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
181	0.009071	0.1747	b3962	sthA	-14.30	0.031527	83 -- 114	34 -- 76	pyridine nucleotide transhydrogenase soluble	_____________82___________________________________________115\n_____________\|____________________________________________\|\n5'-UAC...GAAAC____AAA___AA_______________________AU__AG___GAUAA...CAG-3'\n______________AGAC___GCA__GGC____________CGCUCAGG__AU__CCA\n______________\|\|\|\|___:\|\|__:\|\|____________\|:\|\|\|\|\|\|__\|\|__\|\|\|\n______________UCUG___UGU__UCG____________GUGAGUCC__UA__GGU\n3'-UUU...CCGUU____AUG___G____UUAAGCAACAAA________CC__AA___ACGAA...GCA-5'\n_____________\|____________________________________________\|\n_____________77___________________________________________33\n	99 -- 105	43 -- 49	-23.8174 kcal/mol	4.70621 kcal/mol	4.816 kcal/mol	82 115@LB@ \| \|@LB@5'-UAC...GAAAC AAA AA AU AG GAUAA...CAG-3'@LB@ AGAC GCA GGC CGCUCAGG AU CCA@LB@ \|\|\|\| :\|\| :\|\| \|:\|\|\|\|\|\| \|\| \|\|\|@LB@ UCUG UGU UCG GUGAGUCC UA GGU@LB@3'-UUU...CCGUU AUG G UUAAGCAACAAA CC AA ACGAA...GCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -23.8174 kcal/mol@LB@Unfolding Energy - mRNA 4.70621 kcal/mol@LB@Unfolding Energy - sRNA 4.816 kcal/mol@LB@@LB@Position - mRNA 83 -- 114@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 43 -- 49@LB@
182	0.009082	0.1747	b3998	nfi	-11.38	0.137700	53 -- 76	45 -- 75	endonuclease V; deoxyinosine 3' endonuclease	_____________52______________________________77\n_____________\|_______________________________\|\n5'-UGG...GUAGC________UU_________________G___CGGCG...GAG-3'\n______________GACUAUAC___GCAG______GUUUCG_UCA\n______________\|\|\|\|\|:\|\|___\|\|\|:______\|\|\|\|\|:_\|\|\|\n______________CUGAUGUG___CGUU______CAAAGU_AGU\n3'-UUU...CGUUU________UGU____AAGCAA______G___CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	54 -- 60	68 -- 74	-21.6188 kcal/mol	6.49773 kcal/mol	3.74078 kcal/mol	52 77@LB@ \| \|@LB@5'-UGG...GUAGC UU G CGGCG...GAG-3'@LB@ GACUAUAC GCAG GUUUCG UCA@LB@ \|\|\|\|\|:\|\| \|\|\|: \|\|\|\|\|: \|\|\|@LB@ CUGAUGUG CGUU CAAAGU AGU@LB@3'-UUU...CGUUU UGU AAGCAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.38 kcal/mol@LB@Hybridization Energy -21.6188 kcal/mol@LB@Unfolding Energy - mRNA 6.49773 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 53 -- 76@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 68 -- 74@LB@
183	0.009087	0.1747	b3965	trmA	-11.75	0.116675	18 -- 52	35 -- 74	tRNA m(5)U54 methyltransferase SAM-dependent; tmRNA m(5)U341 methyltransferase	_____________17____________________________________________53\n_____________\|_____________________________________________\|\n5'-UCG...UUACC________U____UCCA_________________________C__UAUUA...UUC-3'\n______________GCUGCGCG_CAGC____GAUUCG______CACU____GGAUU_CC\n______________:\|\|:\|:\|:_\|\|\|\|____:\|\|\|\|\|______\|\|\|\|____\|\|\|\|\|_\|\|\n______________UGAUGUGU_GUCG____UUAAGC______GUGA____CCUAA_GG\n3'-UUU...GUUUC_______________________AACAAA____GUCC_____A__UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________34\n	18 -- 24	68 -- 74	-28.5766 kcal/mol	12.0258 kcal/mol	4.80541 kcal/mol	17 53@LB@ \| \|@LB@5'-UCG...UUACC U UCCA C UAUUA...UUC-3'@LB@ GCUGCGCG CAGC GAUUCG CACU GGAUU CC@LB@ :\|\|:\|:\|: \|\|\|\| :\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UGAUGUGU GUCG UUAAGC GUGA CCUAA GG@LB@3'-UUU...GUUUC AACAAA GUCC A UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -28.5766 kcal/mol@LB@Unfolding Energy - mRNA 12.0258 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 18 -- 52@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
184	0.00937	0.1776	b2467	nudK	-13.30	0.054361	69 -- 94	38 -- 78	GDP-mannose pyrophosphatase	_____________68________________________________________95\n_____________\|_________________________________________\|\n5'-CAA...GGCAG______GU_________________________________AUUGA...AAG-3'\n______________AAGGAC__CAUGCGGCA_______________CAGGGGAUU\n______________\|\|:\|\|\|__\|\|::\|:\|\|\|_______________\|\|\|\|\|\|\|\|\|\n______________UUUCUG__GUGUGUCGU_______________GUCCCCUAA\n3'-UUU...ACCCG______AU_________UAAGCAACAAAGUGA_________AGGUA...GCA-5'\n_____________\|_________________________________________\|\n_____________79________________________________________37\n	88 -- 94	38 -- 44	-30.5001 kcal/mol	12.4248 kcal/mol	4.77973 kcal/mol	68 95@LB@ \| \|@LB@5'-CAA...GGCAG GU AUUGA...AAG-3'@LB@ AAGGAC CAUGCGGCA CAGGGGAUU@LB@ \|\|:\|\|\| \|\|::\|:\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UUUCUG GUGUGUCGU GUCCCCUAA@LB@3'-UUU...ACCCG AU UAAGCAACAAAGUGA AGGUA...GCA-5'@LB@ \| \|@LB@ 79 37@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -30.5001 kcal/mol@LB@Unfolding Energy - mRNA 12.4248 kcal/mol@LB@Unfolding Energy - sRNA 4.77973 kcal/mol@LB@@LB@Position - mRNA 69 -- 94@LB@Position - sRNA 38 -- 78@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 38 -- 44@LB@
185	0.009421	0.1776	b3094	exuR	-10.10	0.235203	51 -- 95	35 -- 75	hexuronate regulon transcriptional repressor; autorepressor	_____________50____________________________________________96\n_____________\|_____________________________________________\|\n5'-CCG...AUAAC___CC_____C____CAUUAAC_______GUA__UUUUA______CUUCA...CUG-3'\n______________GAU__CGCAC_GCAA_______GUUUCGU___AG_____GUUUCC\n______________\|\|:__\|:\|\|\|_\|\|\|\|_______\|\|\|\|\|::___\|\|_____:\|\|\|\|\|\n______________CUG__GUGUG_CGUU_______CAAAGUG___UC_____UAAAGG\n3'-UUU...CGUUU___AU_____U____AAGCAA________AG___CCC________UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________76____________________________________________34\n	73 -- 79	48 -- 54	-21.0703 kcal/mol	6.16224 kcal/mol	4.80541 kcal/mol	50 96@LB@ \| \|@LB@5'-CCG...AUAAC CC C CAUUAAC GUA UUUUA CUUCA...CUG-3'@LB@ GAU CGCAC GCAA GUUUCGU AG GUUUCC@LB@ \|\|: \|:\|\|\| \|\|\|\| \|\|\|\|\|:: \|\| :\|\|\|\|\|@LB@ CUG GUGUG CGUU CAAAGUG UC UAAAGG@LB@3'-UUU...CGUUU AU U AAGCAA AG CCC UACGA...GCA-5'@LB@ \| \|@LB@ 76 34@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -21.0703 kcal/mol@LB@Unfolding Energy - mRNA 6.16224 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 51 -- 95@LB@Position - sRNA 35 -- 75@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 48 -- 54@LB@
186	0.009502	0.1776	b1631	rsxG	-12.74	0.072174	210 -- 253	41 -- 74	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex	_____________209____________________________________________254\n_____________\|______________________________________________\|\n5'-CUG...UGAAA_____CCGAAA________UUA_____G______AUUUG___C___UUCAA...CGA-3'\n______________ACUAU______ACACGGCA___CGUUG___CGCU_____CAG_GGG\n______________\|\|\|\|:______\|\|\|\|:\|\|\|___\|\|\|\|\|___\|:\|\|_____\|\|\|_\|\|\|\n______________UGAUG______UGUGUCGU___GCAAC___GUGA_____GUC_CCC\n3'-UUU...GUUUC___________________UAA_____AAA________________UAAAG...GCA-5'\n_____________\|______________________________________________\|\n_____________75_____________________________________________40\n	222 -- 228	62 -- 68	-28.539 kcal/mol	11.0247 kcal/mol	4.77133 kcal/mol	209 254@LB@ \| \|@LB@5'-CUG...UGAAA CCGAAA UUA G AUUUG C UUCAA...CGA-3'@LB@ ACUAU ACACGGCA CGUUG CGCU CAG GGG@LB@ \|\|\|\|: \|\|\|\|:\|\|\| \|\|\|\|\| \|:\|\| \|\|\| \|\|\|@LB@ UGAUG UGUGUCGU GCAAC GUGA GUC CCC@LB@3'-UUU...GUUUC UAA AAA UAAAG...GCA-5'@LB@ \| \|@LB@ 75 40@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -28.539 kcal/mol@LB@Unfolding Energy - mRNA 11.0247 kcal/mol@LB@Unfolding Energy - sRNA 4.77133 kcal/mol@LB@@LB@Position - mRNA 210 -- 253@LB@Position - sRNA 41 -- 74@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 62 -- 68@LB@
187	0.009506	0.1776	b1243	oppA	-10.52	0.199375	11 -- 17	40 -- 46	oligopeptide ABC transporter periplasmic binding protein	_____________10______18\n_____________\|_______\|\n5'-UGU...CUCGA_______GACAC...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	11 -- 17	40 -- 46	-13.6251 kcal/mol	1.75344 kcal/mol	1.35582 kcal/mol	10 18@LB@ \| \|@LB@5'-UGU...CUCGA GACAC...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -13.6251 kcal/mol@LB@Unfolding Energy - mRNA 1.75344 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 40 -- 46@LB@
188	0.009562	0.1776	b0147	ligT	-10.24	0.223023	2 -- 33	35 -- 66	2'-5' RNA ligase	_____________1_________________________________34\n_____________\|_________________________________\|\n__________5'-C________GCAGCGG___GC____UU_______CGGCC...CGG-3'\n______________CAGCAGUU________CA__CAGG__GAUUUCC\n______________\|\|\|\|\|:\|\|________\|\|__\|\|\|\|__\|\|\|\|\|\|\|\n______________GUCGUUAA________GU__GUCC__CUAAAGG\n3'-UUU...UGUGU________GCAACAAA__GA____C________UACGA...GCA-5'\n_____________\|_________________________________\|\n_____________67________________________________34\n	27 -- 33	35 -- 41	-25.6384 kcal/mol	10.64 kcal/mol	4.7609 kcal/mol	1 34@LB@ \| \|@LB@ 5'-C GCAGCGG GC UU CGGCC...CGG-3'@LB@ CAGCAGUU CA CAGG GAUUUCC@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GUCGUUAA GU GUCC CUAAAGG@LB@3'-UUU...UGUGU GCAACAAA GA C UACGA...GCA-5'@LB@ \| \|@LB@ 67 34@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -25.6384 kcal/mol@LB@Unfolding Energy - mRNA 10.64 kcal/mol@LB@Unfolding Energy - sRNA 4.7609 kcal/mol@LB@@LB@Position - mRNA 2 -- 33@LB@Position - sRNA 35 -- 66@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 35 -- 41@LB@
189	0.009605	0.1776	b0927	ycbL	-15.21	0.018444	14 -- 51	33 -- 78	putative metal-binding enzyme	_____________13__________________________________________________52\n_____________\|___________________________________________________\|\n5'-GGA...GAAGA________U_____UAAAG__________________CGAU__________AUUGA...GCG-3'\n______________AAAG_CUA_CACAC________________GC_CAGG____GGAUUUCCAU\n______________\|\|\|\|_\|\|\|_\|\|\|\|\|________________:\|_\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________UUUC_GAU_GUGUG________________UG_GUCC____CCUAAAGGUA\n3'-UUU...ACCCG____U_________UCGUUAAGCAACAAAG__A__________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________79__________________________________________________32\n	45 -- 51	33 -- 39	-26.8189 kcal/mol	6.79395 kcal/mol	4.81602 kcal/mol	13 52@LB@ \| \|@LB@5'-GGA...GAAGA U UAAAG CGAU AUUGA...GCG-3'@LB@ AAAG CUA CACAC GC CAGG GGAUUUCCAU@LB@ \|\|\|\| \|\|\| \|\|\|\|\| :\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUUC GAU GUGUG UG GUCC CCUAAAGGUA@LB@3'-UUU...ACCCG U UCGUUAAGCAACAAAG A CGAAU...GCA-5'@LB@ \| \|@LB@ 79 32@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -26.8189 kcal/mol@LB@Unfolding Energy - mRNA 6.79395 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 14 -- 51@LB@Position - sRNA 33 -- 78@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 33 -- 39@LB@
190	0.009703	0.1776	b4125	dcuS	-9.98	0.246838	251 -- 265	60 -- 75	sensory histidine kinase in two-component regulatory system with DcuR regulator of anaerobic fumarate respiration	_____________250______________266\n_____________\|________________\|\n5'-UCC...AAAUU__G_____________CUUAA...UAU-3'\n______________GA_UAC_CACAGUGAU\n______________\|\|_\|\|\|_\|\|\|\|\|::\|\|\n______________CU_AUG_GUGUCGUUA\n3'-UUU...CGUUU__G___U_________AGCAA...GCA-5'\n_____________\|________________\|\n_____________76_______________59\n	259 -- 265	60 -- 66	-16.3548 kcal/mol	3.08747 kcal/mol	3.28851 kcal/mol	250 266@LB@ \| \|@LB@5'-UCC...AAAUU G CUUAA...UAU-3'@LB@ GA UAC CACAGUGAU@LB@ \|\| \|\|\| \|\|\|\|\|::\|\|@LB@ CU AUG GUGUCGUUA@LB@3'-UUU...CGUUU G U AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 3.08747 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 60 -- 66@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

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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

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