal/mol@LB@@LB@Position - mRNA 160 -- 209@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 3 -- 9@LB@
46	0.00512	0.3601	b2012	yeeD	-13.46	0.016912	185 -- 206	3 -- 23	putative TusA family sulfurtransferase	_____________184____________________207\n_____________\|______________________\|\n5'-GAU...CAAAU__________G___A_______AUUAA...UAG-3'\n______________UAAGUAAGGU_UAA_GAUGGUG\n______________\|\|\|:\|\|\|:\|\|_\|\|\|_\|\|\|\|:\|:\n______________AUUUAUUUCA_AUU_CUACUAU\n3'-UUU...CCAUU______________A_______CG-5'\n_____________\|______________________\|\n_____________24_____________________2\n	200 -- 206	3 -- 9	-15.4658 kcal/mol	1.89879 kcal/mol	0.104738 kcal/mol	184 207@LB@ \| \|@LB@5'-GAU...CAAAU G A AUUAA...UAG-3'@LB@ UAAGUAAGGU UAA GAUGGUG@LB@ \|\|\|:\|\|\|:\|\| \|\|\| \|\|\|\|:\|:@LB@ AUUUAUUUCA AUU CUACUAU@LB@3'-UUU...CCAUU A CG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -13.46 kcal/mol@LB@Hybridization Energy -15.4658 kcal/mol@LB@Unfolding Energy - mRNA 1.89879 kcal/mol@LB@Unfolding Energy - sRNA 0.104738 kcal/mol@LB@@LB@Position - mRNA 185 -- 206@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 3 -- 9@LB@
47	0.005156	0.3601	b2614	grpE	-12.03	0.036099	152 -- 179	1 -- 26	heat shock protein	_____________151__________________________180\n_____________\|____________________________\|\n5'-GAG...CCCCA_______C________CGA_____AU__GAAAA...CUG-3'\n______________UAAUAAG_GAAGUUAG___GAUGA__GC\n______________\|\|\|\|\|\|:_:\|\|\|\|\|\|:___\|\|\|\|\|__\|\|\n______________AUUAUUU_UUUCAAUU___CUACU__CG\n3'-UUU...CUGCC_______A________A_______AU__-5'\n_____________\|___________________________\|\n_____________27__________________________1\n	161 -- 167	11 -- 17	-17.6467 kcal/mol	5.03361 kcal/mol	0.580494 kcal/mol	151 180@LB@ \| \|@LB@5'-GAG...CCCCA C CGA AU GAAAA...CUG-3'@LB@ UAAUAAG GAAGUUAG GAUGA GC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|: \|\|\|\|\| \|\|@LB@ AUUAUUU UUUCAAUU CUACU CG@LB@3'-UUU...CUGCC A A AU -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -17.6467 kcal/mol@LB@Unfolding Energy - mRNA 5.03361 kcal/mol@LB@Unfolding Energy - sRNA 0.580494 kcal/mol@LB@@LB@Position - mRNA 152 -- 179@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@LB@
48	0.005342	0.3653	b3380	yhfW	-15.20	0.006283	218 -- 233	1 -- 15	phosphopentomutase-related metalloenzyme superfamily protein	_____________217______________234\n_____________\|________________\|\n5'-CUC...GUGGU________U_______UUUGG...GUG-3'\n______________GUUAGUGA_UGAUAGC\n______________\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________CAAUUACU_ACUAUCG\n3'-UUU...UAUUU________________-5'\n_____________\|_______________\|\n_____________16______________1\n	227 -- 233	1 -- 7	-17.7091 kcal/mol	2.46465 kcal/mol	0.0474282 kcal/mol	217 234@LB@ \| \|@LB@5'-CUC...GUGGU U UUUGG...GUG-3'@LB@ GUUAGUGA UGAUAGC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAAUUACU ACUAUCG@LB@3'-UUU...UAUUU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -17.7091 kcal/mol@LB@Unfolding Energy - mRNA 2.46465 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 1 -- 7@LB@
49	0.00563	0.3739	b2239	glpQ	-9.17	0.140723	61 -- 103	1 -- 49	periplasmic glycerophosphodiester phosphodiesterase	_____________60__________________________________________________104\n_____________\|___________________________________________________\|\n5'-CGG...ACCGU____UUC_____CUG__________CUU______U________________GGCAG...UCA-3'\n______________GGAC___UUCGG____GGAUGGCGG_______UA_GG_UAAUGAU__UGGC\n______________:\|\|\|___\|\|\|:\|____\|:\|\|\|:\|\|\|_______\|\|_:\|_\|\|\|\|\|\|\|__\|:\|\|\n______________UCUG___AAGUC____CUUACUGCC_______AU_UC_AUUACUA__AUCG\n3'-UUU...AUUUG____U_______UUUA_________AUUAUUU__U__A_______CU____-5'\n_____________\|__________________________________________________\|\n_____________50_________________________________________________1\n	93 -- 99	7 -- 13	-28.1898 kcal/mol	12.697 kcal/mol	6.32371 kcal/mol	60 104@LB@ \| \|@LB@5'-CGG...ACCGU UUC CUG CUU U GGCAG...UCA-3'@LB@ GGAC UUCGG GGAUGGCGG UA GG UAAUGAU UGGC@LB@ :\|\|\| \|\|\|:\| \|:\|\|\|:\|\|\| \|\| :\| \|\|\|\|\|\|\| \|:\|\|@LB@ UCUG AAGUC CUUACUGCC AU UC AUUACUA AUCG@LB@3'-UUU...AUUUG U UUUA AUUAUUU U A CU -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -28.1898 kcal/mol@LB@Unfolding Energy - mRNA 12.697 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 61 -- 103@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 7 -- 13@LB@
50	0.005695	0.3739	b1086	rluC	-13.13	0.020232	139 -- 168	28 -- 55	23S rRNA pseudouridine(955 2504 2580) synthase	_____________138____________________________169\n_____________\|______________________________\|\n5'-UCC...CAAAA_______UAA____AG_A____________CGAAU...UAC-3'\n______________GUAAAUA___GCAU__A_AAAUGAGUGGCG\n______________\|\|\|\|\|:\|___:\|\|\|__\|_\|\|\|\|\|\|:\|\|:\|\|\n______________CAUUUGU___UGUA__U_UUUACUUACUGC\n3'-UUU...AUCCC_______C______AG_C____________CAUUA...UCG-5'\n_____________\|______________________________\|\n_____________56_____________________________27\n	161 -- 167	29 -- 35	-21.8911 kcal/mol	2.47099 kcal/mol	6.28725 kcal/mol	138 169@LB@ \| \|@LB@5'-UCC...CAAAA UAA AG A CGAAU...UAC-3'@LB@ GUAAAUA GCAU A AAAUGAGUGGCG@LB@ \|\|\|\|\|:\| :\|\|\| \| \|\|\|\|\|\|:\|\|:\|\|@LB@ CAUUUGU UGUA U UUUACUUACUGC@LB@3'-UUU...AUCCC C AG C CAUUA...UCG-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -21.8911 kcal/mol@LB@Unfolding Energy - mRNA 2.47099 kcal/mol@LB@Unfolding Energy - sRNA 6.28725 kcal/mol@LB@@LB@Position - mRNA 139 -- 168@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 29 -- 35@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