Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
191	0.008587	0.1558	b0823	ybiW	-9.49	0.063221	47 -- 54	1 -- 8	putative pyruvate formate lyase	b3951	_____________46_______55\n_____________\|________\|\n5'-ACC...UUUUC________CACAC...CGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	48 -- 54	1 -- 7	-12.4662 kcal/mol	0.878635 kcal/mol	2.11603 kcal/mol	46 55@LB@ \| \|@LB@5'-ACC...UUUUC CACAC...CGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -12.4662 kcal/mol@LB@Unfolding Energy - mRNA 0.878635 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 47 -- 54@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 1 -- 7@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein		_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
104	0.003257	0.1101	b0858	ybjO	-8.07	0.149394	228 -- 257	2 -- 30	DUF2593 family inner membrane protein		_____________227______________________________258\n_____________\|________________________________\|\n5'-AUG...UUUUU____A__________C_____A__CU_G____AAUGU...UUA-3'\n______________AAGA___AACAUCUU_AUCUC_UG__C_CCUG\n______________\|\|\|\|___\|\|\|\|\|\|\|\|_\|:\|\|\|_\|\|__\|_\|\|\|:\n______________UUCU___UUGUAGAA_UGGAG_AC__G_GGAU\n3'-AUU...AGACU____AUC_________________AU______G-5'\n_____________\|________________________________\|\n_____________31_______________________________1\n	234 -- 240	16 -- 22	-20.5501 kcal/mol	4.45089 kcal/mol	8.05308 kcal/mol	227 258@LB@ \| \|@LB@5'-AUG...UUUUU A C A CU G AAUGU...UUA-3'@LB@ AAGA AACAUCUU AUCUC UG C CCUG@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\| \|\| \| \|\|\|:@LB@ UUCU UUGUAGAA UGGAG AC G GGAU@LB@3'-AUU...AGACU AUC AU G-5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -20.5501 kcal/mol@LB@Unfolding Energy - mRNA 4.45089 kcal/mol@LB@Unfolding Energy - sRNA 8.05308 kcal/mol@LB@@LB@Position - mRNA 228 -- 257@LB@Position - sRNA 2 -- 30@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 16 -- 22@LB@
145	0.005462	0.1325	b3239	yhcO	-10.93	0.023720	179 -- 225	2 -- 55	putative barnase inhibitor		_____________178______________________________________________________226\n_____________\|________________________________________________________\|\n5'-CUA...CGCCG___A_______C___________AAC______________A_______________AUGAG...GCG-3'\n______________CGA__ACGUGA_GGU____GG_C____AGAU_GAAUAUUU_UACCUUUG_AUUUUG\n______________\|\|\|__\|\|\|\|\|\|_:\|\|____\|\|_\|____\|\|\|\|_\|\|\|:\|\|:\|_\|\|\|\|\|:\|\|_\|:::\|:\n______________GCU__UGCACU_UCA____CC_G____UCUA_CUUGUAGA_AUGGAGAC_UGGGAU\n3'-AUU...UUUAG___AA__________UUUU__A_ACUU____U_________________A______G-5'\n_____________\|________________________________________________________\|\n_____________56_______________________________________________________1\n	213 -- 219	9 -- 15	-30.2735 kcal/mol	6.67064 kcal/mol	12.6986 kcal/mol	178 226@LB@ \| \|@LB@5'-CUA...CGCCG A C AAC A AUGAG...GCG-3'@LB@ CGA ACGUGA GGU GG C AGAU GAAUAUUU UACCUUUG AUUUUG@LB@ \|\|\| \|\|\|\|\|\| :\|\| \|\| \| \|\|\|\| \|\|\|:\|\|:\| \|\|\|\|\|:\|\| \|:::\|:@LB@ GCU UGCACU UCA CC G UCUA CUUGUAGA AUGGAGAC UGGGAU@LB@3'-AUU...UUUAG AA UUUU A ACUU U A G-5'@LB@ \| \|@LB@ 56 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -30.2735 kcal/mol@LB@Unfolding Energy - mRNA 6.67064 kcal/mol@LB@Unfolding Energy - sRNA 12.6986 kcal/mol@LB@@LB@Position - mRNA 179 -- 225@LB@Position - sRNA 2 -- 55@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 9 -- 15@LB@
146	0.005604	0.1342	b1637	tyrS	-10.18	0.040102	30 -- 71	2 -- 50	tyrosyl-tRNA synthetase		_____________29________________________________________________72\n_____________\|_________________________________________________\|\n5'-CAU...UACCA_______AAU___U_CG________U__U____________________AAAAG...CGA-3'\n______________GCGUGAA____GA_G__UGGAAGAU_GA_CGUCUUGC______ACCCUG\n______________:\|\|\|\|\|\|____:\|_\|__\|\|:\|\|\|\|\|_\|\|_\|:\|\|\|\|:\|______\|\|\|\|\|:\n______________UGCACUU____UU_C__ACUUUCUA_CU_GUAGAAUG______UGGGAU\n3'-AUU...GCUAA_______CAUU__C_AG________U__U________GAGACA______G-5'\n_____________\|_________________________________________________\|\n_____________51________________________________________________1\n	30 -- 36	44 -- 50	-35.883 kcal/mol	13.0482 kcal/mol	12.6769 kcal/mol	29 72@LB@ \| \|@LB@5'-CAU...UACCA AAU U CG U U AAAAG...CGA-3'@LB@ GCGUGAA GA G UGGAAGAU GA CGUCUUGC ACCCUG@LB@ :\|\|\|\|\|\| :\| \| \|\|:\|\|\|\|\| \|\| \|:\|\|\|\|:\| \|\|\|\|\|:@LB@ UGCACUU UU C ACUUUCUA CU GUAGAAUG UGGGAU@LB@3'-AUU...GCUAA CAUU C AG U U GAGACA G-5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -35.883 kcal/mol@LB@Unfolding Energy - mRNA 13.0482 kcal/mol@LB@Unfolding Energy - sRNA 12.6769 kcal/mol@LB@@LB@Position - mRNA 30 -- 71@LB@Position - sRNA 2 -- 50@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 44 -- 50@LB@
154	0.006224	0.1406	b0882	clpA	-11.36	0.017252	127 -- 158	2 -- 32	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________126______________________________159\n_____________\|________________________________\|\n5'-UUU...CGCGA______AU_______CAUUG__G_____G___GAAAA...CGC-3'\n______________GGGAGA__GAGCAUC_____CU_UGUAC_CUA\n______________\|::\|\|\|__\|\|:\|\|\|\|_____\|\|_\|\|\|\|\|_\|\|\|\n______________CUUUCU__CUUGUAG_____GA_ACAUG_GAU\n3'-AUU...CCAGA______AU_______AAUG___G_____G___G-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	135 -- 141	18 -- 24	-27.9684 kcal/mol	7.80814 kcal/mol	8.82442 kcal/mol	126 159@LB@ \| \|@LB@5'-UUU...CGCGA AU CAUUG G G GAAAA...CGC-3'@LB@ GGGAGA GAGCAUC CU UGUAC CUA@LB@ \|::\|\|\| \|\|:\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ CUUUCU CUUGUAG GA ACAUG GAU@LB@3'-AUU...CCAGA AU AAUG G G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -27.9684 kcal/mol@LB@Unfolding Energy - mRNA 7.80814 kcal/mol@LB@Unfolding Energy - sRNA 8.82442 kcal/mol@LB@@LB@Position - mRNA 127 -- 158@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 18 -- 24@LB@
178	0.007695	0.1511	b4567	yjjZ	-7.25	0.231371	185 -- 218	2 -- 33	uncharacterized protein		_____________184_________________________________219\n_____________\|___________________________________\|\n5'-CGG...AUCAA_______GAU___AU___G____AA______G___GGCAG...GGA-3'\n______________UGAAAGA___GAA__CAU_UUGC__C_GUAC_CUG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|_\|\|:\|__\|_\|\|\|\|_\|\|:\n______________ACUUUCU___CUU__GUA_AAUG__G_CAUG_GAU\n3'-AUU...UCCAG_______AU_________G____GA_A____G___G-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	185 -- 191	27 -- 33	-22.8177 kcal/mol	6.54395 kcal/mol	9.04499 kcal/mol	184 219@LB@ \| \|@LB@5'-CGG...AUCAA GAU AU G AA G GGCAG...GGA-3'@LB@ UGAAAGA GAA CAU UUGC C GUAC CUG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|:\| \| \|\|\|\| \|\|:@LB@ ACUUUCU CUU GUA AAUG G CAUG GAU@LB@3'-AUU...UCCAG AU G GA A G G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -7.25 kcal/mol@LB@Hybridization Energy -22.8177 kcal/mol@LB@Unfolding Energy - mRNA 6.54395 kcal/mol@LB@Unfolding Energy - sRNA 9.04499 kcal/mol@LB@@LB@Position - mRNA 185 -- 218@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 27 -- 33@LB@
181	0.007802	0.1516	b1797	yeaR	-7.07	0.254063	142 -- 149	2 -- 9	DUF1971 family protein nitrate-inducible		_____________141______150\n_____________\|________\|\n5'-UGC...CAGGC________AAACG...AAG-3'\n______________GUACCCUG\n______________\|\|\|\|\|\|\|:\n______________CAUGGGAU\n3'-AUU...GGAGA________G-5'\n_____________\|________\|\n_____________10_______1\n	143 -- 149	2 -- 8	-12.2602 kcal/mol	3.09143 kcal/mol	2.12684 kcal/mol	141 150@LB@ \| \|@LB@5'-UGC...CAGGC AAACG...AAG-3'@LB@ GUACCCUG@LB@ \|\|\|\|\|\|\|:@LB@ CAUGGGAU@LB@3'-AUU...GGAGA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -12.2602 kcal/mol@LB@Unfolding Energy - mRNA 3.09143 kcal/mol@LB@Unfolding Energy - sRNA 2.12684 kcal/mol@LB@@LB@Position - mRNA 142 -- 149@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 2 -- 8@LB@
182	0.007896	0.1519	b0686	ybfF	-7.34	0.221050	164 -- 170	2 -- 8	acyl-CoA esterase		_____________163_____171\n_____________\|_______\|\n5'-CUU...CAUAA_______ACCCG...GCG-3'\n______________UACCCUA\n______________\|\|\|\|\|\|\|\n______________AUGGGAU\n3'-AUU...GAGAC_______G-5'\n_____________\|_______\|\n_____________9_______1\n	164 -- 170	2 -- 8	-9.7212 kcal/mol	0.292492 kcal/mol	2.11083 kcal/mol	163 171@LB@ \| \|@LB@5'-CUU...CAUAA ACCCG...GCG-3'@LB@ UACCCUA@LB@ \|\|\|\|\|\|\|@LB@ AUGGGAU@LB@3'-AUU...GAGAC G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -9.7212 kcal/mol@LB@Unfolding Energy - mRNA 0.292492 kcal/mol@LB@Unfolding Energy - sRNA 2.11083 kcal/mol@LB@@LB@Position - mRNA 164 -- 170@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 2 -- 8@LB@
11	3.674e-05	0.01134	b2099	yegU	-10.44	0.033453	166 -- 229	3 -- 59	ADP-ribosylglycohydrolase family protein		_____________165_________________________________________________________________230\n_____________\|___________________________________________________________________\|\n5'-GUG...UCGAU____G____AU____U___CAC______AAGUUAAA_____AC________AU______G_______UUAUG...CAC-3'\n______________GAUC_CGAU__UGCG_UGA___AAGGGG________UGAAA___AGAACGU____UCUC_GUGCUCU\n______________:\|\|\|_\|\|\|\|__\|:\|\|_\|\|\|___\|\|::\|\|________\|\|\|\|\|___\|\|\|\|\|:\|____:\|\|\|_\|\|:\|:\|\|\n______________UUAG_GCUA__AUGC_ACU___UUUUCC________ACUUU___UCUUGUA____GGAG_CAUGGGA\n3'-AUU...UCGGU___________________UCA______AG___________CUA_______GAAU____A_______UG-5'\n_____________\|___________________________________________________________________\|\n_____________60__________________________________________________________________2\n	223 -- 229	3 -- 9	-36.2809 kcal/mol	13.1575 kcal/mol	12.7026 kcal/mol	165 230@LB@ \| \|@LB@5'-GUG...UCGAU G AU U CAC AAGUUAAA AC AU G UUAUG...CAC-3'@LB@ GAUC CGAU UGCG UGA AAGGGG UGAAA AGAACGU UCUC GUGCUCU@LB@ :\|\|\| \|\|\|\| \|:\|\| \|\|\| \|\|::\|\| \|\|\|\|\| \|\|\|\|\|:\| :\|\|\| \|\|:\|:\|\|@LB@ UUAG GCUA AUGC ACU UUUUCC ACUUU UCUUGUA GGAG CAUGGGA@LB@3'-AUU...UCGGU UCA AG CUA GAAU A UG-5'@LB@ \| \|@LB@ 60 2@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -36.2809 kcal/mol@LB@Unfolding Energy - mRNA 13.1575 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 166 -- 229@LB@Position - sRNA 3 -- 59@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 3 -- 9@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